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Conserved domains on  [gi|1487907129|ref|WP_120504037|]
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LysR substrate-binding domain-containing protein [Sulfitobacter mediterraneus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1001158)

LysR family HTH-containing transcriptional regulator

Gene Ontology:  GO:0003677|GO:0003700
PubMed:  19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 super family cl32646
DNA-binding transcriptional activator GcvA; Provisional
 1-291 1.36e-86

DNA-binding transcriptional activator GcvA; Provisional


The actual alignment was detected with superfamily member PRK11139:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 260.93  E-value: 1.36e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   1 MARKLPPLNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAI 80
Cdd:PRK11139    1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  81 ADATESLSER-PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhpG-GAYPG--A 156
Cdd:PRK11139   81 AEATRKLRARsAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRY---GrGNWPGlrV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 157 ELISDAPLYPFAAPGLV--DLPLGEVADLLNYPLLRDRTNGTWDVWFEQAGGVALKdVPQFTWRMSSVLAVEAAIAGQGV 234
Cdd:PRK11139  158 EKLLDEYLLPVCSPALLngGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLN-VQQGPIFSHSSMALQAAIHGQGV 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1487907129 235 LLVSAEVVAGEVAAGRLVQVSDI-GFREGGYHLVRTEGVLRRKPVRIFREWLMAQSAQ 291
Cdd:PRK11139  237 ALGNRVLAQPEIEAGRLVCPFDTvLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-291 1.36e-86

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 260.93  E-value: 1.36e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   1 MARKLPPLNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAI 80
Cdd:PRK11139    1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  81 ADATESLSER-PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhpG-GAYPG--A 156
Cdd:PRK11139   81 AEATRKLRARsAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRY---GrGNWPGlrV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 157 ELISDAPLYPFAAPGLV--DLPLGEVADLLNYPLLRDRTNGTWDVWFEQAGGVALKdVPQFTWRMSSVLAVEAAIAGQGV 234
Cdd:PRK11139  158 EKLLDEYLLPVCSPALLngGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLN-VQQGPIFSHSSMALQAAIHGQGV 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1487907129 235 LLVSAEVVAGEVAAGRLVQVSDI-GFREGGYHLVRTEGVLRRKPVRIFREWLMAQSAQ 291
Cdd:PRK11139  237 ALGNRVLAQPEIEAGRLVCPFDTvLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 94-285 1.45e-48

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: 160.44  E-value: 1.45e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  94 TVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHpgGAYPG--AELISDAPLYPFAAPG 171
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGD--GDWPGleAERLMDEELVPVCSPA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 172 LVD-LPLGEVADLLNYPLLRDRTNGTWDVWFEQAGGVALKDV---PQFTwrmSSVLAVEAAIAGQGVLLVSAEVVAGEVA 247
Cdd:cd08432    79 LLAgLPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDArrgPRFD---DSSLALQAAVAGLGVALAPRALVADDLA 155

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1487907129 248 AGRLVQVSDIGFR-EGGYHLVRTEGVLRRKPVRIFREWL 285
Cdd:cd08432   156 AGRLVRPFDLPLPsGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-291 6.45e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 155.41  E-value: 6.45e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   7 PLNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAIADATES 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  87 LSER---PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEAS---RHLADVARYEADLAIRFVHPGGAYPGAELIS 160
Cdd:COG0583    82 LRALrggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsdRLVDALLEGELDLAIRLGPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 161 DAPLYPFAAPGlvdlplgevadllnYPLLRDRtngtwdvwfeqaggvalkdvPQFTwrmSSVLAVEAAIAGQGVLLVSAE 240
Cdd:COG0583   162 EERLVLVASPD--------------HPLARRA--------------------PLVN---SLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1487907129 241 VVAGEVAAGRLVQVS-DIGFREGGYHLVRTEGVLRRKPVRIFREWLMAQSAQ 291
Cdd:COG0583   205 LAADELAAGRLVALPlPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-66 2.24e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.04  E-value: 2.24e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDG 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 22-276 8.83e-08

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 52.43  E-value: 8.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  22 SFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALD---AIADATESLSERPKgtVTIN 98
Cdd:NF041036   17 SFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDiedSLMDELKSFKGRQR--LSIC 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  99 SEPLFATKWLVPRLGAFTDAFPEI-DVRL---EASRHLADVARYEADLAIrFVHPGGAYPGAELISDAP---LYPFAAPG 171
Cdd:NF041036   95 CTPTFGMAHLPGVLNRFMLRNADVvDLKFlfhSPAQALEGIQNKEFDLAI-IEHCADLDLGRFHTYPLPqdeLVFVSAPS 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 172 LvDLPLG--EVADLLNYPLLRDRTNGTWDVWFEQAGGVALKDVPQFTWRMSS---VLAVEAAIAGQGVLLVSAEVVAGEV 246
Cdd:NF041036  174 L-GLPTPnvTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLDDFRRVVVSddlRLTIQTVLDGGGISFVSRSLVCEYL 252

                         250       260       270
                  ....*....|....*....|....*....|
gi 1487907129 247 AAGRLVQvsdigFREGGYHLVRTEGVLRRK 276
Cdd:NF041036  253 KNGQLRE-----HYVEGFPHVRCRTVVARK 277
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-291 1.36e-86

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 260.93  E-value: 1.36e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   1 MARKLPPLNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAI 80
Cdd:PRK11139    1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  81 ADATESLSER-PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhpG-GAYPG--A 156
Cdd:PRK11139   81 AEATRKLRARsAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRY---GrGNWPGlrV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 157 ELISDAPLYPFAAPGLV--DLPLGEVADLLNYPLLRDRTNGTWDVWFEQAGGVALKdVPQFTWRMSSVLAVEAAIAGQGV 234
Cdd:PRK11139  158 EKLLDEYLLPVCSPALLngGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLN-VQQGPIFSHSSMALQAAIHGQGV 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1487907129 235 LLVSAEVVAGEVAAGRLVQVSDI-GFREGGYHLVRTEGVLRRKPVRIFREWLMAQSAQ 291
Cdd:PRK11139  237 ALGNRVLAQPEIEAGRLVCPFDTvLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQ 294
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 94-285 1.45e-48

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: 160.44  E-value: 1.45e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  94 TVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHpgGAYPG--AELISDAPLYPFAAPG 171
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGD--GDWPGleAERLMDEELVPVCSPA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 172 LVD-LPLGEVADLLNYPLLRDRTNGTWDVWFEQAGGVALKDV---PQFTwrmSSVLAVEAAIAGQGVLLVSAEVVAGEVA 247
Cdd:cd08432    79 LLAgLPLLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDArrgPRFD---DSSLALQAAVAGLGVALAPRALVADDLA 155

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1487907129 248 AGRLVQVSDIGFR-EGGYHLVRTEGVLRRKPVRIFREWL 285
Cdd:cd08432   156 AGRLVRPFDLPLPsGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-291 6.45e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 155.41  E-value: 6.45e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   7 PLNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAIADATES 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  87 LSER---PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEAS---RHLADVARYEADLAIRFVHPGGAYPGAELIS 160
Cdd:COG0583    82 LRALrggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGnsdRLVDALLEGELDLAIRLGPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 161 DAPLYPFAAPGlvdlplgevadllnYPLLRDRtngtwdvwfeqaggvalkdvPQFTwrmSSVLAVEAAIAGQGVLLVSAE 240
Cdd:COG0583   162 EERLVLVASPD--------------HPLARRA--------------------PLVN---SLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1487907129 241 VVAGEVAAGRLVQVS-DIGFREGGYHLVRTEGVLRRKPVRIFREWLMAQSAQ 291
Cdd:COG0583   205 LAADELAAGRLVALPlPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-291 2.62e-33

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 123.96  E-value: 2.62e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAIADA-TES 86
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEiLDI 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  87 LSERPKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRF--VHPGGAYpgAELISDAPL 164
Cdd:PRK10086   96 KNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFddAPSAQLT--HHFLMDEEI 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 165 YPFAAP------GLVDLPlgevADLLNYPLLRDRT-------NGTWDVWFEQAgGVALKDVPQFTWRMSSVLAVEAAIAG 231
Cdd:PRK10086  174 LPVCSPeyaerhALTGNP----DNLRHCTLLHDRQawsndsgTDEWHSWAQHF-GVNLLPPSSGIGFDRSDLAVIAAMNH 248

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1487907129 232 QGVLLVSAEVVAGEVAAGRLVqvsdIGFR------EGGYHLVRTEGVLRRKpVRIFREWLMAQSAQ 291
Cdd:PRK10086  249 IGVAMGRKRLVQKRLASGELV----APFGdmevkcHQHYYVTTLPGRQWPK-IEAFIDWLKEQVKT 309
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 103-285 3.34e-32

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 117.86  E-value: 3.34e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 103 FATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhPGGAYPG--AELISDAPLYPFAAPGLVDLpLGEV 180
Cdd:cd08484    10 FAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRF--GEGAWPGtdATRLFEAPLSPLCTPELARR-LSEP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 181 ADLLNYPLLRDRTNGTWDVWFEQAG-GVALKDVPQFTwrmSSVLAVEAAIAGQGVLLVSAEVVAGEVAAGRLVQVSDIGF 259
Cdd:cd08484    87 ADLANETLLRSYRADEWPQWFEAAGvPPPPINGPVFD---SSLLMVEAALQGAGVALAPPSMFSRELASGALVQPFKITV 163

                         170       180       190
                  ....*....|....*....|....*....|
gi 1487907129 260 REGGYHLVRtegvLRRKP----VRIFREWL 285
Cdd:cd08484   164 STGSYWLTR----LKSKPetpaMSAFSQWL 189
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 95-285 3.87e-31

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: 115.13  E-value: 3.87e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  95 VTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhPGGAYPG--AELISDAPLYPFAAPGL 172
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRY--GNGDWPGleSEPLTAAPFVVVAAPGL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 173 V-DLPLGEVADLLNYPLLRDRTNGTWDVWFEQAgGVALKDVPQFTWrMSSVLAVEAAIAGQGVLLVSAEVVAGEVAAGRL 251
Cdd:cd08483    80 LgDRKVDSLADLAGLPWLQERGTNEQRVWLASM-GVVPDLERGVTF-LPGQLVLEAARAGLGLSIQARALVEPDIAAGRL 157

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1487907129 252 VQVSDIGFREGGYHLVRTEGVLrRKPVRIFREWL 285
Cdd:cd08483   158 TVLFEEEEEGLGYHIVTRPGVL-RPAAKAFVRWL 190
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 94-285 7.96e-30

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: 111.62  E-value: 7.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  94 TVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHPGGAYPGAELISDAPLYPFAAPGLV 173
Cdd:cd08481     1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 174 DL-PLGEVADLLNYPLLRDRTN-GTWDVWFEQAGGVALKDVP-----QFTwrmssvLAVEAAIAGQGVLLVSAEVVAGEV 246
Cdd:cd08481    81 AGrALAAPADLAHLPLLQQTTRpEAWRDWFEEVGLEVPTAYRgmrfeQFS------MLAQAAVAGLGVALLPRFLIEEEL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1487907129 247 AAGRLVQVSDIGFR-EGGYHLVRTEGVLRRKPVRIFREWL 285
Cdd:cd08481   155 ARGRLVVPFNLPLTsDKAYYLVYPEDKAESPPVQAFRDWL 194
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 95-285 1.53e-29

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


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 110.71  E-value: 1.53e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  95 VTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHpgGAYPG--AELISDAPLYPFAAPGL 172
Cdd:cd08487     2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGE--GLWPAthNERLLDAPLSVLCSPEI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 173 VDlPLGEVADLLNYPLLRDRTNGTWDVWFEQAGgvalkdVPQFTWRM----SSVLAVEAAIAGQGVLLVSAEVVAGEVAA 248
Cdd:cd08487    80 AK-RLSHPADLINETLLRSYRTDEWLQWFEAAN------MPPIKIRGpvfdSSRLMVEAAMQGAGVALAPAKMFSREIEN 152

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1487907129 249 GRLVQVSDIGFREGGYHLVRTEGVLRRKPVRIFREWL 285
Cdd:cd08487   153 GQLVQPFKIEVETGSYWLTWLKSKPMTPAMELFRQWI 189
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 103-285 5.15e-26

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 101.45  E-value: 5.15e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 103 FATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhPGGAYPG--AELISDAPLYPFAAPGLVDLpLGEV 180
Cdd:cd08488    10 FAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRF--GSGAWHGidATRLFEAPLSPLCTPELARQ-LREP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 181 ADLLNYPLLRDRTNGTWDVWFEQAGGVALKDVPQFTWRMSSVLAVEAAIAGQGVLLVSAEVVAGEVAAGRLVQVSDIGFR 260
Cdd:cd08488    87 ADLARHTLLRSYRADEWPQWFEAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQPFATTLS 166

                         170       180
                  ....*....|....*....|....*
gi 1487907129 261 EGGYHLVRTEGVLRRKPVRIFREWL 285
Cdd:cd08488   167 TGSYWLTRLQSRPETPAMSAFSAWL 191
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 93-285 2.24e-19

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: 84.03  E-value: 2.24e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  93 GTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhpgGAYPGAELIS----DAPLYPFA 168
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRI----GELPDSSLVArrlgPVRRVLVA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 169 APGLVD---LPLgEVADLLNYPLLRDRTNGTWDVW-FEQAGGVALKDVPQfTWRMSSVLAV-EAAIAGQGVLLVSAEVVA 243
Cdd:cd08422    77 SPAYLArhgTPQ-TPEDLARHRCLGYRLPGRPLRWrFRRGGGEVEVRVRG-RLVVNDGEALrAAALAGLGIALLPDFLVA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1487907129 244 GEVAAGRLVQV-SDIGFREGGYHLVRTEGVLRRKPVRIFREWL 285
Cdd:cd08422   155 EDLASGRLVRVlPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-66 2.24e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.04  E-value: 2.24e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDG 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-290 4.69e-17

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: 77.71  E-value: 4.69e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  93 GTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEAS---RHLADVARYEADLAIRFVHPGGAYPGAELISDAPLYPFAA 169
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGnseELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 170 PG--LVDLPLGEVADLLNYPLL-RDRTNGTWDVWFEQAGGVALKdvPQFTWRMSSVLAV-EAAIAGQGVLLVSAEVVAGE 245
Cdd:pfam03466  82 PDhpLARGEPVSLEDLADEPLIlLPPGSGLRDLLDRALRAAGLR--PRVVLEVNSLEALlQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1487907129 246 VAAGRLVQVSDIGFR-EGGYHLVRTEGVLRRKPVRIFREWLMAQSA 290
Cdd:pfam03466 160 LADGRLVALPLPEPPlPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 107-283 1.23e-14

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 70.98  E-value: 1.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 107 WLVPRLGAFTDAFPEIDVRLEA--SRHLAD-VARYEADLAirFVhpGGAYPGAELISD-----------APLYPFAAPGL 172
Cdd:cd08420    14 LLPRLLARFRKRYPEVRVSLTIgnTEEIAErVLDGEIDLG--LV--EGPVDHPDLIVEpfaedelvlvvPPDHPLAGRKE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 173 VDLplgevADLLNYPL-LRDRTNGTWDVwFEQA---GGVALKDVPQFtWRMSSVLAV-EAAIAGQGVLLVSAEVVAGEVA 247
Cdd:cd08420    90 VTA-----EELAAEPWiLREPGSGTREV-FERAlaeAGLDGLDLNIV-MELGSTEAIkEAVEAGLGISILSRLAVRKELE 162

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1487907129 248 AGRLVQVSDIGF---REggYHLVRTEGVLRRKPVRIFRE 283
Cdd:cd08420   163 LGRLVALPVEGLrltRP--FSLIYHKDKYLSPAAEAFLE 199
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 100-285 4.57e-13

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


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 66.66  E-value: 4.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 100 EPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHPggAYP-GAELISDAP--LYPFAAPGLVD-- 174
Cdd:cd08482     7 SGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDA--PWPaGMQVIELFPerVGPVCSPSLAPtv 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 175 -LPLGEVADLLNYPLLRDRTN-GTWDVWFEQAGGVALKDVPQFTWRMSSVLaVEAAIAGQGVLLVSAEVVAGEVAAGRLv 252
Cdd:cd08482    85 pLRQAPAAALLGAPLLHTRSRpQAWPDWAAAQGLAPEKLGTGQSFEHFYYL-LEAAVAGLGVAIAPWPLVRDDLASGRL- 162

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1487907129 253 qVSDIGFREGGYHLV-RTEGVLRRKPVRIFREWL 285
Cdd:cd08482   163 -VAPWGFIETGSHYVlLRPARLRDSRAGALADWL 195
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 5-256 2.62e-12

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 66.17  E-value: 2.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   5 LPPLNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPAL---DAIA 81
Cdd:PRK14997    1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveaQAAQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  82 DATESLSERPKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRfVHPgGAYPGAELI-- 159
Cdd:PRK14997   81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIR-VRP-RPFEDSDLVmr 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 160 --SDAPLYPFAAPGLVDlPLGE---VADLLNYPLLRDRTNGTWDVWfEQAGGVALKDVPQFTWRM--SSVLAV-EAAIAG 231
Cdd:PRK14997  159 vlADRGHRLFASPDLIA-RMGIpsaPAELSHWPGLSLASGKHIHRW-ELYGPQGARAEVHFTPRMitTDMLALrEAAMAG 236

                         250       260
                  ....*....|....*....|....*
gi 1487907129 232 QGVLLVSAEVVAGEVAAGRLVQVSD 256
Cdd:PRK14997  237 VGLVQLPVLMVKEQLAAGELVAVLE 261
PRK09801 PRK09801
LysR family transcriptional regulator;
22-291 3.66e-12

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 65.83  E-value: 3.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  22 SFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGA---AYLAQVSPALDAIADATESLSERPKGTVTIN 98
Cdd:PRK09801   22 SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQrcyEHALEILTQYQRLVDDVTQIKTRPEGMIRIG 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  99 SEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHPGGAYPGAELISDAPLYPFAAPG-LVDLPL 177
Cdd:PRK09801  102 CSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILCAAPEyLQKYPQ 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 178 GE-VADLLNYPLL----RDRTNGTWdvwfEQAGGVALKDVpQFTWRMSS---VLAVEAAIAGQGVLLVSAEVVAGEVAAG 249
Cdd:PRK09801  182 PQsLQELSRHDCLvtkeRDMTHGIW----ELGNGQEKKSV-KVSGHLSSnsgEIVLQWALEGKGIMLRSEWDVLPFLESG 256

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1487907129 250 RLVQVSDIGFREGGYHLVRTEGVLRRKPVRIFREWLMAQSAQ 291
Cdd:PRK09801  257 KLVQVLPEYAQSANIWAVYREPLYRSMKLRVCVEFLAAWCQQ 298
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-168 1.78e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 63.50  E-value: 1.78e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLaQVSPALDAIAD----A 83
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLL-RYGNRILALCEetcrA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  84 TESLSERPKGTVTINSEPLFATkWLVPRL-GAFTDAFPEIDVRLE--ASRHLA-DVARYEADLAIrfvhPGGAYPgAELI 159
Cdd:CHL00180   86 LEDLKNLQRGTLIIGASQTTGT-YLMPRLiGLFRQRYPQINVQLQvhSTRRIAwNVANGQIDIAI----VGGEVP-TELK 159


                  ....*....
gi 1487907129 160 SDAPLYPFA 168
Cdd:CHL00180  160 KILEITPYV 168
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-150 5.30e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 59.20  E-value: 5.30e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPA---LDAIADAT 84
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAlqdLEAGRRAI 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1487907129  85 ESLSERPKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEA---SRHLADVARYEADLAIRFVHPG 150
Cdd:PRK11242   83 HDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREmsqERIEALLADDELDVGIAFAPVH 151
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-254 2.55e-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 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: 55.93  E-value: 2.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  91 PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADV--ARYeaDLAIRF----------VHPGGAYPGAel 158
Cdd:cd08474     1 PAGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIvaEGF--DAGIRLgesvekdmvaVPLGPPLRMA-- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 159 ISDAPLYpFAAPGLVDLPlgevADLLNYPLLRDR--TNGTWDVW-FEQAGGVALKDVP-QFTWRmSSVLAVEAAIAGQGV 234
Cdd:cd08474    77 VVASPAY-LARHGTPEHP----RDLLNHRCIRYRfpTSGALYRWeFERGGRELEVDVEgPLILN-DSDLMLDAALDGLGI 150

                         170       180
                  ....*....|....*....|
gi 1487907129 235 LLVSAEVVAGEVAAGRLVQV 254
Cdd:cd08474   151 AYLFEDLVAEHLASGRLVRV 170
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-254 5.24e-09

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: 55.01  E-value: 5.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 106 KWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHPGGAYPGAELISDAPLYPFAAPGLVDL--PLGEVADL 183
Cdd:cd08470    14 RFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAYLERhgTPHSLADL 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1487907129 184 LNYPLLRdrtnGTWDVWFEQAGGVALKDVPQFTWRMSSVLAV-EAAIAGQGVLLVSAEVVAGEVAAGRLVQV 254
Cdd:cd08470    94 DRHNCLL----GTSDHWRFQENGRERSVRVQGRWRCNSGVALlDAALKGMGLAQLPDYYVDEHLAAGRLVPV 161
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 105-285 4.75e-08

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 52.12  E-value: 4.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 105 TKWLVPR-LGAFTDAFPEIDVRLEASRH---LADVARYEADLAIRFVHPGGAYPGAELISDAPLYPFAAPG--LVDLPLG 178
Cdd:cd08419    10 AKYFAPRlLGAFCRRHPGVEVSLRVGNReqvLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDhpLAGQKRI 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 179 EVADLLNYP-LLRDRTNGTW---DVWFEQAGgvalkdvpqFTWR----MSSVLAV-EAAIAGQGVLLVSAEVVAGEVAAG 249
Cdd:cd08419    90 PLERLAREPfLLREPGSGTRlamERFFAEHG---------VTLRvrmeLGSNEAIkQAVMAGLGLSVLSLHTLALELATG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1487907129 250 RLVQVSDIGF---REggYHLVRTEGvLRRKPV-RIFREWL 285
Cdd:cd08419   161 RLAVLDVEGFpirRQ--WYVVHRKG-KRLSPAaQAFLDFL 197
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-285 5.24e-08

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: 52.22  E-value: 5.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  94 TVTINSEPLFATKWLVPRLGAFTDAFPEIDVRL---EASRHLADVARYEADLAIRFVHPGGAYPGAELISDAPLYPFAAP 170
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLvegGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 171 G--LVDLPLGEVADLLNYPL-LRDRTNGTW---DVWFEQAGGvalkdVPQFTWRMSSV-LAVEAAIAGQGVLLVSAEVVA 243
Cdd:cd05466    81 DhpLAKRKSVTLADLADEPLiLFERGSGLRrllDRAFAEAGF-----TPNIALEVDSLeAIKALVAAGLGIALLPESAVE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1487907129 244 gEVAAGRLVQVsdigfREGGYHLVRTEGVLRRK------PVRIFREWL 285
Cdd:cd05466   156 -ELADGGLVVL-----PLEDPPLSRTIGLVWRKgrylspAARAFLELL 197
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-254 5.74e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 52.17  E-value: 5.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  91 PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRfVHPGGAYPgAELI----SDAPLYP 166
Cdd:cd08473     1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALR-VRFPPLED-SSLVmrvlGQSRQRL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 167 FAAPGLVDL--PLGEVADLLNYPLL---RDRTNGTWDVWFEQAGGVALKDVPQFtwrMSSVLAV--EAAIAGQGVLLVSA 239
Cdd:cd08473    79 VASPALLARlgRPRSPEDLAGLPTLslgDVDGRHSWRLEGPDGESITVRHRPRL---VTDDLLTlrQAALAGVGIALLPD 155

                         170
                  ....*....|....*
gi 1487907129 240 EVVAGEVAAGRLVQV 254
Cdd:cd08473   156 HLCREALRAGRLVRV 170
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-72 6.71e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 52.64  E-value: 6.71e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1487907129  10 ALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQ 72
Cdd:PRK11074    6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKE 68
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
11-230 7.01e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 52.71  E-value: 7.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  11 LRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAIADATESLSER 90
Cdd:PRK15421    7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  91 PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHL---ADVARYEADLAIRF-------VHPGGAYPGAELIS 160
Cdd:PRK15421   87 QQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFdpqPALQQGELDLVMTSdilprsgLHYSPMFDYEVRLV 166

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1487907129 161 DAPLYPFAAPGLVDLPLGEVADLLNYPLLRDRTngtwDVW--FEQAGGV--ALKDVPQfTWRMSSVLAVEAAIA 230
Cdd:PRK15421  167 LAPDHPLAAKTRITPEDLASETLLIYPVQRSRL----DVWrhFLQPAGVspSLKSVDN-TLLLIQMVAARMGIA 235
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 22-276 8.83e-08

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 52.43  E-value: 8.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  22 SFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALD---AIADATESLSERPKgtVTIN 98
Cdd:NF041036   17 SFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDiedSLMDELKSFKGRQR--LSIC 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  99 SEPLFATKWLVPRLGAFTDAFPEI-DVRL---EASRHLADVARYEADLAIrFVHPGGAYPGAELISDAP---LYPFAAPG 171
Cdd:NF041036   95 CTPTFGMAHLPGVLNRFMLRNADVvDLKFlfhSPAQALEGIQNKEFDLAI-IEHCADLDLGRFHTYPLPqdeLVFVSAPS 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 172 LvDLPLG--EVADLLNYPLLRDRTNGTWDVWFEQAGGVALKDVPQFTWRMSS---VLAVEAAIAGQGVLLVSAEVVAGEV 246
Cdd:NF041036  174 L-GLPTPnvTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLDDFRRVVVSddlRLTIQTVLDGGGISFVSRSLVCEYL 252

                         250       260       270
                  ....*....|....*....|....*....|
gi 1487907129 247 AAGRLVQvsdigFREGGYHLVRTEGVLRRK 276
Cdd:NF041036  253 KNGQLRE-----HYVEGFPHVRCRTVVARK 277
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-254 1.11e-07

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: 51.08  E-value: 1.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  93 GTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhpgGAYPGAELISdAPLYPF----- 167
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRI----GELADSSLVA-RPLAPYrmvlc 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 168 AAPGLVD---LPLgEVADLLNYPLL---RDRTNGTWDvwFEQAGGVALKDVPqftWRMSS---VLAVEAAIAGQGVLLVS 238
Cdd:cd08477    76 ASPDYLArhgTPT-TPEDLARHECLgfsYWRARNRWR--LEGPGGEVKVPVS---GRLTVnsgQALRVAALAGLGIVLQP 149

                         170
                  ....*....|....*.
gi 1487907129 239 AEVVAGEVAAGRLVQV 254
Cdd:cd08477   150 EALLAEDLASGRLVEL 165
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 15-144 1.61e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 51.58  E-value: 1.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  15 EAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLF-RDLPRGLALSPDGAAYLAQVSPAL-DA--IADATESLSER 90
Cdd:PRK12683   11 EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFiRRGKRLTGLTEPGKELLQIVERMLlDAenLRRLAEQFADR 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487907129  91 PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRL-EAS-RHLADVARY-EADLAI 144
Cdd:PRK12683   91 DSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALrQGSpQEIAEMLLNgEADIGI 147
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-72 2.05e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 51.35  E-value: 2.05e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1487907129  10 ALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQ 72
Cdd:PRK10094    6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQ 68
PRK09986 PRK09986
LysR family transcriptional regulator;
8-144 3.32e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 50.88  E-value: 3.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAIADATESL 87
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1487907129  88 SERPKGTVT-INSEPLFATKW--LVPRLGAFTDAFPEIDV---RLEASRHLADVARYEADLAI 144
Cdd:PRK09986   89 EQIGRGEAGrIEIGIVGTALWgrLRPAMRHFLKENPNVEWllrELSPSMQMAALERRELDAGI 151
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-116 4.04e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 50.35  E-value: 4.04e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  11 LRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLF-RDLPrgLALSPDGAAYLAQVSPALDAIADATESLSE 89
Cdd:PRK13348    7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLvRGRP--CRPTPAGQRLLRHLRQVALLEADLLSTLPA 84

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1487907129  90 RPKGTVTI----NSEPLfaTKWLVPRLGAFT 116
Cdd:PRK13348   85 ERGSPPTLaiavNADSL--ATWFLPALAAVL 113
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-254 4.80e-07

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: 49.13  E-value: 4.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  93 GTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhpgGAYPGAELISdAPLYP-----F 167
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRV----GDLPDSSLIA-RKLAPnrrilC 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 168 AAPGLVD---LPLgEVADLLNYPLL----RDRTNGTWDvwFEQAGG-VALKDVPqftwRMSS---VLAVEAAIAGQGVLL 236
Cdd:cd08479    76 ASPAYLErhgAPA-SPEDLARHDCLvireNDEDFGLWR--LRNGDGeATVRVRG----ALSSndgEVVLQWALDGHGIIL 148

                         170
                  ....*....|....*...
gi 1487907129 237 VSAEVVAGEVAAGRLVQV 254
Cdd:cd08479   149 RSEWDVAPYLRSGRLVRV 166
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 91-254 9.46e-07

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: 48.49  E-value: 9.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  91 PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHPGGAYPGAELISDAPLYPFAAP 170
Cdd:cd08478     1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 171 GLVDL---PlGEVADLLNYPLLRDRTNGTWDVW-FEQAGGVALKDVPQFTWRMSSVLAvEAAIAGQGVLLVSAEVVAGEV 246
Cdd:cd08478    81 DYLARhgtP-QSIEDLAQHQLLGFTEPASLNTWpIKDADGNLLKIQPTITASSGETLR-QLALSGCGIACLSDFMTDKDI 158


                  ....*...
gi 1487907129 247 AAGRLVQV 254
Cdd:cd08478   159 AEGRLIPL 166
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-256 1.03e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 48.39  E-value: 1.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 108 LVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRfvhpGGAYPGAELISD-----------APLYpFAAPGlvdlP 176
Cdd:cd08476    14 LLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIR----TGELPDSRLMSRrlgsfrmvlvaSPDY-LARHG----T 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 177 LGEVADLLNYPLLRDR--TNGTWDVW-FEQAGGVALKDVPQfTWRMSSVLA-VEAAIAGQGVLLVSAEVVAGEVAAGRLV 252
Cdd:cd08476    85 PETPADLAEHACLRYRfpTTGKLEPWpLRGDGGDPELRLPT-ALVCNNIEAlIEFALQGLGIACLPDFSVREALADGRLV 163


                  ....
gi 1487907129 253 QVSD 256
Cdd:cd08476   164 TVLD 167
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-254 1.09e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 49.30  E-value: 1.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAIADaTESL 87
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVE-IEQL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  88 SERPKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLaDVARYEADLAIRFVHPGGAYPGAELIS----DAP 163
Cdd:PRK10837   84 FREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQ-DVINAVLDFRVDIGLIEGPCHSPELISepwlEDE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 164 LYPFAAPG--LVDLPLGeVADLLNYP-LLRDRTNGTWDVwfeqAGGVALKDVPQFTWRMSsvLAVEAAI-----AGQGVL 235
Cdd:PRK10837  163 LVVFAAPDspLARGPVT-LEQLAAAPwILRERGSGTREI----VDYLLLSHLPRFELAME--LGNSEAIkhavrHGLGIS 235

                         250
                  ....*....|....*....
gi 1487907129 236 LVSAEVVAGEVAAGRLVQV 254
Cdd:PRK10837  236 CLSRRVIADQLQAGTLVEV 254
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-254 3.70e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 46.74  E-value: 3.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  93 GTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRfvhpGGAYPGAELIS----DAPLYPFA 168
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIR----VGELADSSLVArrlgELRMVTCA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 169 APGLVD---LPlGEVADLLNYPL---LRDRTNGTWDVWFEQAGGVALKDVPqftwrmsSVLAV-------EAAIAGQGVL 235
Cdd:cd08472    77 SPAYLArhgTP-RHPEDLERHRAvgyFSARTGRVLPWEFQRDGEEREVKLP-------SRVSVndseaylAAALAGLGII 148

                         170
                  ....*....|....*....
gi 1487907129 236 LVSAEVVAGEVAAGRLVQV 254
Cdd:cd08472   149 QVPRFMVRPHLASGRLVEV 167
PRK09791 PRK09791
LysR family transcriptional regulator;
8-90 4.25e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 47.45  E-value: 4.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAIADATESL 87
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86


                  ...
gi 1487907129  88 SER 90
Cdd:PRK09791   87 RQR 89
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-127 4.34e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.46  E-value: 4.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  10 ALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRL-NVQLFRDLPrgLALSPDGA---AYLAQVspAL---DAIAD 82
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVgQVLLVRTQP--CRPTEAGQrllRHARQV--RLleaELLGE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1487907129  83 ATESLSERPKGTVTINSEPLfATkWLVPrlgAFTDAFPEIDVRLE 127
Cdd:PRK03635   82 LPALDGTPLTLSIAVNADSL-AT-WFLP---ALAPVLARSGVLLD 121
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-254 4.43e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 46.56  E-value: 4.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  93 GTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFVHPGGAYPGAELISDAPLYPFAAPGL 172
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 173 VD---LPLgEVADLLNYPLLRDRTNGTWDVW-FEQAGGVALKDVPQFTWRMSSVLAVEAAIAGQGVLLVSAEVVAGEVAA 248
Cdd:cd08480    81 LArhgTPL-TPQDLARHNCLGFNFRRALPDWpFRDGGRIVALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAA 159


                  ....*.
gi 1487907129 249 GRLVQV 254
Cdd:cd08480   160 GRLVPV 165
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
15-144 5.58e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 46.89  E-value: 5.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  15 EAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLF-RDLPRGLALSPDGAAYLAQVSPAL---DAIADATESLSER 90
Cdd:PRK12684   11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFtRHGKRLRGLTEPGRIILASVERILqevENLKRVGKEFAAQ 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487907129  91 PKGTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLE--ASRHLAD-VARYEADLAI 144
Cdd:PRK12684   91 DQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILqgSPTQIAEmVLHGQADLAI 147
cbl PRK12679
HTH-type transcriptional regulator Cbl;
15-127 6.64e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 46.73  E-value: 6.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  15 EAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLF-RDLPRGLALSPDGAAYLAQVSPALDAIADA---TESLSER 90
Cdd:PRK12679   11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASNVrrlADLFTND 90

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1487907129  91 PKGTVTINSEPLFATKWLVPRLGAFTDAFPEidVRLE 127
Cdd:PRK12679   91 TSGVLTIATTHTQARYSLPEVIKAFRELFPE--VRLE 125
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
22-145 7.32e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 43.60  E-value: 7.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  22 SFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALDAIADATESL---SERPKGTVTIN 98
Cdd:PRK10632   18 SFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLyafNNTPIGTLRIG 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1487907129  99 SEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIR 145
Cdd:PRK10632   98 CSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIR 144
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 15-144 3.07e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 41.52  E-value: 3.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  15 EAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLF-RDLPRGLALSPDGaaylAQVSPALDAI-ADA------TES 86
Cdd:PRK12682   11 EAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFiRHGKRLKGLTEPG----KAVLDVIERIlREVgnikriGDD 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487907129  87 LSERPKGTVTInseplfAT-----KWLVPR-LGAFTDAFPEIDVRLEASrHLADVARY----EADLAI 144
Cdd:PRK12682   87 FSNQDSGTLTI------ATthtqaRYVLPRvVAAFRKRYPKVNLSLHQG-SPDEIARMvisgEADIGI 147
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-78 5.34e-04

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 40.91  E-value: 5.34e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1487907129   8 LNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQVSPALD 78
Cdd:PRK09906    3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILE 73
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-254 1.06e-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 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: 39.43  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  93 GTVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLEASRHLADVARYEADLAIRFvhpgGAYPGAELIS-----------D 161
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRI----GHLPDSSLVAtrvgsvrrvvcA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 162 APLYpFAAPGLVDLPlgevADLLNYPLLRDRTNGTWDVW-FEQAGGVALKDV-PQFTwrMSSV-LAVEAAIAGQGVLLVS 238
Cdd:cd08471    77 SPAY-LARHGTPKHP----DDLADHDCIAFTGLSPAPEWrFREGGKERSVRVrPRLT--VNTVeAAIAAALAGLGLTRVL 149

                         170
                  ....*....|....*.
gi 1487907129 239 AEVVAGEVAAGRLVQV 254
Cdd:cd08471   150 SYQVAEELAAGRLQRV 165
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
21-73 2.17e-03

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 39.27  E-value: 2.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1487907129  21 QSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQV 73
Cdd:PRK10082   26 RNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQI 78
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-276 4.07e-03

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 37.50  E-value: 4.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129  94 TVTINSEPLFATKWLVPRLGAFTDAFPEIDVRLE---ASRHLADVARYEADLAIRFVHPGGAYPGAELISDAPLY----- 165
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRdvsAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVlvcpk 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487907129 166 --PFAAPGLVDLplgevADLLNYPLLR-DRTNGTW---DVWFEQAGgvALKDVPQFTWRMSSVLA-VEaaiAGQGVLLVS 238
Cdd:cd08440    81 dhPLARRRSVTW-----AELAGYPLIAlGRGSGVRaliDRALAAAG--LTLRPAYEVSHMSTALGmVA---AGLGVAVLP 150

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1487907129 239 AevvagevAAGRLVQVSDIGFRE-GGYHLVRTEGVLRRK 276
Cdd:cd08440   151 A-------LALPLADHPGLVARPlTEPVVTRTVGLIRRR 182
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
19-53 6.02e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 37.69  E-value: 6.02e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1487907129  19 RHqsFSRAAEELGVSHSAISRHVRGLEDRLNVQLF 53
Cdd:PRK03601   16 RH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLF 48
PRK10341 PRK10341
transcriptional regulator TdcA;
5-73 6.54e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 37.53  E-value: 6.54e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1487907129   5 LPPLNALRAFEAAGRHQSFSRAAEELGVSHSAISRHVRGLEDRLNVQLFRDLPRGLALSPDGAAYLAQV 73
Cdd:PRK10341    6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRS 74
 
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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