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Conserved domains on  [gi|937072724|ref|WP_054541489|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Vibrio]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1001158)

LysR family HTH-containing transcriptional regulator

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 super family cl32646
DNA-binding transcriptional activator GcvA; Provisional
 2-289 1.58e-45

DNA-binding transcriptional activator GcvA; Provisional


The actual alignment was detected with superfamily member PRK11139:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 155.39  E-value: 1.58e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   2 LPPLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQPIVAGSLAHLKLQT 81
Cdd:PRK11139   5 LPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEAT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  82 QILFGEKETDVLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVESEDTHCERLFQEH 161
Cdd:PRK11139  85 RKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 162 WQLVCSPQFKSEHQELLSKHDFAALPTVQVKGyRENWLQWLGHNQFE-MTLPKVLLeVSNSLHALEAVKHGIGMLLVR-S 239
Cdd:PRK11139 165 LLPVCSPALLNGGKPLKTPEDLARHTLLHDDS-REDWRAWFRAAGLDdLNVQQGPI-FSHSSMALQAAIHGQGVALGNrV 242

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937072724 240 LAVSElLKKEDLVLASESSMPAESAHYLITKHSRS--AKVNFFCDWLYHQME 289
Cdd:PRK11139 243 LAQPE-IEAGRLVCPFDTVLPSPNAFYLVCPDSQAelPKVAAFRQWLLAEAA 293
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 2-289 1.58e-45

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 155.39  E-value: 1.58e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   2 LPPLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQPIVAGSLAHLKLQT 81
Cdd:PRK11139   5 LPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEAT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  82 QILFGEKETDVLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVESEDTHCERLFQEH 161
Cdd:PRK11139  85 RKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 162 WQLVCSPQFKSEHQELLSKHDFAALPTVQVKGyRENWLQWLGHNQFE-MTLPKVLLeVSNSLHALEAVKHGIGMLLVR-S 239
Cdd:PRK11139 165 LLPVCSPALLNGGKPLKTPEDLARHTLLHDDS-REDWRAWFRAAGLDdLNVQQGPI-FSHSSMALQAAIHGQGVALGNrV 242

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937072724 240 LAVSElLKKEDLVLASESSMPAESAHYLITKHSRS--AKVNFFCDWLYHQME 289
Cdd:PRK11139 243 LAQPE-IEAGRLVCPFDTVLPSPNAFYLVCPDSQAelPKVAAFRQWLLAEAA 293
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-290 3.41e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 3.41e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   4 PLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQPIVAGSLAHL-KLQTQ 82
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELeEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  83 I-LFGEKETDVLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDI------QLVDWPSTnpcQNVDIELTNGKVESEDTHCE 155
Cdd:COG0583   82 LrALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELregnsdRLVDALLE---GELDLAIRLGPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 156 RLFQEHWQLVCSPQfksehqellskHDFAALPTVqvkgyrenwlqwlghnqfemtlpkvlleVSNSLHALEAVKHGIGML 235
Cdd:COG0583  159 PLGEERLVLVASPD-----------HPLARRAPL----------------------------VNSLEALLAAVAAGLGIA 199

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 937072724 236 LVRSLAVSELLKKEDLVLASESSMPAESAHYLITKHSR--SAKVNFFCDWLYHQMED 290
Cdd:COG0583  200 LLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRhlSPAVRAFLDFLREALAE 256
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 92-284 5.42e-29

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: 109.21  E-value: 5.42e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  92 VLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVESEDTHCERLFQEHWQLVCSPQFK 171
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 172 SEHQeLLSKHDFAALPTVQVKGYRENWLQWLGHNQFEMTLPKVLLEVSNSLHALEAVKHGIGMLLVRSLAVSELLKKEDL 251
Cdd:cd08432   81 AGLP-LLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 937072724 252 VLASESSMPAESAHYLITKHSR--SAKVNFFCDWL 284
Cdd:cd08432  160 VRPFDLPLPSGGAYYLVYPPGRaeSPAVAAFRDWL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 4.85e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.67  E-value: 4.85e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724    5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 2-289 1.58e-45

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 155.39  E-value: 1.58e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   2 LPPLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQPIVAGSLAHLKLQT 81
Cdd:PRK11139   5 LPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEAT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  82 QILFGEKETDVLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVESEDTHCERLFQEH 161
Cdd:PRK11139  85 RKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 162 WQLVCSPQFKSEHQELLSKHDFAALPTVQVKGyRENWLQWLGHNQFE-MTLPKVLLeVSNSLHALEAVKHGIGMLLVR-S 239
Cdd:PRK11139 165 LLPVCSPALLNGGKPLKTPEDLARHTLLHDDS-REDWRAWFRAAGLDdLNVQQGPI-FSHSSMALQAAIHGQGVALGNrV 242

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937072724 240 LAVSElLKKEDLVLASESSMPAESAHYLITKHSRS--AKVNFFCDWLYHQME 289
Cdd:PRK11139 243 LAQPE-IEAGRLVCPFDTVLPSPNAFYLVCPDSQAelPKVAAFRQWLLAEAA 293
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-290 3.41e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 145.78  E-value: 3.41e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   4 PLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQPIVAGSLAHL-KLQTQ 82
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELeEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  83 I-LFGEKETDVLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDI------QLVDWPSTnpcQNVDIELTNGKVESEDTHCE 155
Cdd:COG0583   82 LrALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELregnsdRLVDALLE---GELDLAIRLGPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 156 RLFQEHWQLVCSPQfksehqellskHDFAALPTVqvkgyrenwlqwlghnqfemtlpkvlleVSNSLHALEAVKHGIGML 235
Cdd:COG0583  159 PLGEERLVLVASPD-----------HPLARRAPL----------------------------VNSLEALLAAVAAGLGIA 199

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 937072724 236 LVRSLAVSELLKKEDLVLASESSMPAESAHYLITKHSR--SAKVNFFCDWLYHQMED 290
Cdd:COG0583  200 LLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRhlSPAVRAFLDFLREALAE 256
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 92-284 5.42e-29

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: 109.21  E-value: 5.42e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  92 VLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVESEDTHCERLFQEHWQLVCSPQFK 171
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 172 SEHQeLLSKHDFAALPTVQVKGYRENWLQWLGHNQFEMTLPKVLLEVSNSLHALEAVKHGIGMLLVRSLAVSELLKKEDL 251
Cdd:cd08432   81 AGLP-LLSPADLARHTLLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 937072724 252 VLASESSMPAESAHYLITKHSR--SAKVNFFCDWL 284
Cdd:cd08432  160 VRPFDLPLPSGGAYYLVYPPGRaeSPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
11-292 1.77e-28

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 110.86  E-value: 1.77e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  11 FEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQPIVAGSLAHLKLQTQILFGEKET 90
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQELS 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  91 DVLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDI----QLVDWPSTnpcqNVDIELTNGKVESEDTHCERLFQEHWQLVC 166
Cdd:PRK10086 102 GTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTIltgnENVNFQRA----GIDLAIYFDDAPSAQLTHHFLMDEEILPVC 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 167 SPQFKSEHqELLSK----------HDfaalptVQVKGYR---ENWLQWLGHNQFEMTLPKVLLEVSNSLHALEAVKHGIG 233
Cdd:PRK10086 178 SPEYAERH-ALTGNpdnlrhctllHD------RQAWSNDsgtDEWHSWAQHFGVNLLPPSSGIGFDRSDLAVIAAMNHIG 250

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 937072724 234 MLLVRSLAVSELLKKEDLVLA-SESSMPAESAHYLITKHSR-SAKVNFFCDWLYHQMEDGE 292
Cdd:PRK10086 251 VAMGRKRLVQKRLASGELVAPfGDMEVKCHQHYYVTTLPGRqWPKIEAFIDWLKEQVKTTS 311
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 4.85e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 86.67  E-value: 4.85e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724    5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 92-284 1.19e-19

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: 84.65  E-value: 1.19e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  92 VLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVESEDTHCERLFQEHWQLVCSPQFK 171
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 172 SEHQeLLSKHDFAALPTVQVKGYRENWLQWLGHN--------------QFEMtlpkvllevsnslhALEAVKHGIGMLLV 237
Cdd:cd08481   81 AGRA-LAAPADLAHLPLLQQTTRPEAWRDWFEEVglevptayrgmrfeQFSM--------------LAQAAVAGLGVALL 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 937072724 238 RSLAVSELLKKEDLVLASESSMPAESAHYLITKHSR--SAKVNFFCDWL 284
Cdd:cd08481  146 PRFLIEEELARGRLVVPFNLPLTSDKAYYLVYPEDKaeSPPVQAFRDWL 194
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-284 1.32e-19

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 84.65  E-value: 1.32e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   93 LSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDwpSTNPCQ-----NVDIELTNGKVESEDTHCERLFQEHWQLVCS 167
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGN--SEELLDlllegELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  168 PQFKSEHQELLSKHDFAALPTVQVK---GYRENWLQWLGHNQFEmtlPKVLLEVSNSLHALEAVKHGIGMLLVRSLAVSE 244
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPpgsGLRDLLDRALRAAGLR---PRVVLEVNSLEALLQLVAAGLGIALLPRSAVAR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 937072724  245 LLKKEDLVLASESSMPAESAHYLITKHSR--SAKVNFFCDWL 284
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKGRplSPAVRAFIEFL 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
 1-248 2.43e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 68.89  E-value: 2.43e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   1 MLP-PLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYqpivagslahLKL 79
Cdd:CHL00180   2 DLPfTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELL----------LRY 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  80 QTQILFGEKETDVLSLRVNHTFCHN-----------WLLPRLPS-FYKKYPFIRLDIQL-----VDWPSTNpcQNVDIEL 142
Cdd:CHL00180  72 GNRILALCEETCRALEDLKNLQRGTliigasqttgtYLMPRLIGlFRQRYPQINVQLQVhstrrIAWNVAN--GQIDIAI 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 143 TNGKVESE---DTHCERLFQEHWQLVCSP-----QFKSEHQELLSKHDFAAL-PTVQVKGYRENWLQwlgHNQFEMTLPK 213
Cdd:CHL00180 150 VGGEVPTElkkILEITPYVEDELALIIPKshpfaKLKKIQKEDLYRLNFITLdSNSTIRKVIDNILI---QNGIDSKRFK 226

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 937072724 214 VLLEVsNSLHALE-AVKHGIGMLLVRSLAVSELLKK 248
Cdd:CHL00180 227 IEMEL-NSIEAIKnAVQSGLGAAFVSVSAIEKELEL 261
PRK10341 PRK10341
transcriptional regulator TdcA;
1-64 2.47e-12

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 66.04  E-value: 2.47e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 937072724   1 MLPPLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQ 64
Cdd:PRK10341   5 LLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQ 68
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
8-252 4.90e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 64.99  E-value: 4.90e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   8 LVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERsSKGAKLTSAAQhyqpIVAGSLAHLKL-----QTQ 82
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQ----RLLRHLRQVALleadlLST 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  83 ILFGEKETDVLSLRVNHTFCHNWLLPRLPSFYKKyPFIRLDIQLVDWPSTNPcqnvdiELTNGKV------ESE---DTH 153
Cdd:PRK13348  82 LPAERGSPPTLAIAVNADSLATWFLPALAAVLAG-ERILLELIVDDQDHTFA------LLERGEVvgcvstQPKpmrGCL 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 154 CERLFQEHWQLVCSPQFKSEH-QELLSKHDFAALPTVQVK---GYRENWLQWLGhNQFEMTLPKVLLEvsnSLHALE-AV 228
Cdd:PRK13348 155 AEPLGTMRYRCVASPAFAARYfAQGLTRHSALKAPAVAFNrkdTLQDSFLEQLF-GLPVGAYPRHYVP---STHAHLaAI 230

                        250       260
                 ....*....|....*....|....
gi 937072724 229 KHGIGMLLVRSLAVSELLKKEDLV 252
Cdd:PRK13348 231 RHGLGYGMVPELLIGPLLAAGRLV 254
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-284 6.23e-12

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: 63.39  E-value: 6.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  93 LSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDI------QLVDWPSTNpcqNVDIELTNGKVESEDTHCERLFQEHWQLVC 166
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLveggssELLEALLEG---ELDLAIVALPVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 167 SPQFKSEHQELLSKHDFAALPTVQVK---GYRENWLQWLGHNQFEmtlPKVLLEVSNSLHALEAVKHGIGMLLVRSLAVS 243
Cdd:cd05466   79 PPDHPLAKRKSVTLADLADEPLILFErgsGLRRLLDRAFAEAGFT---PNIALEVDSLEAIKALVAAGLGIALLPESAVE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 937072724 244 ElLKKEDLVLASESSMPAESAHYLITKHSR--SAKVNFFCDWL 284
Cdd:cd05466  156 E-LADGGLVVLPLEDPPLSRTIGLVWRKGRylSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-231 5.54e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.90  E-value: 5.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   1 MLppLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYqpIVAGSLAHLKLQ 80
Cdd:PRK11242   1 ML--LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVY--LRYARRALQDLE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  81 TqilfGEKET-DV-------LSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQ----------LVDwpstnpcQNVDIEL 142
Cdd:PRK11242  77 A----GRRAIhDVadlsrgsLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIRemsqeriealLAD-------DELDVGI 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 143 TNGKVESEDTHCERLFQEHWQLVCSPQFK-SEHQELLSKHDFAALPTV----------QVKGY-RENWLQwlghnqfemt 210
Cdd:PRK11242 146 AFAPVHSPEIEAQPLFTETLALVVGRHHPlAARRKALTLDELADEPLVllsaefatreQIDRYfRRHGVT---------- 215

                        250       260
                 ....*....|....*....|..
gi 937072724 211 lPKVLLEVsNSLHA-LEAVKHG 231
Cdd:PRK11242 216 -PRVAIEA-NSISAvLEIVRRG 235
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-128 1.92e-10

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 60.17  E-value: 1.92e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   1 MLPPlRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSS------KGAKLTSAAQHYQPIVAGSL 74
Cdd:PRK03635   1 MLDY-KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQpcrpteAGQRLLRHARQVRLLEAELL 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 937072724  75 AHLKLqtqiLFGEKETdvLSLRVNHTFCHNWLLPRLPSFYKKYPfIRLDIQLVD 128
Cdd:PRK03635  80 GELPA----LDGTPLT--LSIAVNADSLATWFLPALAPVLARSG-VLLDLVVED 126
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 95-284 1.33e-09

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: 56.68  E-value: 1.33e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  95 LRVN--HTFCHNWLLPRLPSFYKKYPFIRLDIQLVDwpstnpcQNVD-IE------LTNGKVESEDTHCERLFQEHWQLV 165
Cdd:cd08422    3 LRISapVSFGRLHLAPLLAEFLARYPDVRLELVLSD-------RLVDlVEegfdlaIRIGELPDSSLVARRLGPVRRVLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 166 CSPQFKSEHQELLSKHDFAALPTVQVkGYRENWLQWL---GHNQFEMTLPKVLleVSNSLHAL-EAVKHGIGMLLVRSLA 241
Cdd:cd08422   76 ASPAYLARHGTPQTPEDLARHRCLGY-RLPGRPLRWRfrrGGGEVEVRVRGRL--VVNDGEALrAAALAGLGIALLPDFL 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 937072724 242 VSELLKKEDLVLASESSMPAESAHYLITKHSR--SAKVNFFCDWL 284
Cdd:cd08422  153 VAEDLASGRLVRVLPDWRPPPLPIYAVYPSRRhlPAKVRAFIDFL 197
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 92-284 3.16e-09

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: 55.45  E-value: 3.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  92 VLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIqlvdwpSTN------PCQNVDIELTNGKVESEDTHCERLFQEHWQLV 165
Cdd:cd08484    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRL------STNnnrvdiAAEGLDFAIRFGEGAWPGTDATRLFEAPLSPL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 166 CSPQFKsehQELLSKHDFAALPTvqVKGYREN-WLQWLGHNQFEMTLPKVLLEVSnSLHALEAVKHGIGMLLVRSLAVSE 244
Cdd:cd08484   75 CTPELA---RRLSEPADLANETL--LRSYRADeWPQWFEAAGVPPPPINGPVFDS-SLLMVEAALQGAGVALAPPSMFSR 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 937072724 245 LLKKEDLV--LASESSMpaeSAHYLITKHSR--SAKVNFFCDWL 284
Cdd:cd08484  149 ELASGALVqpFKITVST---GSYWLTRLKSKpeTPAMSAFSQWL 189
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 93-284 7.68e-09

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: 54.27  E-value: 7.68e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  93 LSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDI----QLVDWPStnpcQNVDIELTNGKVESEDTHCERLFQEHWQLVCSP 168
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLlpsaDLVDLRP----DGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 169 QFKSEhQELLSKHDFAALPTVQVKGYRENWlQWLGHNQFEMTLPKVLLEVSNSLhALEAVKHGIGM-LLVRSLAVSElLK 247
Cdd:cd08483   78 GLLGD-RKVDSLADLAGLPWLQERGTNEQR-VWLASMGVVPDLERGVTFLPGQL-VLEAARAGLGLsIQARALVEPD-IA 153

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 937072724 248 KEDLVLASESSmPAESAHYLITKHSR-SAKVNFFCDWL 284
Cdd:cd08483  154 AGRLTVLFEEE-EEGLGYHIVTRPGVlRPAAKAFVRWL 190
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
5-185 1.34e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 55.02  E-value: 1.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQPIVAGSLAHLKLQTQIL 84
Cdd:PRK15421   4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQAC 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  85 fGEKETDVLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQL-VDWPSTNPCQN--VDIELTNGKVESEDTHCERLFQEH 161
Cdd:PRK15421  84 -NEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSgVTFDPQPALQQgeLDLVMTSDILPRSGLHYSPMFDYE 162

                        170       180
                 ....*....|....*....|....
gi 937072724 162 WQLVCSPQFKSEHQELLSKHDFAA 185
Cdd:PRK15421 163 VRLVLAPDHPLAAKTRITPEDLAS 186
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-65 1.65e-08

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 54.81  E-value: 1.65e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 937072724   1 MLPPlRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQH 65
Cdd:PRK10094   1 MFDP-ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEH 64
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 92-284 3.33e-08

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: 52.53  E-value: 3.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  92 VLSLRVNHTFCHNWLLPRLPSFYKKYPFIrlDIQLvdwpSTN------PCQNVDIELTNGKVESEDTHCERLFQEHWQLV 165
Cdd:cd08488    1 VLHVGAVGTFAVGWLLPRLADFQNRHPFI--DLRL----STNnnrvdiAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 166 CSPQFKSEHQELLSKHDFAALptvqvKGYR-ENWLQWL-----GHNqfeMTLPKVLLeVSNSLHALEAVKHGIGMLLVRS 239
Cdd:cd08488   75 CTPELARQLREPADLARHTLL-----RSYRaDEWPQWFeaagvGHP---CGLPNSIM-FDSSLGMMEAALQGLGVALAPP 145

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 937072724 240 LAVSELLKKEDLVLASESSMPAESahYLITK-HSRSAK--VNFFCDWL 284
Cdd:cd08488  146 SMFSRQLASGALVQPFATTLSTGS--YWLTRlQSRPETpaMSAFSAWL 191
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 92-284 4.70e-08

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


Pssm-ID: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 52.16  E-value: 4.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  92 VLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQ----LVDWPStnpcQNVDIELTNGKVESEDTHCERLFQEHWQLVCS 167
Cdd:cd08487    1 VLTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRtnnnVVDLAT----EGLDFAIRFGEGLWPATHNERLLDAPLSVLCS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 168 PqfksEHQELLSK-HDFAALPTvqVKGYREN-WLQWLGHNQfeMTLPKVLLEV-SNSLHALEAVKHGIGMLLVRSLAVSE 244
Cdd:cd08487   77 P----EIAKRLSHpADLINETL--LRSYRTDeWLQWFEAAN--MPPIKIRGPVfDSSRLMVEAAMQGAGVALAPAKMFSR 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 937072724 245 LLKKEDLVLASESSMPAeSAHYLITKHSR--SAKVNFFCDWL 284
Cdd:cd08487  149 EIENGQLVQPFKIEVET-GSYWLTWLKSKpmTPAMELFRQWI 189
PRK09791 PRK09791
LysR family transcriptional regulator;
5-66 4.74e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.23  E-value: 4.74e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 937072724   5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHY 66
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESF 68
PRK09801 PRK09801
LysR family transcriptional regulator;
3-182 1.65e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 51.57  E-value: 1.65e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   3 PPLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQ-----------HYQPIVA 71
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQrcyehaleiltQYQRLVD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  72 GSlahlklqTQIlfGEKETDVLSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKvESED 151
Cdd:PRK09801  86 DV-------TQI--KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRIND-EIPD 155

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 937072724 152 THCERLFQEHWQLVC-SPQFKSEHQE-----LLSKHD 182
Cdd:PRK09801 156 YYIAHLLTKNKRILCaAPEYLQKYPQpqslqELSRHD 192
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-66 2.27e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 51.10  E-value: 2.27e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 937072724  12 EAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHY 66
Cdd:PRK11074  11 DAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWF 65
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-60 4.36e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 50.41  E-value: 4.36e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937072724   8 LVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLT 60
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLT 68
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 93-284 2.04e-06

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


Pssm-ID: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 47.40  E-value: 2.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  93 LSLRVNHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVE-SEDTHCERLFQEHWQLVCSPQF- 170
Cdd:cd08482    2 LVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPwPAGMQVIELFPERVGPVCSPSLa 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 171 KSEHQELLSKHDFAALPTVQVKGYRENWLQWLGHNQFEMTLPKVLLEVSNSLHALEAVKHGIGmllvrsLAVS-ELLKKE 249
Cdd:cd08482   82 PTVPLRQAPAAALLGAPLLHTRSRPQAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLG------VAIApWPLVRD 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 937072724 250 DL---VLASESSMPAESAHY--LITKHSRSAKVNFFCDWL 284
Cdd:cd08482  156 DLasgRLVAPWGFIETGSHYvlLRPARLRDSRAGALADWL 195
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-284 2.29e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176161  Cd Length: 202  Bit Score: 47.12  E-value: 2.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  95 LRV--NHTFCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVESEDTHCERLFQEHWQLVCSPQFKS 172
Cdd:cd08472    3 LRVdvPGSLARLLLIPALPDFLARYPDIELDLGVSDRPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPAYLA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 173 EHQELLSKHDFAALPTVqvkGYREN-------WLQWLGHNQFEMTLPKVLLeVSNSLHALEAVKHGIGMLLVRSLAVSEL 245
Cdd:cd08472   83 RHGTPRHPEDLERHRAV---GYFSArtgrvlpWEFQRDGEEREVKLPSRVS-VNDSEAYLAAALAGLGIIQVPRFMVRPH 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 937072724 246 LKKEDLV--LA--SESSMPAesahYLITKHSR--SAKVNFFCDWL 284
Cdd:cd08472  159 LASGRLVevLPdwRPPPLPV----SLLYPHRRhlSPRVRVFVDWV 199
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 5-252 2.39e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 48.15  E-value: 2.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKgaKLTsAAQHYQPIVAGSLAHLKLQTQI- 83
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGK--RLV-VNEHGRLLYPRALALLEQAVEIe 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  84 -LFGEketDVLSLRVN-HTFCHNWLLPRLPSFYKK-YPFIRLDIQLVDwpSTNPCQ-----NVDIELTNGKVesedtHCE 155
Cdd:PRK10837  82 qLFRE---DNGALRIYaSSTIGNYILPAMIARYRRdYPQLPLELSVGN--SQDVINavldfRVDIGLIEGPC-----HSP 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 156 RLFQEHW---QLV--CSPQFKSEHQElLSKHDFAALPTV---QVKGYRE--NWLqWLGH-NQFEMtlpkvLLEVSNSLHA 224
Cdd:PRK10837 152 ELISEPWledELVvfAAPDSPLARGP-VTLEQLAAAPWIlreRGSGTREivDYL-LLSHlPRFEL-----AMELGNSEAI 224

                        250       260
                 ....*....|....*....|....*...
gi 937072724 225 LEAVKHGIGMLLVRSLAVSELLKKEDLV 252
Cdd:PRK10837 225 KHAVRHGLGISCLSRRVIADQLQAGTLV 252
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
5-118 1.47e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 45.91  E-value: 1.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQPIVAGSLAHLKLQTQIL 84
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 937072724  85 FGEKETDVLSLRV--NHTFCHNWLLPRLPSFYKKYP 118
Cdd:PRK10632  84 YAFNNTPIGTLRIgcSSTMAQNVLAGLTAKMLKEYP 119
PRK09986 PRK09986
LysR family transcriptional regulator;
5-62 2.43e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 45.10  E-value: 2.43e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 937072724   5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSA 62
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHA 66
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
2-39 3.42e-04

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 39.04  E-value: 3.42e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 937072724   2 LPPLRALVAFEAVARLGSIGAAARELCVTQAAVSQQLK 39
Cdd:COG2522   13 LPAIRALLAKELVERGLSQSEIAKLLGITQAAVSQYLS 50
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 12-125 7.37e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 40.36  E-value: 7.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  12 EAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAK-LTSAAQHYQPI------VAGSLAHLKLQtqil 84
Cdd:PRK12682  11 EAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVierilrEVGNIKRIGDD---- 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 937072724  85 FGEKETDVLSLRVNHTFCHnWLLPR-LPSFYKKYPFIRLDIQ 125
Cdd:PRK12682  87 FSNQDSGTLTIATTHTQAR-YVLPRvVAAFRKRYPKVNLSLH 127
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 5-69 1.61e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 39.28  E-value: 1.61e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937072724   5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQ----HYQPI 69
Cdd:PRK11233   3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKilytHARAI 71
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 5-64 2.97e-03

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 38.60  E-value: 2.97e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724   5 LRALVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQ 64
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGE 62
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 104-252 3.35e-03

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


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 37.86  E-value: 3.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 104 NWLLPR-LPSFYKKYPFIRLDIQLvdwpsTNPCQN--------VDIELTNGKVESEDTHCERLFQEHWQLVCSPQfkseh 174
Cdd:cd08420   12 EYLLPRlLARFRKRYPEVRVSLTI-----GNTEEIaervldgeIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPD----- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724 175 qellskHDFAALPTVQVKG-YRENWL-------------QWLGHNQFEMTLPKVLLEVSNSLHALEAVKHGIGMLLVRSL 240
Cdd:cd08420   82 ------HPLAGRKEVTAEElAAEPWIlrepgsgtrevfeRALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRL 155

                        170
                 ....*....|..
gi 937072724 241 AVSELLKKEDLV 252
Cdd:cd08420  156 AVRKELELGRLV 167
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
8-68 4.71e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 38.07  E-value: 4.71e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 937072724   8 LVAFEAVARLGSIGAAARELCVTQAAVSQQLKSLETFLDTTLFERSSKGAKLTSAAQHYQP 68
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLP 66
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-185 5.34e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 37.32  E-value: 5.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937072724  95 LRVNHT--FCHNWLLPRLPSFYKKYPFIRLDIQLVDWPSTNPCQNVDIELTNGKVESEDTHCERLFQEHWQLVCSPQFKS 172
Cdd:cd08480    3 LRVNASvpFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSYLA 82

                         90
                 ....*....|...
gi 937072724 173 EHQELLSKHDFAA 185
Cdd:cd08480   83 RHGTPLTPQDLAR 95
 
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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