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Conserved domains on  [gi|896107602|ref|WP_049137393|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Enterobacter]

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 1.28e-61

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


The actual alignment was detected with superfamily member cd08431:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 195  Bit Score: 194.02  E-value: 1.28e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQlSDFGFARLGVLEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 174 APHHPLAQEPDPLNRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFIDSG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 896107602 254 ALVEKQVLAQSSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
rbcR super family cl31781
LysR transcriptional regulator; Provisional
 5-120 1.33e-16

LysR transcriptional regulator; Provisional


The actual alignment was detected with superfamily member CHL00180:

Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 78.52  E-value: 1.33e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   5 LDVLIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 896107602  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 1.28e-61

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 194.02  E-value: 1.28e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQlSDFGFARLGVLEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 174 APHHPLAQEPDPLNRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFIDSG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 896107602 254 ALVEKQVLAQSSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 4.90e-55

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 180.91  E-value: 4.90e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   8 LIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQLSDFGFARLGVL 167
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 168 EQVFAVAPHHPLAQEPDPLNRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQ 247
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 896107602 248 RFIDSGALVEKQvLAQSSNES-VWVGWNEQTAGLASAW 284
Cdd:PRK11074 247 PLINSGKLVELT-LENPFPDSpCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 3.09e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 146.16  E-value: 3.09e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   5 LDVLIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGalHEPPQLSDFGFARL 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 165 GVLEQVFAVAPHHPLAQepdplnrrvikgyRAIVVGDSSrpecavssqlldeqeaitvfdfkTKLELQISGLGCGYLPRY 244
Cdd:COG0583  161 GEERLVLVASPDHPLAR-------------RAPLVNSLE-----------------------ALLAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 896107602 245 LAQRFIDSGALVEKQVLAQSSNESVWVGWNEQTA-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 1.78e-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: 90.04  E-value: 1.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALhePPQLSDFGFARLGVLEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRG--PPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  174 APHHPLAQEpDPLNRRVIKGYRAIVVGDSSRP----ECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLARG-EPVSLEDLADEPLILLPPGSGLrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 896107602  250 IDSGALVEKQVLAQSSNESVWVGWN-EQTAGLASAWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-120 1.33e-16

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 78.52  E-value: 1.33e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   5 LDVLIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 896107602  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHS 120
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYP 122
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.31e-12

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 61.63  E-value: 1.31e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602    5 LDVLIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 17-260 2.63e-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: 60.14  E-value: 2.63e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  17 EGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQgwENELV 96
Cdd:NF041036  15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLS 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  97 IGVDDTFPFSLLTPLIEAFYQHH-SVTRLIFINGVLGGSWEALTQGRADIfvgALHEppQLSDFGFARLGVL-----EQV 170
Cdd:NF041036  93 ICCTPTFGMAHLPGVLNRFMLRNaDVVDLKFLFHSPAQALEGIQNKEFDL---AIIE--HCADLDLGRFHTYplpqdELV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 171 FAVAPHHPLAQEPDPLNRrvIKGYRAIvvgdsSRPECAVSSQLL------------DEQEAITVFDFKTKLELQISGLGC 238
Cdd:NF041036 168 FVSAPSLGLPTPNVTLER--LLELCLI-----TRRDGCSSRDLLrrnlaeqgrdldDFRRVVVSDDLRLTIQTVLDGGGI 240

                        250       260
                 ....*....|....*....|..
gi 896107602 239 GYLPRYLAQRFIDSGALVEKQV 260
Cdd:NF041036 241 SFVSRSLVCEYLKNGQLREHYV 262
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-85 1.05e-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: 39.90  E-value: 1.05e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 896107602   11 LDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNiQILDRSGHRARFTRTGQMLLEKGRDvlhtVRELEKQAV 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 1.28e-61

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 194.02  E-value: 1.28e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQlSDFGFARLGVLEQVFAV 173
Cdd:cd08431    1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-GGVKTRPLGEVEFVFAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 174 APHHPLAQEPDPLNRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFIDSG 253
Cdd:cd08431   80 APNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 896107602 254 ALVEKQVLAQSSNESVWVGWNEQTAGLASAWWRDEI 289
Cdd:cd08431  160 ELVEKALEDPRPPQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-284 4.90e-55

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 180.91  E-value: 4.90e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   8 LIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQLSDFGFARLGVL 167
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRFAFRDMGML 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 168 EQVFAVAPHHPLAQEPDPLNRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQ 247
Cdd:PRK11074 167 SWACVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAK 246

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 896107602 248 RFIDSGALVEKQvLAQSSNES-VWVGWNEQTAGLASAW 284
Cdd:PRK11074 247 PLINSGKLVELT-LENPFPDSpCCLTWQQNDMSPALAW 283
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-291 3.09e-42

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 146.16  E-value: 3.09e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   5 LDVLIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGalHEPPQLSDFGFARL 164
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIR--LGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 165 GVLEQVFAVAPHHPLAQepdplnrrvikgyRAIVVGDSSrpecavssqlldeqeaitvfdfkTKLELQISGLGCGYLPRY 244
Cdd:COG0583  161 GEERLVLVASPDHPLAR-------------RAPLVNSLE-----------------------ALLAAVAAGLGIALLPRF 204

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 896107602 245 LAQRFIDSGALVEKQVLAQSSNESVWVGWNEQTA-GLASAWWRDEILA 291
Cdd:COG0583  205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHlSPAVRAFLDFLRE 252
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
18-307 9.32e-39

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 138.79  E-value: 9.32e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  18 GSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQGWENELVI 97
Cdd:PRK10094  17 GSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQVNI 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  98 GVDD-TFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQLSDFGFARLGVLEQVFAVAPH 176
Cdd:PRK10094  97 VINNlLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPLGSVQWRFVMAAD 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 177 HPLAQEPDPLNRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFIDSGALV 256
Cdd:PRK10094 177 HPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLV 256

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 896107602 257 EKQVLAQSSNESVWVGWNEQTAGLASAWwrdeilansaIAAVYSQGSAEKS 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 1.78e-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: 90.04  E-value: 1.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALhePPQLSDFGFARLGVLEQVFAV 173
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRG--PPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  174 APHHPLAQEpDPLNRRVIKGYRAIVVGDSSRP----ECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:pfam03466  81 PPDHPLARG-EPVSLEDLADEPLILLPPGSGLrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 896107602  250 IDSGALVEKQVLAQSSNESVWVGWN-EQTAGLASAWWRDEILANSA 294
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFLREALA 205
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-120 1.33e-16

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 78.52  E-value: 1.33e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   5 LDVLIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 896107602  85 VKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHS 120
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYP 122
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-180 1.37e-14

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 73.13  E-value: 1.37e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   8 LIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTV-RELekQAVK 86
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIsQAL--QACN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  87 LHQgwENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFV-------GALHEPPQLsDF 159
Cdd:PRK15421  85 EPQ--QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMtsdilprSGLHYSPMF-DY 161

                        170       180
                 ....*....|....*....|.
gi 896107602 160 gfarlgvlEQVFAVAPHHPLA 180
Cdd:PRK15421 162 --------EVRLVLAPDHPLA 174
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.31e-12

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 61.63  E-value: 1.31e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602    5 LDVLIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-253 7.60e-11

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 60.31  E-value: 7.60e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALhePPQLSDFGFARLGVLEQVFAV 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVAL--PVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 174 APHHPLAQEPdPLNRRVIKGYRAIVVGDSSRP----ECAVSSQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRF 249
Cdd:cd05466   79 PPDHPLAKRK-SVTLADLADEPLILFERGSGLrrllDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157


                 ....
gi 896107602 250 IDSG 253
Cdd:cd05466  158 ADGG 161
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 17-260 2.63e-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: 60.14  E-value: 2.63e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  17 EGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQgwENELV 96
Cdd:NF041036  15 EGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLS 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  97 IGVDDTFPFSLLTPLIEAFYQHH-SVTRLIFINGVLGGSWEALTQGRADIfvgALHEppQLSDFGFARLGVL-----EQV 170
Cdd:NF041036  93 ICCTPTFGMAHLPGVLNRFMLRNaDVVDLKFLFHSPAQALEGIQNKEFDL---AIIE--HCADLDLGRFHTYplpqdELV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 171 FAVAPHHPLAQEPDPLNRrvIKGYRAIvvgdsSRPECAVSSQLL------------DEQEAITVFDFKTKLELQISGLGC 238
Cdd:NF041036 168 FVSAPSLGLPTPNVTLER--LLELCLI-----TRRDGCSSRDLLrrnlaeqgrdldDFRRVVVSDDLRLTIQTVLDGGGI 240

                        250       260
                 ....*....|....*....|..
gi 896107602 239 GYLPRYLAQRFIDSGALVEKQV 260
Cdd:NF041036 241 SFVSRSLVCEYLKNGQLREHYV 262
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 13-186 2.70e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 59.97  E-value: 2.70e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  13 ALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQML----------LEKGRDVLHTVRELEK 82
Cdd:PRK11242  11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYlryarralqdLEAGRRAIHDVADLSR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  83 qavklhqgweNELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIfingVLGGSWEALTQGRAD--IFVGALHEPPQLSDFG 160
Cdd:PRK11242  91 ----------GSLRLAMTPTFTAYLIGPLIDAFHARYPGITLT----IREMSQERIEALLADdeLDVGIAFAPVHSPEIE 156

                        170       180
                 ....*....|....*....|....*.
gi 896107602 161 FARLGVLEQVFAVAPHHPLAQEPDPL 186
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLAARRKAL 182
PRK09801 PRK09801
LysR family transcriptional regulator;
3-275 1.11e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 55.43  E-value: 1.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   3 PLLDVLIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEK 82
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  83 QAVKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFingVLGGSWEALTQGRADIFVGALHEPPqlsDFGFA 162
Cdd:PRK09801  86 DVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF---ELFDRQIDLVQDNIDLDIRINDEIP---DYYIA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 163 RLGVL-EQVFAVAPHHpLAQEPDPLNRRVIKGYRAIVVGD-------------SSRPECAVSSQLLDEQEAITvfdfktk 228
Cdd:PRK09801 160 HLLTKnKRILCAAPEY-LQKYPQPQSLQELSRHDCLVTKErdmthgiwelgngQEKKSVKVSGHLSSNSGEIV------- 231

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 896107602 229 LELQISGLGCGYLPRYLAQRFIDSGALVekQVL---AQSSNesVWVGWNE 275
Cdd:PRK09801 232 LQWALEGKGIMLRSEWDVLPFLESGKLV--QVLpeyAQSAN--IWAVYRE 277
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 13-182 4.83e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 53.23  E-value: 4.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  13 ALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQGwE 92
Cdd:PRK09906  11 AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE-D 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  93 NELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIfvgALHEPPQLSDfGFARLGVLEQ--V 170
Cdd:PRK09906  90 RQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDV---GFMRHPVYSD-EIDYLELLDEplV 165

                        170
                 ....*....|..
gi 896107602 171 FAVAPHHPLAQE 182
Cdd:PRK09906 166 VVLPVDHPLAHE 177
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
18-111 1.41e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 52.07  E-value: 1.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  18 GSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQGWENELVI 97
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLRI 96

                         90
                 ....*....|....
gi 896107602  98 GVDDTFPFSLLTPL 111
Cdd:PRK10632  97 GCSSTMAQNVLAGL 110
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 9-183 4.43e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 50.46  E-value: 4.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   9 IILDALE------KEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEk 82
Cdd:PRK10837   3 ITLRQLEvfaevlKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  83 qavKLHQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFV--GALHEP-----PQ 155
Cdd:PRK10837  82 ---QLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLieGPCHSPelisePW 158

                        170       180
                 ....*....|....*....|....*...
gi 896107602 156 LSDfgfarlgvlEQVFAVAPHHPLAQEP 183
Cdd:PRK10837 159 LED---------ELVVFAAPDSPLARGP 177
PRK09791 PRK09791
LysR family transcriptional regulator;
16-181 2.22e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 45.14  E-value: 2.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  16 KEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVR---ELEKQAVKLHQGWE 92
Cdd:PRK09791  18 RQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRaaqEDIRQRQGQLAGQI 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  93 NelvIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQLSDFGFARLgvLEQVFA 172
Cdd:PRK09791  98 N---IGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFTFEKL--LEKQFA 172

                        170
                 ....*....|.
gi 896107602 173 VA--PHHPLAQ 181
Cdd:PRK09791 173 VFcrPGHPAIG 183
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
19-67 1.96e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 42.30  E-value: 1.96e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 896107602  19 SFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLL 67
Cdd:PRK10086  30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF 78
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 106-198 2.00e-04

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: 41.49  E-value: 2.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 106 SLLTPLIEAFYQHHSvtRLIFinGVLGGSWEALT----QGRADIFVGALHEPPQLSDFGFARLGVLEQVFAVAPHHPLAQ 181
Cdd:cd08435   13 VLLPPAIARLLARHP--RLTV--RVVEGTSDELLeglrAGELDLAIGRLADDEQPPDLASEELADEPLVVVARPGHPLAR 88

                         90
                 ....*....|....*..
gi 896107602 182 EPdPLNRRVIKGYRAIV 198
Cdd:cd08435   89 RA-RLTLADLADYPWVL 104
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
20-165 2.42e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 41.93  E-value: 2.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  20 FAAASAKLYKTPSALSYTVQKLESDLNIQILDRsgHR--ARFTRTGQMLLEKGRDVLHTVReLEKQAVkLHQGWENELVI 97
Cdd:PRK03601  18 FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTR--HRnnIRLTAAGERLLPYAETLMNTWQ-AAKKEV-AHTSQHNELSI 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 896107602  98 GVDDTFPFSLLTPLIEAFYQHHSVTRLifingvlggswEALTQGRaDIFVGALH----------EPPQLSDFGFARLG 165
Cdd:PRK03601  94 GASASLWECMLTPWLGRLYQNQEALQF-----------EARIAQR-QSLVKQLHerqldllittEAPKMDEFSSQLLG 159
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 105-183 2.52e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 41.40  E-value: 2.52e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896107602 105 FSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGAlhEPPQLSDFGFARLGVLEQVFAVAPHHPLAQEP 183
Cdd:cd08441   12 FDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITS--DPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKE 88
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-282 3.28e-04

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 41.50  E-value: 3.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  11 LDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHrARFTRTGQMLLEKgrdvLHTVRELEKQAVKlHQG 90
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRH----LRQVALLEADLLS-TLP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  91 WENE----LVIGVDDTfpfSLLT---PLIEAFYQHHSVtRLIFINGVLGGSWEALTQGRADIFVGALHEPPQlsDFGFAR 163
Cdd:PRK13348  84 AERGspptLAIAVNAD---SLATwflPALAAVLAGERI-LLELIVDDQDHTFALLERGEVVGCVSTQPKPMR--GCLAEP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 164 LGVLEQVFAVAPHhpLAQE--PDPLNRRVIKGYRAIVVGDSSRPECAVSSQLLDEQEAIT-------VFDFKTKLELqis 234
Cdd:PRK13348 158 LGTMRYRCVASPA--FAARyfAQGLTRHSALKAPAVAFNRKDTLQDSFLEQLFGLPVGAYprhyvpsTHAHLAAIRH--- 232

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 896107602 235 GLGCGYLPRYLAQRFIDSGALVEkqvLAQSSNESV---WVGWNEQTAGLAS 282
Cdd:PRK13348 233 GLGYGMVPELLIGPLLAAGRLVD---LAPGHPVDValyWHHWEVESPTMEA 280
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-119 5.23e-04

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 40.98  E-value: 5.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  19 SFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQAvkLHQGWENELVIG 98
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAKGALTVS 99

                         90       100
                 ....*....|....*....|.
gi 896107602  99 VDDTFPFSLLTPLIEAFYQHH 119
Cdd:PRK11139 100 LLPSFAIQWLVPRLSSFNEAH 120
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 34-84 5.63e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 40.78  E-value: 5.63e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 896107602  34 LSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:PRK11151  32 LSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMA 82
PRK10341 PRK10341
transcriptional regulator TdcA;
8-159 6.22e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.00  E-value: 6.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   8 LIILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKgrdVLHTVRELeKQAVKL 87
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSR---SESITREM-KNMVNE 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 896107602  88 HQGWENELVIGVDDTFP----FSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQLSDF 159
Cdd:PRK10341  88 INGMSSEAVVDVSFGFPsligFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDL 163
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-185 9.57e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.19  E-value: 9.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  30 TPSALSYTVQKLESDLNIQILDRSGHRARFTRTGQMLLEKGRDVLHTVRELeKQAVKLHQG-WENELVIGVDDTFPFSLL 108
Cdd:PRK11716   4 SPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQL-RHTLDQQGPsLSGELSLFCSVTAAYSHL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 109 TPLIEAFYQHHsvtRLIFINGVLGGSWEALTQ---GRADIFVGALhePPQL-SDFGFARLGVLEQVFaVAPHHP-----L 179
Cdd:PRK11716  83 PPILDRFRAEH---PLVEIKLTTGDAADAVEKvqsGEADLAIAAK--PETLpASVAFSPIDEIPLVL-IAPALPcpvrqQ 156


                 ....*.
gi 896107602 180 AQEPDP 185
Cdd:PRK11716 157 LSQEKP 162
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-85 1.05e-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: 39.90  E-value: 1.05e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 896107602   11 LDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNiQILDRSGHRARFTRTGQMLLEKGRDvlhtVRELEKQAV 85
Cdd:TIGR03298   9 LAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLG-QPLLVRTQPCRATEAGQRLLRHARQ----VRLLEAELL 78
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-241 1.20e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.18  E-value: 1.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602   9 IILDALEKEGSFAAASAKLYKTPSALSYTVQKLESDLNIQILDRSGHRAR-FTRTGQMLLEKGRDVLHTVRELEKQAVKL 87
Cdd:PRK12679   8 IIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLF 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  88 HQGWENELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGA--LHEPPQLSDFGFARlg 165
Cdd:PRK12679  88 TNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASerLSNDPQLVAFPWFR-- 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 166 vLEQVFAVAPHHPLAQEP----DPLNRRVIKGYRAIVVGdSSRPECAVSSQLLDEQEAITVFD---FKTKLELqisGLGC 238
Cdd:PRK12679 166 -WHHSLLVPHDHPLTQITpltlESIAKWPLITYRQGITG-RSRIDDAFARKGLLADIVLSAQDsdvIKTYVAL---GLGI 240


                 ...
gi 896107602 239 GYL 241
Cdd:PRK12679 241 GLV 243
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 97-181 1.75e-03

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: 38.87  E-value: 1.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  97 IGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPQLSDFGFARLGVLEQVFAVAPH 176
Cdd:cd08418    4 IGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVARKD 83


                 ....*
gi 896107602 177 HPLAQ 181
Cdd:cd08418   84 HPLQG 88
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-197 2.54e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 38.80  E-value: 2.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  21 AAASAkLYKTPSALSYTVQKLESDLNIQILDRSGHRAR-FTRTGQMLLEKGRDVLHTVRELE---KQAVKLHQGwenELV 96
Cdd:PRK12684  21 EAAKA-LYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKrvgKEFAAQDQG---NLT 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  97 IGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVG--ALHEPPQLSDFGFARlgvLEQVFAVA 174
Cdd:PRK12684  97 IATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAteAIADYKELVSLPCYQ---WNHCVVVP 173

                        170       180
                 ....*....|....*....|...
gi 896107602 175 PHHPLAQEpDPLNRRVIKGYRAI 197
Cdd:PRK12684 174 PDHPLLER-KPLTLEDLAQYPLI 195
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 163-263 3.89e-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 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176161  Cd Length: 202  Bit Score: 37.88  E-value: 3.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 163 RLGVLEQVFAVAPH----HPLAQEPDPLNRRVIKGYRAivvGDSSRP-----ECAVSSQLLDEQEAITVFDFKTKLELQI 233
Cdd:cd08472   66 RLGELRMVTCASPAylarHGTPRHPEDLERHRAVGYFS---ARTGRVlpwefQRDGEEREVKLPSRVSVNDSEAYLAAAL 142

                         90       100       110
                 ....*....|....*....|....*....|
gi 896107602 234 SGLGCGYLPRYLAQRFIDSGALVEkqVLAQ 263
Cdd:cd08472  143 AGLGIIQVPRFMVRPHLASGRLVE--VLPD 170
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 21-184 4.34e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 38.05  E-value: 4.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  21 AAASAkLYKTPSALSYTVQKLESDLNIQILDRSGHR-ARFTRTGQMLLEKGRDVLHTVRELEKQAVKLHQGWENELVIGV 99
Cdd:PRK12682  21 EAAKA-LHTSQPGVSKAIIELEEELGIEIFIRHGKRlKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIAT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602 100 DDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGAlhepPQLSDF-GFARLGVLE--QVFAVAPH 176
Cdd:PRK12682 100 THTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT----ESLADDpDLATLPCYDwqHAVIVPPD 175


                 ....*...
gi 896107602 177 HPLAQEPD 184
Cdd:PRK12682 176 HPLAQEER 183
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 94-183 4.47e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 37.58  E-value: 4.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPqlSDFGFARLGVLEQVFAV 173
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELP--PGLRSQPLFEDRFVCVA 78

                         90
                 ....*....|
gi 896107602 174 APHHPLAQEP 183
Cdd:cd08417   79 RKDHPLAGGP 88
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 94-184 6.38e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 37.14  E-value: 6.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896107602  94 ELVIGVDDTFPFSLLTPLIEAFYQHHSVTRLIFINGVLGGSWEALTQGRADIFVGALHEPPqlSDFGFARLGVLEQVFAV 173
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLP--EDIAFEPLARLPPYVWL 78

                         90
                 ....*....|.
gi 896107602 174 APHHPLAQEPD 184
Cdd:cd08412   79 PADHPLAGKDE 89
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-84 9.94e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 37.18  E-value: 9.94e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 896107602  21 AAASAkLYKTPSALSYTVQKLESDLNIQILDRSG-HRARFTRTGQMLLEKGRDVLHTVRELEKQA 84
Cdd:PRK12681  21 ATAEG-LYTSQPGISKQVRMLEDELGIQIFARSGkHLTQVTPAGEEIIRIAREILSKVESIKSVA 84
 
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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