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Conserved domains on  [gi|581978378|ref|WP_024130600|]
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MULTISPECIES: LysR family transcriptional regulator [Citrobacter]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain; similar to CbbR, AmpR, GalR, YhaJ, and NmcR, which are positive transcriptional regulators of various genes

Gene Ontology:  GO:0003677|GO:0003700|GO:0001216
PubMed:  8257110|19047729
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 94-289 2.26e-60

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd08431:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 195  Bit Score: 190.56  E-value: 2.26e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  94 ELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAINEPPTSAAWSYKmLGTLDNVFVV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRP-LGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 174 APSHPLAAATDGLTNEQLCLHRAVVISDSARFCHPLQSNLMDEQPQIRVDDFDSKVTLLRAGLGCGFLPRHIVRPWLATG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 581978378 254 ELVEKSVISFRQKDVAYMAWRNHSDGLAQRWWREAL 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 8.80e-15

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.41  E-value: 8.80e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378    5 LDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 94-289 2.26e-60

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 190.56  E-value: 2.26e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  94 ELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAINEPPTSAAWSYKmLGTLDNVFVV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRP-LGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 174 APSHPLAAATDGLTNEQLCLHRAVVISDSARFCHPLQSNLMDEQPQIRVDDFDSKVTLLRAGLGCGFLPRHIVRPWLATG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 581978378 254 ELVEKSVISFRQKDVAYMAWRNHSDGLAQRWWREAL 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 3.43e-47

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 160.11  E-value: 3.43e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   8 LLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAVQL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  88 SSGWEKELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAINEPPTSAAWSYKMLGTL 167
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 168 DNVFVVAPSHPLAAATDGLTNEQLCLHRAVVISDSARFCHPLQSNLMDEQPQIRVDDFDSKVTLLRAGLGCGFLPRHIVR 247
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 581978378 248 PWLATGELVEKSVISFRQKDVAYMAWRNHSDGLAQRW 284
Cdd:PRK11074 247 PLINSGKLVELTLENPFPDSPCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-291 9.63e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 152.33  E-value: 9.63e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   3 INLDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEK 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  83 QAVQLSSGWEKELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAinEPPTSAAWSYK 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL--GPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 163 MLGTLDNVFVVAPSHPLAAATdgltneqlclhravvisdsarfchplqsnlmdeqpqIRVDDFDSKVTLLRAGLGCGFLP 242
Cdd:COG0583  159 PLGEERLVLVASPDHPLARRA------------------------------------PLVNSLEALLAAVAAGLGIALLP 202

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 581978378 243 RHIVRPWLATGELVEKSVISFRQKDVAYMAWRNHSD-GLAQRWWREALLA 291
Cdd:COG0583  203 RFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-291 4.22e-21

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: 88.89  E-value: 4.22e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   94 ELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAinEPPTSAAWSYKMLGTLDNVFVV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR--GPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  174 APSHPLAAAtDGLTNEQLCLHRAVVISDSARFCHPLQSNLMDE----QPQIRVDDFDSKVTLLRAGLGCGFLPRHIVRPW 249
Cdd:pfam03466  81 PPDHPLARG-EPVSLEDLADEPLILLPPGSGLRDLLDRALRAAglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 581978378  250 LATGELVEKSVISFRQKDVAYMAWR-NHSDGLAQRWWREALLA 291
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLRE 202
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 8.80e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.41  E-value: 8.80e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378    5 LDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-73 6.91e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 67.74  E-value: 6.91e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   5 LDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKG-RLL 73
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGnRIL 76
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 18-274 2.01e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 63.22  E-value: 2.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  18 GSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAVQLSSgwEKELAI 97
Cdd:NF041036  16 GSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLSI 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  98 ALDDSFPFETLLPVIDAFYALNKQTR-LNFTHHTLAGSWEELTHNGADIilgAINEppTSAAWSYKMLGTLD-----NVF 171
Cdd:NF041036  94 CCTPTFGMAHLPGVLNRFMLRNADVVdLKFLFHSPAQALEGIQNKEFDL---AIIE--HCADLDLGRFHTYPlpqdeLVF 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 172 VVAPSHPLAAATdgLTNEQLCLHRAVVISDSARfCHPLQS-NLmdEQPQIRVDDFDSKVTL--LR-------AGLGCGFL 241
Cdd:NF041036 169 VSAPSLGLPTPN--VTLERLLELCLITRRDGCS-SRDLLRrNL--AEQGRDLDDFRRVVVSddLRltiqtvlDGGGISFV 243

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 581978378 242 PRHIVRPWLATGELVEKSVISF---RQKDVAYMAWR 274
Cdd:NF041036 244 SRSLVCEYLKNGQLREHYVEGFphvRCRTVVARKCR 279
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
10-73 4.48e-05

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 42.12  E-value: 4.48e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 581978378  10 ILDAIDKHGSFAAAAGSLfktpaALSY-----MIQKLENDLDIELLDRS-----GHRAKFTDTGRMMLEKGRLL 73
Cdd:COG2005   26 LLEAIDETGSISAAAKAM-----GMSYkrawdLIDAMNNLLGEPLVERQtggkgGGGARLTPEGRRLLALYRRL 94
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 94-289 2.26e-60

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 190.56  E-value: 2.26e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  94 ELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAINEPPTSAAWSYKmLGTLDNVFVV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRP-LGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 174 APSHPLAAATDGLTNEQLCLHRAVVISDSARFCHPLQSNLMDEQPQIRVDDFDSKVTLLRAGLGCGFLPRHIVRPWLATG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 581978378 254 ELVEKSVISFRQKDVAYMAWRNHSDGLAQRWWREAL 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 3.43e-47

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 160.11  E-value: 3.43e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   8 LLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAVQL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  88 SSGWEKELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAINEPPTSAAWSYKMLGTL 167
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 168 DNVFVVAPSHPLAAATDGLTNEQLCLHRAVVISDSARFCHPLQSNLMDEQPQIRVDDFDSKVTLLRAGLGCGFLPRHIVR 247
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 581978378 248 PWLATGELVEKSVISFRQKDVAYMAWRNHSDGLAQRW 284
Cdd:PRK11074 247 PLINSGKLVELTLENPFPDSPCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-291 9.63e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 152.33  E-value: 9.63e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   3 INLDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEK 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  83 QAVQLSSGWEKELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAinEPPTSAAWSYK 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL--GPPPDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 163 MLGTLDNVFVVAPSHPLAAATdgltneqlclhravvisdsarfchplqsnlmdeqpqIRVDDFDSKVTLLRAGLGCGFLP 242
Cdd:COG0583  159 PLGEERLVLVASPDHPLARRA------------------------------------PLVNSLEALLAAVAAGLGIALLP 202

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 581978378 243 RHIVRPWLATGELVEKSVISFRQKDVAYMAWRNHSD-GLAQRWWREALLA 291
Cdd:COG0583  203 RFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
18-281 9.43e-41

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 143.79  E-value: 9.43e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  18 GSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAVQLSSGWEKELAI 97
Cdd:PRK10094  17 GSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQVNI 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  98 ALDDsfpfetLL----PVIDAFYALNKQ---TRLNFTHHTLAGSWEELTHNGADIILGAINEPPTSAAWSYKMLGTLDNV 170
Cdd:PRK10094  97 VINN------LLynpqAVAQLLAWLNERypfTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPLGSVQWR 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 171 FVVAPSHPLAAATDGLTNEQLCLHRAVVISDSARFCHPLQSNLMDEQPQIRVDDFDSKVTLLRAGLGCGFLPRHIVRPWL 250
Cdd:PRK10094 171 FVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQSMI 250

                        250       260       270
                 ....*....|....*....|....*....|.
gi 581978378 251 ATGELVEKSVISFRQKDVAYMAWRNHSDGLA 281
Cdd:PRK10094 251 DNQQLVSRVIPTMRPPSPLSLAWRKFGSGKA 281
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-291 4.22e-21

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: 88.89  E-value: 4.22e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   94 ELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAinEPPTSAAWSYKMLGTLDNVFVV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR--GPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  174 APSHPLAAAtDGLTNEQLCLHRAVVISDSARFCHPLQSNLMDE----QPQIRVDDFDSKVTLLRAGLGCGFLPRHIVRPW 249
Cdd:pfam03466  81 PPDHPLARG-EPVSLEDLADEPLILLPPGSGLRDLLDRALRAAglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 581978378  250 LATGELVEKSVISFRQKDVAYMAWR-NHSDGLAQRWWREALLA 291
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLRE 202
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 8.80e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 67.41  E-value: 8.80e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378    5 LDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-73 6.91e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 67.74  E-value: 6.91e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   5 LDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKG-RLL 73
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGnRIL 76
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-289 1.13e-11

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 62.62  E-value: 1.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  94 ELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADiiLGAINEPPTSAAWSYKMLGTLDNVFVV 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELD--LAIVALPVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 174 APSHPLAAATdGLTNEQLcLHRAVVISDSARFCHPLQSNLMDE-----QPQIRVDDFDSKVTLLRAGLGCGFLPRHIVRP 248
Cdd:cd05466   79 PPDHPLAKRK-SVTLADL-ADEPLILFERGSGLRRLLDRAFAEagftpNIALEVDSLEAIKALVAAGLGIALLPESAVEE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 581978378 249 wLATGELVEKSVISFRQKDVAYMAWR-NHSDGLAQRWWREAL 289
Cdd:cd05466  157 -LADGGLVVLPLEDPPLSRTIGLVWRkGRYLSPAARAFLELL 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-260 1.18e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 64.27  E-value: 1.18e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   3 INLDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEkgrlLLNAAKDLEK 82
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQ----LANQVLPQIS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  83 QAVQ-LSSGWEKELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAINEPptSAAWSY 161
Cdd:PRK15421  78 QALQaCNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILP--RSGLHY 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 162 KMLGTLDNVFVVAPSHPLAAATDgLTNEQLCLHRAVVisdsarfcHPLQSNLMD----------EQPQIR-VDDFDSKVT 230
Cdd:PRK15421 156 SPMFDYEVRLVLAPDHPLAAKTR-ITPEDLASETLLI--------YPVQRSRLDvwrhflqpagVSPSLKsVDNTLLLIQ 226

                        250       260       270
                 ....*....|....*....|....*....|
gi 581978378 231 LLRAGLGCGFLPRHIVRPWLATGELVEKSV 260
Cdd:PRK15421 227 MVAARMGIAALPHWVVESFERQGLVVTKTL 256
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 18-274 2.01e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 63.22  E-value: 2.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  18 GSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAVQLSSgwEKELAI 97
Cdd:NF041036  16 GSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLSI 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  98 ALDDSFPFETLLPVIDAFYALNKQTR-LNFTHHTLAGSWEELTHNGADIilgAINEppTSAAWSYKMLGTLD-----NVF 171
Cdd:NF041036  94 CCTPTFGMAHLPGVLNRFMLRNADVVdLKFLFHSPAQALEGIQNKEFDL---AIIE--HCADLDLGRFHTYPlpqdeLVF 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 172 VVAPSHPLAAATdgLTNEQLCLHRAVVISDSARfCHPLQS-NLmdEQPQIRVDDFDSKVTL--LR-------AGLGCGFL 241
Cdd:NF041036 169 VSAPSLGLPTPN--VTLERLLELCLITRRDGCS-SRDLLRrNL--AEQGRDLDDFRRVVVSddLRltiqtvlDGGGISFV 243

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 581978378 242 PRHIVRPWLATGELVEKSVISF---RQKDVAYMAWR 274
Cdd:NF041036 244 SRSLVCEYLKNGQLREHYVEGFphvRCRTVVARKCR 279
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 13-191 9.89e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 58.43  E-value: 9.89e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  13 AIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNaakDLE--KQAVQ---- 86
Cdd:PRK11242  11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQ---DLEagRRAIHdvad 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  87 LSSGwekELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADiiLGAINEPPTSAAWSYKMLGT 166
Cdd:PRK11242  88 LSRG---SLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELD--VGIAFAPVHSPEIEAQPLFT 162

                        170       180
                 ....*....|....*....|....*
gi 581978378 167 LDNVFVVAPSHPLAAATDGLTNEQL 191
Cdd:PRK11242 163 ETLALVVGRHHPLAARRKALTLDEL 187
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 20-277 1.18e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 52.08  E-value: 1.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  20 FAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAVQLSSGwEKELAIAL 99
Cdd:PRK09906  18 FTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE-DRQLTIGF 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 100 DDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHngADIILGAINEPPTSAAWSYKMLGTLDNVFVVAPSHPL 179
Cdd:PRK09906  97 VPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRR--GELDVGFMRHPVYSDEIDYLELLDEPLVVVLPVDHPL 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 180 AAAtDGLTNEQlcLHRAVVISDSARFCHPLQSNLMD------EQPQI--RVDDFDSKVTLLRAGLGCGFLPRHIVRpwLA 251
Cdd:PRK09906 175 AHE-KEITAAQ--LDGVNFISTDPAYSGSLAPIIKAwfaqhnSQPNIvqVATNILVTMNLVGMGLGCTIIPGYMNN--FN 249

                        250       260       270
                 ....*....|....*....|....*....|..
gi 581978378 252 TGELVeksvisFRQKDVA------YMAWRNHS 277
Cdd:PRK09906 250 TGQVV------FRPLAGNvpsialLMAWKKGE 275
PRK09801 PRK09801
LysR family transcriptional regulator;
8-112 2.67e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 51.19  E-value: 2.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   8 LLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAVQL 87
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100
                 ....*....|....*....|....*
gi 581978378  88 SSGWEKELAIALDDSFPFETLLPVI 112
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAI 115
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
18-83 2.20e-06

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 48.22  E-value: 2.20e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 581978378  18 GSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQ 83
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQ 82
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-257 2.25e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 48.23  E-value: 2.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  11 LDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRsGHRAKFTDTGRMML---EKGRLLlnaAKDLEKQAVQL 87
Cdd:PRK03635  10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLrhaRQVRLL---EAELLGELPAL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  88 SSGWEKeLAIAL-DDSFpfET-LLPVIDAFyALNKQTRLNFT----HHTLagsweELTHNGAdiILGAI-NEPPTSAAWS 160
Cdd:PRK03635  86 DGTPLT-LSIAVnADSL--ATwFLPALAPV-LARSGVLLDLVvedqDHTA-----ELLRRGE--VVGAVtTEPQPVQGCR 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 161 YKMLGTLDNVFVVAPShpLAAA--TDGLTNEQLC-----------------LHRAVVISDSARFCHPLQSnlmdeqpqir 221
Cdd:PRK03635 155 VDPLGAMRYLAVASPA--FAARyfPDGVTAEALAkapavvfnrkddlqdrfLRQAFGLPPGSVPCHYVPS---------- 222

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 581978378 222 VDDFdskVTLLRAGLGCGFLPRHIVRPWLATGELVE 257
Cdd:PRK03635 223 SEAF---VRAALAGLGWGMIPELQIEPELASGELVD 255
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 11-86 2.65e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 48.10  E-value: 2.65e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 581978378  11 LDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAVQ 86
Cdd:PRK11151   9 LVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQ 84
PRK09791 PRK09791
LysR family transcriptional regulator;
13-183 4.64e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 47.45  E-value: 4.64e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  13 AIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLL---LNAAKDLEKQAVQLSS 89
Cdd:PRK09791  15 EVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLIleeLRAAQEDIRQRQGQLA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  90 GwekELAIALDDSFPfETLLP-VIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAINEPPTSAAWSYKMLGTLD 168
Cdd:PRK09791  95 G---QINIGMGASIA-RSLMPaVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEKLLEKQ 170

                        170
                 ....*....|....*
gi 581978378 169 NVFVVAPSHPLAAAT 183
Cdd:PRK09791 171 FAVFCRPGHPAIGAR 185
PRK12680 PRK12680
LysR family transcriptional regulator;
23-257 5.96e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 46.92  E-value: 5.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  23 AAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAK-FTDTGRMMLEKGRLLLNAAKDLEKQAVQLSSGWEKELAIALDD 101
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 102 SFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADI--ILGAINEPPTSAA---WSYKMLgtldnvFVVAPS 176
Cdd:PRK12680 102 TQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIaiVSTAGGEPSAGIAvplYRWRRL------VVVPRG 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 177 HPLAAATDGLTNEQLCLHRAVVISDSARFCHPLQSNL--MDEQPQIRVDDFDSKV--TLLRAGLGCGFLPRHIV------ 246
Cdd:PRK12680 176 HALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFaqLGLEPSIALTALDADLikTYVRAGLGVGLLAEMAVnanded 255

                        250
                 ....*....|..
gi 581978378 247 -RPWLATGELVE 257
Cdd:PRK12680 256 lRAWPAPAPIAE 267
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 3-191 6.76e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 46.91  E-value: 6.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   3 INLDVLLILDAIDKHG-SFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAK-FTDTGRMMLEKGRLLLNAAKDL 80
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  81 EKQAVQLSSGWEKELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGaineppTSAAWS 160
Cdd:PRK12682  81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA------TESLAD 154

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 581978378 161 YKMLGTL-----DNVFVVAPSHPLAAAtDGLTNEQL 191
Cdd:PRK12682 155 DPDLATLpcydwQHAVIVPPDHPLAQE-ERITLEDL 189
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-82 7.43e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 46.60  E-value: 7.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   1 MRINLDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDL 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80


                 ..
gi 581978378  81 EK 82
Cdd:PRK10837  81 EQ 82
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 164-257 1.72e-05

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: 44.74  E-value: 1.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 164 LGTLDNVFVVAPSHpLAAATDGLTNEQLCLHRAVVISDSA-----RFCHPLQSNLMDEQPQIRVDDFDSKVTLLRAGLGC 238
Cdd:cd08422   67 LGPVRRVLVASPAY-LARHGTPQTPEDLARHRCLGYRLPGrplrwRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGI 145

                         90
                 ....*....|....*....
gi 581978378 239 GFLPRHIVRPWLATGELVE 257
Cdd:cd08422  146 ALLPDFLVAEDLASGRLVR 164
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 12-115 2.01e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 45.22  E-value: 2.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  12 DAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLEKQAvqLSSGW 91
Cdd:PRK11139  15 EAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSA 92

                         90       100
                 ....*....|....*....|....
gi 581978378  92 EKELAIALDDSFPFETLLPVIDAF 115
Cdd:PRK11139  93 KGALTVSLLPSFAIQWLVPRLSSF 116
PRK09986 PRK09986
LysR family transcriptional regulator;
2-242 2.15e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 45.10  E-value: 2.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   2 RINLDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNAAKDLE 81
Cdd:PRK09986   6 RIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  82 KQAVQLSSGWEKELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIILGAINEPPTSAAWSY 161
Cdd:PRK09986  86 ARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTS 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 162 KMLgTLDNVFVVAPS-HPLAAAtDGLTNEQLCLHRAVVI----SDSARFCHplqsNLMDEQ---PQI--RVDDFDSKVTL 231
Cdd:PRK09986 166 RRL-HESAFAVAVPEeHPLASR-SSVPLKALRNEYFITLpfvhSDWGKFLQ----RVCQQAgfsPQIirQVNEPQTVLAM 239

                        250
                 ....*....|.
gi 581978378 232 LRAGLGCGFLP 242
Cdd:PRK09986 240 VSMGIGITLLP 250
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 23-191 3.12e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 44.65  E-value: 3.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  23 AAGSLFKTPAALSYMIQKLENDLDIELLDRSGHR-AKFTDTGRMMLEKGRLLLNAAKDLEKQAVQLSSGWEKELAIALDD 101
Cdd:PRK12683  22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRlTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 102 SFPFETLLPVIDAFYALNKQTRLNFtHHTLAGSWEELTHNG-ADIILG--AINEPPTSAAWSYKmlgTLDNVFVVAPSHP 178
Cdd:PRK12683 102 TQARYALPKVVRQFKEVFPKVHLAL-RQGSPQEIAEMLLNGeADIGIAteALDREPDLVSFPYY---SWHHVVVVPKGHP 177

                        170
                 ....*....|...
gi 581978378 179 LAAAtDGLTNEQL 191
Cdd:PRK12683 178 LTGR-ENLTLEAI 189
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
10-73 4.48e-05

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 42.12  E-value: 4.48e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 581978378  10 ILDAIDKHGSFAAAAGSLfktpaALSY-----MIQKLENDLDIELLDRS-----GHRAKFTDTGRMMLEKGRLL 73
Cdd:COG2005   26 LLEAIDETGSISAAAKAM-----GMSYkrawdLIDAMNNLLGEPLVERQtggkgGGGARLTPEGRRLLALYRRL 94
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-63 4.51e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 44.22  E-value: 4.51e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 581978378  16 KHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTG 63
Cdd:PRK10086  27 RHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG 74
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-257 5.34e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 43.81  E-value: 5.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  11 LDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGH-RAkfTDTGRMML---EKGRLLLNaakDLEKQAVQ 86
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPcRP--TPAGQRLLrhlRQVALLEA---DLLSTLPA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  87 LSSGWEKeLAIALD-DSfpFET-LLPVIDAFYAlNKQTRLNFT----HHTLagsweELTHNGAdiILGAIN---EPPTSA 157
Cdd:PRK13348  85 ERGSPPT-LAIAVNaDS--LATwFLPALAAVLA-GERILLELIvddqDHTF-----ALLERGE--VVGCVStqpKPMRGC 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 158 -AWSykmLGTLDNVFVVAPS------------HPLAAAT-------DGLtnEQLCLHRAVVISDSARFCHPLQSNlmdeq 217
Cdd:PRK13348 154 lAEP---LGTMRYRCVASPAfaaryfaqgltrHSALKAPavafnrkDTL--QDSFLEQLFGLPVGAYPRHYVPST----- 223

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 581978378 218 pqirvddfDSKVTLLRAGLGCGFLPRHIVRPWLATGELVE 257
Cdd:PRK13348 224 --------HAHLAAIRHGLGYGMVPELLIGPLLAAGRLVD 255
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 150-257 1.12e-04

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: 42.16  E-value: 1.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 150 INEPPTSAAWSYKMLGTLDNVFVVAPSHpLAAATDGLTNEQLCLHRAVVISdsaRFCHPLQSNLMDEQ---------PQI 220
Cdd:cd08475   54 IGELADSTGLVARRLGTQRMVLCASPAY-LARHGTPRTLEDLAEHQCIAYG---RGGQPLPWRLADEQgrlvrfrpaPRL 129

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 581978378 221 RVDDFDSKVTLLRAGLGCGFLPRHIVRPWLATGELVE 257
Cdd:cd08475  130 QFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVE 166
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-241 1.60e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 42.49  E-value: 1.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   9 LILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHR-AKFTDTGRMMLEKGRLLLNAAKDLEKQAVQL 87
Cdd:PRK12679   8 IIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILNEASNVRRLADLF 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  88 SSGWEKELAIALDDSFPFETLLPVIDAFYALNKQTRLNFTHhtlaGSWEE----LTHNGADIILGA---INEPPTSA--- 157
Cdd:PRK12679  88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQ----GTPQEiatlLQNGEADIGIASerlSNDPQLVAfpw 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 158 -AWSYKMLgtldnvfvVAPSHPLAAATDgLTNEQLCLHRAVV----ISDSARFCHPLQSNLMdeQPQIRVDDFDSKV--T 230
Cdd:PRK12679 164 fRWHHSLL--------VPHDHPLTQITP-LTLESIAKWPLITyrqgITGRSRIDDAFARKGL--LADIVLSAQDSDVikT 232

                        250
                 ....*....|.
gi 581978378 231 LLRAGLGCGFL 241
Cdd:PRK12679 233 YVALGLGIGLV 243
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
22-191 7.20e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 40.73  E-value: 7.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378  22 AAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAK-FTDTGRMMLEKGRLLLNAAKDLEKQAVQLSSGWEKELAIALD 100
Cdd:PRK12684  21 EAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIATT 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 101 DSFPFETLLPVIDAFYALNKQTRLNFTHHTLAGSWEELTHNGADIilgAInepPTSAAWSYKMLGTLD-----NVFVVAP 175
Cdd:PRK12684 101 HTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADL---AI---ATEAIADYKELVSLPcyqwnHCVVVPP 174

                        170
                 ....*....|....*.
gi 581978378 176 SHPLAAAtDGLTNEQL 191
Cdd:PRK12684 175 DHPLLER-KPLTLEDL 189
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 220-257 7.58e-04

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: 39.80  E-value: 7.58e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 581978378 220 IRVDDFDSKVTLLRAGLGCGFLPRHIVRPWLATGELVE 257
Cdd:cd08472  129 VSVNDSEAYLAAALAGLGIIQVPRFMVRPHLASGRLVE 166
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 217-257 2.50e-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 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: 38.21  E-value: 2.50e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 581978378 217 QPQIRVDDFDSKVTLLRAGLGCGFLPRHIVRPWLATGELVE 257
Cdd:cd08474  129 EGPLILNDSDLMLDAALDGLGIAYLFEDLVAEHLASGRLVR 169
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-110 2.51e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.86  E-value: 2.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378   1 MRINLDVLLILDAIDKHGSFAAAAGSLFKTPAALSYMIQKLENDLDIELLDRSGHRAKFTDTGRMMLEKGRLLLNaAKDl 80
Cdd:PRK15092   9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR-FND- 86

                         90       100       110
                 ....*....|....*....|....*....|.
gi 581978378  81 EKQAVQLSSGWEKELAI-ALDDSfpFETLLP 110
Cdd:PRK15092  87 EACSSLMYSNLQGVLTIgASDDT--ADTILP 115
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 170-249 5.45e-03

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 37.20  E-value: 5.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 170 VFVVAPSHPLAAAtDGLTNEQLCLHRAV---------VISDSARFCHPLQSNLMDEqpqirVDDFDSKVTLLRAGLGCGF 240
Cdd:cd08436   76 VAVVAPDHPLAGR-RRVALADLADEPFVdfppgtgarRQVDRAFAAAGVRRRVAFE-----VSDVDLLLDLVARGLGVAL 149


                 ....*....
gi 581978378 241 LPRHIVRPW 249
Cdd:cd08436  150 LPASVAARL 158
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 170-256 6.09e-03

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 37.12  E-value: 6.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 170 VFVVAPSHPLAAA-----TDGLTNEQLCLHravviSDSArfchpLQSNLMDE--------QPQIRVDDFDSKVTLLRAGL 236
Cdd:cd08421   75 VVVVPRDHPLAGRasvafADTLDHDFVGLP-----AGSA-----LHTFLREAaarlgrrlRLRVQVSSFDAVCRMVAAGL 144

                         90       100
                 ....*....|....*....|
gi 581978378 237 GCGFLPRHIVRPWLATGELV 256
Cdd:cd08421  145 GIGIVPESAARRYARALGLR 164
PBP2_IciA_ArgP cd08428
The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), ...
 164-257 7.91e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176119 [Multi-domain]  Cd Length: 195  Bit Score: 36.84  E-value: 7.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581978378 164 LGTLDNVFVVAPshPLAAA--TDGLTNEQLCLHRAVVIS--DSARFcHPLQSNL---MDEQPQIRVDDFDSKVTLLRAGL 236
Cdd:cd08428   68 LGSMDYLLVASP--DFAARyfPNGLTREALLKAPAVAFNrkDDLHQ-SFLQQHFglpPGSYPCHYVPSSEAFVDLAAQGL 144

                         90       100
                 ....*....|....*....|.
gi 581978378 237 GCGFLPRHIVRPWLATGELVE 257
Cdd:cd08428  145 AYGMIPELQIEPELASGELID 165
 
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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