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Conserved domains on  [gi|516533761|ref|WP_017921567|]
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MULTISPECIES: LysR family transcriptional regulator [Burkholderia]

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];
10-288 6.97e-35

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.52  E-value: 6.97e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  10 DWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASEMEAAAAQLGR- 88
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAe 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  89 -GGPDDSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAV---SLERRETDIALRFGRPEDGDVLARCVA 164
Cdd:COG0583   82 lRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761 165 TLGYGLFAAPslaaglaagaapvfvgfdeaNAHLPEAAWLARHFPKARLALRGGsylaqasaagagAGVALLPNFIGRAD 244
Cdd:COG0583  162 EERLVLVASP--------------------DHPLARRAPLVNSLEALLAAVAAG------------LGIALLPRFLAADE 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 516533761 245 PA---LVPCRLAHAPPAREIWLLTRREARKDLPTRTVADHLGEVFAD 288
Cdd:COG0583  210 LAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-288 6.97e-35

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.52  E-value: 6.97e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  10 DWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASEMEAAAAQLGR- 88
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAe 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  89 -GGPDDSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAV---SLERRETDIALRFGRPEDGDVLARCVA 164
Cdd:COG0583   82 lRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761 165 TLGYGLFAAPslaaglaagaapvfvgfdeaNAHLPEAAWLARHFPKARLALRGGsylaqasaagagAGVALLPNFIGRAD 244
Cdd:COG0583  162 EERLVLVASP--------------------DHPLARRAPLVNSLEALLAAVAAG------------LGIALLPRFLAADE 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 516533761 245 PA---LVPCRLAHAPPAREIWLLTRREARKDLPTRTVADHLGEVFAD 288
Cdd:COG0583  210 LAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
11-69 5.55e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.58  E-value: 5.55e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761   11 WEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAG 69
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-175 1.09e-15

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 75.80  E-value: 1.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761   9 PDWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLG--SASEMEAAAAQL 86
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEhcKAMLVEAQAAQD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  87 GRGGPDDSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFgRP---EDGDVLARCV 163
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRV-RPrpfEDSDLVMRVL 160

                        170
                 ....*....|..
gi 516533761 164 ATLGYGLFAAPS 175
Cdd:PRK14997 161 ADRGHRLFASPD 172
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 14-158 4.98e-13

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 68.03  E-value: 4.98e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  14 IRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASE----MEAAAAQLGRG 89
Cdd:NF040786   6 LEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEmldlWEKLEEEFDRY 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516533761  90 GpdDSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDL-ASDFRAVS--LERRETDIALRFGRPEDGDV 158
Cdd:NF040786  86 G--KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLmISDSIKVIelLLEGEVDIGFTGTKLEKKRL 155
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 97-175 2.29e-12

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: 64.38  E-value: 2.29e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761  97 GLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLARCVATLGYGLFAAPS 175
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPA 79
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
11-61 1.84e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.19  E-value: 1.84e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 516533761    11 WEDIRVFVALARHGSLSAA--ARALSVSHATISRRLQSLEQAlgeRLVERRPD 61
Cdd:smart00347  10 PTQFLVLRILYEEGPLSVSelAKRLGVSPSTVTRVLDRLEKK---GLVRREPS 59
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-288 6.97e-35

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 126.52  E-value: 6.97e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  10 DWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASEMEAAAAQLGR- 88
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAe 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  89 -GGPDDSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAV---SLERRETDIALRFGRPEDGDVLARCVA 164
Cdd:COG0583   82 lRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRlvdALLEGELDLAIRLGPPPDPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761 165 TLGYGLFAAPslaaglaagaapvfvgfdeaNAHLPEAAWLARHFPKARLALRGGsylaqasaagagAGVALLPNFIGRAD 244
Cdd:COG0583  162 EERLVLVASP--------------------DHPLARRAPLVNSLEALLAAVAAG------------LGIALLPRFLAADE 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 516533761 245 PA---LVPCRLAHAPPAREIWLLTRREARKDLPTRTVADHLGEVFAD 288
Cdd:COG0583  210 LAagrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
11-69 5.55e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.58  E-value: 5.55e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761   11 WEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAG 69
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-175 1.09e-15

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 75.80  E-value: 1.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761   9 PDWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLG--SASEMEAAAAQL 86
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEhcKAMLVEAQAAQD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  87 GRGGPDDSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFgRP---EDGDVLARCV 163
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRV-RPrpfEDSDLVMRVL 160

                        170
                 ....*....|..
gi 516533761 164 ATLGYGLFAAPS 175
Cdd:PRK14997 161 ADRGHRLFASPD 172
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-151 4.41e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 73.88  E-value: 4.41e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  16 VFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASEMEAAAAQLGRGGPDDSP 95
Cdd:PRK10086  21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQEL 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 516533761  96 RGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFG 151
Cdd:PRK10086 101 SGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFD 156
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 14-152 9.91e-15

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 72.95  E-value: 9.91e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  14 IRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASEMEAAAAQLGRGGPDD 93
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRAR 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761  94 SPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGR 152
Cdd:PRK11139  91 SAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGR 149
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 14-158 4.98e-13

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 68.03  E-value: 4.98e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  14 IRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASE----MEAAAAQLGRG 89
Cdd:NF040786   6 LEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEmldlWEKLEEEFDRY 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516533761  90 GpdDSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDL-ASDFRAVS--LERRETDIALRFGRPEDGDV 158
Cdd:NF040786  86 G--KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLmISDSIKVIelLLEGEVDIGFTGTKLEKKRL 155
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 97-175 2.29e-12

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: 64.38  E-value: 2.29e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761  97 GLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLARCVATLGYGLFAAPS 175
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPA 79
PRK09791 PRK09791
LysR family transcriptional regulator;
1-69 3.78e-10

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 59.39  E-value: 3.78e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761   1 MADQIRptpdWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAG 69
Cdd:PRK09791   1 MAFQVK----IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAG 65
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-175 5.75e-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 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: 57.91  E-value: 5.75e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761  97 GLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLARCVATLGYGLFAAPS 175
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPA 79
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-287 1.04e-09

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: 56.91  E-value: 1.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761   96 RGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLER---RETDIALRFGRPEDGDVLARCVATLGYGLFA 172
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLlleGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  173 APSLAAGLAAGAAP------VFVGFDEANAHLPEA-AWLARHFPKARLALRGGSYLAQASAAGAGAGVALLPNFIGRADP 245
Cdd:pfam03466  81 PPDHPLARGEPVSLedladePLILLPPGSGLRDLLdRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 516533761  246 A---LVPCRLAHAPPAREIWLLTRREARKDLPTRTVADHLGEVFA 287
Cdd:pfam03466 161 AdgrLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK09801 PRK09801
LysR family transcriptional regulator;
9-149 1.23e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 55.04  E-value: 1.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761   9 PDWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASEMEAAAAQLgr 88
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRL-- 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516533761  89 ggPDD------SPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALR 149
Cdd:PRK09801  84 --VDDvtqiktRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIR 148
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 99-153 1.50e-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: 53.74  E-value: 1.50e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 516533761  99 VRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRP 153
Cdd:cd08432    2 LTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDG 56
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-73 1.21e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 52.12  E-value: 1.21e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516533761  10 DWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTL 73
Cdd:PRK10094   3 DPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLL 66
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
17-128 1.61e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 51.51  E-value: 1.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  17 FVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVER-RPdgYVLTAAGTRTLGSASEMEAAAAQLGRGGPDDSP 95
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRgRP--CRPTPAGQRLLRHLRQVALLEADLLSTLPAERG 87

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 516533761  96 RGL---VRINApPSLAQHFLIARLATLTARHPSLDI 128
Cdd:PRK13348  88 SPPtlaIAVNA-DSLATWFLPALAAVLAGERILLEL 122
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
19-73 9.93e-07

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 46.74  E-value: 9.93e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  19 ALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRP-----DGYVLTAAGTRTL 73
Cdd:COG2005   29 AIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTggkggGGARLTPEGRRLL 88
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 95-174 5.00e-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: 46.18  E-value: 5.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  95 PRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLARCVATLGYGLFAAP 174
Cdd:cd08478    1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80
PRK10341 PRK10341
transcriptional regulator TdcA;
9-74 5.63e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 47.16  E-value: 5.63e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516533761   9 PDWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLG 74
Cdd:PRK10341   7 PKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS 72
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 99-152 1.84e-05

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


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 44.64  E-value: 1.84e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 516533761  99 VRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGR 152
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGN 55
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
16-161 1.98e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 45.14  E-value: 1.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  16 VFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGT-------RTLgsaSEMEAAAAQLgr 88
Cdd:PRK10632   9 VFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRiyyqgcrRML---HEVQDVHEQL-- 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516533761  89 GGPDDSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLAR 161
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSR 156
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-175 2.03e-05

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: 44.61  E-value: 2.03e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761  97 GLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLARCVATLGYGLFAAPS 175
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPA 79
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 14-291 2.35e-05

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 44.95  E-value: 2.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  14 IRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGSASEMEAAAAQLGRGGPD- 92
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDv 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  93 -DSPRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLasdfRAVSLERRET-------DIALRFG--RPEDGDVLARC 162
Cdd:PRK11242  86 aDLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTI----REMSQERIEAlladdelDVGIAFApvHSPEIEAQPLF 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761 163 VATLgyGLFAAPSLAAGLAAGAAPVFVGFDEANAHLPEA--------AWLARHFPKARLALRGGSYLAQASAAGAGAGVA 234
Cdd:PRK11242 162 TETL--ALVVGRHHPLAARRKALTLDELADEPLVLLSAEfatreqidRYFRRHGVTPRVAIEANSISAVLEIVRRGRLAT 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 516533761 235 LLPNFIGRADPALVPCRLAHAPPAREIWLLTRREARKDLPTRTVADHLGEVFADAAD 291
Cdd:PRK11242 240 LLPAAIAREHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAEIGR 296
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-175 2.69e-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: 44.08  E-value: 2.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  95 PRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIAL--RFGRPEDGDVLARCVATLGYGLFA 172
Cdd:cd08473    1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALrvRFPPLEDSSLVMRVLGQSRQRLVA 80


                 ...
gi 516533761 173 APS 175
Cdd:cd08473   81 SPA 83
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-175 2.87e-05

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


Pssm-ID: 176169  Cd Length: 198  Bit Score: 43.86  E-value: 2.87e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761  97 GLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLARCVATLGYGLFAAPS 175
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPS 79
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-175 5.69e-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 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: 42.97  E-value: 5.69e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516533761  97 GLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLARCVATLGYGLFAAPS 175
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPA 79
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
14-166 7.06e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.61  E-value: 7.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  14 IRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVER-RPdgYVLTAAGTRTLGSASEMEAAAAQL-GRGGP 91
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRtQP--CRPTEAGQRLLRHARQVRLLEAELlGELPA 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516533761  92 DDSPRGLVRI--NApPSLAQHFLIArLATLTARHPSLdIDLASDFRAVSLERretdiaLRfgrpeDGDVLArCVATL 166
Cdd:PRK03635  85 LDGTPLTLSIavNA-DSLATWFLPA-LAPVLARSGVL-LDLVVEDQDHTAEL------LR-----RGEVVG-AVTTE 146
PRK09986 PRK09986
LysR family transcriptional regulator;
14-148 1.12e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 42.79  E-value: 1.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  14 IRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGT-------RTLGSASEMEAAAAQL 86
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKilmeesrRLLDNAEQSLARVEQI 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516533761  87 GRGgpddsPRGLVRINAPPSLAQHFLIARLATLTARHPSLDI---DLASDFRAVSLERRETDIAL 148
Cdd:PRK09986  92 GRG-----EAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWllrELSPSMQMAALERRELDAGI 151
rbcR CHL00180
LysR transcriptional regulator; Provisional
 12-69 2.66e-04

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 41.93  E-value: 2.66e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 516533761  12 EDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAG 69
Cdd:CHL00180   8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAG 65
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 105-153 2.70e-04

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


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 41.13  E-value: 2.70e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 516533761 105 PSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRP 153
Cdd:cd08481    8 PTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDP 56
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-161 3.04e-04

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: 41.06  E-value: 3.04e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516533761  97 GLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVLAR 161
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVAR 65
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 11-58 3.19e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 41.52  E-value: 3.19e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 516533761  11 WEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVER 58
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER 53
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-168 3.35e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.55  E-value: 3.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761   1 MADQIRPTP--DWEDIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGTRTLGsase 78
Cdd:PRK15092   1 MINANRPIInlDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLG---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  79 meaAAAQLGRGGPD-------DSPRGLVRINAPPSLAQH---FLIARLATLtarHPSLDIDLA---SDFRAVSLERRETD 145
Cdd:PRK15092  77 ---YARKILRFNDEacsslmySNLQGVLTIGASDDTADTilpFLLNRVSSV---YPKLALDVRvkrNAFMMEMLESQEVD 150

                        170       180
                 ....*....|....*....|....
gi 516533761 146 IALRFGRPEDGD-VLARCVATLGY 168
Cdd:PRK15092 151 LAVTTHRPSSFPaLNLRTSPTLWY 174
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 19-69 4.30e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 41.08  E-value: 4.30e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 516533761  19 ALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAG 69
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAG 62
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 14-153 1.05e-03

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 40.14  E-value: 1.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  14 IRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAGT-------RTLGSASEMEAAAAQL 86
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEvflqdarAILEQAEKAKLRARKI 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516533761  87 GRGgpddspRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLER-RETDIALRFGRP 153
Cdd:PRK09906  86 VQE------DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKlRRGELDVGFMRH 147
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
11-61 1.84e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.19  E-value: 1.84e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 516533761    11 WEDIRVFVALARHGSLSAA--ARALSVSHATISRRLQSLEQAlgeRLVERRPD 61
Cdd:smart00347  10 PTQFLVLRILYEEGPLSVSelAKRLGVSPSTVTRVLDRLEKK---GLVRREPS 59
TrmB pfam01978
Sugar-specific transcriptional regulator TrmB; One member of this family, TrmB, has been shown ...
 13-65 1.93e-03

Sugar-specific transcriptional regulator TrmB; One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.


Pssm-ID: 396525 [Multi-domain]  Cd Length: 67  Bit Score: 35.96  E-value: 1.93e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 516533761   13 DIRVFVALARHGSLSAA--ARALSVSHATISRRLQSLEQAlGerLVERRPDGYVL 65
Cdd:pfam01978  10 EAKVYLALLKLGPATADeiAEESGVPRSKVYEVLRSLEDK-G--LVEREKGRPKK 61
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 13-69 3.75e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 38.47  E-value: 3.75e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 516533761  13 DIRVFVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAG 69
Cdd:PRK11151   5 DLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG 61
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-133 4.50e-03

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: 37.44  E-value: 4.50e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 516533761  95 PRGLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASD 133
Cdd:cd08474    1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVD 39
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
13-73 4.55e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.87  E-value: 4.55e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  13 DIRVFVALARHGSLSAA--ARALSVSHATISRRLQSLEQAlgeRLVERRPDG-------YVLTAAGTRTL 73
Cdd:COG1846   40 QFRVLAALAEAGGLTQSelAERLGLTKSTVSRLLDRLEEK---GLVEREPDPedrravlVRLTEKGRALL 106
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
17-133 5.60e-03

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 37.73  E-value: 5.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  17 FVALARHGSLSAAARALSVSHATISRRLQSLEQALGERLVERRPDGYVLTAAG----TRTLGSASEMEAAAAQLgRGGPD 92
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGkifhSQIRHLLQQLESNLAEL-RGGSD 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 516533761  93 DSPRGlVRINAPPSLAQHFL---IARLATL-TARHPSLDIDLASD 133
Cdd:PRK10082  98 YAQRK-IKIAAAHSLSLGLLpsiISQMPPLfTWAIEAIDVDEAVD 141
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-175 6.26e-03

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: 37.15  E-value: 6.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  97 GLVRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAVSLERRETDIALRFGRPEDGDVL-ARCVATLGYGLFAAPS 175
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADSTGLvARRLGTQRMVLCASPA 80
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-175 6.32e-03

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: 37.19  E-value: 6.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516533761  99 VRINAPPSLAQHFLIARLATLTARHPSLDIDLASDFRAV---SLERRETDIALRFGRPEDGDVLARCVATLGYGLFAAPS 175
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSElleALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81
 
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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