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Conserved domains on  [gi|556318645|ref|WP_023294990|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Enterobacter]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1003592)

LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain, which contains type 2 periplasmic binding fold

CATH:  3.40.190.10
Gene Ontology:  GO:0003700
PubMed:  19047729|8257110|11741199

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 1.37e-61

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: 194.02  E-value: 1.37e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPQlSEFGFARLGVLEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 174 APHHPLANEPEPVTRRVIKNYRAIVVGDSSRPECGISSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFINSG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 556318645 254 ALVEKQVLAQSSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
rbcR super family cl31781
LysR transcriptional regulator; Provisional
 5-120 1.46e-17

LysR transcriptional regulator; Provisional


The actual alignment was detected with superfamily member CHL00180:

Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 81.22  E-value: 1.46e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   5 LDVLVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 556318645  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQRHS 120
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYP 122
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 94-289 1.37e-61

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: 194.02  E-value: 1.37e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPQlSEFGFARLGVLEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 174 APHHPLANEPEPVTRRVIKNYRAIVVGDSSRPECGISSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFINSG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 556318645 254 ALVEKQVLAQSSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 4.73e-53

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 175.52  E-value: 4.73e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   8 LVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYqRH--SVTRLVFINgVLGGSWEALTQGRADIIVGALHEPPQLSEFGFARLG 165
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFY-RHfdDVELIIRQE-VFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMG 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 166 VLEQVFAVAPHHPLANEPEPVTRRVIKNYRAIVVGDSSRPECGISSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYL 245
Cdd:PRK11074 165 MLSWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHF 244

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 556318645 246 AQRFINSGALVEKQvLAQSSNES-VWVGWNEQTAGLASAW 284
Cdd:PRK11074 245 AKPLINSGKLVELT-LENPFPDSpCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 1.21e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.02  E-value: 1.21e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   5 LDVLVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGalHEPPQLSEFGFARL 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 165 GVLEQVFAVAPHHPLANepepvtrrviknyRAIVVGDSsrpecgissqlldeqEAItvfdfktkLELQISGLGCGYLPRY 244
Cdd:COG0583  161 GEERLVLVASPDHPLAR-------------RAPLVNSL---------------EAL--------LAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 556318645 245 LAQRFINSGALVEKQVLAQSSNESVWVGWNEQTA-GLASAWWRDEILA 291
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-294 2.45e-22

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: 92.35  E-value: 2.45e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALhePPQLSEFGFARLGVLEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRG--PPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  174 APHHPLANEpEPVTRRVIKNYRAIVVGDSSRP----ECGISSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLARG-EPVSLEDLADEPLILLPPGSGLrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 556318645  250 INSGALVEKQVLAQSSNESVWVGWN-EQTAGLASAWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-120 1.46e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 81.22  E-value: 1.46e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   5 LDVLVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 556318645  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQRHS 120
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYP 122
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 2.52e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 63.56  E-value: 2.52e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645    5 LDVLVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 8-85 5.71e-04

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 41.05  E-value: 5.71e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556318645    8 LVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTgHRARFTRTGQMLLEKGRDvlhtVRELEKQAV 85
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQ----VRLLEAELL 78
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 94-289 1.37e-61

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: 194.02  E-value: 1.37e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPQlSEFGFARLGVLEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 174 APHHPLANEPEPVTRRVIKNYRAIVVGDSSRPECGISSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFINSG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 556318645 254 ALVEKQVLAQSSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 4.73e-53

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 175.52  E-value: 4.73e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   8 LVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYqRH--SVTRLVFINgVLGGSWEALTQGRADIIVGALHEPPQLSEFGFARLG 165
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFY-RHfdDVELIIRQE-VFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMG 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 166 VLEQVFAVAPHHPLANEPEPVTRRVIKNYRAIVVGDSSRPECGISSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYL 245
Cdd:PRK11074 165 MLSWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHF 244

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 556318645 246 AQRFINSGALVEKQvLAQSSNES-VWVGWNEQTAGLASAW 284
Cdd:PRK11074 245 AKPLINSGKLVELT-LENPFPDSpCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 1.21e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.02  E-value: 1.21e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   5 LDVLVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGalHEPPQLSEFGFARL 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 165 GVLEQVFAVAPHHPLANepepvtrrviknyRAIVVGDSsrpecgissqlldeqEAItvfdfktkLELQISGLGCGYLPRY 244
Cdd:COG0583  161 GEERLVLVASPDHPLAR-------------RAPLVNSL---------------EAL--------LAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 556318645 245 LAQRFINSGALVEKQVLAQSSNESVWVGWNEQTA-GLASAWWRDEILA 291
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
18-301 5.92e-39

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 139.17  E-value: 5.92e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  18 GSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQGWENELVI 97
Cdd:PRK10094  17 GSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQVNI 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  98 GVDD-TFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPQLSEFGFARLGVLEQVFAVAPH 176
Cdd:PRK10094  97 VINNlLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPLGSVQWRFVMAAD 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 177 HPLANEPEPVTRRVIKNYRAIVVGDSSRPECGISSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFINSGALV 256
Cdd:PRK10094 177 HPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLV 256

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 556318645 257 EKQVLAQSSNESVWVGWNEQTAGLASAWwrdeilansaIATVYTQ 301
Cdd:PRK10094 257 SRVIPTMRPPSPLSLAWRKFGSGKAVED----------IVTLFTQ 291
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-294 2.45e-22

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: 92.35  E-value: 2.45e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALhePPQLSEFGFARLGVLEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRG--PPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  174 APHHPLANEpEPVTRRVIKNYRAIVVGDSSRP----ECGISSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLARG-EPVSLEDLADEPLILLPPGSGLrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 556318645  250 INSGALVEKQVLAQSSNESVWVGWN-EQTAGLASAWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-120 1.46e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 81.22  E-value: 1.46e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   5 LDVLVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 556318645  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQRHS 120
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYP 122
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-270 1.95e-16

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 78.14  E-value: 1.95e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   8 LVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTV-RELekQAVK 86
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIsQAL--QACN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  87 LHQgwENELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIV-------GALHEPPQlseF 159
Cdd:PRK15421  85 EPQ--QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMtsdilprSGLHYSPM---F 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 160 GFarlgvlEQVFAVAPHHPLANE----PE----------PVTRRVIKNYRAIVvgdssRPeCGISSQLLDEQEAITVfdf 225
Cdd:PRK15421 160 DY------EVRLVLAPDHPLAAKtritPEdlasetlliyPVQRSRLDVWRHFL-----QP-AGVSPSLKSVDNTLLL--- 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 556318645 226 ktkLELQISGLGCGYLPRYLAQRFINSGALVEKQVlaqssNESVW 270
Cdd:PRK15421 225 ---IQMVAARMGIAALPHWVVESFERQGLVVTKTL-----GEGLW 261
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 2.52e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 63.56  E-value: 2.52e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645    5 LDVLVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-253 4.52e-12

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 63.77  E-value: 4.52e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALhePPQLSEFGFARLGVLEQVFAV 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVAL--PVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 174 APHHPLANEPEpVTRRVIKNYRAIVVGDSSRPecgisSQLLDE---------QEAITVFDFKTKLELQISGLGCGYLPRY 244
Cdd:cd05466   79 PPDHPLAKRKS-VTLADLADEPLILFERGSGL-----RRLLDRafaeagftpNIALEVDSLEAIKALVAAGLGIALLPES 152


                 ....*....
gi 556318645 245 LAQRFINSG 253
Cdd:cd05466  153 AVEELADGG 161
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 13-187 7.38e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.90  E-value: 7.38e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  13 ALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQML----------LEKGRDVLHTVRELEK 82
Cdd:PRK11242  11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYlryarralqdLEAGRRAIHDVADLSR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  83 qavklhqgweNELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLvfingvlggSWEALTQGR------ADII-VGALHEPPQ 155
Cdd:PRK11242  91 ----------GSLRLAMTPTFTAYLIGPLIDAFHARYPGITL---------TIREMSQERieallaDDELdVGIAFAPVH 151

                        170       180       190
                 ....*....|....*....|....*....|..
gi 556318645 156 LSEFGFARLGVLEQVFAVAPHHPLANEPEPVT 187
Cdd:PRK11242 152 SPEIEAQPLFTETLALVVGRHHPLAARRKALT 183
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 16-183 7.36e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 52.77  E-value: 7.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  16 KEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEkqavKLHQGWENEL 95
Cdd:PRK10837  16 KSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE----QLFREDNGAL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  96 VIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADI--IVGALHEPPQLSEfgfarlGVLEQ---V 170
Cdd:PRK10837  92 RIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIglIEGPCHSPELISE------PWLEDelvV 165

                        170
                 ....*....|...
gi 556318645 171 FAvAPHHPLANEP 183
Cdd:PRK10837 166 FA-APDSPLARGP 177
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
18-255 1.13e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 52.46  E-value: 1.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  18 GSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQGWENELVI 97
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLRI 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  98 GVDDTFPFSLLTPLIEAFYQRH---SVtrlvfiNGVLGGSWEALTQGRADII--VGALHEPPQLSEfgfaRLGVLEQVFA 172
Cdd:PRK10632  97 GCSSTMAQNVLAGLTAKMLKEYpglSV------NLVTGIPAPDLIADGLDVVirVGALQDSSLFSR----RLGAMPMVVC 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 173 VAPHHpLANEPEPVTRRVIKNYRAI---VVGDSS----RPEcGISSQLLDEQEAITVfDFKTKLELQISGLGCGYLPRYL 245
Cdd:PRK10632 167 AAKSY-LAQYGTPEKPADLSSHSWLeysVRPDNEfeliAPE-GISTRLIPQGRFVTN-DPQTLVRWLTAGAGIAYVPLMW 243

                        250
                 ....*....|
gi 556318645 246 AQRFINSGAL 255
Cdd:PRK10632 244 VIDEINRGEL 253
PRK09801 PRK09801
LysR family transcriptional regulator;
3-275 1.52e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 51.96  E-value: 1.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   3 PLLDVLVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEK 82
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  83 QAVKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFingVLGGSWEALTQGRADIIVGALHEPPqlsEFGFA 162
Cdd:PRK09801  86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF---ELFDRQIDLVQDNIDLDIRINDEIP---DYYIA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 163 RLGVL-EQVFAVAPHHpLANEPEPVTRRVIKNYRAIVVGDSSRPEcGIsSQLLDEQEAITV--------FDFKTKLELQI 233
Cdd:PRK09801 160 HLLTKnKRILCAAPEY-LQKYPQPQSLQELSRHDCLVTKERDMTH-GI-WELGNGQEKKSVkvsghlssNSGEIVLQWAL 236

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 556318645 234 SGLGCGYLPRYLAQRFINSGALVekQVL---AQSSNesVWVGWNE 275
Cdd:PRK09801 237 EGKGIMLRSEWDVLPFLESGKLV--QVLpeyAQSAN--IWAVYRE 277
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-184 1.73e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 51.69  E-value: 1.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  13 ALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQGwE 92
Cdd:PRK09906  11 AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE-D 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  93 NELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGraDIIVGALHEPPQLSEFGFARLGVLEQVFA 172
Cdd:PRK09906  90 RQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRG--ELDVGFMRHPVYSDEIDYLELLDEPLVVV 167

                        170
                 ....*....|..
gi 556318645 173 VAPHHPLANEPE 184
Cdd:PRK09906 168 LPVDHPLAHEKE 179
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 106-198 3.74e-06

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. 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: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 46.88  E-value: 3.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 106 SLLTPLIEAFYQRHsvtRLVFINGVLGGSW---EALTQGRADIIVGALHEPPQLSEFGFARLGVLEQVFAVAPHHPLAnE 182
Cdd:cd08435   13 VLLPPAIARLLARH---PRLTVRVVEGTSDellEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVVVARPGHPLA-R 88

                         90
                 ....*....|....*.
gi 556318645 183 PEPVTRRVIKNYRAIV 198
Cdd:cd08435   89 RARLTLADLADYPWVL 104
PRK09791 PRK09791
LysR family transcriptional regulator;
16-181 5.40e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 47.06  E-value: 5.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  16 KEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVR---ELEKQAVKLHQGWE 92
Cdd:PRK09791  18 RQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRaaqEDIRQRQGQLAGQI 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  93 NelvIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPQLSEFGFARLgvLEQVFA 172
Cdd:PRK09791  98 N---IGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEKL--LEKQFA 172

                        170
                 ....*....|.
gi 556318645 173 VA--PHHPLAN 181
Cdd:PRK09791 173 VFcrPGHPAIG 183
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
19-119 4.65e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 44.22  E-value: 4.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  19 SFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQML---LEKGRDVL-HTVRELEKQAVklhqgwENE 94
Cdd:PRK10086  30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVfwaLKSSLDTLnQEILDIKNQEL------SGT 103

                         90       100
                 ....*....|....*....|....*
gi 556318645  95 LVIGVDDTFPFSLLTPLIEAFYQRH 119
Cdd:PRK10086 104 LTVYSRPSIAQCWLVPRLADFTRRY 128
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-119 5.06e-05

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 44.06  E-value: 5.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  19 SFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQAvkLHQGWENELVIG 98
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAKGALTVS 99

                         90       100
                 ....*....|....*....|.
gi 556318645  99 VDDTFPFSLLTPLIEAFYQRH 119
Cdd:PRK11139 100 LLPSFAIQWLVPRLSSFNEAH 120
PRK10341 PRK10341
transcriptional regulator TdcA;
8-159 1.52e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 42.93  E-value: 1.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   8 LVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKgrdVLHTVRELeKQAVKL 87
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSR---SESITREM-KNMVNE 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556318645  88 HQGWENELVIGVDDTFP----FSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPQLSEF 159
Cdd:PRK10341  88 INGMSSEAVVDVSFGFPsligFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDL 163
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 34-84 1.76e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 42.32  E-value: 1.76e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 556318645  34 LSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:PRK11151  32 LSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-197 2.47e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 42.27  E-value: 2.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  21 AAASAkLYKTPSALSYTVQKLESDLNIQILDRTGHRAR-FTRTGQMLLEKGRDVLHTVRELE---KQAVKLHQGwenELV 96
Cdd:PRK12684  21 EAAKA-LYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKrvgKEFAAQDQG---NLT 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  97 IGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVG--ALHEPPQLSEFGFARlgvLEQVFAVA 174
Cdd:PRK12684  97 IATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAteAIADYKELVSLPCYQ---WNHCVVVP 173

                        170       180
                 ....*....|....*....|...
gi 556318645 175 PHHPLANEpEPVTRRVIKNYRAI 197
Cdd:PRK12684 174 PDHPLLER-KPLTLEDLAQYPLI 195
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 105-183 3.15e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 41.01  E-value: 3.15e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556318645 105 FSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGAlhEPPQLSEFGFARLGVLEQVFAVAPHHPLANEP 183
Cdd:cd08441   12 FDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITS--DPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKE 88
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-67 4.00e-04

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 41.50  E-value: 4.00e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 556318645  11 LDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHrARFTRTGQMLL 67
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLL 65
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 97-181 4.43e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 40.80  E-value: 4.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  97 IGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPQLSEFGFARLGVLEQVFAVAPH 176
Cdd:cd08418    4 IGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVARKD 83


                 ....*
gi 556318645 177 HPLAN 181
Cdd:cd08418   84 HPLQG 88
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-185 4.90e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.96  E-value: 4.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  30 TPSALSYTVQKLESDLNIQILDRTGHRARFTRTGQMLLEKGRDVLHTVRELeKQAVKLHQG-WENELVIGVDDTFPFSLL 108
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQL-RHTLDQQGPsLSGELSLFCSVTAAYSHL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 109 TPLIEAFYQRHsvtRLVFINGVLGGSWEALTQ---GRADIIVGALhePPQLSE-FGFARLGVLEQVFaVAPHHP-----L 179
Cdd:PRK11716  83 PPILDRFRAEH---PLVEIKLTTGDAADAVEKvqsGEADLAIAAK--PETLPAsVAFSPIDEIPLVL-IAPALPcpvrqQ 156


                 ....*.
gi 556318645 180 ANEPEP 185
Cdd:PRK11716 157 LSQEKP 162
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 8-85 5.71e-04

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 41.05  E-value: 5.71e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556318645    8 LVILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTgHRARFTRTGQMLLEKGRDvlhtVRELEKQAV 85
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQ----VRLLEAELL 78
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-256 2.55e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 38.44  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 106 SLLTPLIEAFYQRHsvTRLVFINGVLGGS--WEALTQGRADIIVG-ALHEPPQLSEFGF--ARLGVLeqvfaVAPHHPLA 180
Cdd:cd08426   13 ELLPSLIARFRQRY--PGVFFTVDVASTAdvLEAVLSGEADIGLAfSPPPEPGIRVHSRqpAPIGAV-----VPPGHPLA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 181 NEPEPVTRRVIKnYRAIVvgdsSRPECGIsSQLLD---EQEAIT---VFD---FKTKLELQISGLGCGYLPRYLAQRFIN 251
Cdd:cd08426   86 RQPSVTLAQLAG-YPLAL----PPPSFSL-RQILDaafARAGVQlepVLIsnsIETLKQLVAAGGGISLLTELAVRREIR 159


                 ....*
gi 556318645 252 SGALV 256
Cdd:cd08426  160 RGQLV 164
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 144-273 2.96e-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 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: 38.31  E-value: 2.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 144 DIIV--GALHEPPQLSefgfAR-LGVLEQVFAVAPHHpLANEPEPVTRRVIKNYRAIVVGDSSRPecgISSQLLDEQEAI 220
Cdd:cd08475   49 DLAVriGELADSTGLV----ARrLGTQRMVLCASPAY-LARHGTPRTLEDLAEHQCIAYGRGGQP---LPWRLADEQGRL 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556318645 221 TVFDFKTKLELQ---------ISGLGCGYLPRYLAQRFINSGALVEkqVLAQ--SSNESVWVGW 273
Cdd:cd08475  121 VRFRPAPRLQFDdgeaiadaaLAGLGIAQLPTWLVADHLQRGELVE--VLPElaPEGLPIHAVW 182
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-183 3.20e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 37.96  E-value: 3.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPqlSEFGFARLGVLEQVFAV 173
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELP--PGLRSQPLFEDRFVCVA 78

                         90
                 ....*....|
gi 556318645 174 APHHPLANEP 183
Cdd:cd08417   79 RKDHPLAGGP 88
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-241 3.93e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 38.25  E-value: 3.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645   9 VILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRTGHRAR-FTRTGQMLLEKGRDVLHTVRELEKQAVKL 87
Cdd:PRK12679   8 IIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLF 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGA--LHEPPQLSEFGFARlg 165
Cdd:PRK12679  88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASerLSNDPQLVAFPWFR-- 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645 166 vLEQVFAVAPHHPLANEP----EPVTRRVIKNYRAIVVGDSSRPECGISSQL-----LDEQEAITVfdfKTKLELqisGL 236
Cdd:PRK12679 166 -WHHSLLVPHDHPLTQITpltlESIAKWPLITYRQGITGRSRIDDAFARKGLladivLSAQDSDVI---KTYVAL---GL 238


                 ....*
gi 556318645 237 GCGYL 241
Cdd:PRK12679 239 GIGLV 243
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 94-184 5.35e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. 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: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 37.49  E-value: 5.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIivGALHEPPQLSEFGFARLGVLEQVFAV 173
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDV--GFVRPPPDPPGLASRPLLREPLVVAL 78

                         90
                 ....*....|.
gi 556318645 174 APHHPLANEPE 184
Cdd:cd08414   79 PADHPLAARES 89
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-151 6.25e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 37.96  E-value: 6.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  21 AAASAkLYKTPSALSYTVQKLESDLNIQILDRTG-HRARFTRTGQMLLEKGRDVLHTVRELEKQA---VKLHQGwenELV 96
Cdd:PRK12681  21 ATAEG-LYTSQPGISKQVRMLEDELGIQIFARSGkHLTQVTPAGEEIIRIAREILSKVESIKSVAgehTWPDKG---SLY 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 556318645  97 IGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRAD--IIVGALH 151
Cdd:PRK12681  97 IATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADfaIATEALH 153
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 110-187 6.33e-03

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 37.19  E-value: 6.33e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556318645 110 PLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVgaLHEPPQLSEFGFARLGVlEQVFAVAPHHPLANEPEPVT 187
Cdd:cd08433   17 PLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLAL--LYGPPPIPGLSTEPLLE-EDLFLVGPADAPLPRGAPVP 91
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 94-184 7.53e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (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 N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 36.75  E-value: 7.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556318645  94 ELVIGVDDTFPFSLLTPLIEAFYQRHSVTRLVFINGVLGGSWEALTQGRADIIVGALHEPPqlSEFGFARLGVLEQVFAV 173
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLP--EDIAFEPLARLPPYVWL 78

                         90
                 ....*....|.
gi 556318645 174 APHHPLANEPE 184
Cdd:cd08412   79 PADHPLAGKDE 89
 
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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