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Conserved domains on  [gi|446086181|ref|WP_000164036|]
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MULTISPECIES: LysR family transcriptional regulator [Gammaproteobacteria]

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];
6-305 9.95e-35

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.90  E-value: 9.95e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   6 LKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNN 85
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  86 FIADYKHEKRGRVTIYAPTGIITYLSKHVIDKIKDIG-DITLSLKTCNLER--NAFYEGvefpdDCDVLISYAPPKDESL 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHpGVRLELREGNSDRlvDALLEG-----ELDLAIRLGPPPDPGL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 163 VASFITQYAVTAYASQRylekHPISRPDElehhscilidsmmiddaniwrfnvagskevrdyrvkgnyVCDNTQSALELA 242
Cdd:COG0583  156 VARPLGEERLVLVASPD----HPLARRAP---------------------------------------LVNSLEALLAAV 192

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446086181 243 RNHLGIVFAPDKSVQSDLQDGTLVPCFQQPYEWWLDLVAIFRKREYQPWRVQYVLDEMLREIR 305
Cdd:COG0583  193 AAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-305 9.95e-35

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.90  E-value: 9.95e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   6 LKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNN 85
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  86 FIADYKHEKRGRVTIYAPTGIITYLSKHVIDKIKDIG-DITLSLKTCNLER--NAFYEGvefpdDCDVLISYAPPKDESL 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHpGVRLELREGNSDRlvDALLEG-----ELDLAIRLGPPPDPGL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 163 VASFITQYAVTAYASQRylekHPISRPDElehhscilidsmmiddaniwrfnvagskevrdyrvkgnyVCDNTQSALELA 242
Cdd:COG0583  156 VARPLGEERLVLVASPD----HPLARRAP---------------------------------------LVNSLEALLAAV 192

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446086181 243 RNHLGIVFAPDKSVQSDLQDGTLVPCFQQPYEWWLDLVAIFRKREYQPWRVQYVLDEMLREIR 305
Cdd:COG0583  193 AAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 149-300 2.31e-26

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: 103.29  E-value: 2.31e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 149 DVLISYAPPKDESLVASFITQYAVTAYASQRYLEKHPI-SRPDELEHHSCILIdsMMIDDANIWRFNVAGskEVRDYRVK 227
Cdd:cd08422   49 DLAIRIGELPDSSLVARRLGPVRRVLVASPAYLARHGTpQTPEDLARHRCLGY--RLPGRPLRWRFRRGG--GEVEVRVR 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446086181 228 GNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVPCFQqpyEWW---LDLVAIFRKREYQPWRVQYVLDEM 300
Cdd:cd08422  125 GRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRVLP---DWRpppLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-66 2.35e-12

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 60.86  E-value: 2.35e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 446086181    9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFG 66
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 21-272 3.09e-12

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 66.02  E-value: 3.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  21 ENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRneqlnnfIADYKHEKR----- 95
Cdd:PRK11139  21 LSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQ-------LAEATRKLRarsak 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  96 GRVTIYA-PTGIITYLSKHVIDKIKDIGDITLSLKTCNLErnafyegVEF-PDDCDVLISYAPPKDESLVASFITQYAVT 173
Cdd:PRK11139  94 GALTVSLlPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRL-------EDFlRDDVDVAIRYGRGNWPGLRVEKLLDEYLL 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 174 AYASQRYLEK-HPISRPDELEHHSciLIDSmmiDDANIWR--FNVAGskeVRDYRVKGNYVCDNTQSALELARNHLGIVF 250
Cdd:PRK11139 167 PVCSPALLNGgKPLKTPEDLARHT--LLHD---DSREDWRawFRAAG---LDDLNVQQGPIFSHSSMALQAAIHGQGVAL 238

                        250       260
                 ....*....|....*....|..
gi 446086181 251 APDKSVQSDLQDGTLVPCFQQP 272
Cdd:PRK11139 239 GNRVLAQPEIEAGRLVCPFDTV 260
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-305 9.95e-35

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.90  E-value: 9.95e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   6 LKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNN 85
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  86 FIADYKHEKRGRVTIYAPTGIITYLSKHVIDKIKDIG-DITLSLKTCNLER--NAFYEGvefpdDCDVLISYAPPKDESL 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHpGVRLELREGNSDRlvDALLEG-----ELDLAIRLGPPPDPGL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 163 VASFITQYAVTAYASQRylekHPISRPDElehhscilidsmmiddaniwrfnvagskevrdyrvkgnyVCDNTQSALELA 242
Cdd:COG0583  156 VARPLGEERLVLVASPD----HPLARRAP---------------------------------------LVNSLEALLAAV 192

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446086181 243 RNHLGIVFAPDKSVQSDLQDGTLVPCFQQPYEWWLDLVAIFRKREYQPWRVQYVLDEMLREIR 305
Cdd:COG0583  193 AAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 149-300 2.31e-26

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: 103.29  E-value: 2.31e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 149 DVLISYAPPKDESLVASFITQYAVTAYASQRYLEKHPI-SRPDELEHHSCILIdsMMIDDANIWRFNVAGskEVRDYRVK 227
Cdd:cd08422   49 DLAIRIGELPDSSLVARRLGPVRRVLVASPAYLARHGTpQTPEDLARHRCLGY--RLPGRPLRWRFRRGG--GEVEVRVR 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446086181 228 GNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVPCFQqpyEWW---LDLVAIFRKREYQPWRVQYVLDEM 300
Cdd:cd08422  125 GRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRVLP---DWRpppLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 146-267 3.25e-16

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: 75.73  E-value: 3.25e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 146 DDCDVLISYAPPKDESLVASFITQYAVTAYASQRYLEKH-PISRPDELEHHSCILIDSMMIDDAniWRFnvAGSKEVRDY 224
Cdd:cd08477   46 EGFDAAFRIGELADSSLVARPLAPYRMVLCASPDYLARHgTPTTPEDLARHECLGFSYWRARNR--WRL--EGPGGEVKV 121

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446086181 225 RVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVP 267
Cdd:cd08477  122 PVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASGRLVE 164
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 149-303 2.55e-14

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: 70.42  E-value: 2.55e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 149 DVLISYAPPKDESLVASFITQYAVTAYASQRYLEKH-PISRPDELEHHSCILIDSmmiddaNIWRFNVAGSKevRDYRVK 227
Cdd:cd08470   49 DLAIRLGRLTDSSLMARRLASRRHYVCASPAYLERHgTPHSLADLDRHNCLLGTS------DHWRFQENGRE--RSVRVQ 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 228 GNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVPC---FQQPYE--WwldlvAIFRKREYQPWRVQYVLDeMLR 302
Cdd:cd08470  121 GRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAAGRLVPVledYRPPDEgiW-----ALYPHNRHLSPKVRLLVD-YLA 194


                 .
gi 446086181 303 E 303
Cdd:cd08470  195 D 195
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 176-276 8.42e-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 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: 69.03  E-value: 8.42e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 176 ASQRYLEKHPI-SRPDELEHHSCILidsmmiddaniWRFNVAGS---------KEVRDYRVKGNYVCDNTQSALELARNH 245
Cdd:cd08474   79 ASPAYLARHGTpEHPRDLLNHRCIR-----------YRFPTSGAlyrwefergGRELEVDVEGPLILNDSDLMLDAALDG 147

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446086181 246 LGIVFAPDKSVQSDLQDGTLVPCFQqpyEWW 276
Cdd:cd08474  148 LGIAYLFEDLVAEHLASGRLVRVLE---DWS 175
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 140-271 2.15e-13

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: 67.92  E-value: 2.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 140 EGVefpdDCdvLISYAPPKDESLVASFITQYAVTAYASQRYLEKH-PISRPDELEHHscILIDSMMIDDANI--WRFNVA 216
Cdd:cd08472   46 EGV----DC--VIRVGELADSSLVARRLGELRMVTCASPAYLARHgTPRHPEDLERH--RAVGYFSARTGRVlpWEFQRD 117

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446086181 217 GskEVRDYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVPCFQQ 271
Cdd:cd08472  118 G--EEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHLASGRLVEVLPD 170
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-66 2.35e-12

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 60.86  E-value: 2.35e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 446086181    9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFG 66
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 146-298 2.83e-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 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: 64.54  E-value: 2.83e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 146 DDCDVLISYAPPKDESLVASFITQYAVTAYASQRYLEKHPI-SRPDELEHHSCILI---DSmmidDANIWRFnVAGSKEV 221
Cdd:cd08479   46 EGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAYLERHGApASPEDLARHDCLVIrenDE----DFGLWRL-RNGDGEA 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 222 RdYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVPCFQQpyeWWL---DLVAIFRKREYQPWRVQYVLD 298
Cdd:cd08479  121 T-VRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRSGRLVRVLPD---WQLpdaDIWAVYPSRLSRSARVRVFVD 196
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 21-272 3.09e-12

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 66.02  E-value: 3.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  21 ENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRneqlnnfIADYKHEKR----- 95
Cdd:PRK11139  21 LSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQ-------LAEATRKLRarsak 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  96 GRVTIYA-PTGIITYLSKHVIDKIKDIGDITLSLKTCNLErnafyegVEF-PDDCDVLISYAPPKDESLVASFITQYAVT 173
Cdd:PRK11139  94 GALTVSLlPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRL-------EDFlRDDVDVAIRYGRGNWPGLRVEKLLDEYLL 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 174 AYASQRYLEK-HPISRPDELEHHSciLIDSmmiDDANIWR--FNVAGskeVRDYRVKGNYVCDNTQSALELARNHLGIVF 250
Cdd:PRK11139 167 PVCSPALLNGgKPLKTPEDLARHT--LLHD---DSREDWRawFRAAG---LDDLNVQQGPIFSHSSMALQAAIHGQGVAL 238

                        250       260
                 ....*....|....*....|..
gi 446086181 251 APDKSVQSDLQDGTLVPCFQQP 272
Cdd:PRK11139 239 GNRVLAQPEIEAGRLVCPFDTV 260
rbcR CHL00180
LysR transcriptional regulator; Provisional
 9-115 3.17e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.20  E-value: 3.17e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIA 88
Cdd:CHL00180   8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALE 87

                         90       100
                 ....*....|....*....|....*..
gi 446086181  89 DYKHEKRGRVTIYAPTGIITYLSKHVI 115
Cdd:CHL00180  88 DLKNLQRGTLIIGASQTTGTYLMPRLI 114
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-305 3.97e-11

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: 61.54  E-value: 3.97e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   95 RGRVTIYAPTGIITYLSKHVIDK-IKDIGDITLSLKTCNLER--NAFYEGvefpdDCDVLISYAPPKDESLVASFITQYA 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARfRERYPDVELELTEGNSEEllDLLLEG-----ELDLAIRRGPPDDPGLEARPLGEEP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  172 VTAYASQRY-LEKHPISRPDELEHHSCILIDSmmiDDANIWRFNVAGSKEVRDYRVkgNYVCDNTQSALELARNHLGIVF 250
Cdd:pfam03466  76 LVLVAPPDHpLARGEPVSLEDLADEPLILLPP---GSGLRDLLDRALRAAGLRPRV--VLEVNSLEALLQLVAAGLGIAL 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446086181  251 APDKSVQSDLQDGTLVPCFQQPYEWWLDLVAIFRKREYQPWRVQYVLDEMLREIR 305
Cdd:pfam03466 151 LPRSAVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK09801 PRK09801
LysR family transcriptional regulator;
9-322 1.85e-10

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 60.82  E-value: 1.85e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIA 88
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  89 DYKHEKRGRVTIYAPTGI-ITYLSKHVIDKIKDIGDITLSLKTCNLERNAFYEGVefpdDCDVLISYAPPkdESLVASFI 167
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFgRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNI----DLDIRINDEIP--DYYIAHLL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 168 TQYAVTAYASQRYLEKHPISRP-DELEHHSCILIDSMMIDDAnIWRfnVAGSKEVRDYRVKGNYVCDNTQSALELARNHL 246
Cdd:PRK09801 163 TKNKRILCAAPEYLQKYPQPQSlQELSRHDCLVTKERDMTHG-IWE--LGNGQEKKSVKVSGHLSSNSGEIVLQWALEGK 239

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446086181 247 GIVFAPDKSVQSDLQDGTLV---PCFQQPYEWWldlvAIFRKREYQPWRVQyvldeMLREIRHQLAQSQQLRPEQAAES 322
Cdd:PRK09801 240 GIMLRSEWDVLPFLESGKLVqvlPEYAQSANIW----AVYREPLYRSMKLR-----VCVEFLAAWCQQRLGKPDEGYQV 309
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 146-299 3.74e-10

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: 58.72  E-value: 3.74e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 146 DDCDVLISYAPPKD-ESLVASFITQYAVTAYASQRYLEKH-PISRPDELEHHSCILI--DSMMIDdaniWRFNVAGSKEV 221
Cdd:cd08475   46 EGIDLAVRIGELADsTGLVARRLGTQRMVLCASPAYLARHgTPRTLEDLAEHQCIAYgrGGQPLP----WRLADEQGRLV 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 222 RdYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVP----CFQQPYEwwldLVAIFRKREYQPWRVQYVL 297
Cdd:cd08475  122 R-FRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEvlpeLAPEGLP----IHAVWPRTRHLPPKVRAAV 196


                 ..
gi 446086181 298 DE 299
Cdd:cd08475  197 DA 198
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 149-300 7.50e-10

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: 57.73  E-value: 7.50e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 149 DVLISYAPPKDESLVASFITQYAVTAYASQRYLEKH--PIsRPDELEHHSCILIDsmMIDDANIWRFNVAGskEVRDYRV 226
Cdd:cd08480   49 DVAIRVGPLPDSSLVARKLGESRRVIVASPSYLARHgtPL-TPQDLARHNCLGFN--FRRALPDWPFRDGG--RIVALPV 123

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446086181 227 KGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVPCFQQPYEWWLDLV-AIFRKREYQPWRVQYVLDEM 300
Cdd:cd08480  124 SGNILVNDGEALRRLALAGAGLARLALFHVADDIAAGRLVPVLEEYNPGDREPIhAVYVGGGRLPARVRAFLDFL 198
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-267 1.62e-09

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: 56.76  E-value: 1.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  96 GRVTIYAPTG--------IIT-YLSKHvidkiKDIgDITLSLktcnLERNA--FYEGVefpddcDVLISYAPPKDESLVA 164
Cdd:cd08471    1 GLLTVTAPVLfgrlhvlpIITdFLDAY-----PEV-SVRLLL----LDRVVnlLEEGV------DVAVRIGHLPDSSLVA 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 165 SFITQYAVTAYASQRYLEKHP-ISRPDELEHHSCILidSMMIDDANIWRFNVAGskEVRDYRVKGNYVCDNTQSALELAR 243
Cdd:cd08471   65 TRVGSVRRVVCASPAYLARHGtPKHPDDLADHDCIA--FTGLSPAPEWRFREGG--KERSVRVRPRLTVNTVEAAIAAAL 140

                        170       180
                 ....*....|....*....|....
gi 446086181 244 NHLGIVFAPDKSVQSDLQDGTLVP 267
Cdd:cd08471  141 AGLGLTRVLSYQVAEELAAGRLQR 164
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 149-267 2.48e-09

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: 56.10  E-value: 2.48e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 149 DVLISYAPPKDESLVASFITQYAVTAYASQRYLEKH-PISRPDELEHHSCILIDSMMIDDANIWRFNVAGSKEvrDYRVK 227
Cdd:cd08476   47 DAVIRTGELPDSRLMSRRLGSFRMVLVASPDYLARHgTPETPADLAEHACLRYRFPTTGKLEPWPLRGDGGDP--ELRLP 124

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446086181 228 GNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVP 267
Cdd:cd08476  125 TALVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVT 164
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-269 2.96e-09

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 57.32  E-value: 2.96e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  16 VIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDrneQLNNFIADYKH-EK 94
Cdd:PRK10086  24 VAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD---TLNQEILDIKNqEL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  95 RGRVTIYAPTGII-TYLSKHVIDKIKDIGDITLSLKTCNLERNAFYEGVefpddcDVLISYAPPKDESLVASFITQYAVT 173
Cdd:PRK10086 101 SGTLTVYSRPSIAqCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGI------DLAIYFDDAPSAQLTHHFLMDEEIL 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 174 AYASQRYLEKHP-ISRPDELEHhsCILidsmmIDDANIWRFNvAGSKEVRDYRVKGNYVCDNTQSALELAR--------- 243
Cdd:PRK10086 175 PVCSPEYAERHAlTGNPDNLRH--CTL-----LHDRQAWSND-SGTDEWHSWAQHFGVNLLPPSSGIGFDRsdlaviaam 246

                        250       260
                 ....*....|....*....|....*.
gi 446086181 244 NHLGIVFAPDKSVQSDLQDGTLVPCF 269
Cdd:PRK10086 247 NHIGVAMGRKRLVQKRLASGELVAPF 272
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 9-132 2.24e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 54.31  E-value: 2.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRN---EQLnn 85
Cdd:PRK10837   6 RQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAveiEQL-- 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446086181  86 fiadYKHEKrGRVTIYAPTGIITYLSKHVIDKI-KDIGDITLSLKTCN 132
Cdd:PRK10837  84 ----FREDN-GALRIYASSTIGNYILPAMIARYrRDYPQLPLELSVGN 126
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 123-266 8.41e-08

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: 51.43  E-value: 8.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 123 DITLSLKTCNlernafyEGVEF-PDDCDVLISYAPPKDESLVASFITQYAVTAYASQRYLEKHPISRPDELEHHSciLID 201
Cdd:cd08432   28 DIDLRLSTSD-------RLVDFaREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLAGLPLLSPADLARHT--LLH 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446086181 202 SMMIDDANIWRFNVAGSKEVRDYRvkGNYVcDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLV 266
Cdd:cd08432   99 DATRPEAWQWWLWAAGVADVDARR--GPRF-DDSSLALQAAVAGLGVALAPRALVADDLAAGRLV 160
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 26-266 9.10e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.69  E-value: 9.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  26 AATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIADYKHEKRGRVTIYAPtg 105
Cdd:PRK14997  22 AGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRGIVKLTCP-- 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 106 iITYLSKHVIDKIKDI----GDITLSLKTCNLERNAFYEGVefpdDCDVLISYAPPKDESLVASFITQYAVTAYASQRYL 181
Cdd:PRK14997 100 -VTLLHVHIGPMLAKFmaryPDVSLQLEATNRRVDVVGEGV----DVAIRVRPRPFEDSDLVMRVLADRGHRLFASPDLI 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 182 EK--HPiSRPDELEHHSCILIDSmmidDANIWRFNVAGSKEVR-DYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQS 258
Cdd:PRK14997 175 ARmgIP-SAPAELSHWPGLSLAS----GKHIHRWELYGPQGARaEVHFTPRMITTDMLALREAAMAGVGLVQLPVLMVKE 249


                 ....*...
gi 446086181 259 DLQDGTLV 266
Cdd:PRK14997 250 QLAAGELV 257
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 22-129 4.19e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 47.68  E-value: 4.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  22 NISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRNEQLNNFIADYKHEKRGRVTI 100
Cdd:PRK12682  18 NLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTI 97

                         90       100       110
                 ....*....|....*....|....*....|
gi 446086181 101 YAPTGIITYLSKHVIDKIKDI-GDITLSLK 129
Cdd:PRK12682  98 ATTHTQARYVLPRVVAAFRKRyPKVNLSLH 127
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 149-298 4.82e-06

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: 46.56  E-value: 4.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 149 DVLISYAPPKDESLVASFITQYAVTAYASQRYLEKH--PiSRPDELEHHSCILIDSMMIddANIWRFNVAGSKEvrdYRV 226
Cdd:cd08478   51 DVAIRIGELTDSTLHARPLGKSRLRILASPDYLARHgtP-QSIEDLAQHQLLGFTEPAS--LNTWPIKDADGNL---LKI 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446086181 227 KGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLVPCF-QQPYEWWLDLVAIFRKREYQPWRVQYVLD 298
Cdd:cd08478  125 QPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLFaEQTSDVRQPINAVYYRNTALSLRIRCFID 197
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 156-267 6.31e-06

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: 46.39  E-value: 6.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 156 PPKDESLVASFITQYAVTAYASQRYLEKHP-ISRPDELEHHSCIlidSMMIDDANI-WRFnVAGSKEVRDYRVKGNYVCD 233
Cdd:cd08473   60 PLEDSSLVMRVLGQSRQRLVASPALLARLGrPRSPEDLAGLPTL---SLGDVDGRHsWRL-EGPDGESITVRHRPRLVTD 135

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446086181 234 NTQSALELARNHLGIVFAPDKSVQSDLQDGTLVP 267
Cdd:cd08473  136 DLLTLRQAALAGVGIALLPDHLCREALRAGRLVR 169
PRK12680 PRK12680
LysR family transcriptional regulator;
1-100 6.37e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 47.31  E-value: 6.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   1 MTKLQLKYrelkIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQL-MLTPFGTALLPYINDMLDR 79
Cdd:PRK12680   1 MTLTQLRY----LVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSE 76

                         90       100
                 ....*....|....*....|.
gi 446086181  80 NEQLNNFIADYKHEKRGRVTI 100
Cdd:PRK12680  77 ANNIRTYAANQRRESQGQLTL 97
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 6-100 1.26e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 46.19  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   6 LKYRELKIISVIAASE-NISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRNEQL 83
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                         90
                 ....*....|....*..
gi 446086181  84 NNFIADYKHEKRGRVTI 100
Cdd:PRK12683  81 RRLAEQFADRDSGHLTV 97
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 146-300 3.95e-05

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: 43.74  E-value: 3.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181 146 DDCDVLISYAPPKDESLVASFITQYAVTAYASQRY-LEKHPISRPDELEHHSCILIDS-MMIDDANIWRFNVAGSKevrd 223
Cdd:cd05466   48 GELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHpLAKRKSVTLADLADEPLILFERgSGLRRLLDRAFAEAGFT---- 123

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446086181 224 YRVKgnYVCDNTQSALELARNHLGIVFAPDKSVQsDLQDGTLVPC-FQQPyEWWLDLVAIFRKREYQPWRVQYVLDEM 300
Cdd:cd05466  124 PNIA--LEVDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLpLEDP-PLSRTIGLVWRKGRYLSPAARAFLELL 197
cbl PRK12679
HTH-type transcriptional regulator Cbl;
6-100 9.68e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 43.64  E-value: 9.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   6 LKYRELKIISVIAASE-NISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRNEQL 83
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNV 80

                         90
                 ....*....|....*..
gi 446086181  84 NNFIADYKHEKRGRVTI 100
Cdd:PRK12679  81 RRLADLFTNDTSGVLTI 97
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
22-100 1.75e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 42.66  E-value: 1.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181  22 NISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRNEQLNNFIADYKHEKRGRVTI 100
Cdd:PRK12684  18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTI 97
PRK10341 PRK10341
transcriptional regulator TdcA;
7-72 2.07e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 42.54  E-value: 2.07e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446086181   7 KYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPY 72
Cdd:PRK10341   8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSR 73
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
6-77 3.34e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 41.93  E-value: 3.34e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446086181   6 LKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDML 77
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL 73
PRK09986 PRK09986
LysR family transcriptional regulator;
9-107 4.69e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 41.25  E-value: 4.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIA 88
Cdd:PRK09986  10 KLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVE 89

                         90
                 ....*....|....*....
gi 446086181  89 DYKHEKRGRVTIyaptGII 107
Cdd:PRK09986  90 QIGRGEAGRIEI----GIV 104
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-56 9.48e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 40.36  E-value: 9.48e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446086181   1 MTKLQLkyRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRT 56
Cdd:PRK11013   1 MAAVSL--RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERV 54
cysB PRK12681
HTH-type transcriptional regulator CysB;
3-100 1.00e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 40.27  E-value: 1.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446086181   3 KL-QLKYrelkIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRN 80
Cdd:PRK12681   2 KLqQLRY----IVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKV 77

                         90       100
                 ....*....|....*....|
gi 446086181  81 EQLNNFIADYKHEKRGRVTI 100
Cdd:PRK12681  78 ESIKSVAGEHTWPDKGSLYI 97
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
17-84 1.79e-03

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 39.40  E-value: 1.79e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446086181  17 IAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLP-------YINDMLDRNEQLN 84
Cdd:PRK10094  13 VAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSqardwlsWLESMPSELQQVN 87
 
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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