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Conserved domains on  [gi|446893046|ref|WP_000970302|]
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MULTISPECIES: LysR family transcriptional regulator [Salmonella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-301 7.64e-40

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.00  E-value: 7.64e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  11 RDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSFQSLLDELR 90
Cdd:COG0583    4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  91 NPDKIIRGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRERSDFFSK--SLEFDeLVFKSGIIESEDLVYRKISP 168
Cdd:COG0583   84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAllEGELD-LAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 169 LKLVLCASPkyirkygriSHPgdLENHiivglhnhglsGPLTlfrqDESYTISGAVnvhlssnnllsvlnlvLEGKGINL 248
Cdd:COG0583  163 ERLVLVASP---------DHP--LARR-----------APLV----NSLEALLAAV----------------AAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446893046 249 MtPAWLATKYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFIED 301
Cdd:COG0583  201 L-PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-301 7.64e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.00  E-value: 7.64e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  11 RDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSFQSLLDELR 90
Cdd:COG0583    4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  91 NPDKIIRGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRERSDFFSK--SLEFDeLVFKSGIIESEDLVYRKISP 168
Cdd:COG0583   84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAllEGELD-LAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 169 LKLVLCASPkyirkygriSHPgdLENHiivglhnhglsGPLTlfrqDESYTISGAVnvhlssnnllsvlnlvLEGKGINL 248
Cdd:COG0583  163 ERLVLVASP---------DHP--LARR-----------APLV----NSLEALLAAV----------------AAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446893046 249 MtPAWLATKYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFIED 301
Cdd:COG0583  201 L-PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 98-299 1.02e-28

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: 109.07  E-value: 1.02e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  98 GSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRER-SDFFSKslEFDeLVFKSGIIESEDLVYRKISPLKLVLCAS 176
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRlVDLVEE--GFD-LAIRIGELPDSSLVARRLGPVRRVLVAS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 177 PKYIRKYGRISHPGDLENHIIVGLHNHGLSGPLTLFRQDESYTIsgAVNVHLSSNNLLSVLNLVLEGKGInLMTPAWLAT 256
Cdd:cd08422   78 PAYLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEV--RVRGRLVVNDGEALRAAALAGLGI-ALLPDFLVA 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 446893046 257 KYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFI 299
Cdd:cd08422  155 EDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-69 2.31e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.73  E-value: 2.31e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046   10 MRDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQ 69
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09801 PRK09801
LysR family transcriptional regulator;
4-306 5.73e-17

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 79.69  E-value: 5.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046   4 LINNRGM-RDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSF 82
Cdd:PRK09801   1 MLNSWPLaKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  83 QSLLDELRN----PDKIIRGSIKFS------APAIVceflankwiwEFTASYPDTKIYLDSRERS-DFFSKSLEFDelvf 151
Cdd:PRK09801  81 QRLVDDVTQiktrPEGMIRIGCSFGfgrshiAPAIT----------ELMRNYPELQVHFELFDRQiDLVQDNIDLD---- 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 152 ksgiIESED-----LVYRKISPLKLVLCASPKYIRKYGRISHPGDLENHIIVGLH----NHGLsGPLTLFRQDESYTISG 222
Cdd:PRK09801 147 ----IRINDeipdyYIAHLLTKNKRILCAAPEYLQKYPQPQSLQELSRHDCLVTKerdmTHGI-WELGNGQEKKSVKVSG 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 223 avnvHLSSNNLLSVLNLVLEGKGINLMTpAWLATKYLKNNELEIILPEWrVPDLPIYLVWRHRQYYSPLFQRFLSFIEDK 302
Cdd:PRK09801 222 ----HLSSNSGEIVLQWALEGKGIMLRS-EWDVLPFLESGKLVQVLPEY-AQSANIWAVYREPLYRSMKLRVCVEFLAAW 295


                 ....
gi 446893046 303 WNNR 306
Cdd:PRK09801 296 CQQR 299
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-301 7.64e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.00  E-value: 7.64e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  11 RDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSFQSLLDELR 90
Cdd:COG0583    4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  91 NPDKIIRGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRERSDFFSK--SLEFDeLVFKSGIIESEDLVYRKISP 168
Cdd:COG0583   84 ALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDAllEGELD-LAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 169 LKLVLCASPkyirkygriSHPgdLENHiivglhnhglsGPLTlfrqDESYTISGAVnvhlssnnllsvlnlvLEGKGINL 248
Cdd:COG0583  163 ERLVLVASP---------DHP--LARR-----------APLV----NSLEALLAAV----------------AAGLGIAL 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446893046 249 MtPAWLATKYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFIED 301
Cdd:COG0583  201 L-PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 98-299 1.02e-28

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: 109.07  E-value: 1.02e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  98 GSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRER-SDFFSKslEFDeLVFKSGIIESEDLVYRKISPLKLVLCAS 176
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRlVDLVEE--GFD-LAIRIGELPDSSLVARRLGPVRRVLVAS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 177 PKYIRKYGRISHPGDLENHIIVGLHNHGLSGPLTLFRQDESYTIsgAVNVHLSSNNLLSVLNLVLEGKGInLMTPAWLAT 256
Cdd:cd08422   78 PAYLARHGTPQTPEDLARHRCLGYRLPGRPLRWRFRRGGGEVEV--RVRGRLVVNDGEALRAAALAGLGI-ALLPDFLVA 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 446893046 257 KYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFI 299
Cdd:cd08422  155 EDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 119-290 2.17e-22

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: 92.58  E-value: 2.17e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 119 EFTASYPDTKIYLDSRER-SDFFSKSleFDeLVFKSGIIESEDLVYRKISPLKLVLCASPKYIRKYGRISHPGDLENHII 197
Cdd:cd08472   22 DFLARYPDIELDLGVSDRpVDLIREG--VD-CVIRVGELADSSLVARRLGELRMVTCASPAYLARHGTPRHPEDLERHRA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 198 VGLHNH--GLSGPLTLFRQDESYTISG----AVN---VHlssnnllsvLNLVLEGKGInLMTPAWLATKYLKNNELEIIL 268
Cdd:cd08472   99 VGYFSArtGRVLPWEFQRDGEEREVKLpsrvSVNdseAY---------LAAALAGLGI-IQVPRFMVRPHLASGRLVEVL 168

                        170       180
                 ....*....|....*....|..
gi 446893046 269 PEWRVPDLPIYLVWRHRQYYSP 290
Cdd:cd08472  169 PDWRPPPLPVSLLYPHRRHLSP 190
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 119-299 4.88e-18

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: 80.74  E-value: 4.88e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 119 EFTASYPDTKIYLDSRERS-DFFSKSleFDeLVFKSGIIESEDLVYRKISPLKLVLCASPKYIRKYGRISHPGDLENHII 197
Cdd:cd08477   22 EYLARYPDVRVDLVLSDRLvDLVEEG--FD-AAFRIGELADSSLVARPLAPYRMVLCASPDYLARHGTPTTPEDLARHEC 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 198 VGLHNHGLSGPLTLFRQD--ESYTISG-------------AVNvhlssnnllsvlnlvleGKGInLMTPAWLATKYLKNN 262
Cdd:cd08477   99 LGFSYWRARNRWRLEGPGgeVKVPVSGrltvnsgqalrvaALA-----------------GLGI-VLQPEALLAEDLASG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 446893046 263 ELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFI 299
Cdd:cd08477  161 RLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-69 2.31e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.73  E-value: 2.31e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046   10 MRDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQ 69
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09801 PRK09801
LysR family transcriptional regulator;
4-306 5.73e-17

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 79.69  E-value: 5.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046   4 LINNRGM-RDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSF 82
Cdd:PRK09801   1 MLNSWPLaKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  83 QSLLDELRN----PDKIIRGSIKFS------APAIVceflankwiwEFTASYPDTKIYLDSRERS-DFFSKSLEFDelvf 151
Cdd:PRK09801  81 QRLVDDVTQiktrPEGMIRIGCSFGfgrshiAPAIT----------ELMRNYPELQVHFELFDRQiDLVQDNIDLD---- 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 152 ksgiIESED-----LVYRKISPLKLVLCASPKYIRKYGRISHPGDLENHIIVGLH----NHGLsGPLTLFRQDESYTISG 222
Cdd:PRK09801 147 ----IRINDeipdyYIAHLLTKNKRILCAAPEYLQKYPQPQSLQELSRHDCLVTKerdmTHGI-WELGNGQEKKSVKVSG 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 223 avnvHLSSNNLLSVLNLVLEGKGINLMTpAWLATKYLKNNELEIILPEWrVPDLPIYLVWRHRQYYSPLFQRFLSFIEDK 302
Cdd:PRK09801 222 ----HLSSNSGEIVLQWALEGKGIMLRS-EWDVLPFLESGKLVQVLPEY-AQSANIWAVYREPLYRSMKLRVCVEFLAAW 295


                 ....
gi 446893046 303 WNNR 306
Cdd:PRK09801 296 CQQR 299
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
15-195 1.42e-16

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 78.65  E-value: 1.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  15 IFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSFQSLLDELRNPDK 94
Cdd:PRK10632   9 VFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNN 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  95 IIRGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSR-ERSDFFSKSLefdELVFKSGIIESEDLVYRKISPLKLVL 173
Cdd:PRK10632  89 TPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGiPAPDLIADGL---DVVIRVGALQDSSLFSRRLGAMPMVV 165

                        170       180
                 ....*....|....*....|..
gi 446893046 174 CASPKYIRKYGRISHPGDLENH 195
Cdd:PRK10632 166 CAAKSYLAQYGTPEKPADLSSH 187
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 10-303 2.66e-16

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 77.72  E-value: 2.66e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  10 MRDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSFQSLLDEL 89
Cdd:PRK14997   4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  90 RNPDKIIRGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLD-SRERSDFFSKSLEFDELVfKSGIIESEDLVYRKISP 168
Cdd:PRK14997  84 AALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEaTNRRVDVVGEGVDVAIRV-RPRPFEDSDLVMRVLAD 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 169 LKLVLCASPKYIRKYGRISHPGDLEN----HIIVGLHNHG--LSGPltlfrqdesytiSGA-VNVHLSSNNLLSVLNLVL 241
Cdd:PRK14997 163 RGHRLFASPDLIARMGIPSAPAELSHwpglSLASGKHIHRweLYGP------------QGArAEVHFTPRMITTDMLALR 230

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446893046 242 EG--KGINLMT-PAWLATKYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFIEDKW 303
Cdd:PRK14997 231 EAamAGVGLVQlPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEY 295
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 119-299 1.03e-14

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: 71.47  E-value: 1.03e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 119 EFTASYPDTKIYLDSRERS-DFFSKSleFDeLVFKSGIIESEDLVYRKISPLKLVLCASPKYIRKYGRISHPGDLENH-I 196
Cdd:cd08479   22 DFAKRYPELEVQLELTDRPvDLVEEG--FD-LDIRVGDLPDSSLIARKLAPNRRILCASPAYLERHGAPASPEDLARHdC 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 197 IVGLHNHGLSGPLTLFRQDESYTISgaVNVHLSSNNLLSVLNLVLEGKGInLMTPAWLATKYLKNNELEIILPEWRVPDL 276
Cdd:cd08479   99 LVIRENDEDFGLWRLRNGDGEATVR--VRGALSSNDGEVVLQWALDGHGI-ILRSEWDVAPYLRSGRLVRVLPDWQLPDA 175

                        170       180
                 ....*....|....*....|...
gi 446893046 277 PIYLVWRHRQYYSPLFQRFLSFI 299
Cdd:cd08479  176 DIWAVYPSRLSRSARVRVFVDFL 198
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-303 2.11e-14

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: 70.78  E-value: 2.11e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046   97 RGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRERSDFFSKSL--EFDeLVFKSGIIESEDLVYRKISPLKLVLC 174
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLegELD-LAIRRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  175 ASPKYIRKYGRISHPGDLENHIIVG--------------LHNHGLSgPLTLFRQDESYTISGAVnvhlssnnllsvlnlv 240
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILlppgsglrdlldraLRAAGLR-PRVVLEVNSLEALLQLV---------------- 142

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446893046  241 LEGKGINLMtPAWLATKYLKNNELEII-LPEWRVPdLPIYLVWRHRQYYSPLFQRFLSFIEDKW 303
Cdd:pfam03466 143 AAGLGIALL-PRSAVARELADGRLVALpLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-298 2.42e-12

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: 64.88  E-value: 2.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  97 RGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRERS-DFFSKSleFD-ELVFKSGIIESEDLVYRKISPLKLVLC 174
Cdd:cd08473    2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRvDLIEEG--IDvALRVRFPPLEDSSLVMRVLGQSRQRLV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 175 ASPKYIRKYGRISHPGDLENHIIVGLHNHGLSGPLTLFRQD-ESYTI--------SGAVNVHlssnnllsvlNLVLEGKG 245
Cdd:cd08473   80 ASPALLARLGRPRSPEDLAGLPTLSLGDVDGRHSWRLEGPDgESITVrhrprlvtDDLLTLR----------QAALAGVG 149

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446893046 246 INLMtPAWLATKYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSF 298
Cdd:cd08473  150 IALL-PDHLCREALRAGRLVRVLPDWTPPRGIVHAVFPSRRGLLPAVRALIDF 201
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 117-284 4.30e-12

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: 64.11  E-value: 4.30e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 117 IWEFTASYPDTKIYLDSrerSDFFSKSLE--FDELVFKSGIIESEDLVYRKISPLKLVLCASPKYIRKYGRISHPGDLEN 194
Cdd:cd08475   20 LLELARRHPELELELSF---SDRFVDLIEegIDLAVRIGELADSTGLVARRLGTQRMVLCASPAYLARHGTPRTLEDLAE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 195 H-IIVGLHNhGLSGPLTLFRQDESYTiSGAVNVHLSSNNLLSVLNLVLEGKGINLMtPAWLATKYLKNNELEIILPEWRV 273
Cdd:cd08475   97 HqCIAYGRG-GQPLPWRLADEQGRLV-RFRPAPRLQFDDGEAIADAALAGLGIAQL-PTWLVADHLQRGELVEVLPELAP 173

                        170
                 ....*....|....
gi 446893046 274 PDLPIYLVW---RH 284
Cdd:cd08475  174 EGLPIHAVWprtRH 187
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 120-302 1.14e-10

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: 60.02  E-value: 1.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 120 FTASYPDTKIYLD-SRERSDFFSKSleFDeLVFKSGIIESEDLVYRKISPLKLVLCASPKYIRKYGRISHPGDLENH-II 197
Cdd:cd08470   23 FMQRYPKLEVDIElTNRVVDLVSEG--FD-LAIRLGRLTDSSLMARRLASRRHYVCASPAYLERHGTPHSLADLDRHnCL 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 198 VGLHNHGL---SGPLTLFRQDESYTISGAVNVHLSSNnllsvlnlvlegKGINL-MTPAWLATKYLKNNELEIILPEWRV 273
Cdd:cd08470  100 LGTSDHWRfqeNGRERSVRVQGRWRCNSGVALLDAAL------------KGMGLaQLPDYYVDEHLAAGRLVPVLEDYRP 167

                        170       180
                 ....*....|....*....|....*....
gi 446893046 274 PDLPIYLVWRHRQYYSPLFQRFLSFIEDK 302
Cdd:cd08470  168 PDEGIWALYPHNRHLSPKVRLLVDYLADA 196
PRK10341 PRK10341
transcriptional regulator TdcA;
14-140 1.52e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.87  E-value: 1.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  14 MIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSFQSLLDELRNPD 93
Cdd:PRK10341  13 VVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMS 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446893046  94 KIIRGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRERSDFF 140
Cdd:PRK10341  93 SEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFL 139
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-299 1.76e-08

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: 53.62  E-value: 1.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  97 RGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRERsdffsksleFDELV---FKSGI-----IEsEDLVYRKISP 168
Cdd:cd08474    2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDG---------LVDIVaegFDAGIrlgesVE-KDMVAVPLGP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 169 -LKLVLCASPKYIRKYGRISHPGDLENHIIVGL---HNHGL----------------SGPLTLfrqDESYTISGAVnvhl 228
Cdd:cd08474   72 pLRMAVVASPAYLARHGTPEHPRDLLNHRCIRYrfpTSGALyrweferggrelevdvEGPLIL---NDSDLMLDAA---- 144

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446893046 229 ssnnllsvlnlvLEGKGInLMTPAWLATKYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFI 299
Cdd:cd08474  145 ------------LDGLGI-AYLFEDLVAEHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-194 2.12e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 54.62  E-value: 2.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  16 FIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKritSSFQSL---LDELRNP 92
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALK---SSLDTLnqeILDIKNQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  93 DkiIRGSIK-FSAPAIVCEFLANKwIWEFTASYPDtkIYLDSR---ERSDF----FSKSLEFDELvfKSGIIESEDLVYR 164
Cdd:PRK10086  99 E--LSGTLTvYSRPSIAQCWLVPR-LADFTRRYPS--ISLTILtgnENVNFqragIDLAIYFDDA--PSAQLTHHFLMDE 171

                        170       180       190
                 ....*....|....*....|....*....|
gi 446893046 165 KISPlklvLCaSPKYIRKYGRISHPGDLEN 194
Cdd:PRK10086 172 EILP----VC-SPEYAERHALTGNPDNLRH 196
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 161-298 3.80e-08

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: 52.53  E-value: 3.80e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 161 LVYRKISPLKLVLCASPKYIRKYGRISHPGDLENHIIVGLHNHGLSGPLTLFRQDESY-----------TISGAVNVhls 229
Cdd:cd08471   62 LVATRVGSVRRVVCASPAYLARHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERsvrvrprltvnTVEAAIAA--- 138

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 230 snnllsvlnlVLEGKGI-NLMtpAWLATKYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSF 298
Cdd:cd08471  139 ----------ALAGLGLtRVL--SYQVAEELAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDF 196
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 16-135 1.20e-06

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 49.18  E-value: 1.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  16 FIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQtAYASMKRitssfQSL--LDE----L 89
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGE-VYLRYAR-----RALqdLEAgrraI 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446893046  90 RNPDKIIRGSIKFSAPAIVCEFLANKWIWEFTASYPDtkIYLDSRE 135
Cdd:PRK11242  83 HDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPG--ITLTIRE 126
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-299 1.53e-06

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: 47.98  E-value: 1.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  99 SIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLDSRERSDFFSKSLEFD-ELVFKSGIIESEDLVYRKISPLKLVLCASP 177
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGElDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 178 KYIRKYGRISHPGDLENHIIVGLHN--------------HGLSgPLTLFRQDESYTISGAVnvhlssnnllsvlnlvLEG 243
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERgsglrrlldrafaeAGFT-PNIALEVDSLEAIKALV----------------AAG 143

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446893046 244 KGINLMtPAWLAtKYLKNNELEIILPEWRVPDLPIYLVWRHRQYYSPLFQRFLSFI 299
Cdd:cd05466  144 LGIALL-PESAV-EELADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09791 PRK09791
LysR family transcriptional regulator;
16-129 2.92e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 47.83  E-value: 2.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  16 FIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSFQSLLDELRNPDKI 95
Cdd:PRK09791  13 FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQ 92

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446893046  96 IRGSIKFSAPAIVCEFLANKWIWEFTASYPDTKI 129
Cdd:PRK09791  93 LAGQINIGMGASIARSLMPAVISRFHQQHPQVKV 126
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
16-90 4.23e-06

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 47.49  E-value: 4.23e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446893046  16 FIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSFQSLLDELR 90
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84
PRK09986 PRK09986
LysR family transcriptional regulator;
16-85 9.81e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 46.25  E-value: 9.81e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446893046  16 FIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITSSF-QSL 85
Cdd:PRK09986  15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAeQSL 85
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 2-69 1.29e-05

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 45.92  E-value: 1.29e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446893046   2 MELinnRGMRdwmIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQ 69
Cdd:PRK09906   1 MEL---RHLR---YFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGE 62
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 119-195 1.38e-05

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: 44.93  E-value: 1.38e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446893046 119 EFTASYPDTKIYLDSRER-SDFFSKSleFDeLVFKSGIIESEDLVYRKISPLKLVLCASPKYIRKYGRISHPGDLENH 195
Cdd:cd08476   20 AFMQRYPEIELDLDFSDRlVDVIDEG--FD-AVIRTGELPDSRLMSRRLGSFRMVLVASPDYLARHGTPETPADLAEH 94
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 24-126 3.05e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 44.83  E-value: 3.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  24 NLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQtAYASmkRITSSFQSLLD---ELRNPDKiiRGSI 100
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQ-RYFL--DIREIFDQLAEatrKLRARSA--KGAL 96

                         90       100       110
                 ....*....|....*....|....*....|
gi 446893046 101 KFSAPAIvcefLANKW----IWEFTASYPD 126
Cdd:PRK11139  97 TVSLLPS----FAIQWlvprLSSFNEAHPD 122
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
16-78 5.16e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 44.19  E-value: 5.16e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446893046  16 FIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDShHLELTGAGQTAYASMKRI 78
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQRLLRHLRQV 71
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 119-217 5.35e-05

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: 43.48  E-value: 5.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 119 EFTASYPDtkIYLD---SRERSDFFsksLEFDELVFKSGIIESEDLVYRKISPLKLVLCASPKYIRKYGRISHPGDLENH 195
Cdd:cd08480   22 AFLARYPE--ILVDlslTDEVVDLL---AERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSYLARHGTPLTPQDLARH 96

                         90       100
                 ....*....|....*....|..
gi 446893046 196 IIVGlHNHGLSGPLTLFRQDES 217
Cdd:cd08480   97 NCLG-FNFRRALPDWPFRDGGR 117
rbcR CHL00180
LysR transcriptional regulator; Provisional
 15-132 5.92e-05

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 43.86  E-value: 5.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  15 IFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRITS----SFQSLLDeLR 90
Cdd:CHL00180  12 ILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlceeTCRALED-LK 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446893046  91 NpdkIIRGSIKFSAPAIVCEFLANKWIWEFTASYPDTKIYLD 132
Cdd:CHL00180  91 N---LQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQ 129
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 15-85 6.80e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 43.83  E-value: 6.80e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446893046  15 IFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAG-------QTAYASMKRITSSFQSL 85
Cdd:PRK11013  11 IFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlrlfeevQRSYYGLDRIVSAAESL 88
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 117-200 1.86e-04

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: 41.94  E-value: 1.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046 117 IWEFTASYPDTKIYLDSRE--------RSDffskslefdeLVFKSGIIESEDLVYRKI--SPLKLVlcASPKYIRKYGRI 186
Cdd:cd08478   22 IAKFRERYPDIELELVSNEgiidlierKTD----------VAIRIGELTDSTLHARPLgkSRLRIL--ASPDYLARHGTP 89

                         90
                 ....*....|....
gi 446893046 187 SHPGDLENHIIVGL 200
Cdd:cd08478   90 QSIEDLAQHQLLGF 103
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 16-78 1.08e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 40.05  E-value: 1.08e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446893046  16 FIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQTAYASMKRI 78
Cdd:PRK11233   9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAI 71
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 19-69 1.25e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 39.93  E-value: 1.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446893046  19 VAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQ 69
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE 63
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
34-101 3.05e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 38.65  E-value: 3.05e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446893046  34 ISISAVSKSLSRLENSIEVTLLRRDSHHLELTGAGQT--AYAsmKRITSSFQSLLDELRNPDKIIRGSIK 101
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEElrPFA--QQTLLQWQQLRHTLDQQGPSLSGELS 70
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 10-57 4.43e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 38.13  E-value: 4.43e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 446893046  10 MRDWMIFIKVAEVGNLSRAARELDISISAVSKSLSRLENSIEVTLLRR 57
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDR 52
 
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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