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Conserved domains on  [gi|1070914336|gb|AOS82103|]
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LysR family transcriptional regulator [Hydrogenophaga sp. PBC]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

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

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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
102-300 9.97e-60

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


The actual alignment was detected with superfamily member cd08431:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 195  Bit Score: 189.40  E-value: 9.97e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 102 QFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVGPGLHAAPLGTAGFVYAVA 181
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 182 PHHPLARLEGTLTEEHMRQHRAVAVADSTQRGRGVSHNLLPGQDVLTVPTMQHKLEAQLRGLGAGFLPTPLAQPYINAGR 261
Cdd:cd08431    81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160
                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1070914336 262 LVVKPVQQGERSFRVAYAWRqtrpSVNNARALHWWLDHL 300
Cdd:cd08431   161 LVEKALEDPRPPQELFLAWR----KDQRGKALAWFVQRL 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
16-72 4.34e-14

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 65.87  E-value: 4.34e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1070914336  16 LALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGE 72
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
102-300 9.97e-60

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


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 189.40  E-value: 9.97e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 102 QFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVGPGLHAAPLGTAGFVYAVA 181
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 182 PHHPLARLEGTLTEEHMRQHRAVAVADSTQRGRGVSHNLLPGQDVLTVPTMQHKLEAQLRGLGAGFLPTPLAQPYINAGR 261
Cdd:cd08431    81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160
                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1070914336 262 LVVKPVQQGERSFRVAYAWRqtrpSVNNARALHWWLDHL 300
Cdd:cd08431   161 LVEKALEDPRPPQELFLAWR----KDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
11-300 3.76e-56

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 183.99  E-value: 3.76e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  11 LSAENLALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVAR 90
Cdd:PRK11074    2 WSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  91 RVKRVATGWEPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALG-VAADSVGPGLHAA 169
Cdd:PRK11074   82 QCQQVANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGaTRAIPVGGRFAFR 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 170 PLGTAGFVYAVAPHHPLARLEGTLTEEHMRQHRAVAVADsTQRGRGVSHN-LLPGQDVLTVPTMQHKLEAQLRGLGAGFL 248
Cdd:PRK11074  162 DMGMLSWACVVSSDHPLASMDGPLSDDELRPYPSLCLED-TSRTLPKRITwLLDNQRRLVVPDWESAINCLSAGLCVGMV 240
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1070914336 249 PTPLAQPYINAGRLVVKPVQQGERSFRVAYAWRQTrpsvNNARALHWWLDHL 300
Cdd:PRK11074  241 PTHFAKPLINSGKLVELTLENPFPDSPCCLTWQQN----DMSPALAWLLDYL 288
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
16-306 3.93e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.77  E-value: 3.93e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  16 LALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVARRVKRV 95
Cdd:COG0583     6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  96 ATGWEPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSvGPGLHAAPLGTAG 175
Cdd:COG0583    86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-DPGLVARPLGEER 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 176 FVYAVAPHHPLARLEgtlteehmrqhravavadstqrgrgvshnllpgqdvLTVPTMQHKLEAQLRGLGAGFLPTPLAQP 255
Cdd:COG0583   165 LVLVASPDHPLARRA------------------------------------PLVNSLEALLAAVAAGLGIALLPRFLAAD 208
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1070914336 256 YINAGRLVVKPVQQGERSFRVAYAWRQTRPsvnNARALHWWLDHLKHAGTR 306
Cdd:COG0583   209 ELAAGRLVALPLPDPPPPRPLYLVWRRRRH---LSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
102-303 1.22e-16

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: 76.94  E-value: 1.22e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 102 QFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALgVAADSVGPGLHAAPLGTAGFVYAVA 181
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAI-RRGPPDDPGLEARPLGEEPLVLVAP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 182 PHHPLARLEgTLTEEHMRQHRAVAVADSTQRGRGVSHNL----LPGQDVLTVPTMQHKLEAQLRGLGAGFLPTPLAQPYI 257
Cdd:pfam03466  82 PDHPLARGE-PVSLEDLADEPLILLPPGSGLRDLLDRALraagLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1070914336 258 NAGRLVVKPVQQGERSFRVAYAWRQTRPsvnNARALHWWLDHLKHA 303
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRP---LSPAVRAFIEFLREA 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
16-72 4.34e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 65.87  E-value: 4.34e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1070914336  16 LALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGE 72
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
20-77 5.02e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 59.63  E-value: 5.02e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1070914336  20 EAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRA 77
Cdd:PRK10086   23 EVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
16-263 1.61e-08

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: 54.92  E-value: 1.61e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  16 LALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSaRRAMLTSAGEELLRAGEFL-LNEFDAVARRVKR 94
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQVrLLEAELLAELPGL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  95 VATGWEPqFTIA--ADALisrATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVgPGLHAAPLG 172
Cdd:TIGR03298  85 APGAPTR-LTIAvnADSL---ATWFLPALAPVLAREGVLLDLVVEDQDHTAELLRSGEVLGAVTTEAKPV-PGCRVVPLG 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 173 TAGFVYAVAP-----HHPLARLEGTLTeehmrqhRAVAVA----DSTQrGRGVSHNL-LPGQ-DVLTVPTMQHKLEAQLR 241
Cdd:TIGR03298 160 AMRYLAVASPafaarYFPDGVTAAALA-------RAPVIVfnrkDDLQ-DRFLRRLFgLPVSpPRHYVPSSEGFVDAARA 231
                         250       260
                  ....*....|....*....|..
gi 1070914336 242 GLGAGFLPTPLAQPYINAGRLV 263
Cdd:TIGR03298 232 GLGWGMVPELQAEPHLAAGRLV 253
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
1-91 6.49e-06

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 44.43  E-value: 6.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336   1 MPPPISARSALSAEN--------LALVEAVARLGSMAAASRELGMvpsalTYR-----IRQIEDALDVLLFDRSA--RR- 64
Cdd:COG2005     1 MSMKLRLKLWLELDGgvflgpgrIELLEAIDETGSISAAAKAMGM-----SYKrawdlIDAMNNLLGEPLVERQTggKGg 75
                          90       100
                  ....*....|....*....|....*....
gi 1070914336  65 --AMLTSAGEELLRAGEFLLNEFDAVARR 91
Cdd:COG2005    76 ggARLTPEGRRLLALYRRLEAEAQRALAA 104
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
102-300 9.97e-60

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


Pssm-ID: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 189.40  E-value: 9.97e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 102 QFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVGPGLHAAPLGTAGFVYAVA 181
Cdd:cd08431     1 ELRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 182 PHHPLARLEGTLTEEHMRQHRAVAVADSTQRGRGVSHNLLPGQDVLTVPTMQHKLEAQLRGLGAGFLPTPLAQPYINAGR 261
Cdd:cd08431    81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160
                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1070914336 262 LVVKPVQQGERSFRVAYAWRqtrpSVNNARALHWWLDHL 300
Cdd:cd08431   161 LVEKALEDPRPPQELFLAWR----KDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
11-300 3.76e-56

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 183.99  E-value: 3.76e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  11 LSAENLALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVAR 90
Cdd:PRK11074    2 WSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRR 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  91 RVKRVATGWEPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALG-VAADSVGPGLHAA 169
Cdd:PRK11074   82 QCQQVANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGaTRAIPVGGRFAFR 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 170 PLGTAGFVYAVAPHHPLARLEGTLTEEHMRQHRAVAVADsTQRGRGVSHN-LLPGQDVLTVPTMQHKLEAQLRGLGAGFL 248
Cdd:PRK11074  162 DMGMLSWACVVSSDHPLASMDGPLSDDELRPYPSLCLED-TSRTLPKRITwLLDNQRRLVVPDWESAINCLSAGLCVGMV 240
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1070914336 249 PTPLAQPYINAGRLVVKPVQQGERSFRVAYAWRQTrpsvNNARALHWWLDHL 300
Cdd:PRK11074  241 PTHFAKPLINSGKLVELTLENPFPDSPCCLTWQQN----DMSPALAWLLDYL 288
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
11-282 7.13e-46

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 157.66  E-value: 7.13e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  11 LSAENLALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVAR 90
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  91 RVKRVATGWEPQFTIAADALI-SRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAA-DSVGPGLHA 168
Cdd:PRK10094   82 ELQQVNDGVERQVNIVINNLLyNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGtEALANTFSL 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 169 APLGTAGFVYAVAPHHPLARLEGTLTEEHMRQHRAVAVADSTQRGRGVSHNLLPGQDVLTVPTMQHKLEAQLRGLGAGFL 248
Cdd:PRK10094  162 DPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFL 241
                         250       260       270
                  ....*....|....*....|....*....|....
gi 1070914336 249 PTPLAQPYINAGRLVVKPVQQGERSFRVAYAWRQ 282
Cdd:PRK10094  242 PKSLCQSMIDNQQLVSRVIPTMRPPSPLSLAWRK 275
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
16-306 3.93e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.77  E-value: 3.93e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  16 LALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVARRVKRV 95
Cdd:COG0583     6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRAL 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  96 ATGWEPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSvGPGLHAAPLGTAG 175
Cdd:COG0583    86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-DPGLVARPLGEER 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 176 FVYAVAPHHPLARLEgtlteehmrqhravavadstqrgrgvshnllpgqdvLTVPTMQHKLEAQLRGLGAGFLPTPLAQP 255
Cdd:COG0583   165 LVLVASPDHPLARRA------------------------------------PLVNSLEALLAAVAAGLGIALLPRFLAAD 208
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1070914336 256 YINAGRLVVKPVQQGERSFRVAYAWRQTRPsvnNARALHWWLDHLKHAGTR 306
Cdd:COG0583   209 ELAAGRLVALPLPDPPPPRPLYLVWRRRRH---LSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
102-303 1.22e-16

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: 76.94  E-value: 1.22e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 102 QFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALgVAADSVGPGLHAAPLGTAGFVYAVA 181
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAI-RRGPPDDPGLEARPLGEEPLVLVAP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 182 PHHPLARLEgTLTEEHMRQHRAVAVADSTQRGRGVSHNL----LPGQDVLTVPTMQHKLEAQLRGLGAGFLPTPLAQPYI 257
Cdd:pfam03466  82 PDHPLARGE-PVSLEDLADEPLILLPPGSGLRDLLDRALraagLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1070914336 258 NAGRLVVKPVQQGERSFRVAYAWRQTRPsvnNARALHWWLDHLKHA 303
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRP---LSPAVRAFIEFLREA 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
16-72 4.34e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 65.87  E-value: 4.34e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1070914336  16 LALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGE 72
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
13-263 2.74e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.07  E-value: 2.74e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  13 AENLAlveAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSaRRAMLTSAGEELLRAGEfLLNEFDAVARRV 92
Cdd:PRK13348    7 LEALA---AVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLR-QVALLEADLLST 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  93 KRVATGWEPQFTIAADAlISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVgPGLHAAPLG 172
Cdd:PRK13348   82 LPAERGSPPTLAIAVNA-DSLATWFLPALAAVLAGERILLELIVDDQDHTFALLERGEVVGCVSTQPKPM-RGCLAEPLG 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 173 TAGFVYAVAPHHPLARLEGTLTEEHMRQHRAVAVADST-------QRGRGVSHNLLPGQdvlTVPTMQHKLEAQLRGLGA 245
Cdd:PRK13348  160 TMRYRCVASPAFAARYFAQGLTRHSALKAPAVAFNRKDtlqdsflEQLFGLPVGAYPRH---YVPSTHAHLAAIRHGLGY 236
                         250
                  ....*....|....*...
gi 1070914336 246 GFLPTPLAQPYINAGRLV 263
Cdd:PRK13348  237 GMVPELLIGPLLAAGRLV 254
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
104-300 8.49e-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: 8.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 104 TIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALgVAADSVGPGLHAAPLGTAGFVYAVAPH 183
Cdd:cd05466     3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAI-VALPVDDPGLESEPLFEEPLVLVVPPD 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 184 HPLARLEgTLTEEHMRQHRAVAVADSTQRGRGV----SHNLLPGQDVLTVPTMQHKLEAQLRGLGAGFLPTPLAQPyINA 259
Cdd:cd05466    82 HPLAKRK-SVTLADLADEPLILFERGSGLRRLLdrafAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE-LAD 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1070914336 260 GRLVVKPVQQGERSFRVAYAWRQTRPsvnNARALHWWLDHL 300
Cdd:cd05466   160 GGLVVLPLEDPPLSRTIGLVWRKGRY---LSPAARAFLELL 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
21-194 2.45e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 60.36  E-value: 2.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  21 AVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVARRVKRVATGWE 100
Cdd:PRK11242   11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADLSR 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 101 PQFTIAADALISRATLFELCEAFYATGAPTRLRLRAEtlsgTLEALQNGLAD--LALGVA-ADSVGPGLHAAPLGTAGFV 177
Cdd:PRK11242   91 GSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREM----SQERIEALLADdeLDVGIAfAPVHSPEIEAQPLFTETLA 166
                         170
                  ....*....|....*..
gi 1070914336 178 YAVAPHHPLARLEGTLT 194
Cdd:PRK11242  167 LVVGRHHPLAARRKALT 183
PRK10341 PRK10341
transcriptional regulator TdcA;
14-177 2.91e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 60.26  E-value: 2.91e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  14 ENLALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVARRVK 93
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  94 RVATGWEPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVGP-GLHAAPLG 172
Cdd:PRK10341   90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLqDLHVEPLF 169

                  ....*
gi 1070914336 173 TAGFV 177
Cdd:PRK10341  170 ESEFV 174
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
20-77 5.02e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 59.63  E-value: 5.02e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1070914336  20 EAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRA 77
Cdd:PRK10086   23 EVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
16-263 1.61e-08

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: 54.92  E-value: 1.61e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  16 LALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSaRRAMLTSAGEELLRAGEFL-LNEFDAVARRVKR 94
Cdd:TIGR03298   6 LAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQVrLLEAELLAELPGL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  95 VATGWEPqFTIA--ADALisrATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVgPGLHAAPLG 172
Cdd:TIGR03298  85 APGAPTR-LTIAvnADSL---ATWFLPALAPVLAREGVLLDLVVEDQDHTAELLRSGEVLGAVTTEAKPV-PGCRVVPLG 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 173 TAGFVYAVAP-----HHPLARLEGTLTeehmrqhRAVAVA----DSTQrGRGVSHNL-LPGQ-DVLTVPTMQHKLEAQLR 241
Cdd:TIGR03298 160 AMRYLAVASPafaarYFPDGVTAAALA-------RAPVIVfnrkDDLQ-DRFLRRLFgLPVSpPRHYVPSSEGFVDAARA 231
                         250       260
                  ....*....|....*....|..
gi 1070914336 242 GLGAGFLPTPLAQPYINAGRLV 263
Cdd:TIGR03298 232 GLGWGMVPELQAEPHLAAGRLV 253
rbcR CHL00180
LysR transcriptional regulator; Provisional
14-82 5.77e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 53.10  E-value: 5.77e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1070914336  14 ENLALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLL 82
Cdd:CHL00180    8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL 76
PRK09791 PRK09791
LysR family transcriptional regulator;
17-152 3.44e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 50.92  E-value: 3.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  17 ALVEaVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVARRVKRVA 96
Cdd:PRK09791   12 AFVE-VARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQ 90
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1070914336  97 TGWEPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLAD 152
Cdd:PRK09791   91 GQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELD 146
PRK09801 PRK09801
LysR family transcriptional regulator;
13-97 1.16e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 49.26  E-value: 1.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  13 AENLALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVARRV 92
Cdd:PRK09801    8 AKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDV 87

                  ....*
gi 1070914336  93 KRVAT 97
Cdd:PRK09801   88 TQIKT 92
PRK09986 PRK09986
LysR family transcriptional regulator;
30-188 1.81e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 48.57  E-value: 1.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  30 AASReLGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVARRVKRVATGWEPQFTIA--A 107
Cdd:PRK09986   27 AAAR-LNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEAGRIEIGivG 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 108 DALISRatLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAAD-SVGPGLHAAPLGTAGFVYAVAPHHPL 186
Cdd:PRK09986  106 TALWGR--LRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADlEPNPGFTSRRLHESAFAVAVPEEHPL 183

                  ..
gi 1070914336 187 AR 188
Cdd:PRK09986  184 AS 185
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
18-190 2.38e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 48.50  E-value: 2.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  18 LVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAM-LTSAGEELLRAGEFLLNEfdavARRVKRVA 96
Cdd:PRK12683    9 IREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLD----AENLRRLA 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  97 TGW----EPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADlaLGVAADSVG--PGLHAAP 170
Cdd:PRK12683   85 EQFadrdSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEAD--IGIATEALDrePDLVSFP 162
                         170       180
                  ....*....|....*....|
gi 1070914336 171 LGTAGFVYAVAPHHPLARLE 190
Cdd:PRK12683  163 YYSWHHVVVVPKGHPLTGRE 182
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
16-263 3.19e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.85  E-value: 3.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  16 LALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSaRRAMLTSAGEELLRAGEFL-LNEFDAVARrvKR 94
Cdd:PRK03635    7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVrLLEAELLGE--LP 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  95 VATGWEPQFTIA--ADALisrATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVgPGLHAAPLG 172
Cdd:PRK03635   84 ALDGTPLTLSIAvnADSL---ATWFLPALAPVLARSGVLLDLVVEDQDHTAELLRRGEVVGAVTTEPQPV-QGCRVDPLG 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 173 TAGFVyAVAPHHPLAR-LEGTLTEEHMRqhRAVAVA----DSTQ-----RGRGVSHNLLPgqdVLTVPTMQHKLEAQLRG 242
Cdd:PRK03635  160 AMRYL-AVASPAFAARyFPDGVTAEALA--KAPAVVfnrkDDLQdrflrQAFGLPPGSVP---CHYVPSSEAFVRAALAG 233
                         250       260
                  ....*....|....*....|.
gi 1070914336 243 LGAGFLPTPLAQPYINAGRLV 263
Cdd:PRK03635  234 LGWGMIPELQIEPELASGELV 254
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
102-295 4.60e-06

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: 46.44  E-value: 4.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 102 QFTIAADALISRATLFELCEAFYATgAP-TRLRLRAETLSGTLEALQNGLADLALGVAaDSVGPGLHAAPLGTAGFVYAV 180
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQE-APgVRLRFVPLDRDDLEEALESGEIDLAIGVF-PELPPGLRSQPLFEDRFVCVA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 181 APHHPLARleGTLTEEHMRQHRAVAVAdSTQRGRGVSHNLLPGQD-----VLTVPTMQhkleAQLRGLGA----GFLPTP 251
Cdd:cd08417    79 RKDHPLAG--GPLTLEDYLAAPHVLVS-PRGRGHGLVDDALAELGlsrrvALTVPHFL----AAPALVAGtdliATVPRR 151
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1070914336 252 LAQPYINAGRLVVKPVQQGERSFRVAYAWrqtRPSVNNARALHW 295
Cdd:cd08417   152 LAEALAERLGLRVLPLPFELPPFTVSLYW---HPRRDRDPAHRW 192
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
14-187 4.97e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 47.32  E-value: 4.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  14 ENLALVEAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEfdaVARRVK 93
Cdd:PRK15421    5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQ---ISQALQ 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  94 RVATGWEPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLalgVAADSVGP--GLHAAPL 171
Cdd:PRK15421   82 ACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDL---VMTSDILPrsGLHYSPM 158
                         170
                  ....*....|....*.
gi 1070914336 172 GTAGFVYAVAPHHPLA 187
Cdd:PRK15421  159 FDYEVRLVLAPDHPLA 174
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
1-91 6.49e-06

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 44.43  E-value: 6.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336   1 MPPPISARSALSAEN--------LALVEAVARLGSMAAASRELGMvpsalTYR-----IRQIEDALDVLLFDRSA--RR- 64
Cdd:COG2005     1 MSMKLRLKLWLELDGgvflgpgrIELLEAIDETGSISAAAKAMGM-----SYKrawdlIDAMNNLLGEPLVERQTggKGg 75
                          90       100
                  ....*....|....*....|....*....
gi 1070914336  65 --AMLTSAGEELLRAGEFLLNEFDAVARR 91
Cdd:COG2005    76 ggARLTPEGRRLLALYRRLEAEAQRALAA 104
cbl PRK12679
HTH-type transcriptional regulator Cbl;
40-189 1.34e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 45.96  E-value: 1.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  40 SALTYRIRQIEDALDVLLFDRSARRAM-LTSAGEELLRAGEFLLNEFDAVARRVKRVATGWEPQFTIAADALISRATLFE 118
Cdd:PRK12679   31 SGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATTHTQARYSLPE 110
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1070914336 119 LCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVGPGLHAAPLGTAGFVYAVAPHHPLARL 189
Cdd:PRK12679  111 VIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQI 181
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
22-71 1.47e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 45.91  E-value: 1.47e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1070914336  22 VARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAG 71
Cdd:PRK10632   13 VVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAG 62
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
31-135 1.96e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 45.39  E-value: 1.96e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  31 ASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLRAGEFLLNEFDAVARRVKRVATGWEpqFTIAADAL 110
Cdd:PRK03601   21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHTSQHNE--LSIGASAS 98
                          90       100
                  ....*....|....*....|....*
gi 1070914336 111 ISRATLFELCEAFYATGAPTRLRLR 135
Cdd:PRK03601   99 LWECMLTPWLGRLYQNQEALQFEAR 123
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
140-297 3.18e-05

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB 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: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 43.87  E-value: 3.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 140 SGTLEALQNGLADLALGVAaDSVGPGLHAAPLGTAGFVYAVAPHHPLARL---EGTLTEEHMRQHRAVAVADSTQRGRGV 216
Cdd:cd08483    36 SADLVDLRPDGIDVAIRYG-NGDWPGLESEPLTAAPFVVVAAPGLLGDRKvdsLADLAGLPWLQERGTNEQRVWLASMGV 114
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 217 SHNLLPGQDVLTVPTMqhkLEAQLRGLGAGFLPTPLAQPYINAGRLVVKpVQQGERSfrVAYaWRQTRPSVNNARALHW- 295
Cdd:cd08483   115 VPDLERGVTFLPGQLV---LEAARAGLGLSIQARALVEPDIAAGRLTVL-FEEEEEG--LGY-HIVTRPGVLRPAAKAFv 187

                  ...
gi 1070914336 296 -WL 297
Cdd:cd08483   188 rWL 190
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
131-285 5.21e-05

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is 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 C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. 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: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 43.28  E-value: 5.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 131 RLRLRAETLSGTLEALQNGLADLALgVAADSVGPGLHAAPLGTAGFVYAVAPHHPLARLEG------------TLTEEH- 197
Cdd:cd08411    31 RLYLREDQTERLLEKLRSGELDAAL-LALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSvtpedlagerllLLEEGHc 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 198 MRQHrAVAVAdstQRGRGVSHNLLPGQDVLTVptmqhkleAQL--RGLGAGFLPTPLAQPYINAG-RLVVKPVQQGERSF 274
Cdd:cd08411   110 LRDQ-ALELC---RLAGAREQTDFEATSLETL--------RQMvaAGLGITLLPELAVPSEELRGdRLVVRPFAEPAPSR 177
                         170
                  ....*....|.
gi 1070914336 275 RVAYAWRQTRP 285
Cdd:cd08411   178 TIGLVWRRSSP 188
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
131-267 1.01e-04

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 42.51  E-value: 1.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 131 RLRLRAETLSGTLEALQNGLADLALGVAaDSVGPGLHAAPLGTAGFVYAVAPHHPLARLEgTLTEEHMRQHRAVAVADST 210
Cdd:cd08440    30 RVRLRDVSAEQVIEAVRSGEVDFGIGSE-PEADPDLEFEPLLRDPFVLVCPKDHPLARRR-SVTWAELAGYPLIALGRGS 107
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1070914336 211 QRGRGVSHNLL-------PGQDVLTVPTMQHKLEAqlrGLGAGFLPTpLAQPYINAGRLVVKPV 267
Cdd:cd08440   108 GVRALIDRALAaagltlrPAYEVSHMSTALGMVAA---GLGVAVLPA-LALPLADHPGLVARPL 167
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
102-285 1.14e-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: 42.34  E-value: 1.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 102 QFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVGPG-LHAAPLGTAGFVYAV 180
Cdd:cd08418     1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKeLISEPLFESDFVVVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 181 APHHPLAR---LEG------TLTEEHM-----------RQHRAVAVADSTQRgRGVSHNLLPGQDVLTVptmqhkleaql 240
Cdd:cd08418    81 RKDHPLQGarsLEElldaswVLPGTRMgyynnllealrRLGYNPRVAVRTDS-IVSIINLVEKADFLTI----------- 148
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1070914336 241 rglgagfLPTPLAQPYINAGRLVVKPVQQGERSFRVAYAWRQTRP 285
Cdd:cd08418   149 -------LSRDMGRGPLDSFRLITIPVEEPLPSADYYLIYRKKSR 186
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
20-190 2.14e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 2.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  20 EAVARLGSMAAASRELGMVPSALTYRIRQIEDALDVLLFDRSARRAM-LTSAGEELLRAGEFLLNEfdavARRVKRVATG 98
Cdd:PRK12682   11 EAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILRE----VGNIKRIGDD 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  99 W----EPQFTIAADALISRATLFELCEAFYATGAPTRLRLRAETLSGTLEALQNGLADlaLGVAADSVG--PGLHAAPLG 172
Cdd:PRK12682   87 FsnqdSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEAD--IGIATESLAddPDLATLPCY 164
                         170
                  ....*....|....*...
gi 1070914336 173 TAGFVYAVAPHHPLARLE 190
Cdd:PRK12682  165 DWQHAVIVPPDHPLAQEE 182
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
143-278 2.17e-04

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. 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: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 41.71  E-value: 2.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 143 LEALQNGLADLALgVAADSVGPGLHAAPLGTAGFVYAVAPHHPLARLEgTLTEEHMRQHRAV---------AVADSTQRG 213
Cdd:cd08420    42 AERVLDGEIDLGL-VEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRK-EVTAEELAAEPWIlrepgsgtrEVFERALAE 119
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1070914336 214 RGVshNLLPGQDVLTVPTMQHKLEAQLRGLGAGFLPTPLAQPYINAGRLVVKPVQQG--ERSFRVAY 278
Cdd:cd08420   120 AGL--DGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVALPVEGLrlTRPFSLIY 184
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
37-76 3.18e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 41.73  E-value: 3.18e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1070914336  37 MVPSALTYRIRQIEDALDVLLFDRSARRAMLTSAGEELLR 76
Cdd:PRK11716    3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRP 42
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
45-201 7.28e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 40.73  E-value: 7.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336  45 RIRQIEDALDVLLFDRSARRAM-LTSAGEELLRAGEFLLNEFDAVARRVKRVATGWEPQFTIAADALISRATLFELCEAF 123
Cdd:PRK12684   36 AIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEF 115
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1070914336 124 YATGAPTRLRLRAETLSGTLEALQNGLADLALGVAADSVGPGLHAAPLGTAGFVYAVAPHHPLARLEGtLTEEHMRQH 201
Cdd:PRK12684  116 KKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADYKELVSLPCYQWNHCVVVPPDHPLLERKP-LTLEDLAQY 192
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
122-190 4.01e-03

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 37.93  E-value: 4.01e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1070914336 122 AFYATGAPTRLRLRAETLSGTLEALQNGLADLALgVAADSVGPGLHAAPLGTAGFVYAVAPHHPLARLE 190
Cdd:cd08415    21 RFRARHPDVRISLHTLSSSTVVEAVLSGQADLGL-ASLPLDHPGLESEPLASGRAVCVLPPGHPLARKD 88
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
128-221 6.52e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 37.17  E-value: 6.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 128 APtRLRLRAETLSG--TLEALQNGLADLALGVAADsVGPGLHAAPLGTAGFVYAVAPHHPLARleGTLTEEHMRQHRAVA 205
Cdd:cd08459    26 AP-GVRIETVRLPVdeLEEALESGEIDLAIGYLPD-LGAGFFQQRLFRERYVCLVRKDHPRIG--STLTLEQFLAARHVV 101
                          90
                  ....*....|....*.
gi 1070914336 206 VadstqRGRGVSHNLL 221
Cdd:cd08459   102 V-----SASGTGHGLV 112
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
152-284 7.36e-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: 7.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070914336 152 DLAL--GVAADSvgPGLHAAPLGTAGFVYAVAPHHpLARLEGTLTEEHMRQHRAVAVAdstQRGRGVSHNLLPGQDVLTV 229
Cdd:cd08475    49 DLAVriGELADS--TGLVARRLGTQRMVLCASPAY-LARHGTPRTLEDLAEHQCIAYG---RGGQPLPWRLADEQGRLVR 122
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1070914336 230 PTMQHKL---------EAQLRGLGAGFLPTPLAQPYINAGRLV-VKPvQQGERSFRVAYAWRQTR 284
Cdd:cd08475   123 FRPAPRLqfddgeaiaDAALAGLGIAQLPTWLVADHLQRGELVeVLP-ELAPEGLPIHAVWPRTR 186
 
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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