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Conserved domains on  [gi|949422723|dbj|BAT35559|]
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predicted DNA-binding transcriptional regulator [Escherichia albertii]

Protein Classification

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 3.25e-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: 193.25  E-value: 3.25e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSsEFGFSRLGELEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPG-GVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 174 APHHPLAQEEEPLNRRVIKRYRAIVVGDTtytgATAVPQ----LLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADT----SRNLPPrssgLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 949422723 250 LDSGALIEKKVVAQTLFESVWIGWNEQTAGLASSWWRDEI 289
Cdd:cd08431  156 LASGELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
rbcR super family cl31781
LysR transcriptional regulator; Provisional
 5-148 4.73e-17

LysR transcriptional regulator; Provisional


The actual alignment was detected with superfamily member CHL00180:

Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 79.68  E-value: 4.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 949422723  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKF-INGVLGGSWEALtQGRADI-IVG 148
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIAWNVA-NGQIDIaIVG 151
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 94-289 3.25e-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: 193.25  E-value: 3.25e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSsEFGFSRLGELEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPG-GVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 174 APHHPLAQEEEPLNRRVIKRYRAIVVGDTtytgATAVPQ----LLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADT----SRNLPPrssgLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 949422723 250 LDSGALIEKKVVAQTLFESVWIGWNEQTAGLASSWWRDEI 289
Cdd:cd08431  156 LASGELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 5.51e-55

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 180.52  E-value: 5.51e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   8 LMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  88 HEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSSEFGFSRLGEL 167
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 168 EQVFAVAPHHPLAQEEEPLNRRVIKRYRAIVVGDTTYTGATAVPQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQ 247
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 949422723 248 RFLDSGALIEKKVVAQTLFESVWIGWNEQTAGLASSW 284
Cdd:PRK11074 247 PLINSGKLVELTLENPFPDSPCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 3.55e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 153.87  E-value: 3.55e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQA 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGamREPPSSSEFGFSRL 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 165 GELEQVFAVAPHHPLAQEEEPLNrrvikryraivvgdttytgatavpqlldeqeaitvfDFKTKLELQISGLGCGYLPRY 244
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPLVN------------------------------------SLEALLAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 949422723 245 LAQRFLDSGALIEKKVVAQTLFESVWIGWNEQTA-GLASSWWRDEILA 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 2.32e-24

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: 97.74  E-value: 2.32e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVgaMREPPSSSEFGFSRLGELEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAI--RRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  174 APHHPLAQeEEPLNRRVIKRYRAIVVGDTTYTGATAVPQL----LDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALraagLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 949422723  250 LDSGALIEKKVVAQTLFESVWIGWN-EQTAGLASSWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-148 4.73e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 79.68  E-value: 4.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 949422723  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKF-INGVLGGSWEALtQGRADI-IVG 148
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIAWNVA-NGQIDIaIVG 151
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 5.20e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 62.79  E-value: 5.20e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723    5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 17-260 9.16e-12

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: 64.37  E-value: 9.16e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  17 EGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKLHEgwENELV 96
Cdd:NF041036  15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLS 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  97 IGVDDTFPFSLLAPLIEAFYQHH-SVTRLKF--------INGVLGGSWE-ALTQGRADIIVGAMREPPsssefgfsrLGE 166
Cdd:NF041036  93 ICCTPTFGMAHLPGVLNRFMLRNaDVVDLKFlfhspaqaLEGIQNKEFDlAIIEHCADLDLGRFHTYP---------LPQ 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 167 LEQVFAVAPH-----HPLAQE---EEPL--------NRRVIKRYRAIVVGDttytgatavpqLLDEQEAITVFDFKTKLE 230
Cdd:NF041036 164 DELVFVSAPSlglptPNVTLErllELCLitrrdgcsSRDLLRRNLAEQGRD-----------LDDFRRVVVSDDLRLTIQ 232

                        250       260       270
                 ....*....|....*....|....*....|
gi 949422723 231 LQISGLGCGYLPRYLAQRFLDSGALIEKKV 260
Cdd:NF041036 233 TVLDGGGISFVSRSLVCEYLKNGQLREHYV 262
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-68 9.17e-03

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: 37.20  E-value: 9.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 949422723   11 LDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRsGHRAKFTRTGRMLLE 68
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLR 65
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 94-289 3.25e-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: 193.25  E-value: 3.25e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSsEFGFSRLGELEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPG-GVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 174 APHHPLAQEEEPLNRRVIKRYRAIVVGDTtytgATAVPQ----LLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADT----SRNLPPrssgLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 949422723 250 LDSGALIEKKVVAQTLFESVWIGWNEQTAGLASSWWRDEI 289
Cdd:cd08431  156 LASGELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 5.51e-55

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 180.52  E-value: 5.51e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   8 LMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  88 HEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSSEFGFSRLGEL 167
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 168 EQVFAVAPHHPLAQEEEPLNRRVIKRYRAIVVGDTTYTGATAVPQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQ 247
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 949422723 248 RFLDSGALIEKKVVAQTLFESVWIGWNEQTAGLASSW 284
Cdd:PRK11074 247 PLINSGKLVELTLENPFPDSPCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 3.55e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 153.87  E-value: 3.55e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQA 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGamREPPSSSEFGFSRL 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 165 GELEQVFAVAPHHPLAQEEEPLNrrvikryraivvgdttytgatavpqlldeqeaitvfDFKTKLELQISGLGCGYLPRY 244
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPLVN------------------------------------SLEALLAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 949422723 245 LAQRFLDSGALIEKKVVAQTLFESVWIGWNEQTA-GLASSWWRDEILA 291
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
18-307 1.16e-41

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 146.10  E-value: 1.16e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  18 GSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKLHEGWENELVI 97
Cdd:PRK10094  17 GSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQVNI 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  98 GVDD-TFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSSEFGFSRLGELEQVFAVAPH 176
Cdd:PRK10094  97 VINNlLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPLGSVQWRFVMAAD 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 177 HPLAQEEEPLNRRVIKRYRAIVVGDTTYTGATAVPQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFLDSGALI 256
Cdd:PRK10094 177 HPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLV 256

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 949422723 257 EKKVVAQTLFESVWIGWNEQTAGLASSWWRDEILANSA-IAGVYAKYDDGKS 307
Cdd:PRK10094 257 SRVIPTMRPPSPLSLAWRKFGSGKAVEDIVTLFTQRRPeISGFLEIFGNPRS 308
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-294 2.32e-24

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: 97.74  E-value: 2.32e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVgaMREPPSSSEFGFSRLGELEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAI--RRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  174 APHHPLAQeEEPLNRRVIKRYRAIVVGDTTYTGATAVPQL----LDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLAR-GEPVSLEDLADEPLILLPPGSGLRDLLDRALraagLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 949422723  250 LDSGALIEKKVVAQTLFESVWIGWN-EQTAGLASSWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-148 4.73e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 79.68  E-value: 4.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 949422723  85 IKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKF-INGVLGGSWEALtQGRADI-IVG 148
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIAWNVA-NGQIDIaIVG 151
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-270 6.98e-17

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 79.68  E-value: 6.98e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   8 LMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVheleKQAIK- 86
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI----SQALQa 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  87 LHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSseFGFSRLGE 166
Cdd:PRK15421  83 CNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSG--LHYSPMFD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 167 LEQVFAVAPHHPLAQEEE--------------PLNRRVIKRYRAIVvgdttyTGATAVPQLLDEQEAITVfdfktkLELQ 232
Cdd:PRK15421 161 YEVRLVLAPDHPLAAKTRitpedlasetlliyPVQRSRLDVWRHFL------QPAGVSPSLKSVDNTLLL------IQMV 228

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 949422723 233 ISGLGCGYLPRYLAQRFLDSGAliekkVVAQTLFESVW 270
Cdd:PRK15421 229 AARMGIAALPHWVVESFERQGL-----VVTKTLGEGLW 261
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-289 3.98e-13

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: 66.85  E-value: 3.98e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVgaMREPPSSSEFGFSRLGELEQVFAV 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAI--VALPVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 174 APHHPLAQEEE-PLNRrvIKRYRAIVVGDTTYTGATAVPQLLDE----QEAITVFDFKTKLELQISGLGCGYLPRYLAQR 248
Cdd:cd05466   79 PPDHPLAKRKSvTLAD--LADEPLILFERGSGLRRLLDRAFAEAgftpNIALEVDSLEAIKALVAAGLGIALLPESAVEE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 949422723 249 FLDSGaLIEKKVVAQTLFESVWIGWN-EQTAGLASSWWRDEI 289
Cdd:cd05466  157 LADGG-LVVLPLEDPPLSRTIGLVWRkGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 5.20e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 62.79  E-value: 5.20e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723    5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGR 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-184 2.28e-12

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 66.33  E-value: 2.28e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  13 ALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKLHEGwE 92
Cdd:PRK09906  11 AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE-D 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  93 NELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGraDIIVGAMREPPSSSEFGFSRLGELEQVFA 172
Cdd:PRK09906  90 RQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRG--ELDVGFMRHPVYSDEIDYLELLDEPLVVV 167

                        170
                 ....*....|..
gi 949422723 173 VAPHHPLAQEEE 184
Cdd:PRK09906 168 LPVDHPLAHEKE 179
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 17-260 9.16e-12

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: 64.37  E-value: 9.16e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  17 EGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKLHEgwENELV 96
Cdd:NF041036  15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLS 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  97 IGVDDTFPFSLLAPLIEAFYQHH-SVTRLKF--------INGVLGGSWE-ALTQGRADIIVGAMREPPsssefgfsrLGE 166
Cdd:NF041036  93 ICCTPTFGMAHLPGVLNRFMLRNaDVVDLKFlfhspaqaLEGIQNKEFDlAIIEHCADLDLGRFHTYP---------LPQ 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 167 LEQVFAVAPH-----HPLAQE---EEPL--------NRRVIKRYRAIVVGDttytgatavpqLLDEQEAITVFDFKTKLE 230
Cdd:NF041036 164 DELVFVSAPSlglptPNVTLErllELCLitrrdgcsSRDLLRRNLAEQGRD-----------LDDFRRVVVSDDLRLTIQ 232

                        250       260       270
                 ....*....|....*....|....*....|
gi 949422723 231 LQISGLGCGYLPRYLAQRFLDSGALIEKKV 260
Cdd:NF041036 233 TVLDGGGISFVSRSLVCEYLKNGQLREHYV 262
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 13-186 3.21e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 62.67  E-value: 3.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  13 ALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTG--------RML--LEKGREILHSVHELEK 82
Cdd:PRK11242  11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGevylryarRALqdLEAGRRAIHDVADLSR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  83 qaiklhegweNELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLkfingvlggSWEALTQGR------ADII-VGAMREPPS 155
Cdd:PRK11242  91 ----------GSLRLAMTPTFTAYLIGPLIDAFHARYPGITL---------TIREMSQERieallaDDELdVGIAFAPVH 151

                        170       180       190
                 ....*....|....*....|....*....|.
gi 949422723 156 SSEFGFSRLGELEQVFAVAPHHPLAQEEEPL 186
Cdd:PRK11242 152 SPEIEAQPLFTETLALVVGRHHPLAARRKAL 182
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
18-185 2.66e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 60.16  E-value: 2.66e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  18 GSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKLHEGWENELVI 97
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLRI 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  98 GVDDTFPFSLLAPLIEAFYQHH---SVtrlkfiNGVLGGSWEALTQGRADII--VGAMREppsSSEFGfSRLGELEQVFA 172
Cdd:PRK10632  97 GCSSTMAQNVLAGLTAKMLKEYpglSV------NLVTGIPAPDLIADGLDVVirVGALQD---SSLFS-RRLGAMPMVVC 166

                        170
                 ....*....|...
gi 949422723 173 VAPHHpLAQEEEP 185
Cdd:PRK10632 167 AAKSY-LAQYGTP 178
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 16-270 1.79e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 57.78  E-value: 1.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  16 KEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEkQAIKLHEGwenEL 95
Cdd:PRK10837  16 KSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE-QLFREDNG---AL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  96 VIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIivGAMREPPSSSEFGFSRLGELEQVFAVAP 175
Cdd:PRK10837  92 RIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDI--GLIEGPCHSPELISEPWLEDELVVFAAP 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 176 HHPLAQeeeplnrrvikryraivvGDTTYTGATAVPQLLDEQEAIT--VFD---------FKTKLELQIS---------G 235
Cdd:PRK10837 170 DSPLAR------------------GPVTLEQLAAAPWILRERGSGTreIVDylllshlprFELAMELGNSeaikhavrhG 231

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 949422723 236 LGCGYLPRYLAQRFLDSGALIEKKVVAQTLFESVW 270
Cdd:PRK10837 232 LGISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLY 266
PRK09801 PRK09801
LysR family transcriptional regulator;
3-126 2.16e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 54.66  E-value: 2.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   3 PLLDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEK 82
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 949422723  83 QAIKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKF 126
Cdd:PRK09801  86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF 129
PRK09791 PRK09791
LysR family transcriptional regulator;
16-181 2.92e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 50.92  E-value: 2.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  16 KEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSV---HELEKQAIKLHEGWE 92
Cdd:PRK09791  18 RQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELraaQEDIRQRQGQLAGQI 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  93 NelvIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSSEFGFSRLGELEQVFA 172
Cdd:PRK09791  98 N---IGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEKLLEKQFAVF 174


                 ....*....
gi 949422723 173 VAPHHPLAQ 181
Cdd:PRK09791 175 CRPGHPAIG 183
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 106-185 6.95e-07

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: 48.81  E-value: 6.95e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 106 SLLAPLIEAFYQHHSVTRLKfingVLGGSWEALT----QGRADIIVGAMREPPSSSEFGFSRLGELEQVFAVAPHHPLAQ 181
Cdd:cd08435   13 VLLPPAIARLLARHPRLTVR----VVEGTSDELLeglrAGELDLAIGRLADDEQPPDLASEELADEPLVVVARPGHPLAR 88


                 ....
gi 949422723 182 EEEP 185
Cdd:cd08435   89 RARL 92
PRK09986 PRK09986
LysR family transcriptional regulator;
13-183 7.62e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 49.72  E-value: 7.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  13 ALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKLHEGWE 92
Cdd:PRK09986  17 AVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  93 NELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSSEFGFSRLGelEQVFA 172
Cdd:PRK09986  97 GRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRRLH--ESAFA 174

                        170
                 ....*....|...
gi 949422723 173 VAPH--HPLAQEE 183
Cdd:PRK09986 175 VAVPeeHPLASRS 187
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-185 8.82e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 46.35  E-value: 8.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  30 TPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELeKQAIKLHEG-WENELVIGVDDTFPFSLL 108
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQL-RHTLDQQGPsLSGELSLFCSVTAAYSHL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 109 APLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSSeFGFSRLGELEQVFaVAPHHP-----LAQEE 183
Cdd:PRK11716  83 PPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPAS-VAFSPIDEIPLVL-IAPALPcpvrqQLSQE 160


                 ..
gi 949422723 184 EP 185
Cdd:PRK11716 161 KP 162
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
19-129 3.33e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 44.61  E-value: 3.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  19 SFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRML---LEKGREIL-HSVHELEKQAIklhegwENE 94
Cdd:PRK10086  30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVfwaLKSSLDTLnQEILDIKNQEL------SGT 103

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 949422723  95 LVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFING 129
Cdd:PRK10086 104 LTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTG 138
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-272 1.02e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 43.26  E-value: 1.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   9 MILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHR-AKFTRTGRMLLEKGREILHSVHELEKQAIKL 87
Cdd:PRK12679   8 IIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILNEASNVRRLADLF 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  88 HEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGA--MREPPSSSEFGFSRlg 165
Cdd:PRK12679  88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASerLSNDPQLVAFPWFR-- 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 166 eLEQVFAVAPHHPLAQEE----EPLNRRVIKRYRAIVVG----DTTYTGATAVPQL-LDEQEAITVfdfKTKLELqisGL 236
Cdd:PRK12679 166 -WHHSLLVPHDHPLTQITpltlESIAKWPLITYRQGITGrsriDDAFARKGLLADIvLSAQDSDVI---KTYVAL---GL 238

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 949422723 237 GCGYLPRYLAQRFLDSGALiekKVVAQTLFES--VWIG 272
Cdd:PRK12679 239 GIGLVAEQSSGEQEESNLI---RLDTRHLFDAntVWLG 273
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 105-183 1.42e-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: 42.17  E-value: 1.42e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 949422723 105 FSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSssEFGFSRLGELEQVFAVAPHHPLAQEE 183
Cdd:cd08441   12 FDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLP--GIAYEPLFDYEVVLVVAPDHPLAAKE 88
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 97-244 1.64e-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: 41.96  E-value: 1.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  97 IGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSSSEFGFSRLGELEQVFAVAPH 176
Cdd:cd08418    4 IGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVARKD 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 949422723 177 HPlaqeeeplnrrvikryraivvgdttYTGATAVPQLLDEQEAITVFDFKTKLELQISGLGCGYLPRY 244
Cdd:cd08418   84 HP-------------------------LQGARSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRV 126
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-119 1.73e-04

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 42.52  E-value: 1.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  19 SFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAikLHEGWENELVIG 98
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAKGALTVS 99

                         90       100
                 ....*....|....*....|.
gi 949422723  99 VDDTFPFSLLAPLIEAFYQHH 119
Cdd:PRK11139 100 LLPSFAIQWLVPRLSSFNEAH 120
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-183 1.93e-04

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: 41.82  E-value: 1.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPSssEFGFSRLGELEQVFAV 173
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPP--GLRSQPLFEDRFVCVA 78

                         90
                 ....*....|
gi 949422723 174 APHHPLAQEE 183
Cdd:cd08417   79 RKDHPLAGGP 88
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 34-184 2.15e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 42.32  E-value: 2.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  34 LSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSVHELEKQAIKLHEGWENELVIGVDDTF-PFslLAPLI 112
Cdd:PRK11151  32 LSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQQGETMSGPLHIGLIPTVgPY--LLPHI 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 113 -----EAF-----YQHHSVTrlkfiNGVLggswEALTQGRAD-IIVGAMREppsSSEFGFSRLGELEQVFAVAPHHPLAQ 181
Cdd:PRK11151 110 ipmlhQTFpklemYLHEAQT-----HQLL----AQLDSGKLDcAILALVKE---SEAFIEVPLFDEPMLLAVYEDHPWAN 177


                 ...
gi 949422723 182 EEE 184
Cdd:PRK11151 178 RDR 180
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 94-184 2.26e-04

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: 41.34  E-value: 2.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIivGAMREPPSSSEFGFSRLGELEQVFAV 173
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDV--GFVRPPPDPPGLASRPLLREPLVVAL 78

                         90
                 ....*....|.
gi 949422723 174 APHHPLAQEEE 184
Cdd:cd08414   79 PADHPLAARES 89
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 94-184 7.11e-04

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: 39.84  E-value: 7.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMREPPssSEFGFSRLGELEQVFAV 173
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLP--EDIAFEPLARLPPYVWL 78

                         90
                 ....*....|.
gi 949422723 174 APHHPLAQEEE 184
Cdd:cd08412   79 PADHPLAGKDE 89
PRK10341 PRK10341
transcriptional regulator TdcA;
8-159 7.78e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 40.62  E-value: 7.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   8 LMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKG----REILHSVHELEKQ 83
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSesitREMKNMVNEINGM 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  84 AiklhegweNELVIGVDDTFP----FSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAMR-------- 151
Cdd:PRK10341  92 S--------SEAVVDVSFGFPsligFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSnemklqdl 163

                        170
                 ....*....|
gi 949422723 152 --EPPSSSEF 159
Cdd:PRK10341 164 hvEPLFESEF 173
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 94-181 1.28e-03

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. 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: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 39.08  E-value: 1.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  94 ELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIivGAMREPPSSSEFGFSRLGELEQVFAV 173
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADL--GLASLPLDHPGLESEPLASGRAVCVL 78


                 ....*...
gi 949422723 174 APHHPLAQ 181
Cdd:cd08415   79 PPGHPLAR 86
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-67 1.44e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 39.57  E-value: 1.44e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 949422723  11 LDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGH-RAkfTRTGRMLL 67
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPcRP--TPAGQRLL 65
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 103-184 2.21e-03

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong 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: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 38.29  E-value: 2.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723 103 FPFSL---LAP-LIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADIIVGAmrEPPSSSEFGFSRLGELEQVFAVAPHHP 178
Cdd:cd08434    6 FLHSLgtsLVPdLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCS--PVPDEPDIEWIPLFTEELVLVVPKDHP 83


                 ....*.
gi 949422723 179 LAQEEE 184
Cdd:cd08434   84 LAGRDS 89
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 5-151 6.52e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 37.70  E-value: 6.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723   5 LDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGRMLLEKGREILHSvhELEKQA 84
Cdd:PRK15092  13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRF--NDEACS 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 949422723  85 IKLHEGWENELVIGV-DDT----FPFsLLAPlIEAFYQHHS----VTRLKFINgvlggswEALTQGRADIIVGAMR 151
Cdd:PRK15092  91 SLMYSNLQGVLTIGAsDDTadtiLPF-LLNR-VSSVYPKLAldvrVKRNAFMM-------EMLESQEVDLAVTTHR 157
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-181 7.79e-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: 36.81  E-value: 7.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949422723  95 LVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWEALTQGRADI-IVGAMREPPSssEFGFSRLGELEQVFAV 173
Cdd:cd08436    2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLaFVGLPERRPP--GLASRELAREPLVAVV 79


                 ....*...
gi 949422723 174 APHHPLAQ 181
Cdd:cd08436   80 APDHPLAG 87
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-68 9.17e-03

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: 37.20  E-value: 9.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 949422723   11 LDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRsGHRAKFTRTGRMLLE 68
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLR 65
 
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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