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Conserved domains on  [gi|556284038|ref|WP_023289829|]
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LysR family transcriptional regulator [Klebsiella quasipneumoniae]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444056)

LysR family transcriptional regulator similar to Pseudomonas aeruginosa HTH-type transcriptional regulator PtxR, which regulates the toxA (exotoxin) and regA genes; substrate binding domain-containing protein is a type 2 periplasmic binding protein (PBP2), similar to the regulatory domain of Vibrio vulnificus virulence gene regulator AphB that has been implicated in acid resistance and pathogenesis

Gene Ontology:  GO:0001216|GO:0032993|GO:0006355
PubMed:  19047729|8257110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-286 3.70e-67

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: 208.06  E-value: 3.70e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYSHFAGQ-RWQFSDaQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIAS 248
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPlRWRFRR-GGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 556284038 249 GALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08422  160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 2.02e-16

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 2.02e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 556284038    8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGE 63
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-286 3.70e-67

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: 208.06  E-value: 3.70e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYSHFAGQ-RWQFSDaQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIAS 248
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPlRWRFRR-GGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 556284038 249 GALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08422  160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-292 6.55e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 152.71  E-value: 6.55e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADEIAGE--RQR 85
Cdd:COG0583    7 RAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAElrALR 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  86 ADPSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPV---SLIGERIDVAIRITDNPEAGAIARRLGVCRSL 162
Cdd:COG0583   87 GGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLGEERLV 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 163 LCAAPRW-LRQHGPLTTLddlqqhncllyshfagqrwqfsdaqgqeasvavngnlsagiSSLLLEAAVAGCGIAMLPELE 241
Cdd:COG0583  167 LVASPDHpLARRAPLVNS-----------------------------------------LEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 556284038 242 ARGAIASGALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDALQRRLGE 292
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK09801 PRK09801
LysR family transcriptional regulator;
8-292 3.00e-36

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 131.70  E-value: 3.00e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAG----ETVLLKTRGLTRIADEIAGER 83
Cdd:PRK09801  12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGqrcyEHALEILTQYQRLVDDVTQIK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  84 QRadPSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLL 163
Cdd:PRK09801  92 TR--PEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRIL 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 164 CAAPRWLRQHGPLTTLDDLQQHNCLLYSH--FAGQRWQFSDAQgQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELE 241
Cdd:PRK09801 170 CAAPEYLQKYPQPQSLQELSRHDCLVTKErdMTHGIWELGNGQ-EKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWD 248

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 556284038 242 ARGAIASGALEVVLPDWTPKAlSVYGIYLSRDYQPDGLPL---FLDA-LQRRLGE 292
Cdd:PRK09801 249 VLPFLESGKLVQVLPEYAQSA-NIWAVYREPLYRSMKLRVcveFLAAwCQQRLGK 302
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-291 4.29e-28

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: 107.37  E-value: 4.29e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   89 SGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINN--HPVSLIGE-RIDVAIRITDNPEAGAIARRLGVCRSLLCA 165
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  166 APRWLRQHGPLTTLDDLQQHNCLLYSHFAGQRWQFSDAqGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGA 245
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRA-LRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 556284038  246 IASGAL-EVVLPDWTPKAlSVYGIYLSRDYQPDGLPLFLDALQRRLG 291
Cdd:pfam03466 160 LADGRLvALPLPEPPLPR-ELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 2.02e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 2.02e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 556284038    8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGE 63
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10341 PRK10341
transcriptional regulator TdcA;
9-82 1.17e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 55.25  E-value: 1.17e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556284038   9 VYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLK----TRGLTRIADEIAGE 82
Cdd:PRK10341  14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRsesiTREMKNMVNEINGM 91
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
12-86 4.68e-05

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 42.12  E-value: 4.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  12 RICELGSLSAAARALGMSRpmvSR---YLEQMESWAGARLIHRST--RR---LTLTPAGETVLLKTRGLTRIADEIAGER 83
Cdd:COG2005   29 AIDETGSISAAAKAMGMSY---KRawdLIDAMNNLLGEPLVERQTggKGgggARLTPEGRRLLALYRRLEAEAQRALAAL 105


                 ...
gi 556284038  84 QRA 86
Cdd:COG2005  106 FEE 108
transpos_IS21 NF033546
IS21 family transposase;
18-98 6.17e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 37.57  E-value: 6.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  18 SLSAAARALGMSRPMVSRYLEQMESWAGARLiHRSTRRLTLTPAGETVLL---------KTRGLTRIADEIagerQRADP 88
Cdd:NF033546  10 SIREIARELGISRNTVRKYLRRAGLDEPPKY-ERRPPRPSKLDPFEPYIPdwleahlrkPGVTATLLWEEL----RAEGY 84

                         90
                 ....*....|
gi 556284038  89 SGTLRVACAH 98
Cdd:NF033546  85 PGSYSTVRRY 94
 
Name Accession Description Interval E-value
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-286 3.70e-67

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: 208.06  E-value: 3.70e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYSHFAGQ-RWQFSDaQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIAS 248
Cdd:cd08422   81 LARHGTPQTPEDLARHRCLGYRLPGRPlRWRFRR-GGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 556284038 249 GALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08422  160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 88-286 3.01e-48

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


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 159.55  E-value: 3.01e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  88 PSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGV-CRSLLCAA 166
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPpLRMAVVAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 167 PRWLRQHGPLTTLDDLQQHNCLLYsHFAGQ----RWQFSDAqGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEA 242
Cdd:cd08474   81 PAYLARHGTPEHPRDLLNHRCIRY-RFPTSgalyRWEFERG-GRELEVDVEGPLILNDSDLMLDAALDGLGIAYLFEDLV 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 556284038 243 RGAIASGALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08474  159 AEHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-286 1.01e-47

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


Pssm-ID: 176166  Cd Length: 197  Bit Score: 158.16  E-value: 1.01e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYSHFAGQ-RWQFSDAQGqEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIAS 248
Cdd:cd08477   81 LARHGTPTTPEDLARHECLGFSYWRARnRWRLEGPGG-EVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 556284038 249 GALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08477  160 GRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 88-286 1.74e-45

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


Pssm-ID: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 152.71  E-value: 1.74e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  88 PSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPE--AGAIARRLGVCRSLLCA 165
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPLedSSLVMRVLGQSRQRLVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 166 APRWLRQHGPLTTLDDLQQHNCL-LYSHFAGQRWQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARG 244
Cdd:cd08473   81 SPALLARLGRPRSPEDLAGLPTLsLGDVDGRHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPDHLCRE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 556284038 245 AIASGALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08473  161 ALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDFL 202
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-292 6.55e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 152.71  E-value: 6.55e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADEIAGE--RQR 85
Cdd:COG0583    7 RAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAElrALR 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  86 ADPSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPV---SLIGERIDVAIRITDNPEAGAIARRLGVCRSL 162
Cdd:COG0583   87 GGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLGEERLV 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 163 LCAAPRW-LRQHGPLTTLddlqqhncllyshfagqrwqfsdaqgqeasvavngnlsagiSSLLLEAAVAGCGIAMLPELE 241
Cdd:COG0583  167 LVASPDHpLARRAPLVNS-----------------------------------------LEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 556284038 242 ARGAIASGALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDALQRRLGE 292
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-284 1.30e-44

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


Pssm-ID: 176161  Cd Length: 202  Bit Score: 150.36  E-value: 1.30e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYSHFAGQR---WQFSDaQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAI 246
Cdd:cd08472   81 LARHGTPRHPEDLERHRAVGYFSARTGRvlpWEFQR-DGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 556284038 247 ASGALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLD 284
Cdd:cd08472  160 ASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVD 197
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-290 2.52e-41

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176159  Cd Length: 197  Bit Score: 141.68  E-value: 2.52e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYSHfagQRWQFSDaQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIASG 249
Cdd:cd08470   81 LERHGTPHSLADLDRHNCLLGTS---DHWRFQE-NGRERSVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAAG 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 556284038 250 ALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDALQRRL 290
Cdd:cd08470  157 RLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADAL 197
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-286 3.40e-40

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 138.88  E-value: 3.40e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYS--HFAGQRWQFSDAQGQeASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIA 247
Cdd:cd08479   81 LERHGAPASPEDLARHDCLVIRenDEDFGLWRLRNGDGE-ATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLR 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 556284038 248 SGALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08479  160 SGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-286 4.48e-38

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


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 133.45  E-value: 4.48e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 105 ISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRI--TDNPeAGAIARRLGVCRSLLCAAPRWLRQHGPLTTLDDL 182
Cdd:cd08475   16 VAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIgeLADS-TGLVARRLGTQRMVLCASPAYLARHGTPRTLEDL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 183 QQHNCLLYSHFAG-QRWQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIASGALEVVLPDWTPK 261
Cdd:cd08475   95 AEHQCIAYGRGGQpLPWRLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAPE 174

                        170       180
                 ....*....|....*....|....*
gi 556284038 262 ALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08475  175 GLPIHAVWPRTRHLPPKVRAAVDAL 199
PRK09801 PRK09801
LysR family transcriptional regulator;
8-292 3.00e-36

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 131.70  E-value: 3.00e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAG----ETVLLKTRGLTRIADEIAGER 83
Cdd:PRK09801  12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGqrcyEHALEILTQYQRLVDDVTQIK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  84 QRadPSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLL 163
Cdd:PRK09801  92 TR--PEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRIL 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 164 CAAPRWLRQHGPLTTLDDLQQHNCLLYSH--FAGQRWQFSDAQgQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELE 241
Cdd:PRK09801 170 CAAPEYLQKYPQPQSLQELSRHDCLVTKErdMTHGIWELGNGQ-EKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWD 248

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 556284038 242 ARGAIASGALEVVLPDWTPKAlSVYGIYLSRDYQPDGLPL---FLDA-LQRRLGE 292
Cdd:PRK09801 249 VLPFLESGKLVQVLPEYAQSA-NIWAVYREPLYRSMKLRVcveFLAAwCQQRLGK 302
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 10-272 1.79e-35

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 129.34  E-value: 1.79e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  10 YLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIAD--EIAGERQRAD 87
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQaaQDAIAALQVE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  88 PSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNP--EAGAIARRLGVCRSLLCA 165
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPfeDSDLVMRVLADRGHRLFA 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 166 APRWLRQHGPLTTLDDLQQHNCL-LYSHFAGQRWQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARG 244
Cdd:PRK14997 170 SPDLIARMGIPSAPAELSHWPGLsLASGKHIHRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLPVLMVKE 249

                        250       260
                 ....*....|....*....|....*...
gi 556284038 245 AIASGALEVVLPDWTPKALSVYGIYLSR 272
Cdd:PRK14997 250 QLAAGELVAVLEEWEPRREVIHAVFPSR 277
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-290 3.38e-34

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


Pssm-ID: 176160  Cd Length: 201  Bit Score: 123.40  E-value: 3.38e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRV-ACAHFTAMQLIsPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPR 168
Cdd:cd08471    1 GLLTVtAPVLFGRLHVL-PIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 169 WLRQHGPLTTLDDLQQHNCLLYS-HFAGQRWQFSDaQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIA 247
Cdd:cd08471   80 YLARHGTPKHPDDLADHDCIAFTgLSPAPEWRFRE-GGKERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 556284038 248 SGALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDALQRRL 290
Cdd:cd08471  159 AGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-259 8.79e-33

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


Pssm-ID: 176165  Cd Length: 197  Bit Score: 119.66  E-value: 8.79e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLisPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08476    1 GRLRVSLPLVGGLLL--PVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYSHFAG---QRWQFSDAQG----QEASVAVNGNLSAgisslLLEAAVAGCGIAMLPELEA 242
Cdd:cd08476   79 LARHGTPETPADLAEHACLRYRFPTTgklEPWPLRGDGGdpelRLPTALVCNNIEA-----LIEFALQGLGIACLPDFSV 153

                        170
                 ....*....|....*..
gi 556284038 243 RGAIASGALEVVLPDWT 259
Cdd:cd08476  154 REALADGRLVTVLDDYV 170
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-276 2.30e-32

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 121.41  E-value: 2.30e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   1 MDRVIAAQVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADEIA 80
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  81 gERQRA---DPSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLG 157
Cdd:PRK10632  81 -EQLYAfnnTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 158 VCRSLLCAAPRWLRQHGPLTTLDDLQQHNCLLYSHFAGQRWQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAML 237
Cdd:PRK10632 160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLTAGAGIAYV 239

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 556284038 238 PELEARGAIASGALEVVLPDWTPKALSVYGIYLSRDYQP 276
Cdd:PRK10632 240 PLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLP 278
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 90-286 4.47e-29

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176169  Cd Length: 198  Bit Score: 109.73  E-value: 4.47e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRW 169
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQHNCLLYSHF-AGQRWQFSDAqGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIAS 248
Cdd:cd08480   81 LARHGTPLTPQDLARHNCLGFNFRrALPDWPFRDG-GRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAA 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 556284038 249 GALEVVLPDWTPKALS-VYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08480  160 GRLVPVLEEYNPGDREpIHAVYVGGGRLPARVRAFLDFL 198
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-291 4.29e-28

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: 107.37  E-value: 4.29e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   89 SGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINN--HPVSLIGE-RIDVAIRITDNPEAGAIARRLGVCRSLLCA 165
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEgELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  166 APRWLRQHGPLTTLDDLQQHNCLLYSHFAGQRWQFSDAqGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGA 245
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRA-LRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 556284038  246 IASGAL-EVVLPDWTPKAlSVYGIYLSRDYQPDGLPLFLDALQRRLG 291
Cdd:pfam03466 160 LADGRLvALPLPEPPLPR-ELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 88-286 1.13e-24

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 98.18  E-value: 1.13e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  88 PSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAP 167
Cdd:cd08478    1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 168 RWLRQHGPLTTLDDLQQHNCLLYSHFAG-QRWQFSDAQGQEasVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAI 246
Cdd:cd08478   81 DYLARHGTPQSIEDLAQHQLLGFTEPASlNTWPIKDADGNL--LKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDI 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 556284038 247 ASGALEVVLPDWT-PKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd08478  159 AEGRLIPLFAEQTsDVRQPINAVYYRNTALSLRIRCFIDFL 199
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 91-284 7.42e-22

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


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 90.33  E-value: 7.42e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  91 TLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRWL 170
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 171 RQHGPLtTLDDLQQHnCLLYSHFAGQRWQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIASGA 250
Cdd:cd08432   81 AGLPLL-SPADLARH-TLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGR 158

                        170       180       190
                 ....*....|....*....|....*....|....
gi 556284038 251 LEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLD 284
Cdd:cd08432  159 LVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRD 192
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 18-257 6.79e-19

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 84.51  E-value: 6.79e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  18 SLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTR-GLTRIADeiAGERQRA-DPSGTLRVA 95
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIReIFDQLAE--ATRKLRArSAKGALTVS 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  96 CAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRWLRQHGP 175
Cdd:PRK11139 100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPALLNGGKP 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 176 LTTLDDLQQHNcLLYSHfAGQRWQ-FSDAQGQEAsVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIASGALEVV 254
Cdd:PRK11139 180 LKTPEDLARHT-LLHDD-SREDWRaWFRAAGLDD-LNVQQGPIFSHSSMALQAAIHGQGVALGNRVLAQPEIEAGRLVCP 256


                 ...
gi 556284038 255 LPD 257
Cdd:PRK11139 257 FDT 259
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-63 2.02e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 2.02e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 556284038    8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGE 63
Cdd:pfam00126   5 RLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-286 8.53e-16

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 74.17  E-value: 8.53e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  91 TLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPV---SLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAP 167
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSElleALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 168 RWLRQHGPLTTLDDLQQHNCLLYSHFAGQRwQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARgAIA 247
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLR-RLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELA 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 556284038 248 SGALEVVLPDWTPKALSVYGIYLSRDYQPDGLPLFLDAL 286
Cdd:cd05466  159 DGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
18-294 3.58e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 74.27  E-value: 3.58e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  18 SLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVL--LKtRGLTRIADEIAgERQRADPSGTLRVA 95
Cdd:PRK10086  30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFwaLK-SSLDTLNQEIL-DIKNQELSGTLTVY 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  96 CAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRL------GVCrsllcaAPRW 169
Cdd:PRK10086 108 SRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLmdeeilPVC------SPEY 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 170 LRQHGPLTTLDDLQQhnCLL------YSHFAGQRWQFSDAQGQEASVAVNgnlSAGI----SSLLLEAAVAGCGIAMLPE 239
Cdd:PRK10086 182 AERHALTGNPDNLRH--CTLlhdrqaWSNDSGTDEWHSWAQHFGVNLLPP---SSGIgfdrSDLAVIAAMNHIGVAMGRK 256

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 556284038 240 LEARGAIASGalEVVLPDWTPKALSVYGIYLS--RDYQPDGLPLFLDALQRRLGETL 294
Cdd:PRK10086 257 RLVQKRLASG--ELVAPFGDMEVKCHQHYYVTtlPGRQWPKIEAFIDWLKEQVKTTS 311
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 99-270 2.69e-13

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 66.94  E-value: 2.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  99 FTAMQLIsPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRWLRQHgPLTT 178
Cdd:cd08481   10 FGTRWLI-PRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGR-ALAA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 179 LDDLqQHNCLLYSHFAGQRW-QFSDAQGQEASVAVNGNLSAGIsSLLLEAAVAGCGIAMLPELEARGAIASGALEVVlpd 257
Cdd:cd08481   88 PADL-AHLPLLQQTTRPEAWrDWFEEVGLEVPTAYRGMRFEQF-SMLAQAAVAGLGVALLPRFLIEEELARGRLVVP--- 162

                        170
                 ....*....|...
gi 556284038 258 WTPKALSVYGIYL 270
Cdd:cd08481  163 FNLPLTSDKAYYL 175
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
13-257 3.64e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 59.60  E-value: 3.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  13 ICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRsTRRLTLTPAGETVLLKTRGLtRI--ADEIAGERQRADPSG 90
Cdd:PRK13348  13 VVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV-ALleADLLSTLPAERGSPP 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  91 TLRVACAHFTAMQLISPLLPDFLARyPLLRLEL--DINNHPVSLIgERIDV--AIRITDNPEAGAIARRLGVCRSLLCAA 166
Cdd:PRK13348  91 TLAIAVNADSLATWFLPALAAVLAG-ERILLELivDDQDHTFALL-ERGEVvgCVSTQPKPMRGCLAEPLGTMRYRCVAS 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 167 PRWLRQHGPLT-TLDDLQQHNCLLYSHFAGQRWQFSDAQGQEASVAVNGNLSAGISSLLLeAAVAGCGIAMLPELEARGA 245
Cdd:PRK13348 169 PAFAARYFAQGlTRHSALKAPAVAFNRKDTLQDSFLEQLFGLPVGAYPRHYVPSTHAHLA-AIRHGLGYGMVPELLIGPL 247

                        250
                 ....*....|..
gi 556284038 246 IASGALEVVLPD 257
Cdd:PRK13348 248 LAAGRLVDLAPG 259
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 107-251 1.06e-09

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. 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: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 56.77  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 107 PLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRL-GVCRSLLCaAPRWLRQhgpLTTLDDLQQH 185
Cdd:cd08488   17 PRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLfEAPLSPLC-TPELARQ---LREPADLARH 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556284038 186 NcLLYSHFAGQRWQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIASGAL 251
Cdd:cd08488   93 T-LLRSYRADEWPQWFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGAL 157
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
18-123 1.22e-09

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 58.06  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  18 SLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLT-LTPAG-------ETVLLKTRGLTRIADEIAGERQradps 89
Cdd:PRK12684  18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGriilasvERILQEVENLKRVGKEFAAQDQ----- 92

                         90       100       110
                 ....*....|....*....|....*....|....
gi 556284038  90 GTLRVACAHFTAMQLISPLLPDFLARYPLLRLEL 123
Cdd:PRK12684  93 GNLTIATTHTQARYALPAAIKEFKKRYPKVRLSI 126
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 101-251 5.92e-09

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 54.68  E-value: 5.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 101 AMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRL-GVCRSLLCaAPRWLRQhgpLTTL 179
Cdd:cd08484   11 AVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLfEAPLSPLC-TPELARR---LSEP 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556284038 180 DDLQQHNcLLYSHFAGQRWQFSDAQGQEASVaVNGNLSAGiSSLLLEAAVAGCGIAMLPELEARGAIASGAL 251
Cdd:cd08484   87 ADLANET-LLRSYRADEWPQWFEAAGVPPPP-INGPVFDS-SLLMVEAALQGAGVALAPPSMFSRELASGAL 155
rbcR CHL00180
LysR transcriptional regulator; Provisional
 17-141 8.77e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 55.41  E-value: 8.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  17 GSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADEI--AGERQRADPSGTLRV 94
Cdd:CHL00180  20 GSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETcrALEDLKNLQRGTLII 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 556284038  95 ACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPV---SLIGERIDVAI 141
Cdd:CHL00180 100 GASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRiawNVANGQIDIAI 149
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 19-195 1.13e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 55.38  E-value: 1.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  19 LSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLT-LTPAGETVL-------LKTRGLTRIADEIAGERqradpSG 90
Cdd:PRK12682  19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLdvierilREVGNIKRIGDDFSNQD-----SG 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  91 TLRVACAHFTAMQLISPLLPDFLARYPLLRLELDiNNHPVS----LIGERIDVAI---RITDNPEAGAIArrlgvCR--- 160
Cdd:PRK12682  94 TLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLH-QGSPDEiarmVISGEADIGIateSLADDPDLATLP-----CYdwq 167

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 556284038 161 -SLLCAAPRWLRQHGPLtTLDDLQQHNCLLYSH-FAG 195
Cdd:PRK12682 168 hAVIVPPDHPLAQEERI-TLEDLAEYPLITYHPgFTG 203
PRK10341 PRK10341
transcriptional regulator TdcA;
9-82 1.17e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 55.25  E-value: 1.17e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556284038   9 VYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLK----TRGLTRIADEIAGE 82
Cdd:PRK10341  14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRsesiTREMKNMVNEINGM 91
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 17-151 1.61e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 54.61  E-value: 1.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  17 GSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAG----ETVLLKTRGLTRIADEIAGERQRADpsGTL 92
Cdd:PRK11013  19 GSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlrlfEEVQRSYYGLDRIVSAAESLREFRQ--GQL 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556284038  93 RVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPV---SLIGERIDVAIRITDNPEAGA 151
Cdd:PRK11013  97 SIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLleeWLSAQRHDLGLTETLHTPAGT 158
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 99-251 4.51e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 52.40  E-value: 4.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  99 FTAMQLIsPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNP-EAGAIARRLG------VCRSLLcaAPRWLR 171
Cdd:cd08482   10 LLMRWLI-PRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPwPAGMQVIELFpervgpVCSPSL--APTVPL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 172 QHGPLTTLDDLQqhncLLYSHFAGQRW-QFSDAQGQEASvavngNLSAGIS----SLLLEAAVAGCGIAMLPELEARGAI 246
Cdd:cd08482   87 RQAPAAALLGAP----LLHTRSRPQAWpDWAAAQGLAPE-----KLGTGQSfehfYYLLEAAVAGLGVAIAPWPLVRDDL 157


                 ....*
gi 556284038 247 ASGAL 251
Cdd:cd08482  158 ASGRL 162
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 19-123 6.40e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 52.74  E-value: 6.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  19 LSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLT-LTPAG-------ETVLLKTRGLTRIADEIAGERqradpSG 90
Cdd:PRK12683  19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGkellqivERMLLDAENLRRLAEQFADRD-----SG 93

                         90       100       110
                 ....*....|....*....|....*....|...
gi 556284038  91 TLRVACAHFTAMQLISPLLPDFLARYPLLRLEL 123
Cdd:PRK12683  94 HLTVATTHTQARYALPKVVRQFKEVFPKVHLAL 126
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-124 7.79e-08

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 52.65  E-value: 7.79e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  10 YLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRiaDEIAGERQRAD-- 87
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQ--DLEAGRRAIHDva 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 556284038  88 --PSGTLRVACA-HFTAMqLISPLLPDFLARYPLLRLELD 124
Cdd:PRK11242  87 dlSRGSLRLAMTpTFTAY-LIGPLIDAFHARYPGITLTIR 125
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 20-129 8.15e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 52.46  E-value: 8.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  20 SAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADE-IAGERQRADPSGTLRVACAH 98
Cdd:PRK09906  19 TKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKaKLRARKIVQEDRQLTIGFVP 98

                         90       100       110
                 ....*....|....*....|....*....|.
gi 556284038  99 FTAMQLISPLLPDFLARYPLLRLELDINNHP 129
Cdd:PRK09906  99 SAEVNLLPKVLPMFRLRHPDTLIELVSLITT 129
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
15-257 1.04e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 52.08  E-value: 1.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  15 ELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRsTRRLTLTPAGETVLLKTRGLTRIADEIAGERQRADPSG-TLR 93
Cdd:PRK03635  15 REGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLGELPALDGTPlTLS 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  94 VAcahFTAMQLISPLLP---DFLARYPLLrLELDINNHPVSLigERI---DV--AIRITDNPEAGAIARRLGVCRSLLCA 165
Cdd:PRK03635  94 IA---VNADSLATWFLPalaPVLARSGVL-LDLVVEDQDHTA--ELLrrgEVvgAVTTEPQPVQGCRVDPLGAMRYLAVA 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 166 APRWLRQHGPL-TTLDDLQQHNCLLYSHfagqrwqfSDA-QGQEASVAVNGNLSAGISSLL------LEAAVAGCGIAML 237
Cdd:PRK03635 168 SPAFAARYFPDgVTAEALAKAPAVVFNR--------KDDlQDRFLRQAFGLPPGSVPCHYVpsseafVRAALAGLGWGMI 239

                        250       260
                 ....*....|....*....|
gi 556284038 238 PELEARGAIASGALEVVLPD 257
Cdd:PRK03635 240 PELQIEPELASGELVDLTPG 259
cysB PRK12681
HTH-type transcriptional regulator CysB;
20-117 1.16e-07

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 52.21  E-value: 1.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  20 SAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLT-LTPAGETV-------LLKTRGLTRIADEIAGERQradpsGT 91
Cdd:PRK12681  20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIiriareiLSKVESIKSVAGEHTWPDK-----GS 94

                         90       100
                 ....*....|....*....|....*.
gi 556284038  92 LRVACAHFTAMQLISPLLPDFLARYP 117
Cdd:PRK12681  95 LYIATTHTQARYALPPVIKGFIERYP 120
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
11-124 2.62e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 51.17  E-value: 2.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  11 LRICelGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLlktrgltRIADEIAGERQRA---- 86
Cdd:PRK15421  13 LRNC--GSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILL-------QLANQVLPQISQAlqac 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 556284038  87 -DPSGT-LRVACAHFTAMQLISPLLPDFLARYPllRLELD 124
Cdd:PRK15421  84 nEPQQTrLRIAIECHSCIQWLTPALENFHKNWP--QVEMD 121
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 92-253 4.37e-07

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 49.27  E-value: 4.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  92 LRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRLGVCRSLLCAAPRWLR 171
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 172 QhgplTTLDDLQQhncllyshFAGQRWQFSDAQGQE----ASVAVNGNLSAGISS----LLLEAAVAGCGIAMLPELEAR 243
Cdd:cd08483   82 D----RKVDSLAD--------LAGLPWLQERGTNEQrvwlASMGVVPDLERGVTFlpgqLVLEAARAGLGLSIQARALVE 149

                        170
                 ....*....|
gi 556284038 244 GAIASGALEV 253
Cdd:cd08483  150 PDIAAGRLTV 159
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 16-141 8.11e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.56  E-value: 8.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  16 LGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADEIAGERQRADP--SGTLR 93
Cdd:PRK11074  16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANgwRGQLS 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 556284038  94 VACAHFTAMQLISPLLPDFLARYPLLRLELDI---NNHPVSLIGERIDVAI 141
Cdd:PRK11074  96 IAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQevfNGVWDALADGRVDIAI 146
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 15-245 3.46e-06

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 47.72  E-value: 3.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  15 ELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADEIAGERQRADPSGTLRV 94
Cdd:PRK15092  24 DLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYSNLQGVLTI 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  95 ACAHFTAmqliSPLLPDFLAR----YPllRLELDINNHPVSLIGE-----RIDVAIRITDNPEAGAIARRlgVCRSLLCA 165
Cdd:PRK15092 104 GASDDTA----DTILPFLLNRvssvYP--KLALDVRVKRNAFMMEmlesqEVDLAVTTHRPSSFPALNLR--TSPTLWYC 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 166 APRWLRQHG---PLTTLDDLQQHNCLLYSHF--AGQRWQFSdaqgQEASvavngNLSAgissllLEAAV-AGCGIA---- 235
Cdd:PRK15092 176 AAEYVLQKGepiPLVLLDEPSPFRDMALATLnaAGIPWRIA----YVAS-----TLSA------VRAAVkAGLGVTarpv 240

                        250
                 ....*....|..
gi 556284038 236 --MLPELEARGA 245
Cdd:PRK15092 241 emMSPDLRVLGE 252
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-256 1.11e-05

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 45.38  E-value: 1.11e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  91 TLRVACAHFTAMQLISPLLPDFLARYPllRLELDINNHPVSLIGERI---DVAIRITDNPEAGAIARRLGVCRSLLCAAP 167
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYP--GVFFTVDVASTADVLEAVlsgEADIGLAFSPPPEPGIRVHSRQPAPIGAVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 168 RwlRQHG----PLTTLDDLQQHNCLLYSHFAGQRwQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEAR 243
Cdd:cd08426   79 P--PGHPlarqPSVTLAQLAGYPLALPPPSFSLR-QILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVR 155

                        170
                 ....*....|...
gi 556284038 244 GAIASGALeVVLP 256
Cdd:cd08426  156 REIRRGQL-VAVP 167
cbl PRK12679
HTH-type transcriptional regulator Cbl;
18-239 1.23e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 45.96  E-value: 1.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  18 SLSAAARALGMSRPMVSRYLEQMESWAGARL-IHRSTRRLTLTPAGETVLLKTRgltRIADEIAGERQRAD-----PSGT 91
Cdd:PRK12679  18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAE---RILNEASNVRRLADlftndTSGV 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  92 LRVACAHFTAMQLISPLLPDFLARYPLLRLELdINNHP---VSLI--GErIDVAI---RITDNPEAGAIArRLGVCRSLL 163
Cdd:PRK12679  95 LTIATTHTQARYSLPEVIKAFRELFPEVRLEL-IQGTPqeiATLLqnGE-ADIGIaseRLSNDPQLVAFP-WFRWHHSLL 171

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556284038 164 CAAPRWLRQHGPLtTLDDLQQHNCLLYSHFAGQRWQFsDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPE 239
Cdd:PRK12679 172 VPHDHPLTQITPL-TLESIAKWPLITYRQGITGRSRI-DDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAE 245
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-127 1.65e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 45.45  E-value: 1.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADEIagERQRAD 87
Cdd:PRK10837   9 EVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI--EQLFRE 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 556284038  88 PSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINN 127
Cdd:PRK10837  87 DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGN 126
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-85 2.12e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 45.18  E-value: 2.12e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556284038  10 YLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLTRIADEIAGERQR 85
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQ 85
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 107-251 3.66e-05

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 43.69  E-value: 3.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 107 PLLPDFLARYPLLRLELDINNHPVSLIGERIDVAIRITDNPEAGAIARRL-GVCRSLLCA---APRwlrqhgpLTTLDDL 182
Cdd:cd08487   17 PRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLlDAPLSVLCSpeiAKR-------LSHPADL 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 183 QqhNCLLYSHFAGQRW-QFSDAQGQEaSVAVNGNLSAGiSSLLLEAAVAGCGIAMLPELEARGAIASGAL 251
Cdd:cd08487   90 I--NETLLRSYRTDEWlQWFEAANMP-PIKIRGPVFDS-SRLMVEAAMQGAGVALAPAKMFSREIENGQL 155
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
12-86 4.68e-05

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 42.12  E-value: 4.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  12 RICELGSLSAAARALGMSRpmvSR---YLEQMESWAGARLIHRST--RR---LTLTPAGETVLLKTRGLTRIADEIAGER 83
Cdd:COG2005   29 AIDETGSISAAAKAMGMSY---KRawdLIDAMNNLLGEPLVERQTggKGgggARLTPEGRRLLALYRRLEAEAQRALAAL 105


                 ...
gi 556284038  84 QRA 86
Cdd:COG2005  106 FEE 108
PRK09791 PRK09791
LysR family transcriptional regulator;
8-135 8.18e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 43.60  E-value: 8.18e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038   8 QVYLRICELGSLSAAARALGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGLT---RIADEIAGERQ 84
Cdd:PRK09791  11 RAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILeelRAAQEDIRQRQ 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 556284038  85 rADPSGTLRVACAHFTAMQLISPLLPDFLARYPLLRLELdINNHPVSLIGE 135
Cdd:PRK09791  91 -GQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI-MEGQLVSMINE 139
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 91-254 4.58e-04

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: 40.27  E-value: 4.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  91 TLRVACAHFTAMQLISPLLPDFLARYPLLRLEL--DINNHPVSLIGE-RIDVAIRITDNPEAGAIARRLGVCRSLLCAAP 167
Cdd:cd08433    1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIveGLSGHLLEWLLNgRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 168 RWLRQHGPLTTLDDLQQHNCLLYSHFAGQRwQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEARGAIA 247
Cdd:cd08433   81 DAPLPRGAPVPLAELARLPLILPSRGHGLR-RLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVA 159


                 ....*..
gi 556284038 248 SGALEVV 254
Cdd:cd08433  160 AGRLVAA 166
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-240 6.00e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.57  E-value: 6.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  28 MSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLlktrgltRIADEIAGE----RQRADP-----SGTLRVACAH 98
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELR-------PFAQQTLLQwqqlRHTLDQqgpslSGELSLFCSV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  99 FTAMQLISPLLPDFLARYPLLRLEL-----------------DI------NNHPVSLIGERID-VAIRItdnpeagaIAR 154
Cdd:PRK11716  76 TAAYSHLPPILDRFRAEHPLVEIKLttgdaadavekvqsgeaDLaiaakpETLPASVAFSPIDeIPLVL--------IAP 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 155 RLGvcrsllCAAPRWLRQHGPlttldDLQQHNCLLYSH-FAGQR---WqFSD--------AQ--GQEASVAVngnlsagi 220
Cdd:PRK11716 148 ALP------CPVRQQLSQEKP-----DWSRIPFILPEHgPARRRidlW-FRRhkikpniyATvsGHEAIVSM-------- 207

                        250       260
                 ....*....|....*....|.
gi 556284038 221 ssllleaaVA-GCGIAMLPEL 240
Cdd:PRK11716 208 --------VAlGCGVGLLPEV 220
PBP2_IciA_ArgP cd08428
The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), ...
 107-258 6.55e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. 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: 176119 [Multi-domain]  Cd Length: 195  Bit Score: 39.92  E-value: 6.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 107 PLLPDFLARYP-LLRLELDINNHPVSLI--GERIDvAIRITDNPEAGAIARRLGVCRSLLCAAPRWLRQHGP--LT---- 177
Cdd:cd08428   17 PALAPVLKRERiLLDLIVDDEDRTHDLLrdGEVVG-CISTQAQPMQGCRSDYLGSMDYLLVASPDFAARYFPngLTreal 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 178 ---------TLDDLQQHncLLYSHFAGqrwqfsdAQGQEASVAVNGnlsagiSSLLLEAAVAGCGIAMLPELEARGAIAS 248
Cdd:cd08428   96 lkapavafnRKDDLHQS--FLQQHFGL-------PPGSYPCHYVPS------SEAFVDLAAQGLAYGMIPELQIEPELAS 160

                        170
                 ....*....|
gi 556284038 249 GALEVVLPDW 258
Cdd:cd08428  161 GELIDLAPGH 170
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 91-260 1.04e-03

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: 39.32  E-value: 1.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  91 TLRVACAHFTAMQLISPLLPDFLARYPLLRLELDINNHPVS---LIGERIDVAI--RITDNP--EAGAIARRLGVCrsLL 163
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVeqwLSAQQCDLGLvsTLHEPPgiERERLLRIDGVC--VL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038 164 CAAPRWLRQhgPLTTLDDLQQHNCLLYSHFAGQRwQFSDAQGQEASVAVNGNLSAGISSLLLEAAVAGCGIAMLPELEAR 243
Cdd:cd08456   79 PPGHRLAVK--KVLTPSDLEGEPFISLARTDGTR-QRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTAL 155

                        170
                 ....*....|....*..
gi 556284038 244 GAIASGaleVVLPDWTP 260
Cdd:cd08456  156 DYAAAG---LVVRRFSP 169
transpos_IS21 NF033546
IS21 family transposase;
18-98 6.17e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 37.57  E-value: 6.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556284038  18 SLSAAARALGMSRPMVSRYLEQMESWAGARLiHRSTRRLTLTPAGETVLL---------KTRGLTRIADEIagerQRADP 88
Cdd:NF033546  10 SIREIARELGISRNTVRKYLRRAGLDEPPKY-ERRPPRPSKLDPFEPYIPdwleahlrkPGVTATLLWEEL----RAEGY 84

                         90
                 ....*....|
gi 556284038  89 SGTLRVACAH 98
Cdd:NF033546  85 PGSYSTVRRY 94
PRK09986 PRK09986
LysR family transcriptional regulator;
21-72 7.16e-03

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 37.39  E-value: 7.16e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 556284038  21 AAARaLGMSRPMVSRYLEQMESWAGARLIHRSTRRLTLTPAGETVLLKTRGL 72
Cdd:PRK09986  27 AAAR-LNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRL 77
 
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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