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Conserved domains on  [gi|495708310|ref|WP_008432889|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [unclassified Pseudomonas]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1001158)

LysR family HTH-containing transcriptional regulator

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 super family cl32646
DNA-binding transcriptional activator GcvA; Provisional
 1-285 6.99e-70

DNA-binding transcriptional activator GcvA; Provisional


The actual alignment was detected with superfamily member PRK11139:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 218.17  E-value: 6.99e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   1 MRQLPSLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIE 80
Cdd:PRK11139   2 SRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  81 RALHAVRVPNLRQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA--EIDCQVRFGLEAATQCSSELLV 158
Cdd:PRK11139  82 EATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLrdDVDVAIRYGRGNWPGLRVEKLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 159 MERHIAVASPELFSDGQPP----DLRRFPLLHIlhDGKRLkvWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLA 234
Cdd:PRK11139 162 DEYLLPVCSPALLNGGKPLktpeDLARHTLLHD--DSRED--WRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVA 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495708310 235 VIDRQMIERELANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:PRK11139 238 LGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWL 288
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-285 6.99e-70

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 218.17  E-value: 6.99e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   1 MRQLPSLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIE 80
Cdd:PRK11139   2 SRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  81 RALHAVRVPNLRQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA--EIDCQVRFGLEAATQCSSELLV 158
Cdd:PRK11139  82 EATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLrdDVDVAIRYGRGNWPGLRVEKLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 159 MERHIAVASPELFSDGQPP----DLRRFPLLHIlhDGKRLkvWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLA 234
Cdd:PRK11139 162 DEYLLPVCSPALLNGGKPLktpeDLARHTLLHD--DSRED--WRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVA 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495708310 235 VIDRQMIERELANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:PRK11139 238 LGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWL 288
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-285 1.67e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 164.65  E-value: 1.67e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   6 SLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHA 85
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  86 VRVPN--LRQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA-----EIDCQVRFGLEAATQCSSELLV 158
Cdd:COG0583   82 LRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDallegELDLAIRLGPPPDPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 159 MERHIAVASPElfsdgqppdlrrfpllHILhdgkrlkvwenwlaamgredidAGQGLEFSTLDQVIHTALAGGGLAVIDR 238
Cdd:COG0583  162 EERLVLVASPD----------------HPL----------------------ARRAPLVNSLEALLAAVAAGLGIALLPR 203

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 495708310 239 QMIERELANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 94-285 3.71e-41

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: 140.79  E-value: 3.71e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA--EIDCQVRFGLEAATQCSSELLVMERHIAVASPELF 171
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAreGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 172 SDGQPP---DLRRFPLLHILHdgkRLKVWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELANG 248
Cdd:cd08432   81 AGLPLLspaDLARHTLLHDAT---RPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAG 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495708310 249 SLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08432  158 RLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-65 1.45e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 90.91  E-value: 1.45e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 495708310    7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAG 65
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
21-83 6.76e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.26  E-value: 6.76e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495708310    21 SFSQAAVGLNVTQGAVSRQIKQLEDylgvALFIRTPQG--------LSLTEAGFALSPHLSDAFDHIERAL 83
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLEK----KGLVRREPSpedrrsvlVSLTEEGRELIEQLLEARSETLAEL 92
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-285 6.99e-70

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 218.17  E-value: 6.99e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   1 MRQLPSLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIE 80
Cdd:PRK11139   2 SRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  81 RALHAVRVPNLRQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA--EIDCQVRFGLEAATQCSSELLV 158
Cdd:PRK11139  82 EATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLrdDVDVAIRYGRGNWPGLRVEKLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 159 MERHIAVASPELFSDGQPP----DLRRFPLLHIlhDGKRLkvWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLA 234
Cdd:PRK11139 162 DEYLLPVCSPALLNGGKPLktpeDLARHTLLHD--DSRED--WRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVA 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495708310 235 VIDRQMIERELANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:PRK11139 238 LGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWL 288
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
6-285 1.67e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 164.65  E-value: 1.67e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   6 SLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHA 85
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  86 VRVPN--LRQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA-----EIDCQVRFGLEAATQCSSELLV 158
Cdd:COG0583   82 LRALRggPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDallegELDLAIRLGPPPDPGLVARPLG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 159 MERHIAVASPElfsdgqppdlrrfpllHILhdgkrlkvwenwlaamgredidAGQGLEFSTLDQVIHTALAGGGLAVIDR 238
Cdd:COG0583  162 EERLVLVASPD----------------HPL----------------------ARRAPLVNSLEALLAAVAAGLGIALLPR 203

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 495708310 239 QMIERELANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:COG0583  204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 94-285 3.71e-41

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: 140.79  E-value: 3.71e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA--EIDCQVRFGLEAATQCSSELLVMERHIAVASPELF 171
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAreGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 172 SDGQPP---DLRRFPLLHILHdgkRLKVWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELANG 248
Cdd:cd08432   81 AGLPLLspaDLARHTLLHDAT---RPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGLGVALAPRALVADDLAAG 157

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495708310 249 SLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08432  158 RLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
7-285 2.15e-38

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 137.06  E-value: 2.15e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHAV 86
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  87 RVPNLRQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASL--AEIDCQVRFGLEAATQCSSELLVMERHIA 164
Cdd:PRK10086  96 KNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFqrAGIDLAIYFDDAPSAQLTHHFLMDEEILP 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 165 VASPE------LFSDgqPPDLRRFPLLH---ILHDGKRLKVWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLAV 235
Cdd:PRK10086 176 VCSPEyaerhaLTGN--PDNLRHCTLLHdrqAWSNDSGTDEWHSWAQHFGVNLLPPSSGIGFDRSDLAVIAAMNHIGVAM 253

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495708310 236 IDRQMIERELANGSL-LPITPVEVIGPYGYWLDVASDKQGlSKVRLFTQWL 285
Cdd:PRK10086 254 GRKRLVQKRLASGELvAPFGDMEVKCHQHYYVTTLPGRQW-PKIEAFIDWL 303
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 101-285 7.77e-35

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: 124.72  E-value: 7.77e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 101 PTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFGLEAATQCSSELLVMERHIAVASPELFSD---GQ 175
Cdd:cd08481    8 PTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQgsFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPALLAGralAA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 176 PPDLRRFPLLHILHdgkRLKVWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELANGSLLPITP 255
Cdd:cd08481   88 PADLAHLPLLQQTT---RPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEELARGRLVVPFN 164

                        170       180       190
                 ....*....|....*....|....*....|
gi 495708310 256 VEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08481  165 LPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-65 1.45e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 90.91  E-value: 1.45e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 495708310    7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAG 65
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-285 8.90e-23

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: 93.12  E-value: 8.90e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   92 RQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA-----EIDCQVRFGLEAATQCSSELLVMERHIAVA 166
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDlllegELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  167 SPELFSDGQPP----DLRRFPLLHILHDGKRLKVWENWLAAMGredIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIE 242
Cdd:pfam03466  81 PPDHPLARGEPvsleDLADEPLILLPPGSGLRDLLDRALRAAG---LRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 495708310  243 RELANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:pfam03466 158 RELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-127 8.90e-20

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 86.93  E-value: 8.90e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIE---RAL 83
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEagrRAI 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 495708310  84 HAVRvpNL-RQRLRIVAPPTWaTRWLSAHL-RRFCERYPDINLSVT 127
Cdd:PRK11242  83 HDVA--DLsRGSLRLAMTPTF-TAYLIGPLiDAFHARYPGITLTIR 125
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-258 1.23e-19

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 86.56  E-value: 1.23e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  10 LRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQgLSLTEAGFALSPHL-------SDAFDHIERA 82
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLrqvalleADLLSTLPAE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  83 LHAvrvpnlRQRLRI-VAPPTWATrWLSAHLRRFCERyPDI--NLSVTHQN-THASLAE---IDCqVRFGLEAATQCSSE 155
Cdd:PRK13348  86 RGS------PPTLAIaVNADSLAT-WFLPALAAVLAG-ERIllELIVDDQDhTFALLERgevVGC-VSTQPKPMRGCLAE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 156 LLVMERHIAVASPEL----FSDG-QPPDLRRFPLlhILHDGK-RLKvwENWLAAMGREDIDAGQGLEFSTLDQVIHTALA 229
Cdd:PRK13348 157 PLGTMRYRCVASPAFaaryFAQGlTRHSALKAPA--VAFNRKdTLQ--DSFLEQLFGLPVGAYPRHYVPSTHAHLAAIRH 232

                        250       260       270
                 ....*....|....*....|....*....|..
gi 495708310 230 GGGLAVIDRQMIERELANGSL---LPITPVEV 258
Cdd:PRK13348 233 GLGYGMVPELLIGPLLAAGRLvdlAPGHPVDV 264
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-285 2.50e-17

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: 78.25  E-value: 2.50e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFGLEAATQCSSELLVMERHIAVASPELF 171
Cdd:cd08422    2 RLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEegFDLAIRIGELPDSSLVARRLGPVRRVLVASPAYL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 172 SD----GQPPDLRRFPLLHILHDGkRLKVWENWLAAmGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELAN 247
Cdd:cd08422   82 ARhgtpQTPEDLARHRCLGYRLPG-RPLRWRFRRGG-GEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLAS 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 495708310 248 GSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08422  160 GRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 95-250 1.77e-16

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: 75.84  E-value: 1.77e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  95 LRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFGLEAATQCSSELLVMERHIAVASPELFS 172
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPdgIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 173 D---GQPPDLRRFPLlhiLHDGKRLKVWEnWLAAMGREDiDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELANGS 249
Cdd:cd08483   82 DrkvDSLADLAGLPW---LQERGTNEQRV-WLASMGVVP-DLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGR 156


                 .
gi 495708310 250 L 250
Cdd:cd08483  157 L 157
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 95-285 4.42e-16

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: 74.71  E-value: 4.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  95 LRIVAPPTWATRWLSAHLRRFCERYPDINLSV-THQNTHASLAE-IDCQVRFGlEAATQCSSELLVMERHIAV-ASPELF 171
Cdd:cd08484    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLsTNNNRVDIAAEgLDFAIRFG-EGAWPGTDATRLFEAPLSPlCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 172 SD-GQPPDLRRFPLLHilhdGKRLKVWENWLAAMGREDIDAgQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELANGSL 250
Cdd:cd08484   81 RRlSEPADLANETLLR----SYRADEWPQWFEAAGVPPPPI-NGPVFDSSLLMVEAALQGAGVALAPPSMFSRELASGAL 155

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 495708310 251 LPITPVEVIGPyGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08484  156 VQPFKITVSTG-SYWLTRLKSKPETPAMSAFSQWL 189
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-268 2.56e-15

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 74.42  E-value: 2.56e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  10 LRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTpQGLSLTEAGFALSPHL-------SDAFDHIeRA 82
Cdd:PRK03635   7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHArqvrlleAELLGEL-PA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  83 LHAVRVpnlrqRLRIV------AppTWatrWLSAhLRRFCERYP-DINLSVTHQN-THASLaeidcqvRFG--------L 146
Cdd:PRK03635  85 LDGTPL-----TLSIAvnadslA--TW---FLPA-LAPVLARSGvLLDLVVEDQDhTAELL-------RRGevvgavttE 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 147 EAATQ-CSSELL-VMeRHIAVASPEL----FSDGQPPD-LRRFPLLHI-----LHDgkrlkvweNWLAAMGREDIDAGQG 214
Cdd:PRK03635 147 PQPVQgCRVDPLgAM-RYLAVASPAFaaryFPDGVTAEaLAKAPAVVFnrkddLQD--------RFLRQAFGLPPGSVPC 217

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495708310 215 LEFSTLDQVIHTALAGGGLAVIDRQMIERELANGSLLPITPvevigpyGYWLDV 268
Cdd:PRK03635 218 HYVPSSEAFVRAALAGLGWGMIPELQIEPELASGELVDLTP-------GRPLDV 264
PRK09986 PRK09986
LysR family transcriptional regulator;
6-169 5.21e-15

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 73.60  E-value: 5.21e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   6 SLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHA 85
Cdd:PRK09986   8 DLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLAR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  86 VRVPNLRQRLRIVAPPTWATRW--LSAHLRRFCERYPDINLSVTHQNTHASLA-----EIDCQV-RFGLEAATQCSSELL 157
Cdd:PRK09986  88 VEQIGRGEAGRIEIGIVGTALWgrLRPAMRHFLKENPNVEWLLRELSPSMQMAalerrELDAGIwRMADLEPNPGFTSRR 167

                        170
                 ....*....|..
gi 495708310 158 VMERHIAVASPE 169
Cdd:PRK09986 168 LHESAFAVAVPE 179
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 4-253 6.64e-15

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 73.49  E-value: 6.64e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   4 LPSLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERAL 83
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  84 HAVRVPNLRQR--LRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA----EIDCQVRFGLEAATQCSSELL 157
Cdd:PRK14997  81 DAIAALQVEPRgiVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVgegvDVAIRVRPRPFEDSDLVMRVL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 158 VMERHIAVASPELFS----DGQPPDLRRFPLLHiLHDGKRLKVWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGL 233
Cdd:PRK14997 161 ADRGHRLFASPDLIArmgiPSAPAELSHWPGLS-LASGKHIHRWELYGPQGARAEVHFTPRMITTDMLALREAAMAGVGL 239

                        250       260
                 ....*....|....*....|
gi 495708310 234 AVIDRQMIERELANGSLLPI 253
Cdd:PRK14997 240 VQLPVLMVKEQLAAGELVAV 259
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 95-285 2.86e-14

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: 69.50  E-value: 2.86e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  95 LRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFGLEAATQCSSELLVMERHIAVASPELFS 172
Cdd:cd08487    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATegLDFAIRFGEGLWPATHNERLLDAPLSVLCSPEIAK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 173 D-GQPPDLRRFPLLHilhdGKRLKVWENWLAAMGREDIDAgQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELANGSLL 251
Cdd:cd08487   82 RlSHPADLINETLLR----SYRTDEWLQWFEAANMPPIKI-RGPVFDSSRLMVEAAMQGAGVALAPAKMFSREIENGQLV 156

                        170       180       190
                 ....*....|....*....|....*....|....
gi 495708310 252 PITPVEVIGPyGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08487  157 QPFKIEVETG-SYWLTWLKSKPMTPAMELFRQWI 189
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 94-258 1.44e-13

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: 67.90  E-value: 1.44e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAEI-DCQVRFGL-EAatQCSSELLVME-----RHIAVA 166
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVlDGEIDLGLvEG--PVDHPDLIVEpfaedELVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 167 SPE--LFSDGQPP--DLRRFPLlhILHD---GKRlKVWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQ 239
Cdd:cd08420   79 PPDhpLAGRKEVTaeELAAEPW--ILREpgsGTR-EVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRL 155

                        170       180
                 ....*....|....*....|.
gi 495708310 240 MIERELANGSL--LPITPVEV 258
Cdd:cd08420  156 AVRKELELGRLvaLPVEGLRL 176
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 95-285 2.38e-13

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: 67.17  E-value: 2.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  95 LRIVAPPTWATRWLSAHLRRFCERYPDINLSV-THQNTHASLAE-IDCQVRFGlEAATQCSSELLVMERHIAV-ASPELF 171
Cdd:cd08488    2 LHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLsTNNNRVDIAAEgLDYAIRFG-SGAWHGIDATRLFEAPLSPlCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 172 SD-GQPPDLRRFPLLHilhdGKRLKVWENWLAAMG-REDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELANGS 249
Cdd:cd08488   81 RQlREPADLARHTLLR----SYRADEWPQWFEAAGvGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQLASGA 156

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495708310 250 LL-PITPVEVIGpyGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08488  157 LVqPFATTLSTG--SYWLTRLQSRPETPAMSAFSAWL 191
PRK10341 PRK10341
transcriptional regulator TdcA;
4-65 2.79e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 68.74  E-value: 2.79e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495708310   4 LPSLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAG 65
Cdd:PRK10341   6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAG 67
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 7-183 8.04e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 67.32  E-value: 8.04e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   7 LNMLRVFEEVARHR-SFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRtpQG---LSLTEAGFALSPhlsdafdHIERA 82
Cdd:PRK12682   3 LQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIR--HGkrlKGLTEPGKAVLD-------VIERI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  83 LHAVRvpNLRQ-----------RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVtHQNTHASLAEIdcqvrfgleaatq 151
Cdd:PRK12682  74 LREVG--NIKRigddfsnqdsgTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSL-HQGSPDEIARM------------- 137

                        170       180       190
                 ....*....|....*....|....*....|..
gi 495708310 152 csseLLVMERHIAVASPELFSDgqpPDLRRFP 183
Cdd:PRK12682 138 ----VISGEADIGIATESLADD---PDLATLP 162
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-126 9.89e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 66.97  E-value: 9.89e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   4 LP-SLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFAL---SPHLSDAFDHI 79
Cdd:CHL00180   3 LPfTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLlryGNRILALCEET 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 495708310  80 ERALHAVRvpNL-RQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSV 126
Cdd:CHL00180  83 CRALEDLK--NLqRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQL 128
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
7-137 2.14e-12

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 66.15  E-value: 2.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   7 LNMLRVFEEVARHR-SFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGL-SLTEAGFALsphlsdaFDHIERALH 84
Cdd:PRK12684   3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPGRII-------LASVERILQ 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495708310  85 AVRvpNLRQ-----------RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVtHQNTHASLAE 137
Cdd:PRK12684  76 EVE--NLKRvgkefaaqdqgNLTIATTHTQARYALPAAIKEFKKRYPKVRLSI-LQGSPTQIAE 136
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-291 6.15e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 64.83  E-value: 6.15e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   9 MLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAF------------ 76
Cdd:PRK10094   6 TLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLswlesmpselqq 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  77 --DHIERALHAVrVPNLRQRLRIVAPP-TWATRWLSA---HLRRFCER-------YPDINLSVTHQNTHaSLAEidcqvR 143
Cdd:PRK10094  86 vnDGVERQVNIV-INNLLYNPQAVAQLlAWLNERYPFtqfHISRQIYMgvwdsllYEGFSLAIGVTGTE-ALAN-----T 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 144 FGLEAATQCSSELLVMERHIAVASPELFSDGQppdLRRFPLLHILHDGKRLKVWENWLAAmGREDIdagqglEFSTLDQV 223
Cdd:PRK10094 159 FSLDPLGSVQWRFVMAADHPLANVEEPLTEAQ---LRRFPAVNIEDSARTLTKRVAWRLP-GQKEI------IVPDMETK 228

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 224 IHTALAGGGLAVIDRQMIERELANGSLL--------PITPVEVIgpygyWLDVASDKQGLSKVRLFTQ-------WLNRV 288
Cdd:PRK10094 229 IAAHLAGVGIGFLPKSLCQSMIDNQQLVsrviptmrPPSPLSLA-----WRKFGSGKAVEDIVTLFTQrrpeisgFLEIF 303


                 ...
gi 495708310 289 SNP 291
Cdd:PRK10094 304 GNP 306
PRK09791 PRK09791
LysR family transcriptional regulator;
7-95 1.28e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 64.01  E-value: 1.28e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALsphlsdaFDHIERALHAV 86
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESF-------YQHASLILEEL 79

                         90
                 ....*....|.
gi 495708310  87 RVP--NLRQRL 95
Cdd:PRK09791  80 RAAqeDIRQRQ 90
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-139 8.00e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 61.32  E-value: 8.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERA-LHA 85
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAkLRA 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 495708310  86 VRVPNLRQRLRIVAPPTWATRWLSAHLRRFCERYPD-----INLSVTHQNTHASLAEID 139
Cdd:PRK09906  83 RKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDtlielVSLITTQQEEKLRRGELD 141
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-65 1.28e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 60.73  E-value: 1.28e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 495708310  10 LRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAG 65
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAG 62
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 6-261 1.43e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 60.47  E-value: 1.43e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   6 SLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPhlsdafdhieRAL-- 83
Cdd:PRK10837   4 TLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYP----------RALal 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  84 --HAVRVPNLRQR----LRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASL-AEIDCQVRFGLEAATQCSSEL 156
Cdd:PRK10837  74 leQAVEIEQLFREdngaLRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVInAVLDFRVDIGLIEGPCHSPEL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 157 LV---MERHIAV-ASPELFSDGQPPDLRRFPLLH-ILHD---GKRLKVWENWLAAMGREDIdagqGLEFSTLDQVIHTAL 228
Cdd:PRK10837 154 ISepwLEDELVVfAAPDSPLARGPVTLEQLAAAPwILRErgsGTREIVDYLLLSHLPRFEL----AMELGNSEAIKHAVR 229

                        250       260       270
                 ....*....|....*....|....*....|...
gi 495708310 229 AGGGLAVIDRQMIERELANGSLlpitpVEVIGP 261
Cdd:PRK10837 230 HGLGISCLSRRVIADQLQAGTL-----VEVAVP 257
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 10-183 1.64e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 60.44  E-value: 1.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  10 LRVFEEVARhRSF--SQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLS-LTEAGFALSPhlsdafdHIERALhaV 86
Cdd:PRK12683   6 LRIIREAVR-QNFnlTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQ-------IVERML--L 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  87 RVPNLRQ-----------RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVtHQnthASLAEIdcqvrfgleaatqcSSE 155
Cdd:PRK12683  76 DAENLRRlaeqfadrdsgHLTVATTHTQARYALPKVVRQFKEVFPKVHLAL-RQ---GSPQEI--------------AEM 137

                        170       180
                 ....*....|....*....|....*...
gi 495708310 156 LLVMERHIAVASPELfsdGQPPDLRRFP 183
Cdd:PRK12683 138 LLNGEADIGIATEAL---DREPDLVSFP 162
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 100-285 1.65e-10

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: 59.34  E-value: 1.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 100 PPTWATRWLSAHLRRFCERYPDIN--LSVTHQNTHASLAEIDCQVRFGLEAATQ-CSSELLVMERHIAVASPELFS---- 172
Cdd:cd08482    7 SGSLLMRWLIPRLPAFQAALPDIDlqLSASDGPVDSLRDGIDAAIRFNDAPWPAgMQVIELFPERVGPVCSPSLAPtvpl 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 173 -DGQPPDLRRFPLLHILhdgKRLKVWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELANGSLL 251
Cdd:cd08482   87 rQAPAAALLGAPLLHTR---SRPQAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGRLV 163

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495708310 252 -PITPVEVIGPYGYWL--DVASdkqglSKVRLFTQWL 285
Cdd:cd08482  164 aPWGFIETGSHYVLLRpaRLRD-----SRAGALADWL 195
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-71 3.65e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 59.26  E-value: 3.65e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495708310   9 MLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPH 71
Cdd:PRK03601   5 LLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPY 67
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
10-124 4.00e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 59.65  E-value: 4.00e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  10 LRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHAVRVP 89
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEP 86

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 495708310  90 NlRQRLRIVAPPTWATRWLSAHLRRFCERYPDINL 124
Cdd:PRK15421  87 Q-QTRLRIAIECHSCIQWLTPALENFHKNWPQVEM 120
PRK09801 PRK09801
LysR family transcriptional regulator;
10-255 4.82e-10

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 59.28  E-value: 4.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  10 LRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHAVRVP 89
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  90 NLRQR--LRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFGLEAATQCSSELLVMERHIAV 165
Cdd:PRK09801  91 KTRPEgmIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQdnIDLDIRINDEIPDYYIAHLLTKNKRILC 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 166 ASPELFSD-GQPPDLRRFPLLHILHDGKRLKVWENWLAAMGRE--DIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIE 242
Cdd:PRK09801 171 AAPEYLQKyPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEkkSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDVL 250

                        250
                 ....*....|...
gi 495708310 243 RELANGSLLPITP 255
Cdd:PRK09801 251 PFLESGKLVQVLP 263
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-253 5.12e-10

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


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 57.86  E-value: 5.12e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNThasLAEI-----DCQVRFG--LEA---ATQCSSELlvmeRHI 163
Cdd:cd08474    4 TLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDG---LVDIvaegfDAGIRLGesVEKdmvAVPLGPPL----RMA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 164 AVASPELFSD----GQPPDLR-------RFPllhilHDGkRLKVWEnwLAAMGRE-DID-AGQgLEFSTLDQVIHTALAG 230
Cdd:cd08474   77 VVASPAYLARhgtpEHPRDLLnhrciryRFP-----TSG-ALYRWE--FERGGRElEVDvEGP-LILNDSDLMLDAALDG 147

                        170       180
                 ....*....|....*....|...
gi 495708310 231 GGLAVIDRQMIERELANGSLLPI 253
Cdd:cd08474  148 LGIAYLFEDLVAEHLASGRLVRV 170
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-281 1.42e-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 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: 56.48  E-value: 1.42e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWatRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFGLEAATQCSSELLVMERHIAVASPELF 171
Cdd:cd08476    2 RLRVSLPLVG--GLLLPVLAAFMQRYPEIELDLDFSDRLVDVIDegFDAVIRTGELPDSRLMSRRLGSFRMVLVASPDYL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 172 SD----GQPPDLRRFPLLH--ILHDGKrLKVWEnwLAAM-GREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERE 244
Cdd:cd08476   80 ARhgtpETPADLAEHACLRyrFPTTGK-LEPWP--LRGDgGDPELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREA 156

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 495708310 245 LANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLF 281
Cdd:cd08476  157 LADGRLVTVLDDYVEERGQFRLLWPSSRHLSPKLRVF 193
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-285 1.78e-08

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


Pssm-ID: 176161  Cd Length: 202  Bit Score: 53.28  E-value: 1.78e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDIN--LSVTHQNTHASLAEIDCQVRFG-LEAATqcsselLVMeRHIA------ 164
Cdd:cd08472    2 RLRVDVPGSLARLLLIPALPDFLARYPDIEldLGVSDRPVDLIREGVDCVIRVGeLADSS------LVA-RRLGelrmvt 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 165 VASPE-LFSDG---QPPDLRRFPLLHIL-HDGKRLKVWENWLAAmGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQ 239
Cdd:cd08472   75 CASPAyLARHGtprHPEDLERHRAVGYFsARTGRVLPWEFQRDG-EEREVKLPSRVSVNDSEAYLAAALAGLGIIQVPRF 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 495708310 240 MIERELANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08472  154 MVRPHLASGRLVEVLPDWRPPPLPVSLLYPHRRHLSPRVRVFVDWV 199
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-257 2.16e-08

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 52.99  E-value: 2.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA-----EIDCQVRFGLEAATQCSSELLVMERHIAVASP 168
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEallegELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 169 E-LFSDGQ---PPDLRRFPLLhILHDGKRL-KVWENWLAAMGredIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIEr 243
Cdd:cd05466   81 DhPLAKRKsvtLADLADEPLI-LFERGSGLrRLLDRAFAEAG---FTPNIALEVDSLEAIKALVAAGLGIALLPESAVE- 155

                        170
                 ....*....|....
gi 495708310 244 ELANGSLLPITPVE 257
Cdd:cd05466  156 ELADGGLVVLPLED 169
cysB PRK12681
HTH-type transcriptional regulator CysB;
7-137 3.04e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 53.75  E-value: 3.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   7 LNMLRVFEEVARHR-SFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLS-LTEAG---FALSPHLSDAFDHIER 81
Cdd:PRK12681   3 LQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGeeiIRIAREILSKVESIKS 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 495708310  82 ALHAVRVPNlRQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVtHQNTHASLAE 137
Cdd:PRK12681  83 VAGEHTWPD-KGSLYIATTHTQARYALPPVIKGFIERYPRVSLHM-HQGSPTQIAE 136
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 6-129 3.63e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 53.46  E-value: 3.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310   6 SLNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALsphlsdaFDHIERALHA 85
Cdd:PRK11013   5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRL-------FEEVQRSYYG 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495708310  86 V-RVPN----LRQ----RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQ 129
Cdd:PRK11013  78 LdRIVSaaesLREfrqgQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQ 130
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-255 4.85e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 52.17  E-value: 4.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  92 RQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDC--QVRFGLEAATQcsselLVME-----RH 162
Cdd:cd08473    2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEegIDValRVRFPPLEDSS-----LVMRvlgqsRQ 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 163 IAVASPELFSDGQPP----DLRRFPLLHiLHDGKRLKVWENWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDR 238
Cdd:cd08473   77 RLVASPALLARLGRPrspeDLAGLPTLS-LGDVDGRHSWRLEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLPD 155

                        170
                 ....*....|....*..
gi 495708310 239 QMIERELANGSLLPITP 255
Cdd:cd08473  156 HLCREALRAGRLVRVLP 172
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
13-87 9.58e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 52.36  E-value: 9.58e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 495708310  13 FEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHAVR 87
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELR 93
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-68 1.18e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 51.95  E-value: 1.18e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495708310   7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFAL 68
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQL 74
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 21-137 3.68e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 50.45  E-value: 3.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  21 SFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHAVRvpNLRQRLR---- 96
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVH--NVGQALSgqvs 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 495708310  97 -IVAPPTWATRWLSAHLRRFCERYPDINLSVtHQNTHASLAE 137
Cdd:PRK11233  95 iGLAPGTAASSLTMPLLQAVRAEFPGIVLYL-HENSGATLNE 135
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 94-253 4.74e-07

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 49.26  E-value: 4.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFG------LEAATQCSSELLV------M 159
Cdd:cd08478    4 LLRVDAATPFVLHLLAPLIAKFRERYPDIELELVSNEGIIDLIErkTDVAIRIGeltdstLHARPLGKSRLRIlaspdyL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 160 ERHIAVASPE------LFSDGQPPDLRRFPLLHilHDGKRLKVwenwlaamgREDIDAGQGlefSTLDQVihtALAGGGL 233
Cdd:cd08478   84 ARHGTPQSIEdlaqhqLLGFTEPASLNTWPIKD--ADGNLLKI---------QPTITASSG---ETLRQL---ALSGCGI 146

                        170       180
                 ....*....|....*....|
gi 495708310 234 AVIDRQMIERELANGSLLPI 253
Cdd:cd08478  147 ACLSDFMTDKDIAEGRLIPL 166
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 17-68 4.75e-07

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 50.03  E-value: 4.75e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495708310  17 ARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFAL 68
Cdd:PRK11151  13 AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLL 64
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-255 5.96e-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 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: 49.09  E-value: 5.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFG-LEAATQCSSELLVMERHIAVASPE- 169
Cdd:cd08475    2 RLRIDLPVAFGRLCVAPLLLELARRHPELELELSFSDRFVDLIEegIDLAVRIGeLADSTGLVARRLGTQRMVLCASPAy 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 170 LFSDGQP---PDLRRFPLLHILHDGKRLKvWenWLAAMGREDID---AGQgLEFSTLDQVIHTALAGGGLAVIDRQMIER 243
Cdd:cd08475   82 LARHGTPrtlEDLAEHQCIAYGRGGQPLP-W--RLADEQGRLVRfrpAPR-LQFDDGEAIADAALAGLGIAQLPTWLVAD 157

                        170
                 ....*....|..
gi 495708310 244 ELANGSLLPITP 255
Cdd:cd08475  158 HLQRGELVEVLP 169
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-122 8.19e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.43  E-value: 8.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  30 NVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERALHAVRV--PNLRQRLRIVAPPTWATRW 107
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQqgPSLSGELSLFCSVTAAYSH 81

                         90
                 ....*....|....*
gi 495708310 108 LSAHLRRFCERYPDI 122
Cdd:PRK11716  82 LPPILDRFRAEHPLV 96
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
7-74 1.08e-06

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 49.05  E-value: 1.08e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 495708310   7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSD 74
Cdd:PRK10216  10 LNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLAE 77
cbl PRK12679
HTH-type transcriptional regulator Cbl;
10-158 1.71e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 48.65  E-value: 1.71e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  10 LRVFEEVAR-HRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQG-LSLTEAGFALsphLSDAFDHIERALHAVR 87
Cdd:PRK12679   6 LKIIREAARqDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKAL---LVIAERILNEASNVRR 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495708310  88 VPNL-----RQRLRIVAPPTWATRWLSAHLRRFCERYPDINLSVtHQNTHaslAEIDCQVRFGlEAATQCSSELLV 158
Cdd:PRK12679  83 LADLftndtSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLEL-IQGTP---QEIATLLQNG-EADIGIASERLS 153
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 94-250 3.81e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 46.45  E-value: 3.81e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLA-----EIDC-----QVRFGLEAATQCSSELLVMerhi 163
Cdd:cd08442    1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQavlegRLDGafvagPVEHPRLEQEPVFQEELVL---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 164 aVASPELFSDGQPPDLRRFPLLHILHD-GKRLKVwENWLAAMGredIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIE 242
Cdd:cd08442   77 -VSPKGHPPVSRAEDLAGSTLLAFRAGcSYRRRL-EDWLAEEG---VSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLD 151


                 ....*...
gi 495708310 243 RELANGSL 250
Cdd:cd08442  152 SLQGRGSV 159
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-285 6.76e-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 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: 45.68  E-value: 6.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFGLEAatqcSSEL----LVMERHIAVAS 167
Cdd:cd08477    2 KLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEegFDAAFRIGELA----DSSLvarpLAPYRMVLCAS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 168 PE-LFSDGQP--P-DL-----------RRFPLLHILHDGKRLKVwenwlAAMGREDIDAGQGLEFStldqvihtALAGGG 232
Cdd:cd08477   78 PDyLARHGTPttPeDLarheclgfsywRARNRWRLEGPGGEVKV-----PVSGRLTVNSGQALRVA--------ALAGLG 144

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495708310 233 LAVIDRQMIERELANGSLLPITPVEVIGPYGYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08477  145 IVLQPEALLAEDLASGRLVELLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197
PBP2_CrgA_like_1 cd08470
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-285 4.33e-05

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: 43.45  E-value: 4.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  95 LRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFG-LE----AATQCSSellvmERHIAVAS 167
Cdd:cd08470    3 LRITCPVAYGERFIAPLVNDFMQRYPKLEVDIELTNRVVDLVSegFDLAIRLGrLTdsslMARRLAS-----RRHYVCAS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 168 PELFSDGQPP----DLRRFPLL-------HILHDGKR--LKVWENWLAAMGREDIDAgqglefstldqvihtALAGGGLA 234
Cdd:cd08470   78 PAYLERHGTPhslaDLDRHNCLlgtsdhwRFQENGRErsVRVQGRWRCNSGVALLDA---------------ALKGMGLA 142

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 495708310 235 VIDRQMIERELANGSLlpitpVEVIGPY-----GYWLDVASDKQGLSKVRLFTQWL 285
Cdd:cd08470  143 QLPDYYVDEHLAAGRL-----VPVLEDYrppdeGIWALYPHNRHLSPKVRLLVDYL 193
PRK11482 PRK11482
DNA-binding transcriptional regulator;
7-83 4.85e-05

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 43.94  E-value: 4.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495708310   7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAGFALSPHLSDAFDHIERAL 83
Cdd:PRK11482  31 LNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGAL 107
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
7-65 2.48e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 42.05  E-value: 2.48e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 495708310   7 LNMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAG 65
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAG 62
PRK12680 PRK12680
LysR family transcriptional regulator;
25-139 7.07e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 40.76  E-value: 7.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  25 AAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGL-SLTEAGFALsphlsdafdhIERALHA-VRVPNLR-----QR--- 94
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEV----------IERARAVlSEANNIRtyaanQRres 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 495708310  95 ---LRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAEID 139
Cdd:PRK12680  92 qgqLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLG 139
nhaR PRK11062
transcriptional activator NhaR; Provisional
 8-65 1.45e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.61  E-value: 1.45e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495708310   8 NMLRVFEEVARHRSFSQAAVGLNVTQGAVSRQIKQLEDYLGVALFIRTPQGLSLTEAG 65
Cdd:PRK11062   7 NHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-187 3.69e-03

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 37.50  E-value: 3.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSV---THQNTHASLA--EIDCQVRFGLEAATQCSSELLVMERHIAVASP 168
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLrdvSAEQVIEAVRsgEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                         90       100
                 ....*....|....*....|...
gi 495708310 169 ELFSDGQPP----DLRRFPLLHI 187
Cdd:cd08440   81 DHPLARRRSvtwaELAGYPLIAL 103
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-285 3.92e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 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: 37.58  E-value: 3.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310  94 RLRIVAPPTWATRWLSAHLRRFCERYPDINLSVTHQNTHASLAE--IDCQVRFGLEAATQCSSELLVMERHIAVASPE-L 170
Cdd:cd08479    2 LLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEegFDLDIRVGDLPDSSLIARKLAPNRRILCASPAyL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495708310 171 FSDGQP---PDLRRFPLLHILHDGKRLKVWEnWLAAMGREDIDAGQGLEFSTLDQVIHTALAGGGLAVIDRQMIERELAN 247
Cdd:cd08479   82 ERHGAPaspEDLARHDCLVIRENDEDFGLWR-LRNGDGEATVRVRGALSSNDGEVVLQWALDGHGIILRSEWDVAPYLRS 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 495708310 248 GSLlpitpVEVIGPYGY-----WLdVASDKQGLS-KVRLFTQWL 285
Cdd:cd08479  161 GRL-----VRVLPDWQLpdadiWA-VYPSRLSRSaRVRVFVDFL 198
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
21-83 6.76e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.26  E-value: 6.76e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495708310    21 SFSQAAVGLNVTQGAVSRQIKQLEDylgvALFIRTPQG--------LSLTEAGFALSPHLSDAFDHIERAL 83
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLEK----KGLVRREPSpedrrsvlVSLTEEGRELIEQLLEARSETLAEL 92
 
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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