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Conserved domains on  [gi|2096623015|ref|WP_223229206|]
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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];
21-307 7.53e-52

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.20  E-value: 7.53e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAT 100
Cdd:COG0583     9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 101 PKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIA---DDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLC 177
Cdd:COG0583    89 PRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnsDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERLVLV 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 178 VAPElletgpspsaaeftdwiqqlpYVAHMREPATvtfacdseirgdlrfvpnlrgNTVDAVLAMAREGMGVALLPDLAV 257
Cdd:COG0583   169 ASPD---------------------HPLARRAPLV---------------------NSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 2096623015 258 AEDLAGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAILALRHRLSE 307
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
21-307 7.53e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.20  E-value: 7.53e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAT 100
Cdd:COG0583     9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 101 PKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIA---DDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLC 177
Cdd:COG0583    89 PRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnsDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERLVLV 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 178 VAPElletgpspsaaeftdwiqqlpYVAHMREPATvtfacdseirgdlrfvpnlrgNTVDAVLAMAREGMGVALLPDLAV 257
Cdd:COG0583   169 ASPD---------------------HPLARRAPLV---------------------NSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 2096623015 258 AEDLAGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAILALRHRLSE 307
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 107-295 2.42e-38

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: 134.49  E-value: 2.42e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 107 ITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLETG 186
Cdd:cd08422     5 ISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAYLARH 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 187 PSPSAAEftDwIQQLPYVAHMREPATV--TFACDSEIRgDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDLAGG 264
Cdd:cd08422    85 GTPQTPE--D-LARHRCLGYRLPGRPLrwRFRRGGGEV-EVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2096623015 265 RLVRVCSAHNPAPVPIYAVHAYDALVPLSVR 295
Cdd:cd08422   161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVR 191
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
19-298 2.43e-33

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 124.49  E-value: 2.43e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  19 MSFLA-IVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAY 97
Cdd:PRK10632    7 MSVFAkVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  98 GATPKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLC 177
Cdd:PRK10632   87 NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMVVC 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 178 VAPELLE---TGPSPSAAEFTDWIQQLPYVAHMRE---PATVTfacdseirgdLRFVPNLRGNTVDA--VLAMAREGMGV 249
Cdd:PRK10632  167 AAKSYLAqygTPEKPADLSSHSWLEYSVRPDNEFEliaPEGIS----------TRLIPQGRFVTNDPqtLVRWLTAGAGI 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2096623015 250 ALLPDLAVAEDLAGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAI 298
Cdd:PRK10632  237 AYVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCI 285
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
21-74 1.45e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.45e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGE 74
Cdd:pfam00126   7 FVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
21-307 7.53e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.20  E-value: 7.53e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAT 100
Cdd:COG0583     9 FVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 101 PKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIA---DDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLC 177
Cdd:COG0583    89 PRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREgnsDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERLVLV 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 178 VAPElletgpspsaaeftdwiqqlpYVAHMREPATvtfacdseirgdlrfvpnlrgNTVDAVLAMAREGMGVALLPDLAV 257
Cdd:COG0583   169 ASPD---------------------HPLARRAPLV---------------------NSLEALLAAVAAGLGIALLPRFLA 206

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 2096623015 258 AEDLAGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAILALRHRLSE 307
Cdd:COG0583   207 ADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 107-295 2.42e-38

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: 134.49  E-value: 2.42e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 107 ITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLETG 186
Cdd:cd08422     5 ISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAYLARH 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 187 PSPSAAEftDwIQQLPYVAHMREPATV--TFACDSEIRgDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDLAGG 264
Cdd:cd08422    85 GTPQTPE--D-LARHRCLGYRLPGRPLrwRFRRGGGEV-EVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASG 160

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2096623015 265 RLVRVCSAHNPAPVPIYAVHAYDALVPLSVR 295
Cdd:cd08422   161 RLVRVLPDWRPPPLPIYAVYPSRRHLPAKVR 191
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
19-298 2.43e-33

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 124.49  E-value: 2.43e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  19 MSFLA-IVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAY 97
Cdd:PRK10632    7 MSVFAkVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  98 GATPKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLC 177
Cdd:PRK10632   87 NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAMPMVVC 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 178 VAPELLE---TGPSPSAAEFTDWIQQLPYVAHMRE---PATVTfacdseirgdLRFVPNLRGNTVDA--VLAMAREGMGV 249
Cdd:PRK10632  167 AAKSYLAqygTPEKPADLSSHSWLEYSVRPDNEFEliaPEGIS----------TRLIPQGRFVTNDPqtLVRWLTAGAGI 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2096623015 250 ALLPDLAVAEDLAGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAI 298
Cdd:PRK10632  237 AYVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKLPLKVQVCI 285
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 21-295 1.16e-32

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 122.41  E-value: 1.16e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAT 100
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 101 PKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLP--DSSLKAQRVGALCDTLCV 178
Cdd:PRK14997   90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRPfeDSDLVMRVLADRGHRLFA 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 179 APELLETGPSPSA-AEFTDWiqqlP--YVAHMREPATVTFACDSEIRGDLRFVPNLRGNTVDAVLAMAREGMGVALLPDL 255
Cdd:PRK14997  170 SPDLIARMGIPSApAELSHW----PglSLASGKHIHRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGLVQLPVL 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 2096623015 256 AVAEDLAGGRLVRVCSAHNPAPVPIYAVHA-YDALVPlSVR 295
Cdd:PRK14997  246 MVKEQLAAGELVAVLEEWEPRREVIHAVFPsRRGLLP-SVR 285
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-305 2.20e-26

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: 102.99  E-value: 2.20e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 103 GPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPEL 182
Cdd:cd08471     1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDRVVNLLEEGVDVAVRIGHLPDSSLVATRVGSVRRVVCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 183 LETGPSPSAAeftDWIQQLPYVAHMREPATV--TFACDSEIRGdLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAED 260
Cdd:cd08471    81 LARHGTPKHP---DDLADHDCIAFTGLSPAPewRFREGGKERS-VRVRPRLTVNTVEAAIAAALAGLGLTRVLSYQVAEE 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2096623015 261 LAGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAILALRHRL 305
Cdd:cd08471   157 LAAGRLQRVLEDFEPPPLPVHLVHPEGRLAPAKVRAFVDFAVPRL 201
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-301 2.72e-22

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: 92.23  E-value: 2.72e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 107 ITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSS-LKAQRVGALCDTLCVAPELLET 185
Cdd:cd08475     5 IDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEEGIDLAVRIGELADSTgLVARRLGTQRMVLCASPAYLAR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 186 GPSP-SAAEFtdwiQQLPYVAHMREPATVTFACDSEIRGDLRFVPN--LRGNTVDAVLAMAREGMGVALLPDLAVAEDLA 262
Cdd:cd08475    85 HGTPrTLEDL----AEHQCIAYGRGGQPLPWRLADEQGRLVRFRPAprLQFDDGEAIADAALAGLGIAQLPTWLVADHLQ 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2096623015 263 GGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAILAL 301
Cdd:cd08475   161 RGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-298 3.72e-22

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: 91.52  E-value: 3.72e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 107 ITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLETG 186
Cdd:cd08477     5 ISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDYLARH 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 187 PSPSAAE---------FTDWIQQLPYvaHMREPatvtfacDSEIRGDLRfvPNLRGNTVDAVLAMAREGMGVALLPDLAV 257
Cdd:cd08477    85 GTPTTPEdlarheclgFSYWRARNRW--RLEGP-------GGEVKVPVS--GRLTVNSGQALRVAALAGLGIVLQPEALL 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2096623015 258 AEDLAGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAI 298
Cdd:cd08477   154 AEDLASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFI 194
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 101-283 9.39e-22

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: 90.69  E-value: 9.39e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 101 PKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLP--DSSLKAQRVGALCDTLCV 178
Cdd:cd08473     1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPleDSSLVMRVLGQSRQRLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 179 APELLETGPSPSAAEFtdwIQQLPYVAHMREPATVTF---ACDSEIRgDLRFVPNLRGNTVDAVLAMAREGMGVALLPDL 255
Cdd:cd08473    81 SPALLARLGRPRSPED---LAGLPTLSLGDVDGRHSWrleGPDGESI-TVRHRPRLVTDDLLTLRQAALAGVGIALLPDH 156

                         170       180
                  ....*....|....*....|....*...
gi 2096623015 256 AVAEDLAGGRLVRVCSAHNPAPVPIYAV 283
Cdd:cd08473   157 LCREALRAGRLVRVLPDWTPPRGIVHAV 184
PRK09801 PRK09801
LysR family transcriptional regulator;
13-269 1.50e-21

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 92.79  E-value: 1.50e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  13 MLSPLPMS-----FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALS 87
Cdd:PRK09801    1 MLNSWPLAkdlqvLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  88 HSARTEMEAYGATPKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGD-LPDSSL-- 164
Cdd:PRK09801   81 QRLVDDVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDeIPDYYIah 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 165 ---KAQRVgalcdtLCVAPELLETGPSPSAaeftdwIQQLPyvahmREPATVTFACD----------SEIRGDLRFVPNL 231
Cdd:PRK09801  161 lltKNKRI------LCAAPEYLQKYPQPQS------LQELS-----RHDCLVTKERDmthgiwelgnGQEKKSVKVSGHL 223

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 2096623015 232 RGNTVDAVLAMAREGMGVALLPDLAVAEDLAGGRLVRV 269
Cdd:PRK09801  224 SSNSGEIVLQWALEGKGIMLRSEWDVLPFLESGKLVQV 261
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-295 4.20e-21

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: 89.11  E-value: 4.20e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 103 GPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPEL 182
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 183 LETGPSPSAAEFTDWIQQLPYV-AHMREPATVTFACDSEIRgDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDL 261
Cdd:cd08472    81 LARHGTPRHPEDLERHRAVGYFsARTGRVLPWEFQRDGEER-EVKLPSRVSVNDSEAYLAAALAGLGIIQVPRFMVRPHL 159

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2096623015 262 AGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVR 295
Cdd:cd08472   160 ASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVR 193
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-305 5.31e-21

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: 88.52  E-value: 5.31e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 107 ITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLETG 186
Cdd:cd08470     5 ITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSEGFDLAIRLGRLTDSSLMARRLASRRHYVCASPAYLERH 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 187 PSPSAaeftdwIQQLPyvAHMREPATVT---FACDSEIRgDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDLAG 263
Cdd:cd08470    85 GTPHS------LADLD--RHNCLLGTSDhwrFQENGRER-SVRVQGRWRCNSGVALLDAALKGMGLAQLPDYYVDEHLAA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2096623015 264 GRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAILALRHRL 305
Cdd:cd08470   156 GRLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYLADAL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
21-74 1.45e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.45e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGE 74
Cdd:pfam00126   7 FVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 103-306 1.01e-17

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 80.03  E-value: 1.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 103 GPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDAR--LDLVAGG-IDLALTVGDLPDSSLKAQRVGALCDTLCVA 179
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEelLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 180 PEL-LETGPSPSAAEFTDWIQ-QLPYVAHMREPATVTFAcdseiRGDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAV 257
Cdd:pfam03466  82 PDHpLARGEPVSLEDLADEPLiLLPPGSGLRDLLDRALR-----AAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2096623015 258 AEDLAGGRLVRVCSAHNPAPVPIYAVHAYDALVPLSVREAILALRHRLS 306
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 113-283 8.12e-17

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: 77.28  E-value: 8.12e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 113 LIAPVVAPALAQMLRRFsslqPRVIAD----DARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLETGPS 188
Cdd:cd08476     9 LVGGLLLPVLAAFMQRY----PEIELDldfsDRLVDVIDEGFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDYLARHGT 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 189 PSAAEftDWIQQLpyVAHMREPATVTFA----CDSEIRGDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDLAGG 264
Cdd:cd08476    85 PETPA--DLAEHA--CLRYRFPTTGKLEpwplRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALADG 160

                         170
                  ....*....|....*....
gi 2096623015 265 RLVRVCSAHNPAPVPIYAV 283
Cdd:cd08476   161 RLVTVLDDYVEERGQFRLL 179
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-295 1.14e-15

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 74.17  E-value: 1.14e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 118 VAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLETGPSPSAAE---- 193
Cdd:cd08479    16 IAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAYLERHGAPASPEdlar 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 194 ------------FTDWIqqlpyVAHMREPATVtfacdseirgdlRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDL 261
Cdd:cd08479    96 hdclvirendedFGLWR-----LRNGDGEATV------------RVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYL 158

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2096623015 262 AGGRLVRVCSAHNPAPVPIYAVhaYDALVPLSVR 295
Cdd:cd08479   159 RSGRLVRVLPDWQLPDADIWAV--YPSRLSRSAR 190
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 29-269 3.58e-15

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 74.49  E-value: 3.58e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  29 SITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAtpKGPFVIT 108
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSA--KGALTVS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 109 APHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRvgaLCDT----LCvAPELLE 184
Cdd:PRK11139  100 LLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEK---LLDEyllpVC-SPALLN 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 185 TG-PSPSAAEFT--------------DWIQQLPyVAHMREPATVTFAcDSeirgdlrfvpnlrgntvDAVLAMAREGMGV 249
Cdd:PRK11139  176 GGkPLKTPEDLArhtllhddsredwrAWFRAAG-LDDLNVQQGPIFS-HS-----------------SMALQAAIHGQGV 236

                         250       260
                  ....*....|....*....|
gi 2096623015 250 ALLPDLAVAEDLAGGRLVRV 269
Cdd:PRK11139  237 ALGNRVLAQPEIEAGRLVCP 256
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 122-295 7.87e-15

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 71.60  E-value: 7.87e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 122 LAQMLRRFSSLQPRVIAD----DARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLETGPSPSAAEFTDW 197
Cdd:cd08480    16 LLPLLPAFLARYPEILVDlsltDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSYLARHGTPLTPQDLAR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 198 IQQLPYvAHMREPATVTFACDSEIRgDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDLAGGRLVRVCSAHNPAP 277
Cdd:cd08480    96 HNCLGF-NFRRALPDWPFRDGGRIV-ALPVSGNILVNDGEALRRLALAGAGLARLALFHVADDIAAGRLVPVLEEYNPGD 173

                         170
                  ....*....|....*....
gi 2096623015 278 V-PIYAVHAYDALVPLSVR 295
Cdd:cd08480   174 RePIHAVYVGGGRLPARVR 192
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
21-164 5.23e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 71.19  E-value: 5.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDivALSHSARTEMEAYGAT 100
Cdd:PRK10086   22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKS--SLDTLNQEILDIKNQE 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2096623015 101 PKGPFVITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSL 164
Cdd:PRK10086  100 LSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQL 163
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-281 5.47e-13

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


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 66.72  E-value: 5.47e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 107 ITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVA-PELLET 185
Cdd:cd08474     7 INAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKDMVAVPLGPPLRMAVVAsPAYLAR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 186 GPSPSAaeftdwIQQLpyVAH----MREPATVT-----FACDSE-----IRGDLRFvpnlrgNTVDAVLAMAREGMGVAL 251
Cdd:cd08474    87 HGTPEH------PRDL--LNHrcirYRFPTSGAlyrweFERGGRelevdVEGPLIL------NDSDLMLDAALDGLGIAY 152

                         170       180       190
                  ....*....|....*....|....*....|
gi 2096623015 252 LPDLAVAEDLAGGRLVRVCSAHNPAPVPIY 281
Cdd:cd08474   153 LFEDLVAEHLASGRLVRVLEDWSPPFPGGY 182
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
21-281 1.32e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 66.72  E-value: 1.32e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRtTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAT 100
Cdd:PRK03635   10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVRLLEAELLGELPALDGT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 101 PkgpfvITAPHAL----IAPVVAPALAQMLRRFSSLQPRVIADDAR-LDL-----VAGgidlALTVGDLPDSSLKAQRVG 170
Cdd:PRK03635   89 P-----LTLSIAVnadsLATWFLPALAPVLARSGVLLDLVVEDQDHtAELlrrgeVVG----AVTTEPQPVQGCRVDPLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 171 ALcDTLCVA-PELLET----GPSPSAaeftdwIQQLPYVA-------HMREPATVTfacdseiRGDLRFVPNLRGNTVDA 238
Cdd:PRK03635  160 AM-RYLAVAsPAFAARyfpdGVTAEA------LAKAPAVVfnrkddlQDRFLRQAF-------GLPPGSVPCHYVPSSEA 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 2096623015 239 VLAMAREGMGVALLPDLAVAEDLAGGRLVRVCSAHnPAPVPIY 281
Cdd:PRK03635  226 FVRAALAGLGWGMIPELQIEPELASGELVDLTPGR-PLDVPLY 267
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
13-136 1.71e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 66.75  E-value: 1.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  13 MLSPLPM-SFLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSAR 91
Cdd:PRK10094    1 MFDPETLrTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2096623015  92 TEMEAYGATPKGPFVITAPHALIAP-VVAPALAQMLRRFSSLQPRV 136
Cdd:PRK10094   81 SELQQVNDGVERQVNIVINNLLYNPqAVAQLLAWLNERYPFTQFHI 126
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 118-302 2.70e-12

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: 64.52  E-value: 2.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 118 VAPALAQM-----LRRFSSLQP----RVIADDARLDLVAGGIDLALTVGDLPDSSLKAQR-----VGALCdtlcvAPELL 183
Cdd:cd08432     6 VTPSFAARwliprLARFQARHPdidlRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERlmdeeLVPVC-----SPALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 184 ETGPSPSAAEftdwIQQLPYVAHMREPATVTFACDSEIRGDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDLAG 263
Cdd:cd08432    81 AGLPLLSPAD----LARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2096623015 264 GRLVRvcsahnPAPVPIYAVHAYDALVPLSVRE--AILALR 302
Cdd:cd08432   157 GRLVR------PFDLPLPSGGAYYLVYPPGRAEspAVAAFR 191
PRK12680 PRK12680
LysR family transcriptional regulator;
21-306 1.53e-11

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 64.26  E-value: 1.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAG-SITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRF-TLTPAGERYYQRCKDIVALSHSARTEMEAYG 98
Cdd:PRK12680    9 LVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  99 ATPKGPFVITAPHALIAPVVAPALAQMLRRFS--SLQPRVIADDARLDLVA-GGIDLAL--TVGDLPDSSL-----KAQR 168
Cdd:PRK12680   89 RESQGQLTLTTTHTQARFVLPPAVAQIKQAYPqvSVHLQQAAESAALDLLGqGDADIAIvsTAGGEPSAGIavplyRWRR 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 169 V-----GALCDTLCVAPELLETGPSPsaaeftdwiqQLPYVAHMREPATVTFACDSeirgdLRFVPNLRGNTVDAVL--A 241
Cdd:PRK12680  169 LvvvprGHALDTPRRAPDMAALAEHP----------LISYESSTRPGSSLQRAFAQ-----LGLEPSIALTALDADLikT 233

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 242 MAREGMGVALLPDLAVA---EDLAGGrlvrvcsahnPAPVPIYAVHAYdALVPLS--VREAILALRHRLS 306
Cdd:PRK12680  234 YVRAGLGVGLLAEMAVNandEDLRAW----------PAPAPIAECIAW-AVLPRDrvLRDYALELVHVLA 292
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 21-78 3.77e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 59.58  E-value: 3.77e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQ 78
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLR 66
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 107-298 4.02e-10

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: 58.38  E-value: 4.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 107 ITAPHALIAPVVAPALAQMLRRFSSLQPRVIADDARL---DLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPE-L 182
Cdd:cd05466     4 IGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSElleALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDhP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 183 LETGPSPSAAEftdwIQQLPYVahMREPATVTFACDSEIRGDLRFVPN--LRGNTVDAVLAMAREGMGVALLPDLAVAED 260
Cdd:cd05466    84 LAKRKSVTLAD----LADEPLI--LFERGSGLRRLLDRAFAEAGFTPNiaLEVDSLEAIKALVAAGLGIALLPESAVEEL 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2096623015 261 LAGGrlVRVCSAHNPAP-VPIYAVHAYDALVPLSVREAI 298
Cdd:cd05466   158 ADGG--LVVLPLEDPPLsRTIGLVWRKGRYLSPAARAFL 194
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 21-129 2.22e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.38  E-value: 2.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAT 100
Cdd:PRK11233    9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQA 88

                          90       100       110
                  ....*....|....*....|....*....|
gi 2096623015 101 PKGPFVI-TAPHALIAPVVAPALAQMLRRF 129
Cdd:PRK11233   89 LSGQVSIgLAPGTAASSLTMPLLQAVRAEF 118
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
21-281 2.40e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 57.29  E-value: 2.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRtTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAT 100
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVALLEADLLSTLPAERGS 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 101 PkgpfvITAPHALIAPVVA----PALAQMLRRFSSLQPRVIAD-DARLDLVAGG-IDLALTVGDLPDSSLKAQRVGALCD 174
Cdd:PRK13348   89 P-----PTLAIAVNADSLAtwflPALAAVLAGERILLELIVDDqDHTFALLERGeVVGCVSTQPKPMRGCLAEPLGTMRY 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 175 TLCVAPELLET----GPSPSAAeftdwiQQLPYVAHMREPATVTFACDSeiRGDLR-------FVPnlrgnTVDAVLAMA 243
Cdd:PRK13348  164 RCVASPAFAARyfaqGLTRHSA------LKAPAVAFNRKDTLQDSFLEQ--LFGLPvgayprhYVP-----STHAHLAAI 230

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 2096623015 244 REGMGVALLPDLAVAEDLAGGRLVRVCSAHnPAPVPIY 281
Cdd:PRK13348  231 RHGLGYGMVPELLIGPLLAAGRLVDLAPGH-PVDVALY 267
PRK09791 PRK09791
LysR family transcriptional regulator;
20-136 4.07e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.61  E-value: 4.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  20 SFLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGA 99
Cdd:PRK09791   12 AFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQG 91

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2096623015 100 TPKGPFVITAPhALIAPVVAPalaQMLRRFSSLQPRV 136
Cdd:PRK09791   92 QLAGQINIGMG-ASIARSLMP---AVISRFHQQHPQV 124
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 116-295 2.33e-07

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 50.42  E-value: 2.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 116 PVVAPALAQMLRRFSSLQPRV----IADDARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLETGPSPSA 191
Cdd:cd08478    12 PFVLHLLAPLIAKFRERYPDIelelVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDYLARHGTPQS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 192 AEFTDWIQQLPYVahmrEPATV-TFACDSEIRGDLRFVPNLRGNTVDAVLAMAREGMGVALLPDLAVAEDLAGGRLVRV- 269
Cdd:cd08478    92 IEDLAQHQLLGFT----EPASLnTWPIKDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRLIPLf 167

                         170       180
                  ....*....|....*....|....*.
gi 2096623015 270 CSAHNPAPVPIYAVHAYDALVPLSVR 295
Cdd:cd08478   168 AEQTSDVRQPINAVYYRNTALSLRIR 193
PRK10341 PRK10341
transcriptional regulator TdcA;
19-136 2.84e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.02  E-value: 2.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  19 MSFLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYG 98
Cdd:PRK10341   13 VVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMS 92

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2096623015  99 ATPKGPFVITAPhALIAPVVapaLAQMLRRFSSLQPRV 136
Cdd:PRK10341   93 SEAVVDVSFGFP-SLIGFTF---MSDMINKFKEVFPKA 126
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 21-91 3.94e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 50.54  E-value: 3.94e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSAR 91
Cdd:PRK09906    9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAK 79
rbcR CHL00180
LysR transcriptional regulator; Provisional
 23-86 4.50e-07

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 50.40  E-value: 4.50e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2096623015  23 AIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGE---RYYQRckdIVAL 86
Cdd:CHL00180   15 AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllRYGNR---ILAL 78
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 23-74 1.94e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 48.40  E-value: 1.94e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2096623015  23 AIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGE 74
Cdd:PRK11074   12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE 63
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 114-301 4.49e-06

The 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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 46.44  E-value: 4.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 114 IAPVVAPALAQMLRRFSSLQPRVI-ADDARL--DLVAGGIDLALtVGDLPDSSLkaqrvgALCDTLCVAPEL-------- 182
Cdd:cd08423    11 AAALLPPALAALRARHPGLEVRLReAEPPESldALRAGELDLAV-VFDYPVTPP------PDDPGLTRVPLLddpldlvl 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 183 -----LETGPSPSAAEFTD--WIQQLPYVahmREPATVTFACDSeiRGdlrFVPNLRGNTVD--AVLAMAREGMGVALLP 253
Cdd:cd08423    84 padhpLAGREEVALADLADepWIAGCPGS---PCHRWLVRACRA--AG---FTPRIAHEADDyaTVLALVAAGLGVALVP 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2096623015 254 DLAVAEDLAGGRLVRVcsahnpAPVP---IYAVHAYDALVPLSVREAILAL 301
Cdd:cd08423   156 RLALGARPPGVVVRPL------RPPPtrrIYAAVRAGAARRPAVAAALEAL 200
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 30-136 2.36e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 45.42  E-value: 2.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  30 ITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFT-LTPAGERYYQRCKDIVALSHSARTEMEAYGATPKGPFVIT 108
Cdd:PRK12683   19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVA 98

                          90       100
                  ....*....|....*....|....*...
gi 2096623015 109 APHALiapvVAPALAQMLRRFSSLQPRV 136
Cdd:PRK12683   99 TTHTQ----ARYALPKVVRQFKEVFPKV 122
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
39-257 2.62e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 44.81  E-value: 2.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  39 VAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGATPKGPFVI----TAPHALi 114
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcsvTAAYSH- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 115 apvvapaLAQMLRRFSSLQPRV-IA----DDAR-LDLV-AGGIDLALTV--GDLPDS-----------SLKAQRVGalcd 174
Cdd:PRK11716   82 -------LPPILDRFRAEHPLVeIKlttgDAADaVEKVqSGEADLAIAAkpETLPASvafspideiplVLIAPALP---- 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 175 tlCVAPELLETGPSpsaaeftDWiQQLPYVahMREPATVTFACDSEIRgDLRFVPNL----RGNtvDAVLAMAREGMGVA 250
Cdd:PRK11716  151 --CPVRQQLSQEKP-------DW-SRIPFI--LPEHGPARRRIDLWFR-RHKIKPNIyatvSGH--EAIVSMVALGCGVG 215


                  ....*..
gi 2096623015 251 LLPDLAV 257
Cdd:PRK11716  216 LLPEVVL 222
GbsR COG1510
DNA-binding transcriptional regulator GbsR, MarR family [Transcription];
13-95 3.05e-05

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


Pssm-ID: 441119  Cd Length: 164  Bit Score: 43.38  E-value: 3.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  13 MLSPLPMSFLAIVEAgsitgaadaLGVAKSAVSQNLKHLEDtlgVKLAIRTTRRftltpaGER--YYQRCKDIVALSHSA 90
Cdd:COG1510    37 YLSDEPLTADELAEE---------LGVSKSSVSTALRELED---WGLVRRVRKP------GDRkdYFRAEKDVWELFRRV 98


                  ....*
gi 2096623015  91 RTEME 95
Cdd:COG1510    99 FRERL 103
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 126-276 5.45e-05

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


Pssm-ID: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 43.10  E-value: 5.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 126 LRRFSSLQPRV---IADDARL-DLVAGGIDLALTVGDLPDSSLKAQRVGALCDTLCVAPELLE--TGPSPSAAEFTDWIQ 199
Cdd:cd08483    19 LGSFWAKHPEIelsLLPSADLvDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLGdrKVDSLADLAGLPWLQ 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2096623015 200 QLPyvahmREPATVTFACDSEIRGDLRFVPNLRGNTVdavLAMAREGMGVALLPDLAVAEDLAGGRLVRVCSAHNPA 276
Cdd:cd08483    99 ERG-----TNEQRVWLASMGVVPDLERGVTFLPGQLV---LEAARAGLGLSIQARALVEPDIAAGRLTVLFEEEEEG 167
PRK09986 PRK09986
LysR family transcriptional regulator;
21-137 5.85e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 43.94  E-value: 5.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIVALSHSARTEMEAYGAT 100
Cdd:PRK09986   15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRG 94

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2096623015 101 PKGPFVItaphALIAPVVAPALAQMLRRFSSLQPRVI 137
Cdd:PRK09986   95 EAGRIEI----GIVGTALWGRLRPAMRHFLKENPNVE 127
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 120-268 7.16e-05

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


Pssm-ID: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 42.90  E-value: 7.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 120 PALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRV-GALCDTLCVaPELLETGPSPS-------- 190
Cdd:cd08488    17 PRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLfEAPLSPLCT-PELARQLREPAdlarhtll 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 191 ----AAEFTDWIQQLPYVAHMREPATVTFacDSEIrgdlrfvpnlrgntvdAVLAMAREGMGVALLPDLAVAEDLAGGRL 266
Cdd:cd08488    96 rsyrADEWPQWFEAAGVGHPCGLPNSIMF--DSSL----------------GMMEAALQGLGVALAPPSMFSRQLASGAL 157


                  ..
gi 2096623015 267 VR 268
Cdd:cd08488   158 VQ 159
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
23-257 9.16e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 43.47  E-value: 9.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  23 AIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQRCKDIvaLSHSARTeMEAYGATPK 102
Cdd:PRK15421   12 ALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQV--LPQISQA-LQACNEPQQ 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 103 GPFVITAP-HALIApVVAPALAQMLRRFsslqPRVIAD-------DARLDLVAGGIDLALTVGDLPDSSLKAQRVGALCD 174
Cdd:PRK15421   89 TRLRIAIEcHSCIQ-WLTPALENFHKNW----PQVEMDfksgvtfDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEV 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 175 TLCVAPE-----LLETGPSPSAAE----FTDWIQQLPYVAHMREPATVTfacdseirgdlrfvPNLRgnTVDAVL---AM 242
Cdd:PRK15421  164 RLVLAPDhplaaKTRITPEDLASEtlliYPVQRSRLDVWRHFLQPAGVS--------------PSLK--SVDNTLlliQM 227

                         250
                  ....*....|....*
gi 2096623015 243 AREGMGVALLPDLAV 257
Cdd:PRK15421  228 VAARMGIAALPHWVV 242
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 122-269 1.25e-04

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: 42.09  E-value: 1.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 122 LAQMLRRFSSLQPRVIADDARL---DLVAGGIDLALTVGDLPDSSLKAQRVG--ALCdtLCVAPEL-LETGPSPSAAEft 195
Cdd:cd08420    19 LARFRKRYPEVRVSLTIGNTEEiaeRVLDGEIDLGLVEGPVDHPDLIVEPFAedELV--LVVPPDHpLAGRKEVTAEE-- 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 196 dwIQQLPYVahMREP-----ATVtfacDSEIRGDLRFVPNLR-----GNTvDAVLAMAREGMGVALLPDLAVAEDLAGGR 265
Cdd:cd08420    95 --LAAEPWI--LREPgsgtrEVF----ERALAEAGLDGLDLNivmelGST-EAIKEAVEAGLGISILSRLAVRKELELGR 165


                  ....
gi 2096623015 266 LVRV 269
Cdd:cd08420   166 LVAL 169
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 122-270 1.45e-04

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


Pssm-ID: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 41.90  E-value: 1.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 122 LAQMLRRFSSLQPRVIAD----DARLDLVAGGIDLALTVGDlPDSSlkaqrvGALCDTLC-------VAPELLETGPSPS 190
Cdd:cd08481    15 LIPRLPDFLARHPDITVNlvtrDEPFDFSQGSFDAAIHFGD-PVWP------GAESEYLMdeevvpvCSPALLAGRALAA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 191 AAEftdwIQQLPYVAHMREP-------ATVTFACDSEIRGdLRFvpnlrgNTVDAVLAMAREGMGVALLPDLAVAEDLAG 263
Cdd:cd08481    88 PAD----LAHLPLLQQTTRPeawrdwfEEVGLEVPTAYRG-MRF------EQFSMLAQAAVAGLGVALLPRFLIEEELAR 156


                  ....*..
gi 2096623015 264 GRLVRVC 270
Cdd:cd08481   157 GRLVVPF 163
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
33-75 1.90e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 42.31  E-value: 1.90e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2096623015  33 AADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGER 75
Cdd:PRK03601   21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGER 63
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 21-79 1.98e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 42.37  E-value: 1.98e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2096623015  21 FLAIVEAGSITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAGERYYQR 79
Cdd:PRK10837   11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPR 69
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 231-278 1.04e-03

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is 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 C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. 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: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 39.43  E-value: 1.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2096623015 231 LRGNTVDAVLAMAREGMGVALLPDLAVAEDLAGGRLVRVCSAHNPAPV 278
Cdd:cd08411   129 FEATSLETLRQMVAAGLGITLLPELAVPSEELRGDRLVVRPFAEPAPS 176
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
29-154 2.57e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 38.80  E-value: 2.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015  29 SITGAADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFT-LTPAGERyyqrckdIVALSHSARTEMEA-------YGAT 100
Cdd:PRK12684   18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRI-------ILASVERILQEVENlkrvgkeFAAQ 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2096623015 101 PKGPFVITAPHALIAPVVAPALAQMLRRF-----SSLQ--PRVIADdarlDLVAGGIDLAL 154
Cdd:PRK12684   91 DQGNLTIATTHTQARYALPAAIKEFKKRYpkvrlSILQgsPTQIAE----MVLHGQADLAI 147
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
21-53 3.97e-03

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 37.17  E-value: 3.97e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2096623015  21 FLAIVEAGSITGA--ADALGVAKSAVSQNLKHLED 53
Cdd:COG3398   103 LLYLLENPGATNKelAEELGISRSTVSWHLKRLEE 137
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 120-268 7.54e-03

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 36.97  E-value: 7.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 120 PALAQMLRRFSSLQPRVIADDARLDLVAGGIDLALTVGDLPDSSLKAQRV-GALCDTLCvAPELLETGPSPS-------- 190
Cdd:cd08484    17 PRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEGAWPGTDATRLfEAPLSPLC-TPELARRLSEPAdlanetll 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096623015 191 ----AAEFTDWIQQlpyvahmrepATVTfacdseirgdlrfVPNLRGNTVDAVLAM---AREGMGVALLPDLAVAEDLAG 263
Cdd:cd08484    96 rsyrADEWPQWFEA----------AGVP-------------PPPINGPVFDSSLLMveaALQGAGVALAPPSMFSRELAS 152


                  ....*
gi 2096623015 264 GRLVR 268
Cdd:cd08484   153 GALVQ 157
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 33-73 9.23e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 37.32  E-value: 9.23e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2096623015  33 AADALGVAKSAVSQNLKHLEDTLGVKLAIRTTRRFTLTPAG 73
Cdd:PRK11151   21 AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG 61
 
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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