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Conserved domains on  [gi|1741674064|ref|WP_149687261|]
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LysR family transcriptional regulator [Shimia marina]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 7.79e-52

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 7.79e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   8 FDWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVAL 87
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  88 VASGQRQTVAGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDD---VQDLMRREADIAVRHVRPEQPDLIARLV 164
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 165 REANGYFYAATDYLerrgrpqaledltahdfigsgnvarmLAHLTPLgfpiteenfrtgSDSGLVAWEMCKQGFGIAPMA 244
Cdd:COG0583   161 GEERLVLVASPDHP--------------------------LARRAPL------------VNSLEALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1741674064 245 EEVAE---MTPGVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTLAAHLA 294
Cdd:COG0583   203 RFLAAdelAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 7.79e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 7.79e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   8 FDWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVAL 87
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  88 VASGQRQTVAGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDD---VQDLMRREADIAVRHVRPEQPDLIARLV 164
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 165 REANGYFYAATDYLerrgrpqaledltahdfigsgnvarmLAHLTPLgfpiteenfrtgSDSGLVAWEMCKQGFGIAPMA 244
Cdd:COG0583   161 GEERLVLVASPDHP--------------------------LARRAPL------------VNSLEALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1741674064 245 EEVAE---MTPGVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTLAAHLA 294
Cdd:COG0583   203 RFLAAdelAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 98-289 2.58e-24

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: 97.13  E-value: 2.58e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDY 177
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 178 LERRGRPQALEDLTAHDFIGsgnvARMLAHLTPLGFPITEENFR---TG---SDSGLVAWEMCKQGFGIAPM-----AEE 246
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLG----YRLPGRPLRWRFRRGGGEVEvrvRGrlvVNDGEALRAAALAGLGIALLpdflvAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1741674064 247 VAEMTpgVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTL 289
Cdd:cd08422   157 LASGR--LVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-68 7.08e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.97  E-value: 7.08e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1741674064  10 WNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAG 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-192 1.75e-17

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 80.80  E-value: 1.75e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   9 DWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAM----RAAADR 84
Cdd:PRK14997    3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMlveaQAAQDA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  85 VALVASGQRQTVAGRVVITASDVYsvylLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRhVRP---EQPDLIA 161
Cdd:PRK14997   83 IAALQVEPRGIVKLTCPVTLLHVH----IGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIR-VRPrpfEDSDLVM 157

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1741674064 162 RLVREANGYFYAATDYLERRGRPQALEDLTA 192
Cdd:PRK14997  158 RVLADRGHRLFASPDLIARMGIPSAPAELSH 188
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-294 7.79e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 170.82  E-value: 7.79e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   8 FDWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVAL 87
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  88 VASGQRQTVAGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDD---VQDLMRREADIAVRHVRPEQPDLIARLV 164
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSdrlVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 165 REANGYFYAATDYLerrgrpqaledltahdfigsgnvarmLAHLTPLgfpiteenfrtgSDSGLVAWEMCKQGFGIAPMA 244
Cdd:COG0583   161 GEERLVLVASPDHP--------------------------LARRAPL------------VNSLEALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1741674064 245 EEVAE---MTPGVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTLAAHLA 294
Cdd:COG0583   203 RFLAAdelAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 98-289 2.58e-24

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: 97.13  E-value: 2.58e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDY 177
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 178 LERRGRPQALEDLTAHDFIGsgnvARMLAHLTPLGFPITEENFR---TG---SDSGLVAWEMCKQGFGIAPM-----AEE 246
Cdd:cd08422    81 LARHGTPQTPEDLARHRCLG----YRLPGRPLRWRFRRGGGEVEvrvRGrlvVNDGEALRAAALAGLGIALLpdflvAED 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1741674064 247 VAEMTpgVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTL 289
Cdd:cd08422   157 LASGR--LVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
10-68 7.08e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.97  E-value: 7.08e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1741674064  10 WNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAG 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 97-294 8.08e-19

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: 82.72  E-value: 8.08e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  97 AGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDD---VQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYA 173
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSeelLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 174 ATDYLERRGRPQALEDLTAHDFI----GSGNVARMLAHLTPLGFPIteeNFRTGSDSGLVAWEMCKQGFGIAPMAEEVAE 249
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLIllppGSGLRDLLDRALRAAGLRP---RVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1741674064 250 ---MTPGVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTLAAHLA 294
Cdd:pfam03466 158 relADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-192 1.75e-17

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 80.80  E-value: 1.75e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   9 DWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAM----RAAADR 84
Cdd:PRK14997    3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMlveaQAAQDA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  85 VALVASGQRQTVAGRVVITASDVYsvylLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRhVRP---EQPDLIA 161
Cdd:PRK14997   83 IAALQVEPRGIVKLTCPVTLLHVH----IGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIR-VRPrpfEDSDLVM 157

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1741674064 162 RLVREANGYFYAATDYLERRGRPQALEDLTA 192
Cdd:PRK14997  158 RVLADRGHRLFASPDLIARMGIPSAPAELSH 188
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 12-148 1.99e-17

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 80.58  E-value: 1.99e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  12 HIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVALVAsg 91
Cdd:PRK09906    5 HLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA-- 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1741674064  92 qRQTVAGRVVITASDVYS--VYLLPPILRELRAKAPRLIIDVVASDDVQD---LMRREADIA 148
Cdd:PRK09906   83 -RKIVQEDRQLTIGFVPSaeVNLLPKVLPMFRLRHPDTLIELVSLITTQQeekLRRGELDVG 143
PRK09801 PRK09801
LysR family transcriptional regulator;
23-291 9.81e-17

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 78.92  E-value: 9.81e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  23 GSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVALVASGQRQTVAGRVVI 102
Cdd:PRK09801   21 GSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEGMIRI 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 103 TASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRhVRPEQPD-LIARLVREANGYFYAATDYLERR 181
Cdd:PRK09801  101 GCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIR-INDEIPDyYIAHLLTKNKRILCAAPEYLQKY 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 182 GRPQALEDLTAHDFIGSGNvaRMLAH-LTPLGFPITEENFRT----GSDSGLVAWEMCKQGFGIapMAEEVAEMTPGVE- 255
Cdd:PRK09801  180 PQPQSLQELSRHDCLVTKE--RDMTHgIWELGNGQEKKSVKVsghlSSNSGEIVLQWALEGKGI--MLRSEWDVLPFLEs 255

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1741674064 256 ----RILPKLDPIVfPIWLTTHRELHNSRRMRLVFDTLAA 291
Cdd:PRK09801  256 gklvQVLPEYAQSA-NIWAVYREPLYRSMKLRVCVEFLAA 294
PRK12680 PRK12680
LysR family transcriptional regulator;
22-258 6.66e-15

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 73.89  E-value: 6.66e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  22 EGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSL-ALTVAGGELLEHVRAMRAAADRVALVASGQRQTVAGRV 100
Cdd:PRK12680   16 ELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 101 VITASDVYSVYLLPPILRELRAKAPRLIIDV--VASDDVQDLMRR-EADIAVRHVRPEQP-DLIA-------RLVREANG 169
Cdd:PRK12680   96 TLTTTHTQARFVLPPAVAQIKQAYPQVSVHLqqAAESAALDLLGQgDADIAIVSTAGGEPsAGIAvplyrwrRLVVVPRG 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 170 YfyaatdYLERRGRPQALEDLTAHDFIG-------SGNVARMLAH--------LTPLGFPITEENFRTGSDSGLVAwEMC 234
Cdd:PRK12680  176 H------ALDTPRRAPDMAALAEHPLISyesstrpGSSLQRAFAQlglepsiaLTALDADLIKTYVRAGLGVGLLA-EMA 248

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1741674064 235 KQGF--------GIAPMAEEVAEMTPGVERIL 258
Cdd:PRK12680  249 VNANdedlrawpAPAPIAECIAWAVLPRDRVL 280
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-289 1.11e-14

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: 71.09  E-value: 1.11e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  99 RVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDD---VQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAAT 175
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSselLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 176 DYLERRGRPQALEDLTAHDFI----GSGNVARMLAHLTPLGFPIteeNFRTGSDSGLVAWEMCKQGFGIAPMAEEVAE-- 249
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLIlferGSGLRRLLDRAFAEAGFTP---NIALEVDSLEAIKALVAAGLGIALLPESAVEel 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1741674064 250 MTPGVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTL 289
Cdd:cd05466   158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 11-193 1.65e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 72.18  E-value: 1.65e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  11 NHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRA----MRAAADRVa 86
Cdd:PRK11139    9 NALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREifdqLAEATRKL- 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  87 lvasgQRQTVAGRVVITASDVYSVYLLPPILRELRAKAPRliIDV--VASDDVQDLMRREADIAVRHVRPEQPDLIARLV 164
Cdd:PRK11139   88 -----RARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPD--IDVrlKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL 160

                         170       180
                  ....*....|....*....|....*....
gi 1741674064 165 REANGYFYAATDYLERRGRPQALEDLTAH 193
Cdd:PRK11139  161 LDEYLLPVCSPALLNGGKPLKTPEDLARH 189
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 97-289 1.86e-14

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: 70.45  E-value: 1.86e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  97 AGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATD 176
Cdd:cd08478     2 SGLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 177 YLERRGRPQALEDLTAHDFIGSGNVARM----LAHLTPLGFPIteeNFRTGSDSGLVAWEMCKQGFGIAPMAEEVA--EM 250
Cdd:cd08478    82 YLARHGTPQSIEDLAQHQLLGFTEPASLntwpIKDADGNLLKI---QPTITASSGETLRQLALSGCGIACLSDFMTdkDI 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1741674064 251 TPG--VERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTL 289
Cdd:cd08478   159 AEGrlIPLFAEQTSDVRQPINAVYYRNTALSLRIRCFIDFL 199
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 10-133 2.47e-14

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 71.95  E-value: 2.47e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  10 WNHI---RAFLTTaeeGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVA 86
Cdd:PRK11013    6 LRHIeifHAVMTA---GSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIV 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1741674064  87 LVASGQRQTVAGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVA 133
Cdd:PRK11013   83 SAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVP 129
PRK09986 PRK09986
LysR family transcriptional regulator;
13-254 2.86e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 71.68  E-value: 2.86e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  13 IRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAAD----RVALV 88
Cdd:PRK09986   12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEqslaRVEQI 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  89 ASGQRQTVAGRVVITAsdVYSVYLlpPILRELRAKAPRLII---DVVASDDVQDLMRREADIAV-RHVRPEQ-PDLIARL 163
Cdd:PRK09986   92 GRGEAGRIEIGIVGTA--LWGRLR--PAMRHFLKENPNVEWllrELSPSMQMAALERRELDAGIwRMADLEPnPGFTSRR 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 164 VREANGYFYAATDYLERRGRPQALEDLTAHDFI----GSGNVARML------AHLTPLgfpITEEnfrtgSDSGLVAWEM 233
Cdd:PRK09986  168 LHESAFAVAVPEEHPLASRSSVPLKALRNEYFItlpfVHSDWGKFLqrvcqqAGFSPQ---IIRQ-----VNEPQTVLAM 239

                         250       260
                  ....*....|....*....|..
gi 1741674064 234 CKQGFGIAPMAEEVAEMT-PGV 254
Cdd:PRK09986  240 VSMGIGITLLPDSYAQIPwPGV 261
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-196 2.66e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 68.83  E-value: 2.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  12 HIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVR-AMRA-AADRVAL-- 87
Cdd:PRK11242    5 HIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARrALQDlEAGRRAIhd 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  88 VASGQRqtvaGRVVITASDVYSVYLLPPILRELRAKAP--RLIIDVVASDDVQD-LMRREADIAVRHVRPEQPDLIAR-L 163
Cdd:PRK11242   85 VADLSR----GSLRLAMTPTFTAYLIGPLIDAFHARYPgiTLTIREMSQERIEAlLADDELDVGIAFAPVHSPEIEAQpL 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1741674064 164 VREANGYFYAATDYLERRGRPQALEDLTAHDFI 196
Cdd:PRK11242  161 FTETLALVVGRHHPLAARRKALTLDELADEPLV 193
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-282 3.55e-13

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 66.87  E-value: 3.55e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDY 177
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 178 LERRGRPQALEDLTAHDFIG-SGNVARMLAHLT-PLGFPITEENFRTGSDSGLVAWEMCKQGFGIAPMAEEV--AEMTPG 253
Cdd:cd08477    81 LARHGTPTTPEDLARHECLGfSYWRARNRWRLEgPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALlaEDLASG 160

                         170       180       190
                  ....*....|....*....|....*....|
gi 1741674064 254 V-ERILPKLDPIVFPIWLTTHRElhnsRRM 282
Cdd:cd08477   161 RlVELLPDYLPPPRPMHLLYPPD----RRP 186
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-289 6.45e-13

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 66.04  E-value: 6.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQP-DLIARLVREANGYFYAATD 176
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADStGLVARRLGTQRMVLCASPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 177 YLERRGRPQALEDLTAHDFIGSGNVARML------AHLTPLGFPITEenfRTGSDSGLVAWEMCKQGFGIAPM-----AE 245
Cdd:cd08475    81 YLARHGTPRTLEDLAEHQCIAYGRGGQPLpwrladEQGRLVRFRPAP---RLQFDDGEAIADAALAGLGIAQLptwlvAD 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1741674064 246 EVAEMTpgVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTL 289
Cdd:cd08475   158 HLQRGE--LVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-76 1.49e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 66.75  E-value: 1.49e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1741674064   1 MIDPNMpfdwnhIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVR 76
Cdd:PRK10094    1 MFDPET------LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQAR 70
rbcR CHL00180
LysR transcriptional regulator; Provisional
 6-149 6.11e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.04  E-value: 6.11e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   6 MPFDWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELL---EHVRAMRAAA 82
Cdd:CHL00180    3 LPFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLrygNRILALCEET 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1741674064  83 DRVAL-VASGQRqtvaGRVVITASDVYSVYLLPPILRELRAKAPRLIIDV-VASDDV--QDLMRREADIAV 149
Cdd:CHL00180   83 CRALEdLKNLQR----GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRiaWNVANGQIDIAI 149
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 25-149 7.18e-12

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 64.63  E-value: 7.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  25 LSAAARKLGQTQPTVGRQVAALEADLGVMLFERVG-RSLALTVAGGELLEHVRAMRAAAD---RVALVASGQRqtvAGRV 100
Cdd:PRK12682   19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREVGnikRIGDDFSNQD---SGTL 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1741674064 101 VITASDVYSVYLLPPILRELRAKAPRliIDVV---ASDD--VQDLMRREADIAV 149
Cdd:PRK12682   96 TIATTHTQARYVLPRVVAAFRKRYPK--VNLSlhqGSPDeiARMVISGEADIGI 147
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-198 7.75e-12

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: 63.10  E-value: 7.75e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDY 177
Cdd:cd08470     1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAY 80

                          90       100
                  ....*....|....*....|..
gi 1741674064 178 LERRGRPQALEDLTAHD-FIGS 198
Cdd:cd08470    81 LERHGTPHSLADLDRHNcLLGT 102
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-197 1.21e-11

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 62.35  E-value: 1.21e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDY 177
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                          90       100
                  ....*....|....*....|
gi 1741674064 178 LERRGRPQALEDLTAHDFIG 197
Cdd:cd08480    81 LARHGTPLTPQDLARHNCLG 100
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-184 2.46e-11

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 63.12  E-value: 2.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   1 MIDPNMP---FDWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRA 77
Cdd:PRK15092    1 MINANRPiinLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  78 MRAAADRVAlvASGQRQTVAGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDD---VQDLMRREADIAVRHVRP 154
Cdd:PRK15092   81 ILRFNDEAC--SSLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNafmMEMLESQEVDLAVTTHRP 158

                         170       180       190
                  ....*....|....*....|....*....|
gi 1741674064 155 eqPDLIARLVREANGYFYAATDYLERRGRP 184
Cdd:PRK15092  159 --SSFPALNLRTSPTLWYCAAEYVLQKGEP 186
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 25-149 5.43e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 59.29  E-value: 5.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  25 LSAAARKLGQTQPTVGRQVAALEADLGVMLFERVG-RSLALTVAGGELLEHVRAMRAAADRVALVASGQRQTVAGRVVIT 103
Cdd:PRK12683   19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVA 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1741674064 104 ASDVYSVYLLPPILRELRAKAPRLIIDV---VASDDVQDLMRREADIAV 149
Cdd:PRK12683   99 TTHTQARYALPKVVRQFKEVFPKVHLALrqgSPQEIAEMLLNGEADIGI 147
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-289 6.57e-10

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 57.61  E-value: 6.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 115 PILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDYLERRGRPQALEDLTAHD 194
Cdd:cd08479    18 PALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAYLERHGAPASPEDLARHD 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 195 --FIGSGNVARMLAHLTPLGfpiTEENFR-TG---SDSGLVAWEMCKQGFGIAPMAE-EVAEMTPGVE--RILPKLDPIV 265
Cdd:cd08479    98 clVIRENDEDFGLWRLRNGD---GEATVRvRGalsSNDGEVVLQWALDGHGIILRSEwDVAPYLRSGRlvRVLPDWQLPD 174

                         170       180
                  ....*....|....*....|....
gi 1741674064 266 FPIWLTTHRELHNSRRMRLVFDTL 289
Cdd:cd08479   175 ADIWAVYPSRLSRSARVRVFVDFL 198
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
8-139 7.82e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.44  E-value: 7.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   8 FDWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERvGRSLALTVAGGELLEHVRAMR---AAADR 84
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVAlleADLLS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1741674064  85 VALVASGQRQTVAgrvVITASDVYSVYLLpPILRELRAKaPRLIIDVVASDdvQD 139
Cdd:PRK13348   81 TLPAERGSPPTLA---IAVNADSLATWFL-PALAAVLAG-ERILLELIVDD--QD 128
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
12-193 1.50e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 57.85  E-value: 1.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  12 HIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVALVASG 91
Cdd:PRK10632    6 RMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  92 QRQTVAGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYF 171
Cdd:PRK10632   86 FNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMVV 165

                         170       180
                  ....*....|....*....|..
gi 1741674064 172 YAATDYLERRGRPQALEDLTAH 193
Cdd:PRK10632  166 CAAKSYLAQYGTPEKPADLSSH 187
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
38-149 2.62e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 56.75  E-value: 2.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  38 TVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVALVASGQRQTVAGRVVI----TASdvYSvyLL 113
Cdd:PRK11716    7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcsvTAA--YS--HL 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1741674064 114 PPILRELRAKAPRLII-----DvvASDDVQDLMRREADIAV 149
Cdd:PRK11716   83 PPILDRFRAEHPLVEIklttgD--AADAVEKVQSGEADLAI 121
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
24-149 2.67e-09

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 56.91  E-value: 2.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  24 SLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVG-RSLALTVAGGELLEHV-RAMRAAAD--RVALVASGQRQtvaGR 99
Cdd:PRK12684   18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVeRILQEVENlkRVGKEFAAQDQ---GN 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1741674064 100 VVITASDVYSVYLLPPILRELRAKAPRL-----------IIDVVASDdvqdlmrrEADIAV 149
Cdd:PRK12684   95 LTIATTHTQARYALPAAIKEFKKRYPKVrlsilqgsptqIAEMVLHG--------QADLAI 147
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-286 1.01e-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 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: 54.06  E-value: 1.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 112 LLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDYLERRGRPQALEDLT 191
Cdd:cd08472    15 LLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAYLARHGTPRHPEDLE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 192 AHDFIG-----SGNVArmlahltPLGFPITEENFR---------TGSDSGLVAwemCKQGFGIAPMAEEVAEmtPGVER- 256
Cdd:cd08472    95 RHRAVGyfsarTGRVL-------PWEFQRDGEEREvklpsrvsvNDSEAYLAA---ALAGLGIIQVPRFMVR--PHLASg 162

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1741674064 257 ----ILPKLDPIVFPIWLTTHRELHNSRRMRlVF 286
Cdd:cd08472   163 rlveVLPDWRPPPLPVSLLYPHRRHLSPRVR-VF 195
PRK09791 PRK09791
LysR family transcriptional regulator;
6-132 2.70e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 54.00  E-value: 2.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064   6 MPFD--WNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVR----AMR 79
Cdd:PRK09791    1 MAFQvkIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASlileELR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1741674064  80 AAADRVAlvasgQRQ-TVAGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVV 132
Cdd:PRK09791   81 AAQEDIR-----QRQgQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIM 129
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-289 3.66e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 52.46  E-value: 3.66e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  97 AGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVR---HVrpeQPDLIA-RLVREANGYFY 172
Cdd:cd08474     2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRlgeSV---EKDMVAvPLGPPLRMAVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 173 AATDYLERRGRPQALEDLTAHDFIgsgnvarmlahltplgfpiteeNFRTGSDSGLVAWE-------------------- 232
Cdd:cd08474    79 ASPAYLARHGTPEHPRDLLNHRCI----------------------RYRFPTSGALYRWEferggrelevdvegplilnd 136

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1741674064 233 ------MCKQGFGIAPMAEEVAEmtPGVE-----RILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTL 289
Cdd:cd08474   137 sdlmldAALDGLGIAYLFEDLVA--EHLAsgrlvRVLEDWSPPFPGGYLYYPSRRRVPPALRAFIDFL 202
PRK10341 PRK10341
transcriptional regulator TdcA;
12-78 4.52e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 53.33  E-value: 4.52e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1741674064  12 HIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAM 78
Cdd:PRK10341   11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESI 77
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-203 4.83e-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: 4.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRhVRP---EQPDLIARLVREANGYFYAA 174
Cdd:cd08473     3 GTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALR-VRFpplEDSSLVMRVLGQSRQRLVAS 81

                          90       100
                  ....*....|....*....|....*....
gi 1741674064 175 TDYLERRGRPQALEDLTAHDFIGSGNVAR 203
Cdd:cd08473    82 PALLARLGRPRSPEDLAGLPTLSLGDVDG 110
cysB PRK12681
HTH-type transcriptional regulator CysB;
26-126 4.88e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 53.36  E-value: 4.88e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  26 SAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSL-ALTVAG-------GELLEHVRAMRAaadrvalVASGQRQTVA 97
Cdd:PRK12681   20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGeeiiriaREILSKVESIKS-------VAGEHTWPDK 92

                          90       100
                  ....*....|....*....|....*....
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPR 126
Cdd:PRK12681   93 GSLYIATTHTQARYALPPVIKGFIERYPR 121
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 35-127 1.53e-07

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 51.57  E-value: 1.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  35 TQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVALVASGQRQTVAGRVVITASDVYSVYLLP 114
Cdd:PRK11151   28 SQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQGETMSGPLHIGLIPTVGPYLLP 107

                          90
                  ....*....|...
gi 1741674064 115 PILRELRAKAPRL 127
Cdd:PRK11151  108 HIIPMLHQTFPKL 120
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 16-283 9.37e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 49.30  E-value: 9.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  16 FLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVALVASGQRqt 95
Cdd:PRK10837   11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLFREDN-- 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  96 vaGRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDvQDLMRREADIAVRHVRPE----QPDLIARLVREANGYF 171
Cdd:PRK10837   89 --GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNS-QDVINAVLDFRVDIGLIEgpchSPELISEPWLEDELVV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 172 YAATDYlERRGRPQALEDLTAHDFI----GSGN---VARML-AHLTplGFPITEEnfrtgsdsgLVAWEMCKQ----GFG 239
Cdd:PRK10837  166 FAAPDS-PLARGPVTLEQLAAAPWIlrerGSGTreiVDYLLlSHLP--RFELAME---------LGNSEAIKHavrhGLG 233

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1741674064 240 IAPMAEEVAE--MTPG--VERILPkLDPIVFPIWLTTHRELHNSRRMR 283
Cdd:PRK10837  234 ISCLSRRVIAdqLQAGtlVEVAVP-LPRLMRTLYRIHHRQKHLSNALQ 280
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
12-130 1.30e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 48.86  E-value: 1.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  12 HIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRvALVASG 91
Cdd:PRK15421    6 HLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQ-ALQACN 84

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1741674064  92 QRQTVAGRVVITASDVysVYLLPPILRELRAKAPRLIID 130
Cdd:PRK15421   85 EPQQTRLRIAIECHSC--IQWLTPALENFHKNWPQVEMD 121
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 20-97 2.08e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 48.40  E-value: 2.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  20 AEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVR-------AMRAAADRvalVASGQ 92
Cdd:PRK11074   14 ARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARsvikkmqETRRQCQQ---VANGW 90


                  ....*
gi 1741674064  93 RQTVA 97
Cdd:PRK11074   91 RGQLS 95
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-293 2.23e-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 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: 47.52  E-value: 2.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  98 GRVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVR--HVrpeqPD--LIARLVREANGYFYA 173
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRigHL----PDssLVATRVGSVRRVVCA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 174 ATDYLERRGRPQALEDLTAHDFIGSGNvarmLAHLTPLGFPITEENFRTGSDSGLV------AWEMCKQGFGIAPM---- 243
Cdd:cd08471    77 SPAYLARHGTPKHPDDLADHDCIAFTG----LSPAPEWRFREGGKERSVRVRPRLTvntveaAIAAALAGLGLTRVlsyq 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1741674064 244 -AEEVAEMTpgVERILPKLDPIVFPIWLTTHRELHNSRRMRLVFDTLAAHL 293
Cdd:cd08471   153 vAEELAAGR--LQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
8-79 2.60e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.85  E-value: 2.60e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1741674064   8 FDWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERvGRSLALTVAGGELLEHVRAMR 79
Cdd:PRK03635    2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVR 72
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 16-129 6.99e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 46.60  E-value: 6.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  16 FLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAM--RAAADRVALVASGqr 93
Cdd:PRK11233    9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAIlrQCEQAQLAVHNVG-- 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1741674064  94 QTVAGRVVI-----TASDVYSVyllpPILRELRAKAPRLII 129
Cdd:PRK11233   87 QALSGQVSIglapgTAASSLTM----PLLQAVRAEFPGIVL 123
nhaR PRK11062
transcriptional activator NhaR; Provisional
 9-62 9.71e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 46.16  E-value: 9.71e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1741674064   9 DWNHIRAFLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSL 62
Cdd:PRK11062    5 NYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGL 58
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
16-160 4.31e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 44.27  E-value: 4.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  16 FLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAGGELLEHVRAMRAAADRVALVASGQRQT 95
Cdd:PRK10082   19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1741674064  96 VAGRVVITASDVYSVYLLPPILRELrakaPRLIIDVVASDDVqdlmrreaDIAVRHVRPEQPDLI 160
Cdd:PRK10082   99 AQRKIKIAAAHSLSLGLLPSIISQM----PPLFTWAIEAIDV--------DEAVDKLREGQSDCI 151
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 99-166 7.24e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 42.97  E-value: 7.24e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1741674064  99 RVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDD---VQDLMRREADIAVRHVRPEQPDLIARLVRE 166
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRddlEEALESGEIDLAIGVFPELPPGLRSQPLFE 71
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-200 8.30e-05

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: 42.51  E-value: 8.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  99 RVVITASDVYSVYLLPPILRELRAKAPRL---IIDVVASDDVQDLMRREADIAVRHVRPEQPDLIAR-LVREANGYFYAA 174
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIrvrLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEpLLRDPFVLVCPK 80

                          90       100
                  ....*....|....*....|....*.
gi 1741674064 175 TDYLERRgRPQALEDLTAHDFIGSGN 200
Cdd:cd08440    81 DHPLARR-RSVTWAELAGYPLIALGR 105
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-68 1.18e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 43.07  E-value: 1.18e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1741674064  16 FLTTAEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVGRSLALTVAG 68
Cdd:PRK10086   22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG 74
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-196 1.20e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 42.27  E-value: 1.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 100 VVITASDVYSVYLLPPILRELRAKAP--RLIIDVVASDDVQDLMRR-EADIAVrhVRPEQ--PDLIARLVREANGYFYAA 174
Cdd:cd08461     2 LVIAATDYAQKAILPPLLAALRQEAPgvRVAIRDLESDNLEAQLERgEVDLAL--TTPEYapDGLRSRPLFEERYVCVTR 79

                          90       100
                  ....*....|....*....|..
gi 1741674064 175 TDYLERRGRPqALEDLTAHDFI 196
Cdd:cd08461    80 RGHPLLQGPL-SLDQFCALDHI 100
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 99-259 1.65e-04

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 41.55  E-value: 1.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  99 RVVITASDVYSVYLLPPILRELRAKAPRLIIDVV--ASDDVQD-LMRREADIAVRHVRPeqPDLIARLVREANGYFYAAT 175
Cdd:cd08439     1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVckRTPRLMEmLERGEVDLALITHPP--PGASATILRRSPTVWYCAA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 176 DYLERRGRPQAL----EDLTAHDFigsgnvarMLAHLTPLGFPItEENFRTGSDSGLVAweMCKQGFGIAPMAEevaEMT 251
Cdd:cd08439    79 GYILAPGEPLPLalldEPTLDRRA--------ALAALDAAGIPW-RIAYAASSLSGLRA--AVRAGLGITARTQ---EMV 144


                  ....*...
gi 1741674064 252 PGVERILP 259
Cdd:cd08439   145 PPDLRILG 152
cbl PRK12679
HTH-type transcriptional regulator Cbl;
24-149 2.56e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 42.10  E-value: 2.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  24 SLSAAARKLGQTQPTVGRQVAALEADLGVMLFERVG-RSLALTVAGGELLEHVRAMRAAADRVALVASGQRQTVAGRVVI 102
Cdd:PRK12679   18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTI 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1741674064 103 TASDVYSVYLLPPILRELRAKAPRLIIDVVA---SDDVQDLMRREADIAV 149
Cdd:PRK12679   98 ATTHTQARYSLPEVIKAFRELFPEVRLELIQgtpQEIATLLQNGEADIGI 147
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 102-202 6.25e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 40.25  E-value: 6.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 102 ITASDVYSVYLLPPILRELRAKAPRLIIDVV--ASDDVQDLMRR-EADIAVRHVrpeqPDLIARLVREA---NGYFYAAt 175
Cdd:cd08459     4 IAMSDIGEMYFLPRLLAALREVAPGVRIETVrlPVDELEEALESgEIDLAIGYL----PDLGAGFFQQRlfrERYVCLV- 78

                          90       100
                  ....*....|....*....|....*..
gi 1741674064 176 dyleRRGRPQALEDLTAHDFIGSGNVA 202
Cdd:cd08459    79 ----RKDHPRIGSTLTLEQFLAARHVV 101
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 99-199 1.24e-03

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: 39.01  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064  99 RVVITASDVYSVYLLPPILRELRAKAPRLIIDVVASDD---VQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAAT 175
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTeeiAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                          90       100
                  ....*....|....*....|....*....
gi 1741674064 176 DY-LERRGRPQAlEDLTAHDFI----GSG 199
Cdd:cd08420    81 DHpLAGRKEVTA-EELAAEPWIlrepGSG 108
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 115-196 1.37e-03

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: 39.10  E-value: 1.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 115 PILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDYLERRGRPQAlEDLTAHD 194
Cdd:cd08432    17 PRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALLAGLPLLSP-ADLARHT 95


                  ..
gi 1741674064 195 FI 196
Cdd:cd08432    96 LL 97
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-196 1.64e-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 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: 38.76  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 112 LLPPILRELRAKAPRLIIDVVASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDYLERRGRPQALEDLT 191
Cdd:cd08476    13 LLLPVLAAFMQRYPEIELDLDFSDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDYLARHGTPETPADLA 92


                  ....*
gi 1741674064 192 AHDFI 196
Cdd:cd08476    93 EHACL 97
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 112-206 2.33e-03

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has 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: 176124  Cd Length: 198  Bit Score: 38.35  E-value: 2.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1741674064 112 LLPPILRELRAKAPRLIIDVV---ASDDVQDLMRREADIAVRHVRPEQPDLIARLVREANGYFYAATDYLERRGRPQALE 188
Cdd:cd08433    14 LAVPLLRAVRRRYPGIRLRIVeglSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAPLPRGAPVPLA 93

                          90       100
                  ....*....|....*....|
gi 1741674064 189 DLTAHDFI--GSGNVARMLA 206
Cdd:cd08433    94 ELARLPLIlpSRGHGLRRLV 113
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
20-86 2.61e-03

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 37.11  E-value: 2.61e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1741674064  20 AEEGSLSAAARKLGQTQPTVGRQVAALEADLGVMLFERV--GRS---LALTVAGGELLEHVRAMRAAADRVA 86
Cdd:COG2005    31 DETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQtgGKGgggARLTPEGRRLLALYRRLEAEAQRAL 102
 
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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