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Conserved domains on  [gi|2588820560|ref|WP_314602096|]
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LysR substrate-binding domain-containing protein [Enterobacter sichuanensis]

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 7.80e-63

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: 197.11  E-value: 7.80e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQlSDFGFARLGVLEQVFAV 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 174 APHHPLAQEPEPINRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFIDSG 253
Cdd:cd08431    80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2588820560 254 ALVEKQVLAQNSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431   160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
rbcR super family cl31781
LysR transcriptional regulator; Provisional
5-120 2.95e-16

LysR transcriptional regulator; Provisional


The actual alignment was detected with superfamily member CHL00180:

Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 77.37  E-value: 2.95e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   5 LDVLIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQA 84
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2588820560  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHS 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 7.80e-63

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: 197.11  E-value: 7.80e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQlSDFGFARLGVLEQVFAV 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 174 APHHPLAQEPEPINRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFIDSG 253
Cdd:cd08431    80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2588820560 254 ALVEKQVLAQNSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431   160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
8-284 5.84e-54

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 177.83  E-value: 5.84e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   8 LIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQAVKL 87
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQLSDFGFARLGVL 167
Cdd:PRK11074   87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 168 EQVFAVAPHHPLAQEPEPINRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQ 247
Cdd:PRK11074  167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246
                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 2588820560 248 RFIDSGALVEKQvLAQNSNES-VWVGWNEQTAGLASAW 284
Cdd:PRK11074  247 PLINSGKLVELT-LENPFPDSpCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 3.82e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 146.16  E-value: 3.82e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   5 LDVLIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQA 84
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGalHEPPQLSDFGFARL 164
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 165 GVLEQVFAVAPHHPLAQepepinrrvikgyRAIVVGDSsrpecavssqlldeqEAItvfdfktkLELQISGLGCGYLPRY 244
Cdd:COG0583   161 GEERLVLVASPDHPLAR-------------RAPLVNSL---------------EAL--------LAAVAAGLGIALLPRF 204
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 2588820560 245 LAQRFIDSGALVEKQVLAQNSNESVWVGWNEQTA-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 3.16e-21

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 89.27  E-value: 3.16e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALhePPQLSDFGFARLGVLEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRG--PPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 174 APHHPLAQEpEPINRRVIKGYRAIVVGDSSRP----ECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLARG-EPVSLEDLADEPLILLPPGSGLrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2588820560 250 IDSGALVEKQVLAQNSNESVWVGWN-EQTAGLASAWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
5-120 2.95e-16

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 77.37  E-value: 2.95e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   5 LDVLIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQA 84
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2588820560  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHS 120
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYP 122
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 9.22e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 62.02  E-value: 9.22e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   5 LDVLIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
17-260 1.46e-10

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: 60.91  E-value: 1.46e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  17 EGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQAVKLHQgwENELV 96
Cdd:NF041036   15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLS 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  97 IGVDDTFPFSLLTPLIEAFYQHH-SVTRLIF--------INGVLGGSWD-ALTQGRSDIFVGALHEPPQLSDfgfarlgv 166
Cdd:NF041036   93 ICCTPTFGMAHLPGVLNRFMLRNaDVVDLKFlfhspaqaLEGIQNKEFDlAIIEHCADLDLGRFHTYPLPQD-------- 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 167 lEQVFAVAPHHPLAQEPEPINRrvIKGYRAIvvgdsSRPECAVSSQLL------------DEQEAITVFDFKTKLELQIS 234
Cdd:NF041036  165 -ELVFVSAPSLGLPTPNVTLER--LLELCLI-----TRRDGCSSRDLLrrnlaeqgrdldDFRRVVVSDDLRLTIQTVLD 236
                         250       260
                  ....*....|....*....|....*.
gi 2588820560 235 GLGCGYLPRYLAQRFIDSGALVEKQV 260
Cdd:NF041036  237 GGGISFVSRSLVCEYLKNGQLREHYV 262
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
11-85 3.39e-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: 41.44  E-value: 3.39e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2588820560  11 LDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNiQILDRSGHRARFTRTGQMLLEKGREvlhtVRELEKQAV 85
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLG-QPLLVRTQPCRATEAGQRLLRHARQ----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 7.80e-63

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: 197.11  E-value: 7.80e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQlSDFGFARLGVLEQVFAV 173
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 174 APHHPLAQEPEPINRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFIDSG 253
Cdd:cd08431    80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2588820560 254 ALVEKQVLAQNSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431   160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
8-284 5.84e-54

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 177.83  E-value: 5.84e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   8 LIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQAVKL 87
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQLSDFGFARLGVL 167
Cdd:PRK11074   87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 168 EQVFAVAPHHPLAQEPEPINRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQ 247
Cdd:PRK11074  167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246
                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 2588820560 248 RFIDSGALVEKQvLAQNSNES-VWVGWNEQTAGLASAW 284
Cdd:PRK11074  247 PLINSGKLVELT-LENPFPDSpCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 3.82e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 146.16  E-value: 3.82e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   5 LDVLIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQA 84
Cdd:COG0583     3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGalHEPPQLSDFGFARL 164
Cdd:COG0583    83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 165 GVLEQVFAVAPHHPLAQepepinrrvikgyRAIVVGDSsrpecavssqlldeqEAItvfdfktkLELQISGLGCGYLPRY 244
Cdd:COG0583   161 GEERLVLVASPDHPLAR-------------RAPLVNSL---------------EAL--------LAAVAAGLGIALLPRF 204
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 2588820560 245 LAQRFIDSGALVEKQVLAQNSNESVWVGWNEQTA-GLASAWWRDEILA 291
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
18-307 1.21e-37

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 135.70  E-value: 1.21e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  18 GSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQAVKLHQGWENELVI 97
Cdd:PRK10094   17 GSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQVNI 96
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  98 GVDD-TFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQLSDFGFARLGVLEQVFAVAPH 176
Cdd:PRK10094   97 VINNlLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPLGSVQWRFVMAAD 176
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 177 HPLAQEPEPINRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFIDSGALV 256
Cdd:PRK10094  177 HPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLV 256
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2588820560 257 EKQVLAQNSNESVWVGWNEQTAGLASAWwrdeilansaIAAVYAQGSVEKS 307
Cdd:PRK10094  257 SRVIPTMRPPSPLSLAWRKFGSGKAVED----------IVTLFTQRRPEIS 297
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
94-294 3.16e-21

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 89.27  E-value: 3.16e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALhePPQLSDFGFARLGVLEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRG--PPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 174 APHHPLAQEpEPINRRVIKGYRAIVVGDSSRP----ECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLARG-EPVSLEDLADEPLILLPPGSGLrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2588820560 250 IDSGALVEKQVLAQNSNESVWVGWN-EQTAGLASAWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
5-120 2.95e-16

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 77.37  E-value: 2.95e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   5 LDVLIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQA 84
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2588820560  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHS 120
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYP 122
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-270 1.88e-14

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 72.74  E-value: 1.88e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   8 LIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTV-RELekQAVK 86
Cdd:PRK15421    7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIsQAL--QACN 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  87 LHQgwENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFV-------GALHEPPQLsDF 159
Cdd:PRK15421   85 EPQ--QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMtsdilprSGLHYSPMF-DY 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 160 gfarlgvlEQVFAVAPHHPLAQE----PE----------PINRRVIKGYRAIVVGDSSRPEC-AVSSQLLdeqeaitvfd 224
Cdd:PRK15421  162 --------EVRLVLAPDHPLAAKtritPEdlasetlliyPVQRSRLDVWRHFLQPAGVSPSLkSVDNTLL---------- 223
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 2588820560 225 fktKLELQISGLGCGYLPRYLAQRFIDSGALVEKQVlaqnsNESVW 270
Cdd:PRK15421  224 ---LIQMVAARMGIAALPHWVVESFERQGLVVTKTL-----GEGLW 261
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 9.22e-13

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 62.02  E-value: 9.22e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   5 LDVLIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
17-260 1.46e-10

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: 60.91  E-value: 1.46e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  17 EGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQAVKLHQgwENELV 96
Cdd:NF041036   15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLS 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  97 IGVDDTFPFSLLTPLIEAFYQHH-SVTRLIF--------INGVLGGSWD-ALTQGRSDIFVGALHEPPQLSDfgfarlgv 166
Cdd:NF041036   93 ICCTPTFGMAHLPGVLNRFMLRNaDVVDLKFlfhspaqaLEGIQNKEFDlAIIEHCADLDLGRFHTYPLPQD-------- 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 167 lEQVFAVAPHHPLAQEPEPINRrvIKGYRAIvvgdsSRPECAVSSQLL------------DEQEAITVFDFKTKLELQIS 234
Cdd:NF041036  165 -ELVFVSAPSLGLPTPNVTLER--LLELCLI-----TRRDGCSSRDLLrrnlaeqgrdldDFRRVVVSDDLRLTIQTVLD 236
                         250       260
                  ....*....|....*....|....*.
gi 2588820560 235 GLGCGYLPRYLAQRFIDSGALVEKQV 260
Cdd:NF041036  237 GGGISFVSRSLVCEYLKNGQLREHYV 262
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
94-253 2.27e-10

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: 59.15  E-value: 2.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALhePPQLSDFGFARLGVLEQVFAV 173
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVAL--PVDDPGLESEPLFEEPLVLVV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 174 APHHPLAQEPEpINRRVIKGYRAIVVGDSSRP----ECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:cd05466    79 PPDHPLAKRKS-VTLADLADEPLILFERGSGLrrllDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157

                  ....
gi 2588820560 250 IDSG 253
Cdd:cd05466   158 ADGG 161
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
13-186 2.44e-09

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 57.27  E-value: 2.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  13 ALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQML----------LEKGREVLHTVRELEK 82
Cdd:PRK11242   11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYlryarralqdLEAGRRAIHDVADLSR 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  83 qavklhqgweNELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLifingvlggSWDALTQGR------SDIF-VGALHEPPQ 155
Cdd:PRK11242   91 ----------GSLRLAMTPTFTAYLIGPLIDAFHARYPGITL---------TIREMSQERieallaDDELdVGIAFAPVH 151
                         170       180       190
                  ....*....|....*....|....*....|.
gi 2588820560 156 LSDFGFARLGVLEQVFAVAPHHPLAQEPEPI 186
Cdd:PRK11242  152 SPEIEAQPLFTETLALVVGRHHPLAARRKAL 182
PRK09801 PRK09801
LysR family transcriptional regulator;
3-275 6.54e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 56.20  E-value: 6.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   3 PLLDVLIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEK 82
Cdd:PRK09801    6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  83 QAVKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFingVLGGSWDALTQGRSDIFVGALHEPPqlsDFGFA 162
Cdd:PRK09801   86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF---ELFDRQIDLVQDNIDLDIRINDEIP---DYYIA 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 163 RLGVL-EQVFAVAPHHpLAQEPEPINRRVIKGYRAIVVGD-------------SSRPECAVSSQLLDEQEAITvfdfktk 228
Cdd:PRK09801  160 HLLTKnKRILCAAPEY-LQKYPQPQSLQELSRHDCLVTKErdmthgiwelgngQEKKSVKVSGHLSSNSGEIV------- 231
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 2588820560 229 LELQISGLGCGYLPRYLAQRFIDSGALVekQVL---AQNSNesVWVGWNE 275
Cdd:PRK09801  232 LQWALEGKGIMLRSEWDVLPFLESGKLV--QVLpeyAQSAN--IWAVYRE 277
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
18-111 1.33e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 52.07  E-value: 1.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  18 GSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQAVKLHQGWENELVI 97
Cdd:PRK10632   17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLRI 96
                          90
                  ....*....|....
gi 2588820560  98 GVDDTFPFSLLTPL 111
Cdd:PRK10632   97 GCSSTMAQNVLAGL 110
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
13-184 3.46e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 50.92  E-value: 3.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  13 ALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQAVKLHQGwE 92
Cdd:PRK09906   11 AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE-D 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  93 NELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIfvgALHEPPQLSDfGFARLGVLEQ--V 170
Cdd:PRK09906   90 RQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDV---GFMRHPVYSD-EIDYLELLDEplV 165
                         170
                  ....*....|....
gi 2588820560 171 FAVAPHHPLAQEPE 184
Cdd:PRK09906  166 VVLPVDHPLAHEKE 179
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
9-183 6.93e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 49.69  E-value: 6.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   9 IILDALE------KEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEk 82
Cdd:PRK10837    3 ITLRQLEvfaevlKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE- 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  83 qavKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFingVLGGSWD---ALTQGRSDIFV--GALHEP---- 153
Cdd:PRK10837   82 ---QLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLEL---SVGNSQDvinAVLDFRVDIGLieGPCHSPelis 155
                         170       180       190
                  ....*....|....*....|....*....|.
gi 2588820560 154 -PQLSDfgfarlgvlEQVFAVAPHHPLAQEP 183
Cdd:PRK10837  156 ePWLED---------ELVVFAAPDSPLARGP 177
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
9-185 2.36e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 48.12  E-value: 2.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   9 IILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRArftrTGqmLLEKGREVLHTV----------R 78
Cdd:PRK12683    8 IIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRL----TG--LTEPGKELLQIVermlldaenlR 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  79 ELEKQAVKLHQGwenELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVG--ALHEPPQL 156
Cdd:PRK12683   82 RLAEQFADRDSG---HLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIAteALDREPDL 158
                         170       180
                  ....*....|....*....|....*....
gi 2588820560 157 SDFGFARLgvlEQVFAVAPHHPLAQEPEP 185
Cdd:PRK12683  159 VSFPYYSW---HHVVVVPKGHPLTGRENL 184
PRK09791 PRK09791
LysR family transcriptional regulator;
16-181 2.28e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 45.14  E-value: 2.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  16 KEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGR---EVLHTVRELEKQAVKLHQGWE 92
Cdd:PRK09791   18 RQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASlilEELRAAQEDIRQRQGQLAGQI 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  93 NelvIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQLSDFGFARLgvLEQVFA 172
Cdd:PRK09791   98 N---IGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEKL--LEKQFA 172
                         170
                  ....*....|.
gi 2588820560 173 VA--PHHPLAQ 181
Cdd:PRK09791  173 VFcrPGHPAIG 183
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
106-185 2.45e-05

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: 44.19  E-value: 2.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 106 SLLTPLIEAFYQHHSvtRLIFinGVLGGSWDALT----QGRSDIFVGALHEPPQLSDFGFARLGVLEQVFAVAPHHPLAQ 181
Cdd:cd08435    13 VLLPPAIARLLARHP--RLTV--RVVEGTSDELLeglrAGELDLAIGRLADDEQPPDLASEELADEPLVVVARPGHPLAR 88

                  ....
gi 2588820560 182 EPEP 185
Cdd:cd08435    89 RARL 92
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
19-119 1.65e-04

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 42.52  E-value: 1.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  19 SFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQAvkLHQGWENELVIG 98
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAKGALTVS 99
                          90       100
                  ....*....|....*....|.
gi 2588820560  99 VDDTFPFSLLTPLIEAFYQHH 119
Cdd:PRK11139  100 LLPSFAIQWLVPRLSSFNEAH 120
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
19-67 2.09e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 42.30  E-value: 2.09e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2588820560  19 SFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLL 67
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF 78
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
11-85 3.39e-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: 41.44  E-value: 3.39e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2588820560  11 LDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNiQILDRSGHRARFTRTGQMLLEKGREvlhtVRELEKQAV 85
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLG-QPLLVRTQPCRATEAGQRLLRHARQ----VRLLEAELL 78
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
34-84 4.58e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 41.17  E-value: 4.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2588820560  34 LSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELEKQA 84
Cdd:PRK11151   32 LSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
97-181 6.37e-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: 40.03  E-value: 6.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  97 IGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQLSDFGFARLGVLEQVFAVAPH 176
Cdd:cd08418     4 IGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVARKD 83

                  ....*
gi 2588820560 177 HPLAQ 181
Cdd:cd08418    84 HPLQG 88
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-241 7.65e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.56  E-value: 7.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   9 IILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRAR-FTRTGQMLLEKGREVLHTVRELEKQAVKL 87
Cdd:PRK12679    8 IIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLF 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGA--LHEPPQLSDFGFARlg 165
Cdd:PRK12679   88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASerLSNDPQLVAFPWFR-- 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 166 vLEQVFAVAPHHPLAQEP----EPINRRVIKGYRAIVVGdSSRPECAVSSQLLDEQEAITVFD---FKTKLELqisGLGC 238
Cdd:PRK12679  166 -WHHSLLVPHDHPLTQITpltlESIAKWPLITYRQGITG-RSRIDDAFARKGLLADIVLSAQDsdvIKTYVAL---GLGI 240

                  ...
gi 2588820560 239 GYL 241
Cdd:PRK12679  241 GLV 243
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-185 8.98e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.19  E-value: 8.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  30 TPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGREVLHTVRELeKQAVKLHQG-WENELVIGVDDTFPFSLL 108
Cdd:PRK11716    4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQL-RHTLDQQGPsLSGELSLFCSVTAAYSHL 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 109 TPLIEAFYQHHsvtRLIFINGVLGGSWDALTQ---GRSDIFVGALhePPQL-SDFGFARLGVLEQVFaVAPHHP-----L 179
Cdd:PRK11716   83 PPILDRFRAEH---PLVEIKLTTGDAADAVEKvqsGEADLAIAAK--PETLpASVAFSPIDEIPLVL-IAPALPcpvrqQ 156

                  ....*.
gi 2588820560 180 AQEPEP 185
Cdd:PRK11716  157 LSQEKP 162
PRK10341 PRK10341
transcriptional regulator TdcA;
8-159 1.13e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 40.23  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560   8 LIILDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKgreVLHTVRELeKQAVKL 87
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSR---SESITREM-KNMVNE 87
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2588820560  88 HQGWENELVIGVDDTFP----FSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGALHEPPQLSDF 159
Cdd:PRK10341   88 INGMSSEAVVDVSFGFPsligFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDL 163
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
105-183 1.30e-03

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: 39.09  E-value: 1.30e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2588820560 105 FSLLTPLIEAFYQHHSVTRLIFINGVLGGSWDALTQGRSDIFVGAlhEPPQLSDFGFARLGVLEQVFAVAPHHPLAQEP 183
Cdd:cd08441    12 FDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITS--DPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKE 88
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-67 1.41e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 39.57  E-value: 1.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2588820560  11 LDALEKEGSFAAASAKLFKTPSALSYTVQKLESDLNIQILDRSGHrARFTRTGQMLL 67
Cdd:PRK13348   10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLL 65
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
20-124 2.78e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 38.84  E-value: 2.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560  20 FAAASAKLFKTPSALSYTVQKLESDLNIQILDRsgHR--ARFTRTGQMLLEKGrEVLHTVRELEKQAVkLHQGWENELVI 97
Cdd:PRK03601   18 FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTR--HRnnIRLTAAGERLLPYA-ETLMNTWQAAKKEV-AHTSQHNELSI 93
                          90       100
                  ....*....|....*....|....*..
gi 2588820560  98 GVDDTFPFSLLTPLIEAFYQHHSVTRL 124
Cdd:PRK03601   94 GASASLWECMLTPWLGRLYQNQEALQF 120
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
152-273 5.45e-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: 37.15  E-value: 5.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2588820560 152 EPPQLSDFGFARLGVLEQVFAVAPHHpLAQEPEPINRRVIKGYRAIVVGDSSRPecaVSSQLLDEQEAITVFDFKTKLEL 231
Cdd:cd08475    56 ELADSTGLVARRLGTQRMVLCASPAY-LARHGTPRTLEDLAEHQCIAYGRGGQP---LPWRLADEQGRLVRFRPAPRLQF 131
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2588820560 232 Q---------ISGLGCGYLPRYLAQRFIDSGALVEkqVLAQNSNES--VWVGW 273
Cdd:cd08475   132 DdgeaiadaaLAGLGIAQLPTWLVADHLQRGELVE--VLPELAPEGlpIHAVW 182
 
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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