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Conserved domains on  [gi|857688505|emb|CDU02755|]
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Glycine cleavage system transcriptional activator [Vibrio coralliirubri]

Protein Classification

transcriptional regulator GcvA( domain architecture ID 11485222)

transcriptional regulator GcvA is a LysR-type transcriptional regulator protein that mediates activation of gcv by glycine and repression by purines

Gene Ontology:  GO:0006355|GO:0006351|GO:0003677
PubMed:  8188587|19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-297 0e+00

DNA-binding transcriptional activator GcvA; Provisional


:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 572.17  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   1 MSRRLPPLNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  81 AEATDKVLERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLRADKL 160
Cdd:PRK11139  81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 161 YQEYLIPLCSPSVLLGVKPLESLSDLACHTLLHDTSRKDWKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGN 240
Cdd:PRK11139 161 LDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGN 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 857688505 241 NVLAQPEIEAGRLIAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWMLAKAQSEQE 297
Cdd:PRK11139 241 RVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQE 297
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-297 0e+00

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 572.17  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   1 MSRRLPPLNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  81 AEATDKVLERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLRADKL 160
Cdd:PRK11139  81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 161 YQEYLIPLCSPSVLLGVKPLESLSDLACHTLLHDTSRKDWKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGN 240
Cdd:PRK11139 161 LDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGN 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 857688505 241 NVLAQPEIEAGRLIAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWMLAKAQSEQE 297
Cdd:PRK11139 241 RVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQE 297
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-288 5.91e-80

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: 240.56  E-value: 5.91e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  95 ALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPSvL 174
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPA-L 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 175 LGVKPLESLSDLACHTLLHDTSRKD-WKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEAGRL 253
Cdd:cd08432   80 LAGLPLLSPADLARHTLLHDATRPEaWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 857688505 254 IAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08432  160 VRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-294 4.27e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 189.69  E-value: 4.27e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   7 PLNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDK 86
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  87 V--LERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGS---LTDDVDVAIYYGRGNWSGLRADKLY 161
Cdd:COG0583   82 LraLRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVdalLEGELDLAIRLGPPPDPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 162 QEYLIPLCSPSvllgvkpleslsdlacHTLLHdtsrkdwkqfakqngidgvnvnHGPIFSHSTMVLQAAAHGQGIALGNN 241
Cdd:COG0583  162 EERLVLVASPD----------------HPLAR----------------------RAPLVNSLEALLAAVAAGLGIALLPR 203

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 857688505 242 VLAQPEIEAGRLIAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWMLAKAQS 294
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-293 1.59e-28

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: 108.53  E-value: 1.59e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGS---LTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCS 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLdllLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  171 PSVLLGVKPLESLSDLACHTLLH-DTSRKDWKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIE 249
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILlPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 857688505  250 AGRLIA-PFDEVLVSkNAFYVVCHEKQADMGRIATFRDWMLAKAQ 293
Cdd:pfam03466 162 DGRLVAlPLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-297 0e+00

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 572.17  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   1 MSRRLPPLNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSL 80
Cdd:PRK11139   1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  81 AEATDKVLERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLRADKL 160
Cdd:PRK11139  81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 161 YQEYLIPLCSPSVLLGVKPLESLSDLACHTLLHDTSRKDWKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGN 240
Cdd:PRK11139 161 LDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGN 240

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 857688505 241 NVLAQPEIEAGRLIAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWMLAKAQSEQE 297
Cdd:PRK11139 241 RVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQE 297
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-288 5.91e-80

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: 240.56  E-value: 5.91e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  95 ALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPSvL 174
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPA-L 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 175 LGVKPLESLSDLACHTLLHDTSRKD-WKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEAGRL 253
Cdd:cd08432   80 LAGLPLLSPADLARHTLLHDATRPEaWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAGRL 159

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 857688505 254 IAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08432  160 VRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-296 1.41e-67

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 212.94  E-value: 1.41e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   2 SRRLPPLNS-----LRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDI 76
Cdd:PRK10086   5 EMRNRLLNGwqlskLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSS 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  77 FTSLAEATDKVLERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLR 156
Cdd:PRK10086  85 LDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPSAQLT 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 157 ADKLYQEYLIPLCSPSVLLGVKPLESLSDLACHTLLHD------TSRKD-WKQFAKQNGIDGVNVNHGPIFSHSTMVLQA 229
Cdd:PRK10086 165 HHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDrqawsnDSGTDeWHSWAQHFGVNLLPPSSGIGFDRSDLAVIA 244

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 857688505 230 AAHGQGIALGNNVLAQPEIEAGRLIAPF-DEVLVSKNAFYVVC-HEKQAdmGRIATFRDWMLAKAQSEQ 296
Cdd:PRK10086 245 AMNHIGVAMGRKRLVQKRLASGELVAPFgDMEVKCHQHYYVTTlPGRQW--PKIEAFIDWLKEQVKTTS 311
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-294 4.27e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 189.69  E-value: 4.27e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   7 PLNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDK 86
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  87 V--LERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGS---LTDDVDVAIYYGRGNWSGLRADKLY 161
Cdd:COG0583   82 LraLRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVdalLEGELDLAIRLGPPPDPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 162 QEYLIPLCSPSvllgvkpleslsdlacHTLLHdtsrkdwkqfakqngidgvnvnHGPIFSHSTMVLQAAAHGQGIALGNN 241
Cdd:COG0583  162 EERLVLVASPD----------------HPLAR----------------------RAPLVNSLEALLAAVAAGLGIALLPR 203

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 857688505 242 VLAQPEIEAGRLIAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWMLAKAQS 294
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 96-288 1.14e-51

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: 168.24  E-value: 1.14e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  96 LTISLPPSFAIQWLVPRLADFNQQEPDIDV----RIKAVDMDEGSLtddvDVAIYYGRGNWSGLRADKLYQEYLIPLCSP 171
Cdd:cd08481    2 LELAVLPTFGTRWLIPRLPDFLARHPDITVnlvtRDEPFDFSQGSF----DAAIHFGDPVWPGAESEYLMDEEVVPVCSP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 172 SvLLGVKPLESLSDLACHTLLHDTSRKD-WKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEA 250
Cdd:cd08481   78 A-LLAGRALAAPADLAHLPLLQQTTRPEaWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELAR 156

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 857688505 251 GRLIAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08481  157 GRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 95-288 2.16e-36

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: 129.00  E-value: 2.16e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  95 ALTISLPPSFAIQWLVPRLADFNQQEPDIDVRI----KAVDMDEgsltDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCS 170
Cdd:cd08483    1 PLTVTLTPSFASNWLMPRLGSFWAKHPEIELSLlpsaDLVDLRP----DGIDVAIRYGNGDWPGLESEPLTAAPFVVVAA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 171 PSvLLGVKPLESLSDLACHTLLHDTSRKDWKQFAKQNGIDGVNVNhGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEA 250
Cdd:cd08483   77 PG-LLGDRKVDSLADLAGLPWLQERGTNEQRVWLASMGVVPDLER-GVTFLPGQLVLEAARAGLGLSIQARALVEPDIAA 154

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 857688505 251 GRLIAPFDEVLVSKnAFYVVcHEKQADMGRIATFRDWM 288
Cdd:cd08483  155 GRLTVLFEEEEEGL-GYHIV-TRPGVLRPAAKAFVRWL 190
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 95-288 1.15e-33

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: 121.74  E-value: 1.15e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  95 ALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNW-SGLRADKLYQEYLIPLCSPSv 173
Cdd:cd08482    1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWpAGMQVIELFPERVGPVCSPS- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 174 LLGVKPL--ESLSDLACHTLLHDTSRKD-WKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEA 250
Cdd:cd08482   80 LAPTVPLrqAPAAALLGAPLLHTRSRPQaWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 857688505 251 GRLIAPFDevLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08482  160 GRLVAPWG--FIETGSHYVLLRPARLRDSRAGALADWL 195
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 96-288 1.54e-32

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


Pssm-ID: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 118.63  E-value: 1.54e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  96 LTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKA----VDMdegsLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSP 171
Cdd:cd08484    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTnnnrVDI----AAEGLDFAIRFGEGAWPGTDATRLFEAPLSPLCTP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 172 SVllgVKPLESLSDLACHTLLHDTSRKDWKQFAKQNGIdGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEAG 251
Cdd:cd08484   78 EL---ARRLSEPADLANETLLRSYRADEWPQWFEAAGV-PPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSRELASG 153

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 857688505 252 RLIAPFDeVLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08484  154 ALVQPFK-ITVSTGSYWLTRLKSKPETPAMSAFSQWL 189
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 96-288 2.56e-30

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: 113.02  E-value: 2.56e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  96 LTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPSVll 175
Cdd:cd08487    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEI-- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 176 gVKPLESLSDLACHTLLHDTSRKDWKQFAKQNGIDGVNVNhGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEAGRLIA 255
Cdd:cd08487   80 -AKRLSHPADLINETLLRSYRTDEWLQWFEAANMPPIKIR-GPVFDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLVQ 157

                        170       180       190
                 ....*....|....*....|....*....|...
gi 857688505 256 PFDeVLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08487  158 PFK-IEVETGSYWLTWLKSKPMTPAMELFRQWI 189
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 103-288 1.19e-28

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: 108.77  E-value: 1.19e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 103 SFAIQWLVPRLADFNQQEPDIDVRIKA----VDM-DEGsltddVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPSVllgV 177
Cdd:cd08488    9 TFAVGWLLPRLADFQNRHPFIDLRLSTnnnrVDIaAEG-----LDYAIRFGSGAWHGIDATRLFEAPLSPLCTPEL---A 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 178 KPLESLSDLACHTLLHDTSRKDWKQFAKQNGIDG-VNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEAGRLIAP 256
Cdd:cd08488   81 RQLREPADLARHTLLRSYRADEWPQWFEAAGVGHpCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGALVQP 160

                        170       180       190
                 ....*....|....*....|....*....|..
gi 857688505 257 FDeVLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08488  161 FA-TTLSTGSYWLTRLQSRPETPAMSAFSAWL 191
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-293 1.59e-28

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: 108.53  E-value: 1.59e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGS---LTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCS 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLdllLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  171 PSVLLGVKPLESLSDLACHTLLH-DTSRKDWKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIE 249
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILlPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 857688505  250 AGRLIA-PFDEVLVSkNAFYVVCHEKQADMGRIATFRDWMLAKAQ 293
Cdd:pfam03466 162 DGRLVAlPLPEPPLP-RELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 3.06e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 92.83  E-value: 3.06e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505    8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQ 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-288 5.60e-22

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: 90.96  E-value: 5.60e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRI----KAVDM-DEGsltddVDVAIYYGRGNWSGLRADKLYQEYLIPL 168
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELvlsdRLVDLvEEG-----FDLAIRIGELPDSSLVARRLGPVRRVLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 169 CSPSVLLGVKPLESLSDLACHTLL---HDTSRKDWkQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQ 245
Cdd:cd08422   76 ASPAYLARHGTPQTPEDLARHRCLgyrLPGRPLRW-RFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVA 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 857688505 246 PEIEAGRLIAPFDEVLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08422  155 EDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-128 5.88e-19

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 85.07  E-value: 5.88e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQsYFLDIKDIFTSLAEATDKV 87
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGE-LLLRYGNRILALCEETCRA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 857688505  88 LE---RSEKGALTISlppsfAIQ----WLVPRL-ADFNQQEPDIDVRIK 128
Cdd:CHL00180  86 LEdlkNLQRGTLIIG-----ASQttgtYLMPRLiGLFRQRYPQINVQLQ 129
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-145 1.56e-18

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 83.85  E-value: 1.56e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDKV 87
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 857688505  88 LERSE--KGALTISLPPSFAiQWLV-PRLADFNQQEPDIDVRIKAVDMD--EGSLTDD-VDVAI 145
Cdd:PRK11242  83 HDVADlsRGSLRLAMTPTFT-AYLIgPLIDAFHARYPGITLTIREMSQEriEALLADDeLDVGI 145
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-259 3.55e-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 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: 78.04  E-value: 3.55e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRI----KAVDM-DEGsltddVDVAIYYGRGNWSGLRADKLyQEYLIPL 168
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLvlsdRLVDLvEEG-----FDAAFRIGELADSSLVARPL-APYRMVL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 169 C-SPSVLLGVKPLESLSDLACHTLL---HDTSRKDWkQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLA 244
Cdd:cd08477   75 CaSPDYLARHGTPTTPEDLARHECLgfsYWRARNRW-RLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALL 153

                        170
                 ....*....|....*
gi 857688505 245 QPEIEAGRLIAPFDE 259
Cdd:cd08477  154 AEDLASGRLVELLPD 168
PRK09986 PRK09986
LysR family transcriptional regulator;
8-125 1.10e-13

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 69.75  E-value: 1.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDKV 87
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 857688505  88 --LERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDV 125
Cdd:PRK09986  89 eqIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEW 128
PRK09801 PRK09801
LysR family transcriptional regulator;
1-269 3.21e-13

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 68.91  E-value: 3.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   1 MSRRLPPLNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSL 80
Cdd:PRK09801   1 MLNSWPLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  81 AEATDKV--LERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLRAD 158
Cdd:PRK09801  81 QRLVDDVtqIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAH 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 159 KLYQEYLIPLCSPSVLLGVKPLESLSDLACHTLL----HDTSRKDWKQfakQNGIDGVNVN-HGPIFSHS-TMVLQAAAH 232
Cdd:PRK09801 161 LLTKNKRILCAAPEYLQKYPQPQSLQELSRHDCLvtkeRDMTHGIWEL---GNGQEKKSVKvSGHLSSNSgEIVLQWALE 237

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 857688505 233 GQGIALGNNVLAQPEIEAGRLIAPFDEVLVSKNAFYV 269
Cdd:PRK09801 238 GKGIMLRSEWDVLPFLESGKLVQVLPEYAQSANIWAV 274
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
11-209 5.29e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 68.12  E-value: 5.29e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  11 LRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDKVLEr 90
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNE- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  91 SEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKA---VDMDEGSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIP 167
Cdd:PRK15421  86 PQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSgvtFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRL 165

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 857688505 168 LCSPSVLLGVKPLESLSDLACHTLL---HDTSRKD-WKQFAKQNGI 209
Cdd:PRK15421 166 VLAPDHPLAAKTRITPEDLASETLLiypVQRSRLDvWRHFLQPAGV 211
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 94-288 1.06e-12

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: 65.44  E-value: 1.06e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPSV 173
Cdd:cd08478    3 GLLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRLRILASPDY 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 174 LLGVKPLESLSDLACHTLLHDTSRK---DWKqfAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEA 250
Cdd:cd08478   83 LARHGTPQSIEDLAQHQLLGFTEPAslnTWP--IKDADGNLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDIAE 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 857688505 251 GRLIAPF-DEVLVSKNAFYVVCHEKQADMGRIATFRDWM 288
Cdd:cd08478  161 GRLIPLFaEQTSDVRQPINAVYYRNTALSLRIRCFIDFL 199
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-134 2.68e-12

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 65.95  E-value: 2.68e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIftsLAEAtDKV 87
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAI---LEQA-EKA 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 857688505  88 LERS-----EKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDE 134
Cdd:PRK09906  79 KLRArkivqEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQ 130
PRK09791 PRK09791
LysR family transcriptional regulator;
8-127 3.02e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 65.94  E-value: 3.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDKV 87
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 857688505  88 LER--SEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRI 127
Cdd:PRK09791  87 RQRqgQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI 128
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-261 1.64e-11

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 62.14  E-value: 1.64e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVD-----MDEGsltddVDVAIYYGRGNWSGLRADKLYQEYLIPL 168
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLGVSDrpvdlIREG-----VDCVIRVGELADSSLVARRLGELRMVTC 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 169 CSPSVL--LGVkPlESLSDLACHTLLHDTSRK-----DWkQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNN 241
Cdd:cd08472   76 ASPAYLarHGT-P-RHPEDLERHRAVGYFSARtgrvlPW-EFQRDGEEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPR 152

                        170       180
                 ....*....|....*....|
gi 857688505 242 VLAQPEIEAGRLIapfdEVL 261
Cdd:cd08472  153 FMVRPHLASGRLV----EVL 168
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-72 3.79e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 62.65  E-value: 3.79e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 857688505  10 SLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQsYFLD 72
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE-WFVK 67
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-238 4.25e-11

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: 61.08  E-value: 4.25e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  96 LTISLPPSFAIQWLVPRLADFNQQEPDIDVRIK---AVDMDEGSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPS 172
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVeggSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 173 VLLGVKPLESLSDLACHTLL----HDTSRKDWKQFAKQNGIdgvNVNHGPIFSHSTMVLQAAAHGQGIAL 238
Cdd:cd05466   82 HPLAKRKSVTLADLADEPLIlferGSGLRRLLDRAFAEAGF---TPNIALEVDSLEAIKALVAAGLGIAL 148
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-77 1.48e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 60.98  E-value: 1.48e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 857688505  10 SLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIF 77
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-255 2.17e-09

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 55.99  E-value: 2.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVD-----MDEGsltddVDVAIYYGRGNWSGLRADKLYQEYLIpL 168
Cdd:cd08471    1 GLLTVTAPVLFGRLHVLPIITDFLDAYPEVSVRLLLLDrvvnlLEEG-----VDVAVRIGHLPDSSLVATRVGSVRRV-V 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 169 C-SPSVLLGVKPLESLSDLACHTLLHDT---SRKDWkQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIAlgnNVL- 243
Cdd:cd08471   75 CaSPAYLARHGTPKHPDDLADHDCIAFTglsPAPEW-RFREGGKERSVRVRPRLTVNTVEAAIAAALAGLGLT---RVLs 150

                        170
                 ....*....|....
gi 857688505 244 --AQPEIEAGRLIA 255
Cdd:cd08471  151 yqVAEELAAGRLQR 164
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 5-145 2.40e-09

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 57.31  E-value: 2.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   5 LPPLNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEAT 84
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 857688505  85 DKV--LERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKAVDMDEGSLTDDVDVAI 145
Cdd:PRK14997  81 DAIaaLQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAI 143
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 8-134 2.57e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 57.31  E-value: 2.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLR-VFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLL-LTEEGQSYFLDIKDIFTSLA--EA 83
Cdd:PRK12682   3 LQQLRfVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGniKR 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 857688505  84 TDKVLERSEKGALTISLPPSFAiQWLVPR-LADFNQQEPDIDVRIKAVDMDE 134
Cdd:PRK12682  83 IGDDFSNQDSGTLTIATTHTQA-RYVLPRvVAAFRKRYPKVNLSLHQGSPDE 133
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
8-145 9.51e-09

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 55.37  E-value: 9.51e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLR-VFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLL-LTEEG-------QSYFLDIKDIFT 78
Cdd:PRK12684   3 LHQLRfVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGriilasvERILQEVENLKR 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 857688505  79 SLAEATDKvlersEKGALTI---------SLPPsfAIQWlvprladFNQQEPDIDVRIK---AVDMDEGSLTDDVDVAI 145
Cdd:PRK12684  83 VGKEFAAQ-----DQGNLTIatthtqaryALPA--AIKE-------FKKRYPKVRLSILqgsPTQIAEMVLHGQADLAI 147
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-128 1.28e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 55.03  E-value: 1.28e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDKV 87
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSL 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 857688505  88 LERSEKGALTISLPPSFA----------IQWLVPRLAdfnqqepdIDVRIK 128
Cdd:PRK15092  93 MYSNLQGVLTIGASDDTAdtilpfllnrVSSVYPKLA--------LDVRVK 135
nhaR PRK11062
transcriptional activator NhaR; Provisional
 22-70 1.35e-08

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 55.01  E-value: 1.35e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 857688505  22 SFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYF 70
Cdd:PRK11062  20 SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVF 68
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 11-68 7.36e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 52.74  E-value: 7.36e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  11 LR-VFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLL-LTEEGQS 68
Cdd:PRK12683   6 LRiIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKE 65
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-254 1.13e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 51.06  E-value: 1.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRI----KAVDMDEgsltDDVDVAIYYGRGNWSGLRADKLYQEYLIpLC 169
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLeltdRPVDLVE----EGFDLDIRVGDLPDSSLIARKLAPNRRI-LC 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 170 -SPSVLLGVKPLESLSDLACHTLL----HDTSRKDWKqFAKQNGIDGVNVNhGPIFS-HSTMVLQAAAHGQGIALGNNVL 243
Cdd:cd08479   76 aSPAYLERHGAPASPEDLARHDCLvireNDEDFGLWR-LRNGDGEATVRVR-GALSSnDGEVVLQWALDGHGIILRSEWD 153

                        170
                 ....*....|.
gi 857688505 244 AQPEIEAGRLI 254
Cdd:cd08479  154 VAPYLRSGRLV 164
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-120 1.26e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 51.90  E-value: 1.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  11 LRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFrRRNRSLLLTEEGQSYFLDIKDIftSLAEA-TDKVLE 89
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL-VRGRPCRPTPAGQRLLRHLRQV--ALLEAdLLSTLP 83

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 857688505  90 RSEKGALTISLppsfAIQ------WLVPRLADFNQQE 120
Cdd:PRK13348  84 AERGSPPTLAI----AVNadslatWFLPALAAVLAGE 116
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
8-199 1.82e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 51.68  E-value: 1.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIftsLAEATDkV 87
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRM---LHEVQD-V 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  88 LER------SEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVR----IKAVDMdegsLTDDVDVAIYYGRGNWSGLRA 157
Cdd:PRK10632  80 HEQlyafnnTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNlvtgIPAPDL----IADGLDVVIRVGALQDSSLFS 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 857688505 158 DKLYQEYLIPLCSPSVLLGVKPLESLSDLACHTLLHDTSRKD 199
Cdd:PRK10632 156 RRLGAMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPD 197
cbl PRK12679
HTH-type transcriptional regulator Cbl;
15-123 5.86e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 50.19  E-value: 5.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  15 EAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLL-LTEEGQSYFLDIKDIftsLAEATD-----KVL 88
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERI---LNEASNvrrlaDLF 87

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 857688505  89 ERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDI 123
Cdd:PRK12679  88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEV 122
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-270 6.76e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 48.78  E-value: 6.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIqwLVPRLADFNQQEPDIDVRI----KAVDM-DEGsltddVDVAIYYGRGNWSGLRADKLyQEYLIPL 168
Cdd:cd08476    1 GRLRVSLPLVGGL--LLPVLAAFMQRYPEIELDLdfsdRLVDViDEG-----FDAVIRTGELPDSRLMSRRL-GSFRMVL 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 169 C-SPSVLLGVKPLESLSDLACHTLLH---DTSRK--DWkQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNV 242
Cdd:cd08476   73 VaSPDYLARHGTPETPADLAEHACLRyrfPTTGKlePW-PLRGDGGDPELRLPTALVCNNIEALIEFALQGLGIACLPDF 151

                        170       180
                 ....*....|....*....|....*...
gi 857688505 243 LAQPEIEAGRLIAPFDEVLVSKNAFYVV 270
Cdd:cd08476  152 SVREALADGRLVTVLDDYVEERGQFRLL 179
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
22-282 8.37e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 49.67  E-value: 8.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  22 SFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIF----TSLAE---ATDKVLERSEKG 94
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLqqleSNLAElrgGSDYAQRKIKIA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  95 A---LTISLPPSFAIQwlVPRLADFNQQEPDIDvriKAVDM-DEGSltddVDVAIYYGRGNWSGLRAD--KLYQEYLIPL 168
Cdd:PRK10082 107 AahsLSLGLLPSIISQ--MPPLFTWAIEAIDVD---EAVDKlREGQ----SDCIFSFHDEDLLEAPFDhiRLFESQLFPV 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 169 CSPSvllgvKPLESLSDLA-CHTLLHDTSRKDWK-QFAKQNGIDGVNVNHGPIF--SHSTMVLQAAAHGQGIALGNNVLA 244
Cdd:PRK10082 178 CASD-----EHGEALFNLAqPHFPLLNYSRNSYMgRLINRTLTRHSELSFSTFFvsSMSELLKQVALDGCGIAWLPEYAI 252

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 857688505 245 QPEIEAGRLIA-PFDEVLVSKNAFyvvCHEKQADMGRIA 282
Cdd:PRK10082 253 QQEIRSGQLVVlNRDELVIPIQAY---AYRMNTRMNPVA 288
PRK10341 PRK10341
transcriptional regulator TdcA;
5-67 9.02e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 49.48  E-value: 9.02e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 857688505   5 LPPLNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQ 67
Cdd:PRK10341   6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQ 68
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-255 2.03e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 47.33  E-value: 2.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIkavdmdegSLTDDV--------DVAIYYGRGNWSGLRADKLYQEYL 165
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDL--------SLTDEVvdllaertDVAIRVGPLPDSSLVARKLGESRR 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 166 IPLCSPSVL--LGvKPLEsLSDLACHTLL---HDTSRKDWKqfAKQNGIDGVNVNHGPIFSHSTMVL-QAAAHGQGIALG 239
Cdd:cd08480   73 VIVASPSYLarHG-TPLT-PQDLARHNCLgfnFRRALPDWP--FRDGGRIVALPVSGNILVNDGEALrRLALAGAGLARL 148

                        170
                 ....*....|....*.
gi 857688505 240 NNVLAQPEIEAGRLIA 255
Cdd:cd08480  149 ALFHVADDIAAGRLVP 164
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 22-192 2.10e-06

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 48.53  E-value: 2.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  22 SFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDKVLERSE--KGALTIS 99
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNVGQalSGQVSIG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 100 LPPSFAIQWL-VPRLADFNQQEPDIDVRIK---AVDMDEGSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPSvll 175
Cdd:PRK11233  97 LAPGTAASSLtMPLLQAVRAEFPGIVLYLHensGATLNEKLMNGQLDMAVIYEHSPVAGLSSQPLLKEDLFLVGTQD--- 173

                        170
                 ....*....|....*....
gi 857688505 176 gvKPLES--LSDLACHTLL 192
Cdd:PRK11233 174 --CPGQSvdLAAVAQMNLF 190
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 11-66 2.45e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 48.10  E-value: 2.45e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 857688505  11 LRVFE---AAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEG 66
Cdd:PRK11151   3 IRDLEylvALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG 61
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-255 2.84e-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 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: 47.16  E-value: 2.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIKA----VD-MDEGsltddVDVAIYYgRGNW---SGLRADKLYQEYL 165
Cdd:cd08473    3 GTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEAtnrrVDlIEEG-----IDVALRV-RFPPledSSLVMRVLGQSRQ 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 166 IPLCSPSVLLGVKPLESLSDLACHTLLH---DTSRKDWKQFAKQNGIdgVNVNHGPIFSHSTMVL--QAAAHGQGIALGN 240
Cdd:cd08473   77 RLVASPALLARLGRPRSPEDLAGLPTLSlgdVDGRHSWRLEGPDGES--ITVRHRPRLVTDDLLTlrQAALAGVGIALLP 154

                        170
                 ....*....|....*
gi 857688505 241 NVLAQPEIEAGRLIA 255
Cdd:cd08473  155 DHLCREALRAGRLVR 169
PRK12680 PRK12680
LysR family transcriptional regulator;
8-151 2.88e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 48.08  E-value: 2.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAA-RHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSL--------LLTEEGQSYFLDIKDIFT 78
Cdd:PRK12680   3 LTQLRYLVAIAdAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLesvtpagvEVIERARAVLSEANNIRT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  79 SLAEAtdkvlERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIDVRIK------AVD-MDEGsltdDVDVAIYYGRGN 151
Cdd:PRK12680  83 YAANQ-----RRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQqaaesaALDlLGQG----DADIAIVSTAGG 153
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-259 3.67e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 46.92  E-value: 3.67e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 103 SFAIQWLVPRLADFNQQEPDI--DVRIKAV-DMDEGSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPSVLLGVKP 179
Cdd:cd08426    9 GLAAELLPSLIARFRQRYPGVffTVDVASTaDVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 180 LESLSDLACHTLLHDTsrkdwKQFAKQNGIDGV----NVNHGPIF--SHSTMVLQAAAHGQGIALGNNVLAQPEIEAGRL 253
Cdd:cd08426   89 SVTLAQLAGYPLALPP-----PSFSLRQILDAAfaraGVQLEPVLisNSIETLKQLVAAGGGISLLTELAVRREIRRGQL 163


                 ....*..
gi 857688505 254 IA-PFDE 259
Cdd:cd08426  164 VAvPLAD 170
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-121 3.83e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.46  E-value: 3.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  11 LRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFrRRNRSLLLTEEGQsyfldikdiftSLAEATDKV--L 88
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLL-VRTQPCRPTEAGQ-----------RLLRHARQVrlL 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 857688505  89 ER---SEKGALTiSLPPSFAI--------QWLVPRLADFNQQEP 121
Cdd:PRK03635  75 EAellGELPALD-GTPLTLSIavnadslaTWFLPALAPVLARSG 117
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-255 3.98e-06

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: 46.53  E-value: 3.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRI----KAVDMDEGSltddVDVAIYYGRGNWSGLRADKLYQEYLIPLC 169
Cdd:cd08470    1 GLLRITCPVAYGERFIAPLVNDFMQRYPKLEVDIeltnRVVDLVSEG----FDLAIRLGRLTDSSLMARRLASRRHYVCA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 170 SPSVLLGVKPLESLSDLACHTLLHDTSRKdWKqFaKQNG------IDG-VNVNHGPIfshstmVLQAAAHGQGIALGNNV 242
Cdd:cd08470   77 SPAYLERHGTPHSLADLDRHNCLLGTSDH-WR-F-QENGrersvrVQGrWRCNSGVA------LLDAALKGMGLAQLPDY 147

                        170
                 ....*....|...
gi 857688505 243 LAQPEIEAGRLIA 255
Cdd:cd08470  148 YVDEHLAAGRLVP 160
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-270 4.16e-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 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: 46.39  E-value: 4.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  94 GALTISLPPSFAIQWLVPRLADFNQQEPDIDVRI----KAVDMDEgsltDDVDVAIYYG-RGNWSGLRADKLYQEYLIpL 168
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELsfsdRFVDLIE----EGIDLAVRIGeLADSTGLVARRLGTQRMV-L 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 169 C-SPSVLLGVKPLESLSDLACH---TLLHDTSRKDWkQFAKQNG-IDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVL 243
Cdd:cd08475   76 CaSPAYLARHGTPRTLEDLAEHqciAYGRGGQPLPW-RLADEQGrLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWL 154

                        170       180
                 ....*....|....*....|....*..
gi 857688505 244 AQPEIEAGRLIAPFDEVLVSKNAFYVV 270
Cdd:cd08475  155 VADHLQRGELVEVLPELAPEGLPIHAV 181
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
19-127 4.33e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 47.32  E-value: 4.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  19 RHlsFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSLAEATDKVLERSEKGALTI 98
Cdd:PRK03601  16 RH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHTSQHNELSI 93

                         90       100       110
                 ....*....|....*....|....*....|.
gi 857688505  99 SLPPSFAIQWLVPRLADFNQQEPD--IDVRI 127
Cdd:PRK03601  94 GASASLWECMLTPWLGRLYQNQEAlqFEARI 124
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 10-127 4.40e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 47.29  E-value: 4.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  10 SLR---VFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRR-RNR------SLLLTEEGQSYFLDIKDIfTS 79
Cdd:PRK11013   5 SLRhieIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERvRGRlhptvqGLRLFEEVQRSYYGLDRI-VS 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 857688505  80 LAEAtdkvLERSEKGALTISLPPSFAiQWLVPRL-ADFNQQEPDIDVRI 127
Cdd:PRK11013  84 AAES----LREFRQGQLSIACLPVFS-QSLLPGLcQPFLARYPDVSLNI 127
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-254 6.40e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 46.99  E-value: 6.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQsyfLDIKDIFTSLAEATD-K 86
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGR---LLYPRALALLEQAVEiE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  87 VLERSEKGALTISLPPSFAIQWLVPRLADFNQQEPDI----------DVrIKAVdmdegsLTDDVDVAIYYGRGNWSGLR 156
Cdd:PRK10837  82 QLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLplelsvgnsqDV-INAV------LDFRVDIGLIEGPCHSPELI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 157 ADKLYQEYLIPLCSPSVLLGVKPLeSLSDLAchtllhdtsRKDWKQFAKQNG----IDGVNVNHGPIFS------HSTMV 226
Cdd:PRK10837 155 SEPWLEDELVVFAAPDSPLARGPV-TLEQLA---------AAPWILRERGSGtreiVDYLLLSHLPRFElamelgNSEAI 224

                        250       260
                 ....*....|....*....|....*....
gi 857688505 227 LQAAAHGQGIA-LGNNVLAQpEIEAGRLI 254
Cdd:PRK10837 225 KHAVRHGLGIScLSRRVIAD-QLQAGTLV 252
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 108-272 2.35e-05

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: 44.40  E-value: 2.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 108 WLVPRLADFNQQEPDIDVRI------KAVDMdegSLTDDVDVAIYYGRGNWSGLRADKLYQEYLIPLCSPSVLLGVKPLE 181
Cdd:cd08420   14 LLPRLLARFRKRYPEVRVSLtignteEIAER---VLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505 182 SLSDLACHTLL----HDTSRKDWKQFAKQNGIDGVNVNHGPIFSHSTMVLQAAAHGQGIALGNNVLAQPEIEAGRLIA-P 256
Cdd:cd08420   91 TAEELAAEPWIlrepGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVAlP 170

                        170
                 ....*....|....*.
gi 857688505 257 FDEVLVSKNaFYVVCH 272
Cdd:cd08420  171 VEGLRLTRP-FSLIYH 185
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-67 2.10e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 39.03  E-value: 2.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 857688505  31 FVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQ 67
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGE 38
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 96-186 2.13e-03

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 38.35  E-value: 2.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  96 LTISLPPSFAIQWLVPRLADFNQQEPDIDVRIkaVDMDEGSLTD-----DVDVAIYYGRGNWSGLRADKLYQEYLIPLCS 170
Cdd:cd08433    2 VSVGLPPSAASVLAVPLLRAVRRRYPGIRLRI--VEGLSGHLLEwllngRLDLALLYGPPPIPGLSTEPLLEEDLFLVGP 79

                         90
                 ....*....|....*....
gi 857688505 171 PSVLLGVK---PLESLSDL 186
Cdd:cd08433   80 ADAPLPRGapvPLAELARL 98
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
11-80 4.12e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 38.11  E-value: 4.12e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505  11 LRVFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLLLTEEGQSYFLDIKDIFTSL 80
Cdd:PRK15243   9 LKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFL 78
cysB PRK12681
HTH-type transcriptional regulator CysB;
8-145 9.07e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 37.18  E-value: 9.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857688505   8 LNSLR-VFEAAARHLSFTRAAEELFVTQAAVSHQIKALEEFLSLKLFRRRNRSLL-LTEEGQsYFLDIKDIFTSLAEATD 85
Cdd:PRK12681   3 LQQLRyIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGE-EIIRIAREILSKVESIK 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 857688505  86 KVLE---RSEKGALTISLPPSFAIQWLVPRLADFNQQEPDIdvrikAVDMDEGSLTD--------DVDVAI 145
Cdd:PRK12681  82 SVAGehtWPDKGSLYIATTHTQARYALPPVIKGFIERYPRV-----SLHMHQGSPTQiaeaaakgNADFAI 147
 
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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