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Conserved domains on  [gi|1578827486|ref|WP_130206642|]
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MULTISPECIES: LysR family transcriptional regulator [unclassified Escherichia]

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 2.33e-34

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.13  E-value: 2.33e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   6 LKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNN 85
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  86 FIADYKHEKRGRVTIYAPTGIITYLSKHVIDKIKDIG-EITLSLKTCNLER--NAFYEGvefpdDCDVLISYAPPKDESL 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHpGVRLELREGNSDRlvDALLEG-----ELDLAIRLGPPPDPGL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 163 VASFITQYAVTAYASqtylEKHPISRPDElehhscilidsmmiddaniwrfnvagskevrdyrvkgnyVCDNTQSALELA 242
Cdd:COG0583   156 VARPLGEERLVLVAS----PDHPLARRAP---------------------------------------LVNSLEALLAAV 192

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1578827486 243 RNHLGIVFAPDKSVQSDLQDGTLIPCFQQPYEWWLDLVAIFRKREYQPWRVQYVLDEMLREIR 305
Cdd:COG0583   193 AAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-305 2.33e-34

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.13  E-value: 2.33e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   6 LKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNN 85
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  86 FIADYKHEKRGRVTIYAPTGIITYLSKHVIDKIKDIG-EITLSLKTCNLER--NAFYEGvefpdDCDVLISYAPPKDESL 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHpGVRLELREGNSDRlvDALLEG-----ELDLAIRLGPPPDPGL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 163 VASFITQYAVTAYASqtylEKHPISRPDElehhscilidsmmiddaniwrfnvagskevrdyrvkgnyVCDNTQSALELA 242
Cdd:COG0583   156 VARPLGEERLVLVAS----PDHPLARRAP---------------------------------------LVNSLEALLAAV 192

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1578827486 243 RNHLGIVFAPDKSVQSDLQDGTLIPCFQQPYEWWLDLVAIFRKREYQPWRVQYVLDEMLREIR 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 6.66e-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: 102.13  E-value: 6.66e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 149 DVLISYAPPKDESLVASFITQYAVTAYASQTYLEKHPI-SRPDELEHHSCILIdsMMIDDANIWRFNVAGskEVRDYRVK 227
Cdd:cd08422    49 DLAIRIGELPDSSLVARRLGPVRRVLVASPAYLARHGTpQTPEDLARHRCLGY--RLPGRPLRWRFRRGG--GEVEVRVR 124

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1578827486 228 GNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIPCFQqpyEWW---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 1578827486   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFG 66
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
rbcR CHL00180
LysR transcriptional regulator; Provisional
 9-115 3.96e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.81  E-value: 3.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIA 88
Cdd:CHL00180    8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALE 87

                          90       100
                  ....*....|....*....|....*..
gi 1578827486  89 DYKHEKRGRVTIYAPTGIITYLSKHVI 115
Cdd:CHL00180   88 DLKNLQRGTLIIGASQTTGTYLMPRLI 114
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-305 2.33e-34

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.13  E-value: 2.33e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   6 LKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNN 85
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  86 FIADYKHEKRGRVTIYAPTGIITYLSKHVIDKIKDIG-EITLSLKTCNLER--NAFYEGvefpdDCDVLISYAPPKDESL 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHpGVRLELREGNSDRlvDALLEG-----ELDLAIRLGPPPDPGL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 163 VASFITQYAVTAYASqtylEKHPISRPDElehhscilidsmmiddaniwrfnvagskevrdyrvkgnyVCDNTQSALELA 242
Cdd:COG0583   156 VARPLGEERLVLVAS----PDHPLARRAP---------------------------------------LVNSLEALLAAV 192

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1578827486 243 RNHLGIVFAPDKSVQSDLQDGTLIPCFQQPYEWWLDLVAIFRKREYQPWRVQYVLDEMLREIR 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 6.66e-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: 102.13  E-value: 6.66e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 149 DVLISYAPPKDESLVASFITQYAVTAYASQTYLEKHPI-SRPDELEHHSCILIdsMMIDDANIWRFNVAGskEVRDYRVK 227
Cdd:cd08422    49 DLAIRIGELPDSSLVARRLGPVRRVLVASPAYLARHGTpQTPEDLARHRCLGY--RLPGRPLRWRFRRGG--GEVEVRVR 124

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1578827486 228 GNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIPCFQqpyEWW---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 2.22e-15

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: 73.42  E-value: 2.22e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 146 DDCDVLISYAPPKDESLVASFITQYAVTAYASQTYLEKH-PISRPDELEHHSCILIDSMMIDDAniWRFnvAGSKEVRDY 224
Cdd:cd08477    46 EGFDAAFRIGELADSSLVARPLAPYRMVLCASPDYLARHgTPTTPEDLARHECLGFSYWRARNR--WRL--EGPGGEVKV 121

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1578827486 225 RVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIP 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 4.25e-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: 69.65  E-value: 4.25e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 149 DVLISYAPPKDESLVASFITQYAVTAYASQTYLEKH-PISRPDELEHHSCILIDSmmiddaNIWRFNVAGSKevRDYRVK 227
Cdd:cd08470    49 DLAIRLGRLTDSSLMARRLASRRHYVCASPAYLERHgTPHSLADLDRHNCLLGTS------DHWRFQENGRE--RSVRVQ 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 228 GNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIPC---FQQPYE--WwldlvAIFRKREYQPWRVQYVLDeMLR 302
Cdd:cd08470   121 GRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAAGRLVPVledYRPPDEgiW-----ALYPHNRHLSPKVRLLVD-YLA 194


                  .
gi 1578827486 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 1.42e-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 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: 68.26  E-value: 1.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 176 ASQTYLEKHPI-SRPDELEHHSCILidsmmiddaniWRFNVAGS---------KEVRDYRVKGNYVCDNTQSALELARNH 245
Cdd:cd08474    79 ASPAYLARHGTpEHPRDLLNHRCIR-----------YRFPTSGAlyrwefergGRELEVDVEGPLILNDSDLMLDAALDG 147

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1578827486 246 LGIVFAPDKSVQSDLQDGTLIPCFQqpyEWW 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 3.61e-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: 67.15  E-value: 3.61e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 140 EGVefpdDCdvLISYAPPKDESLVASFITQYAVTAYASQTYLEKH-PISRPDELEHHscILIDSMMIDDANI--WRFNVA 216
Cdd:cd08472    46 EGV----DC--VIRVGELADSSLVARRLGELRMVTCASPAYLARHgTPRHPEDLERH--RAVGYFSARTGRVlpWEFQRD 117

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1578827486 217 GskEVRDYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIPCFQQ 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 1578827486   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFG 66
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
rbcR CHL00180
LysR transcriptional regulator; Provisional
 9-115 3.96e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.81  E-value: 3.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIA 88
Cdd:CHL00180    8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALE 87

                          90       100
                  ....*....|....*....|....*..
gi 1578827486  89 DYKHEKRGRVTIYAPTGIITYLSKHVI 115
Cdd:CHL00180   88 DLKNLQRGTLIIGASQTTGTYLMPRLI 114
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 21-272 4.17e-12

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 65.63  E-value: 4.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  21 ENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRneqlnnfIADYKHEKR----- 95
Cdd:PRK11139   21 LSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQ-------LAEATRKLRarsak 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  96 GRVTIYA-PTGIITYLSKHVIDKIKDIGEITLSLKTCNLErnafyegVEF-PDDCDVLISYAPPKDESLVASFITQYAVT 173
Cdd:PRK11139   94 GALTVSLlPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRL-------EDFlRDDVDVAIRYGRGNWPGLRVEKLLDEYLL 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 174 AYASQTYLEK-HPISRPDELEHHSciLIDSmmiDDANIWR--FNVAGskeVRDYRVKGNYVCDNTQSALELARNHLGIVF 250
Cdd:PRK11139  167 PVCSPALLNGgKPLKTPEDLARHT--LLHD---DSREDWRawFRAAG---LDDLNVQQGPIFSHSSMALQAAIHGQGVAL 238

                         250       260
                  ....*....|....*....|..
gi 1578827486 251 APDKSVQSDLQDGTLIPCFQQP 272
Cdd:PRK11139  239 GNRVLAQPEIEAGRLVCPFDTV 260
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 146-298 1.77e-11

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: 62.23  E-value: 1.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 146 DDCDVLISYAPPKDESLVASFITQYAVTAYASQTYLEKHPI-SRPDELEHHSCILI---DSmmidDANIWRFnVAGSKEV 221
Cdd:cd08479    46 EGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAYLERHGApASPEDLARHDCLVIrenDE----DFGLWRL-RNGDGEA 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 222 RdYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIPCFQQpyeWWL---DLVAIFRKREYQPWRVQYVLD 298
Cdd:cd08479   121 T-VRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRSGRLVRVLPD---WQLpdaDIWAVYPSRLSRSARVRVFVD 196
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-305 1.05e-10

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: 60.38  E-value: 1.05e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  95 RGRVTIYAPTGIITYLSKHVIDK-IKDIGEITLSLKTCNLER--NAFYEGvefpdDCDVLISYAPPKDESLVASFITQYA 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARfRERYPDVELELTEGNSEEllDLLLEG-----ELDLAIRRGPPDDPGLEARPLGEEP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 172 VTAYASQTY--LEKHPISrPDELEHHSCILIDSmmiDDANIWRFNVAGSKEVRDYRVkgNYVCDNTQSALELARNHLGIV 249
Cdd:pfam03466  76 LVLVAPPDHplARGEPVS-LEDLADEPLILLPP---GSGLRDLLDRALRAAGLRPRV--VLEVNSLEALLQLVAAGLGIA 149

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 250 FAPDKSVQSDLQDGTL----IPCFQQPYEWWLdlvaIFRKREYQPWRVQYVLDEMLREIR 305
Cdd:pfam03466 150 LLPRSAVARELADGRLvalpLPEPPLPRELYL----VWRKGRPLSPAVRAFIEFLREALA 205
PRK09801 PRK09801
LysR family transcriptional regulator;
9-319 1.27e-10

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 61.20  E-value: 1.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIA 88
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  89 DYKHEKRGRVTIYAPTGI-ITYLSKHVIDKIKDIGEITLSLKTCNLERNAFYEGVefpdDCDVLISYAPPkdESLVASFI 167
Cdd:PRK09801   89 QIKTRPEGMIRIGCSFGFgRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNI----DLDIRINDEIP--DYYIAHLL 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 168 TQYAVTAYASQTYLEKHPISRP-DELEHHSCILIDSMMIDDAnIWRfnVAGSKEVRDYRVKGNYVCDNTQSALELARNHL 246
Cdd:PRK09801  163 TKNKRILCAAPEYLQKYPQPQSlQELSRHDCLVTKERDMTHG-IWE--LGNGQEKKSVKVSGHLSSNSGEIVLQWALEGK 239

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1578827486 247 GIVFAPDKSVQSDLQDGTLI---PCFQQPYEWWldlvAIFRKREYQPWRVQyvldeMLREIRHQLAQSQQLRPEQA 319
Cdd:PRK09801  240 GIMLRSEWDVLPFLESGKLVqvlPEYAQSANIW----AVYREPLYRSMKLR-----VCVEFLAAWCQQRLGKPDEG 306
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 146-299 7.39e-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: 57.57  E-value: 7.39e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 146 DDCDVLISYAPPKD-ESLVASFITQYAVTAYASQTYLEKH-PISRPDELEHHSCILI--DSMMIDdaniWRFNVAGSKEV 221
Cdd:cd08475    46 EGIDLAVRIGELADsTGLVARRLGTQRMVLCASPAYLARHgTPRTLEDLAEHQCIAYgrGGQPLP----WRLADEQGRLV 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 222 RdYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIP----CFQQPYEwwldLVAIFRKREYQPWRVQYVL 297
Cdd:cd08475   122 R-FRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEvlpeLAPEGLP----IHAVWPRTRHLPPKVRAAV 196


                  ..
gi 1578827486 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 1.12e-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 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: 57.35  E-value: 1.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 149 DVLISYAPPKDESLVASFITQYAVTAYASQTYLEKH--PIsRPDELEHHSCILIDsmMIDDANIWRFNVAGskEVRDYRV 226
Cdd:cd08480    49 DVAIRVGPLPDSSLVARKLGESRRVIVASPSYLARHgtPL-TPQDLARHNCLGFN--FRRALPDWPFRDGG--RIVALPV 123

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1578827486 227 KGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIPCFQQPYEWWLDLV-AIFRKREYQPWRVQYVLDEM 300
Cdd:cd08480   124 SGNILVNDGEALRRLALAGAGLARLALFHVADDIAAGRLVPVLEEYNPGDREPIhAVYVGGGRLPARVRAFLDFL 198
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 149-267 2.60e-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: 2.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 149 DVLISYAPPKDESLVASFITQYAVTAYASQTYLEKH-PISRPDELEHHSCILIDSMMIDDANIWRFNVAGSKEvrDYRVK 227
Cdd:cd08476    47 DAVIRTGELPDSRLMSRRLGSFRMVLVASPDYLARHgTPETPADLAEHACLRYRFPTTGKLEPWPLRGDGGDP--ELRLP 124

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1578827486 228 GNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIP 267
Cdd:cd08476   125 TALVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVT 164
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 140-267 6.10e-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: 55.22  E-value: 6.10e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 140 EGVefpddcDVLISYAPPKDESLVASFITQYAVTAYASQTYLEKHP-ISRPDELEHHSCILidSMMIDDANIWRFNVAGs 218
Cdd:cd08471    46 EGV------DVAVRIGHLPDSSLVATRVGSVRRVVCASPAYLARHGtPKHPDDLADHDCIA--FTGLSPAPEWRFREGG- 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1578827486 219 kEVRDYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIP 267
Cdd:cd08471   117 -KERSVRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEELAAGRLQR 164
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-269 1.47e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 55.01  E-value: 1.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  16 VIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDrneQLNNFIADYKH-EK 94
Cdd:PRK10086   24 VAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD---TLNQEILDIKNqEL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  95 RGRVTIYAPTGII-TYLskhvIDKIKDIGE----ITLSLKTCNLERNAFYEGVefpddcDVLISYAPPKDESLVASFITQ 169
Cdd:PRK10086  101 SGTLTVYSRPSIAqCWL----VPRLADFTRrypsISLTILTGNENVNFQRAGI------DLAIYFDDAPSAQLTHHFLMD 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 170 YAVTAYASQTYLEKHP-ISRPDELEHhsCILidsmmIDDANIWRFNvAGSKEVRDYRVKGNYVCDNTQSALELAR----- 243
Cdd:PRK10086  171 EEILPVCSPEYAERHAlTGNPDNLRH--CTL-----LHDRQAWSND-SGTDEWHSWAQHFGVNLLPPSSGIGFDRsdlav 242

                         250       260       270
                  ....*....|....*....|....*....|
gi 1578827486 244 ----NHLGIVFAPDKSVQSDLQDGTLIPCF 269
Cdd:PRK10086  243 iaamNHIGVAMGRKRLVQKRLASGELVAPF 272
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 9-132 4.03e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 53.54  E-value: 4.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   9 RELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRN---EQLnn 85
Cdd:PRK10837    6 RQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAveiEQL-- 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1578827486  86 fiadYKHEKrGRVTIYAPTGIITYLSKHVIDKI-KDIGEITLSLKTCN 132
Cdd:PRK10837   84 ----FREDN-GALRIYASSTIGNYILPAMIARYrRDYPQLPLELSVGN 126
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 26-266 2.97e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 51.14  E-value: 2.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  26 AATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDRNEQLNNFIADYKHEKRGRVTIYAPtg 105
Cdd:PRK14997   22 AGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRGIVKLTCP-- 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 106 iITYLSKHVIDKIKDI----GEITLSLKTCNLERNAFYEGVefpdDCDVLISYAPPKDESLVASFITQYAVTAYASQTYL 181
Cdd:PRK14997  100 -VTLLHVHIGPMLAKFmaryPDVSLQLEATNRRVDVVGEGV----DVAIRVRPRPFEDSDLVMRVLADRGHRLFASPDLI 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 182 EK--HPiSRPDELEHHSCILIDSmmidDANIWRFNVAGSKEVR-DYRVKGNYVCDNTQSALELARNHLGIVFAPDKSVQS 258
Cdd:PRK14997  175 ARmgIP-SAPAELSHWPGLSLAS----GKHIHRWELYGPQGARaEVHFTPRMITTDMLALREAAMAGVGLVQLPVLMVKE 249


                  ....*...
gi 1578827486 259 DLQDGTLI 266
Cdd:PRK14997  250 QLAAGELV 257
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 123-266 1.18e-06

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: 48.35  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 123 EITLSLKTCNlernafyEGVEF-PDDCDVLISYAPPKDESLVASFITQYAVTAYASQTYLEKHPISRPDELEHHSciLID 201
Cdd:cd08432    28 DIDLRLSTSD-------RLVDFaREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLAGLPLLSPADLARHT--LLH 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1578827486 202 SMMIDDANIWRFNVAGSKEVRDYRvkGNYVcDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLI 266
Cdd:cd08432    99 DATRPEAWQWWLWAAGVADVDARR--GPRF-DDSSLALQAAVAGLGVALAPRALVADDLAAGRLV 160
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 149-298 2.39e-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: 47.33  E-value: 2.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 149 DVLISYAPPKDESLVASFITQYAVTAYASQTYLEKH--PiSRPDELEHHSCILIDSMMIddANIWRFNVAGSKEvrdYRV 226
Cdd:cd08478    51 DVAIRIGELTDSTLHARPLGKSRLRILASPDYLARHgtP-QSIEDLAQHQLLGFTEPAS--LNTWPIKDADGNL---LKI 124

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1578827486 227 KGNYVCDNTQSALELARNHLGIVFAPDKSVQSDLQDGTLIPCF-QQPYEWWLDLVAIFRKREYQPWRVQYVLD 298
Cdd:cd08478   125 QPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLFaEQTSDVRQPINAVYYRNTALSLRIRCFID 197
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 22-101 5.70e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 47.29  E-value: 5.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  22 NISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRNEQLNNFIADYKHEKRGRVTI 100
Cdd:PRK12682   18 NLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTI 97


                  .
gi 1578827486 101 Y 101
Cdd:PRK12682   98 A 98
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 1578827486   1 MTKLQLKYrelkIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQL-MLTPFGTALLPYINDMLDR 79
Cdd:PRK12680    1 MTLTQLRY----LVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSE 76

                          90       100
                  ....*....|....*....|.
gi 1578827486  80 NEQLNNFIADYKHEKRGRVTI 100
Cdd:PRK12680   77 ANNIRTYAANQRRESQGQLTL 97
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 6-100 1.25e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 46.19  E-value: 1.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   6 LKYRELKIISVIAASE-NISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRNEQL 83
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                          90
                  ....*....|....*..
gi 1578827486  84 NNFIADYKHEKRGRVTI 100
Cdd:PRK12683   81 RRLAEQFADRDSGHLTV 97
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 156-267 1.75e-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 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: 44.85  E-value: 1.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 156 PPKDESLVASFITQYAVTAYASQTYLEKHP-ISRPDELEHHSCIlidSMMIDDANI-WRFnVAGSKEVRDYRVKGNYVCD 233
Cdd:cd08473    60 PLEDSSLVMRVLGQSRQRLVASPALLARLGrPRSPEDLAGLPTL---SLGDVDGRHsWRL-EGPDGESITVRHRPRLVTD 135

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1578827486 234 NTQSALELARNHLGIVFAPDKSVQSDLQDGTLIP 267
Cdd:cd08473   136 DLLTLRQAALAGVGIALLPDHLCREALRAGRLVR 169
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 146-300 5.43e-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: 43.36  E-value: 5.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486 146 DDCDVLISYAPPKDESLVASFITQYAVTAYASQTY-LEKHPISRPDELEHHSCILIDS-MMIDDANIWRFNVAGSKevrd 223
Cdd:cd05466    48 GELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHpLAKRKSVTLADLADEPLILFERgSGLRRLLDRAFAEAGFT---- 123

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1578827486 224 YRVKgnYVCDNTQSALELARNHLGIVFAPDKSVQsDLQDGTLIPC-FQQPyEWWLDLVAIFRKREYQPWRVQYVLDEM 300
Cdd:cd05466   124 PNIA--LEVDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLpLEDP-PLSRTIGLVWRKGRYLSPAARAFLELL 197
cbl PRK12679
HTH-type transcriptional regulator Cbl;
6-100 9.59e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 43.64  E-value: 9.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   6 LKYRELKIISVIAASE-NISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRNEQL 83
Cdd:PRK12679    1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNV 80

                          90
                  ....*....|....*..
gi 1578827486  84 NNFIADYKHEKRGRVTI 100
Cdd:PRK12679   81 RRLADLFTNDTSGVLTI 97
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
22-100 1.73e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 42.66  E-value: 1.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486  22 NISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRNEQLNNFIADYKHEKRGRVTI 100
Cdd:PRK12684   18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTI 97
PRK10341 PRK10341
transcriptional regulator TdcA;
7-72 2.11e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 42.54  E-value: 2.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1578827486   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 1578827486   6 LKYRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDML 77
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL 73
PRK09986 PRK09986
LysR family transcriptional regulator;
4-107 4.21e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 41.25  E-value: 4.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   4 LQLKYR-ELKIIS---VIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLMLTPFGTALLPYINDMLDR 79
Cdd:PRK09986    1 MERLYRiDLKLLRyflAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDN 80

                          90       100
                  ....*....|....*....|....*...
gi 1578827486  80 NEQLNNFIADYKHEKRGRVTIyaptGII 107
Cdd:PRK09986   81 AEQSLARVEQIGRGEAGRIEI----GIV 104
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-56 8.67e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 40.36  E-value: 8.67e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1578827486   1 MTKLQLkyRELKIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRT 56
Cdd:PRK11013    1 MAAVSL--RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERV 54
cysB PRK12681
HTH-type transcriptional regulator CysB;
3-100 9.76e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 40.27  E-value: 9.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1578827486   3 KL-QLKYrelkIISVIAASENISHAATVLGIAQANVSKYLADFESKVGLKVFDRTTRQLM-LTPFGTALLPYINDMLDRN 80
Cdd:PRK12681    2 KLqQLRY----IVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKV 77

                          90       100
                  ....*....|....*....|
gi 1578827486  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 1578827486  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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