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Conserved domains on  [gi|1543042950|ref|WP_125952954|]
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MULTISPECIES: LysR family transcriptional regulator [unclassified Variovorax]

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 ...
 100-300 1.43e-70

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: 217.14  E-value: 1.43e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASlaltaTGIRTRPIGELRFV 179
Cdd:cd08431     2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-----GGVKTRPLGEVEFV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 180 YAVAPHHPLARLPQPLSDAVMRQHRAVAAADSARHGPSMTVNLMGGQDVLTVPSMQAKIAAQLHGLGGGFLPDPMARPYI 259
Cdd:cd08431    77 FAVAPNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPEL 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1543042950 260 EAGHLVELKTERKPPMGTMHCAWRvrsAGKPGRALEWWLEQ 300
Cdd:cd08431   157 ASGELVEKALEDPRPPQELFLAWR---KDQRGKALAWFVQR 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
29-68 3.00e-08

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 49.69  E-value: 3.00e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1543042950  29 ARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAG 68
Cdd:pfam00126  20 AERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 100-300 1.43e-70

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: 217.14  E-value: 1.43e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASlaltaTGIRTRPIGELRFV 179
Cdd:cd08431     2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-----GGVKTRPLGEVEFV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 180 YAVAPHHPLARLPQPLSDAVMRQHRAVAAADSARHGPSMTVNLMGGQDVLTVPSMQAKIAAQLHGLGGGFLPDPMARPYI 259
Cdd:cd08431    77 FAVAPNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPEL 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1543042950 260 EAGHLVELKTERKPPMGTMHCAWRvrsAGKPGRALEWWLEQ 300
Cdd:cd08431   157 ASGELVEKALEDPRPPQELFLAWR---KDQRGKALAWFVQR 194
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 31-299 6.69e-52

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 172.82  E-value: 6.69e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  31 ELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAVDSVIAR 110
Cdd:PRK11074   25 ELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRGQLSIAVDNIVRP 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 111 DPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGavldaASLALTATG-IRTRPIGELRFVYAVAPHHPLA 189
Cdd:PRK11074  105 DRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIG-----ATRAIPVGGrFAFRDMGMLSWACVVSSDHPLA 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 190 RLPQPLSDAVMRQHRAVAAADSARHGPSMTVNLMGGQDVLTVPSMQAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKT 269
Cdd:PRK11074  180 SMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAKPLINSGKLVELTL 259

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1543042950 270 ERKPPmgTMHC--AWRVRSAGKpgrALEWWLE 299
Cdd:PRK11074  260 ENPFP--DSPCclTWQQNDMSP---ALAWLLD 286
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
30-307 1.28e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.61  E-value: 1.28e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  30 RELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAVDSVIA 109
Cdd:COG0583    23 ERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGTLRIGAPPSLA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 110 RDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAvldaasLALTATGIRTRPIGELRFVYAVAPHHPLA 189
Cdd:COG0583   103 RYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL------GPPPDPGLVARPLGEERLVLVASPDHPLA 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 190 RLPQplsdavmrqhravaaadsarhgpsmtvnlmggqdvlTVPSMQAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKT 269
Cdd:COG0583   177 RRAP------------------------------------LVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVALPL 220

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1543042950 270 ERKPPMGTMHCAWRVRSAGKPgrALEWWLEQFEHEGTR 307
Cdd:COG0583   221 PDPPPPRPLYLVWRRRRHLSP--AVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 100-301 2.08e-15

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: 73.48  E-value: 2.08e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAvldaasLALTATGIRTRPIGELRFV 179
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR------GPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 180 YAVAPHHPLARLpQPLSDAVMRQHRAVAAADSARHGPSMTVNLMGG----QDVLTVPSMQAKIAAQLHGLGGGFLPDPMA 255
Cdd:pfam03466  78 LVAPPDHPLARG-EPVSLEDLADEPLILLPPGSGLRDLLDRALRAAglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1543042950 256 RPYIEAGHLVELKTERKPPMGTMHCAWRVRSAGKPgrALEWWLEQF 301
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVWRKGRPLSP--AVRAFIEFL 200
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 8-271 2.30e-14

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: 72.26  E-value: 2.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950   8 LTPDALAMLQTVAAAGSFAAAARELNLVPSALSYRVRQIEDALDVLLFDRSaRQARLTEAGAELLREADRL-LNEIDAVA 86
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQVrLLEAELLA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  87 NRVKRVATGWEPmLTIAVDSviarDPL----LDlACAFFALEPPTRLKLRDETLLGTIEALTSGEadlAIGAVldaASLA 162
Cdd:TIGR03298  80 ELPGLAPGAPTR-LTIAVNA----DSLatwfLP-ALAPVLAREGVLLDLVVEDQDHTAELLRSGE---VLGAV---TTEA 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 163 LTATGIRTRPIGELRFVYAVAP-----HHPLARLPQPLSDA---VMRQHRAVAAADSARHgpsmtVNLMGGQDVLTVPSM 234
Cdd:TIGR03298 148 KPVPGCRVVPLGAMRYLAVASPafaarYFPDGVTAAALARApviVFNRKDDLQDRFLRRL-----FGLPVSPPRHYVPSS 222

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1543042950 235 QAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKTER 271
Cdd:TIGR03298 223 EGFVDAARAGLGWGMVPELQAEPHLAAGRLVELAPGR 259
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 30-268 4.95e-10

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 59.55  E-value: 4.95e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  30 RELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAVDSVIA 109
Cdd:NF040786   23 KKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVLRIGASTIPG 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 110 RDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAI-GAVLDAASLALTatgirtrPIGELRFVYAVAPHHPL 188
Cdd:NF040786  103 QYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFtGTKLEKKRLVYT-------PFYKDRLVLITPNGTEK 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 189 AR---LPQPLSDA-----VMRQH----RAVAAADSARHG---PSMTVnlmggqdVLTVPSMQAKIAAQLHGLGGGFLPDP 253
Cdd:NF040786  176 YRmlkEEISISELqkepfIMREEgsgtRKEAEKALKSLGislEDLNV-------VASLGSTEAIKQSVEAGLGISVISEL 248

                         250
                  ....*....|....*
gi 1543042950 254 MARPYIEAGHLVELK 268
Cdd:NF040786  249 AAEKEVERGRVLIFP 263
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
29-68 3.00e-08

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 49.69  E-value: 3.00e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1543042950  29 ARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAG 68
Cdd:pfam00126  20 AERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
rbcR CHL00180
LysR transcriptional regulator; Provisional
 9-79 9.34e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 52.71  E-value: 9.34e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1543042950   9 TPDALAMLQTVAAAGSFAAAARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLL 79
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL 76
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 29-266 5.24e-07

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: 50.12  E-value: 5.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  29 ARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATgwEPMLTIAVDSVI 108
Cdd:NF041036   22 AEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLSICCTPTF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 109 ARDPLLDLACAFFALE-PPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASLALTATgiRTRPIGELRFVYAvaphhP 187
Cdd:NF041036  100 GMAHLPGVLNRFMLRNaDVVDLKFLFHSPAQALEGIQNKEFDLAIIEHCADLDLGRFHT--YPLPQDELVFVSA-----P 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 188 LARLPQPLSD-AVMRQHRAVAAADSARHGPSMTVNLMG-GQD------VLTVPSMQAKIAAQLHGLGGGFLPDPMARPYI 259
Cdd:NF041036  173 SLGLPTPNVTlERLLELCLITRRDGCSSRDLLRRNLAEqGRDlddfrrVVVSDDLRLTIQTVLDGGGISFVSRSLVCEYL 252


                  ....*..
gi 1543042950 260 EAGHLVE 266
Cdd:NF041036  253 KNGQLRE 259
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 100-300 1.43e-70

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: 217.14  E-value: 1.43e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASlaltaTGIRTRPIGELRFV 179
Cdd:cd08431     2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPP-----GGVKTRPLGEVEFV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 180 YAVAPHHPLARLPQPLSDAVMRQHRAVAAADSARHGPSMTVNLMGGQDVLTVPSMQAKIAAQLHGLGGGFLPDPMARPYI 259
Cdd:cd08431    77 FAVAPNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPEL 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1543042950 260 EAGHLVELKTERKPPMGTMHCAWRvrsAGKPGRALEWWLEQ 300
Cdd:cd08431   157 ASGELVEKALEDPRPPQELFLAWR---KDQRGKALAWFVQR 194
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 31-299 6.69e-52

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 172.82  E-value: 6.69e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  31 ELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAVDSVIAR 110
Cdd:PRK11074   25 ELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRGQLSIAVDNIVRP 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 111 DPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGavldaASLALTATG-IRTRPIGELRFVYAVAPHHPLA 189
Cdd:PRK11074  105 DRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIG-----ATRAIPVGGrFAFRDMGMLSWACVVSSDHPLA 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 190 RLPQPLSDAVMRQHRAVAAADSARHGPSMTVNLMGGQDVLTVPSMQAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKT 269
Cdd:PRK11074  180 SMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCVGMVPTHFAKPLINSGKLVELTL 259

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1543042950 270 ERKPPmgTMHC--AWRVRSAGKpgrALEWWLE 299
Cdd:PRK11074  260 ENPFP--DSPCclTWQQNDMSP---ALAWLLD 286
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-289 4.76e-47

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 160.74  E-value: 4.76e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950   8 LTPDALAMLQTVAAAGSFAAAARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVAN 87
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  88 RVKRVATGWEPMLTIAVDSVI-ARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGaVLDAASLALTat 166
Cdd:PRK10094   82 ELQQVNDGVERQVNIVINNLLyNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIG-VTGTEALANT-- 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 167 gIRTRPIGELRFVYAVAPHHPLARLPQPLSDAVMRQHRAVAAADSARHGPSMTVNLMGGQDVLTVPSMQAKIAAQLHGLG 246
Cdd:PRK10094  159 -FSLDPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVG 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1543042950 247 GGFLPDPMARPYIEAGHLV--ELKTERKPpmGTMHCAWRVRSAGK 289
Cdd:PRK10094  238 IGFLPKSLCQSMIDNQQLVsrVIPTMRPP--SPLSLAWRKFGSGK 280
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
30-307 1.28e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 134.61  E-value: 1.28e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  30 RELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAVDSVIA 109
Cdd:COG0583    23 ERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRALRGGPRGTLRIGAPPSLA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 110 RDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAvldaasLALTATGIRTRPIGELRFVYAVAPHHPLA 189
Cdd:COG0583   103 RYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL------GPPPDPGLVARPLGEERLVLVASPDHPLA 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 190 RLPQplsdavmrqhravaaadsarhgpsmtvnlmggqdvlTVPSMQAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKT 269
Cdd:COG0583   177 RRAP------------------------------------LVNSLEALLAAVAAGLGIALLPRFLAADELAAGRLVALPL 220

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1543042950 270 ERKPPMGTMHCAWRVRSAGKPgrALEWWLEQFEHEGTR 307
Cdd:COG0583   221 PDPPPPRPLYLVWRRRRHLSP--AVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 100-301 2.08e-15

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: 73.48  E-value: 2.08e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAvldaasLALTATGIRTRPIGELRFV 179
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRR------GPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 180 YAVAPHHPLARLpQPLSDAVMRQHRAVAAADSARHGPSMTVNLMGG----QDVLTVPSMQAKIAAQLHGLGGGFLPDPMA 255
Cdd:pfam03466  78 LVAPPDHPLARG-EPVSLEDLADEPLILLPPGSGLRDLLDRALRAAglrpRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1543042950 256 RPYIEAGHLVELKTERKPPMGTMHCAWRVRSAGKPgrALEWWLEQF 301
Cdd:pfam03466 157 ARELADGRLVALPLPEPPLPRELYLVWRKGRPLSP--AVRAFIEFL 200
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 8-271 2.30e-14

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: 72.26  E-value: 2.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950   8 LTPDALAMLQTVAAAGSFAAAARELNLVPSALSYRVRQIEDALDVLLFDRSaRQARLTEAGAELLREADRL-LNEIDAVA 86
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQVrLLEAELLA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  87 NRVKRVATGWEPmLTIAVDSviarDPL----LDlACAFFALEPPTRLKLRDETLLGTIEALTSGEadlAIGAVldaASLA 162
Cdd:TIGR03298  80 ELPGLAPGAPTR-LTIAVNA----DSLatwfLP-ALAPVLAREGVLLDLVVEDQDHTAELLRSGE---VLGAV---TTEA 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 163 LTATGIRTRPIGELRFVYAVAP-----HHPLARLPQPLSDA---VMRQHRAVAAADSARHgpsmtVNLMGGQDVLTVPSM 234
Cdd:TIGR03298 148 KPVPGCRVVPLGAMRYLAVASPafaarYFPDGVTAAALARApviVFNRKDDLQDRFLRRL-----FGLPVSPPRHYVPSS 222

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1543042950 235 QAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKTER 271
Cdd:TIGR03298 223 EGFVDAARAGLGWGMVPELQAEPHLAAGRLVELAPGR 259
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
29-287 2.30e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 69.23  E-value: 2.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  29 ARELNLVPSALSYRVRQIEDALDVLLFDRSaRQARLTEAGAELLREADRL-LNEIDAVaNRVKRVATGWePMLTIAVDSv 107
Cdd:PRK13348   23 ARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVaLLEADLL-STLPAERGSP-PTLAIAVNA- 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 108 iarDPL----LDLACAFFAlEPPTRLKLRDETLLGTIEALTSGEadlAIGAVldaASLALTATGIRTRPIGELRFVYAVA 183
Cdd:PRK13348   99 ---DSLatwfLPALAAVLA-GERILLELIVDDQDHTFALLERGE---VVGCV---STQPKPMRGCLAEPLGTMRYRCVAS 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 184 P-----HHP-------LARLP-------QPLSDAVMRQHRAVAAADSARHgpsmtvnlmggqdvlTVPSMQAKIAAQLHG 244
Cdd:PRK13348  169 PafaarYFAqgltrhsALKAPavafnrkDTLQDSFLEQLFGLPVGAYPRH---------------YVPSTHAHLAAIRHG 233

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1543042950 245 LGGGFLPDPMARPYIEAGHLVELKTERKPPMGTMHCAWRVRSA 287
Cdd:PRK13348  234 LGYGMVPELLIGPLLAAGRLVDLAPGHPVDVALYWHHWEVESP 276
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
29-271 1.34e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 64.02  E-value: 1.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  29 ARELNLVPSALSYRVRQIEDALDVLLFDRSaRQARLTEAGAELLREADRL-LNEIDAVANrvKRVATGWEPMLTIAV--D 105
Cdd:PRK03635   23 AQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVrLLEAELLGE--LPALDGTPLTLSIAVnaD 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 106 S-------VIARdplldlacafFALEPPTRLKLR--DETLlgTIEALTSGEadlAIGAVldaASLALTATGIRTRPIGEL 176
Cdd:PRK03635  100 SlatwflpALAP----------VLARSGVLLDLVveDQDH--TAELLRRGE---VVGAV---TTEPQPVQGCRVDPLGAM 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 177 RFVyAVA-------------PHHPLARLP-------QPLSDAVMRQHRAVAAADSARHgpsmtvnlmggqdvlTVPSMQA 236
Cdd:PRK03635  162 RYL-AVAspafaaryfpdgvTAEALAKAPavvfnrkDDLQDRFLRQAFGLPPGSVPCH---------------YVPSSEA 225

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1543042950 237 KIAAQLHGLGGGFLPDPMARPYIEAGHLVELKTER 271
Cdd:PRK03635  226 FVRAALAGLGWGMIPELQIEPELASGELVDLTPGR 260
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 37-201 4.28e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 62.75  E-value: 4.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  37 SALSYRVRQIEDALDVLLFDRSA-RQARLTEAGAELLREADRLLNEidavANRVKRVATGW----EPMLTIAVDSVIARD 111
Cdd:PRK12683   31 SGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLD----AENLRRLAEQFadrdSGHLTVATTHTQARY 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 112 PLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIgavldaASLALTAT-GIRTRPIGELRFVYAVAPHHPLAR 190
Cdd:PRK12683  107 ALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGI------ATEALDREpDLVSFPYYSWHHVVVVPKGHPLTG 180

                         170
                  ....*....|.
gi 1543042950 191 LPQPLSDAVMR 201
Cdd:PRK12683  181 RENLTLEAIAE 191
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 37-196 8.78e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.51  E-value: 8.78e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  37 SALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAV-----DSVIArd 111
Cdd:PRK11242   30 PTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADLSRGSLRLAMtptftAYLIG-- 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 112 PLLDlacAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVldaaslALTATGIRTRPIGELRFVYAVAPHHPLARL 191
Cdd:PRK11242  108 PLID---AFHARYPGITLTIREMSQERIEALLADDELDVGIAFA------PVHSPEIEAQPLFTETLALVVGRHHPLAAR 178


                  ....*
gi 1543042950 192 PQPLS 196
Cdd:PRK11242  179 RKALT 183
PRK09986 PRK09986
LysR family transcriptional regulator;
32-252 1.86e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 60.51  E-value: 1.86e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  32 LNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAVDSVIARD 111
Cdd:PRK09986   31 LNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQIGRGEAGRIEIGIVGTALWG 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 112 PLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASLAltatGIRTRPIGELRFVYAVAPHHPLARL 191
Cdd:PRK09986  111 RLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNP----GFTSRRLHESAFAVAVPEEHPLASR 186

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1543042950 192 pqplsdavmrqhravaaadsarhgPSMTVNLMGGQDVLTVPSMQAKIAAQLHG--LGGGFLPD 252
Cdd:PRK09986  187 ------------------------SSVPLKALRNEYFITLPFVHSDWGKFLQRvcQQAGFSPQ 225
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 100-299 3.27e-10

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 58.77  E-value: 3.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIgavldaASLALTATGIRTRPIGELRFV 179
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAI------VALPVDDPGLESEPLFEEPLV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 180 YAVAPHHPLARLPQ-PLSDA-----VMR----QHRAVAAADSARHGPSMTVnlmggqdVLTVPSMQAKIAAQLHGLGGGF 249
Cdd:cd05466    76 LVVPPDHPLAKRKSvTLADLadeplILFergsGLRRLLDRAFAEAGFTPNI-------ALEVDSLEAIKALVAAGLGIAL 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1543042950 250 LPDpMARPYIEAGHLVELKTERKPPMGTMHCAWrvRSAGKPGRALEWWLE 299
Cdd:cd05466   149 LPE-SAVEELADGGLVVLPLEDPPLSRTIGLVW--RKGRYLSPAARAFLE 195
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 30-268 4.95e-10

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 59.55  E-value: 4.95e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  30 RELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAVDSVIA 109
Cdd:NF040786   23 KKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVLRIGASTIPG 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 110 RDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAI-GAVLDAASLALTatgirtrPIGELRFVYAVAPHHPL 188
Cdd:NF040786  103 QYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFtGTKLEKKRLVYT-------PFYKDRLVLITPNGTEK 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 189 AR---LPQPLSDA-----VMRQH----RAVAAADSARHG---PSMTVnlmggqdVLTVPSMQAKIAAQLHGLGGGFLPDP 253
Cdd:NF040786  176 YRmlkEEISISELqkepfIMREEgsgtRKEAEKALKSLGislEDLNV-------VASLGSTEAIKQSVEAGLGISVISEL 248

                         250
                  ....*....|....*
gi 1543042950 254 MARPYIEAGHLVELK 268
Cdd:NF040786  249 AAEKEVERGRVLIFP 263
cbl PRK12679
HTH-type transcriptional regulator Cbl;
37-165 2.05e-08

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 54.82  E-value: 2.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  37 SALSYRVRQIEDALDVLLF-DRSARQARLTEAGAELLREADRLLNEidavANRVKRVATGW----EPMLTIAVDSVIARD 111
Cdd:PRK12679   31 SGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNE----ASNVRRLADLFtndtSGVLTIATTHTQARY 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1543042950 112 PLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASLALTA 165
Cdd:PRK12679  107 SLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVA 160
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
29-68 3.00e-08

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 49.69  E-value: 3.00e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1543042950  29 ARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAG 68
Cdd:pfam00126  20 AERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 37-193 4.67e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 53.46  E-value: 4.67e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  37 SALSYRVRQIEDALDVLLFDRSA-RQARLTEAGAELLREADRLLNEIdavaNRVKRVATGW----EPMLTIAVDSVIARD 111
Cdd:PRK12682   31 PGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREV----GNIKRIGDDFsnqdSGTLTIATTHTQARY 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 112 PLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGavldAASLALTaTGIRTRPIGELRFVYAVAPHHPLARL 191
Cdd:PRK12682  107 VLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA----TESLADD-PDLATLPCYDWQHAVIVPPDHPLAQE 181


                  ..
gi 1543042950 192 PQ 193
Cdd:PRK12682  182 ER 183
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-274 8.45e-08

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: 51.74  E-value: 8.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKL----RDETLLGtiealtsGEADLAI-GAVLDAASLAltatgirTRPIG 174
Cdd:cd08472     3 LRVDVPGSLARLLLIPALPDFLARYPDIELDLgvsdRPVDLIR-------EGVDCVIrVGELADSSLV-------ARRLG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 175 ELRFVYAVAPHHpLARLPQPLSDAVMRQHRAVAAAdSARHGPSMTVNLM-GGQDV-LTVPSM------QAKIAAQLHGLG 246
Cdd:cd08472    69 ELRMVTCASPAY-LARHGTPRHPEDLERHRAVGYF-SARTGRVLPWEFQrDGEEReVKLPSRvsvndsEAYLAAALAGLG 146

                         170       180
                  ....*....|....*....|....*...
gi 1543042950 247 GGFLPDPMARPYIEAGHLVELKTERKPP 274
Cdd:cd08472   147 IIQVPRFMVRPHLASGRLVEVLPDWRPP 174
rbcR CHL00180
LysR transcriptional regulator; Provisional
 9-79 9.34e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 52.71  E-value: 9.34e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1543042950   9 TPDALAMLQTVAAAGSFAAAARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLL 79
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL 76
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-193 2.57e-07

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: 50.22  E-value: 2.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASlaltatGIRTRPIGELRFV 179
Cdd:cd08440     2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADP------DLEFEPLLRDPFV 75

                          90
                  ....*....|....
gi 1543042950 180 YAVAPHHPLARLPQ 193
Cdd:cd08440    76 LVCPKDHPLARRRS 89
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 29-266 5.24e-07

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: 50.12  E-value: 5.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  29 ARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATgwEPMLTIAVDSVI 108
Cdd:NF041036   22 AEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKG--RQRLSICCTPTF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 109 ARDPLLDLACAFFALE-PPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASLALTATgiRTRPIGELRFVYAvaphhP 187
Cdd:NF041036  100 GMAHLPGVLNRFMLRNaDVVDLKFLFHSPAQALEGIQNKEFDLAIIEHCADLDLGRFHT--YPLPQDELVFVSA-----P 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 188 LARLPQPLSD-AVMRQHRAVAAADSARHGPSMTVNLMG-GQD------VLTVPSMQAKIAAQLHGLGGGFLPDPMARPYI 259
Cdd:NF041036  173 SLGLPTPNVTlERLLELCLITRRDGCSSRDLLRRNLAEqGRDlddfrrVVVSDDLRLTIQTVLDGGGISFVSRSLVCEYL 252


                  ....*..
gi 1543042950 260 EAGHLVE 266
Cdd:NF041036  253 KNGQLRE 259
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
40-152 5.31e-07

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 50.36  E-value: 5.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  40 SYRVRQIEDALDVLLFDRSARQAR-LTEAGAELLREADRLLNEIDA---VANRVKRVATGwepMLTIAVDSVIARDPLLD 115
Cdd:PRK12684   34 SKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENlkrVGKEFAAQDQG---NLTIATTHTQARYALPA 110

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1543042950 116 LACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAI 152
Cdd:PRK12684  111 AIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 149-282 1.43e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. 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 further 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: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 47.82  E-value: 1.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 149 DLAI--GAVLDaaslaltaTGIRTRPIGELRFVYAVAPHHpLARLPQPLSDAVMRQHRAVAAAdsaRHGPSMTVNLMGGQ 226
Cdd:cd08422    49 DLAIriGELPD--------SSLVARRLGPVRRVLVASPAY-LARHGTPQTPEDLARHRCLGYR---LPGRPLRWRFRRGG 116

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1543042950 227 DVLTVP--------SMQAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKTERKPPMGTMHCAW 282
Cdd:cd08422   117 GEVEVRvrgrlvvnDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRVLPDWRPPPLPIYAVY 180
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 149-282 1.62e-06

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: 47.94  E-value: 1.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 149 DLAI--GAVLDAASLAltatgirTRPIGELRFVYAVAPHHpLARLPQPLSDAVMRQHRAVAAAdsaRHGPSMTVNLMGGQ 226
Cdd:cd08475    49 DLAVriGELADSTGLV-------ARRLGTQRMVLCASPAY-LARHGTPRTLEDLAEHQCIAYG---RGGQPLPWRLADEQ 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1543042950 227 DVLTVPSM---------QAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKTERKPPMGTMHCAW 282
Cdd:cd08475   118 GRLVRFRPaprlqfddgEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAPEGLPIHAVW 182
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
32-101 5.87e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 46.93  E-value: 5.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  32 LNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRV-----------ATGWEPML 100
Cdd:PRK03601   25 LYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHTsqhnelsigasASLWECML 104


                  .
gi 1543042950 101 T 101
Cdd:PRK03601  105 T 105
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
30-88 7.55e-06

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 46.92  E-value: 7.55e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1543042950  30 RELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAG----AELLREADRLLNEIDAVANR 88
Cdd:PRK10086   36 DELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGkrvfWALKSSLDTLNQEILDIKNQ 98
PRK09791 PRK09791
LysR family transcriptional regulator;
29-152 9.68e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 46.29  E-value: 9.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  29 ARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIAVDSVI 108
Cdd:PRK09791   26 SRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQLAGQINIGMGASI 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1543042950 109 ARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAI 152
Cdd:PRK09791  106 ARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTI 149
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 99-193 1.10e-05

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: 45.25  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  99 MLTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIgavldaASLALTATGIRTRPIGELRF 178
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGL------ASLPLDHPGLESEPLASGRA 74

                          90
                  ....*....|....*
gi 1543042950 179 VYAVAPHHPLARLPQ 193
Cdd:cd08415    75 VCVLPPGHPLARKDV 89
PRK10341 PRK10341
transcriptional regulator TdcA;
13-157 1.74e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 45.62  E-value: 1.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  13 LAMLQTVAAAGSFAAAARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELL-------READRLLNEIDAV 85
Cdd:PRK10341   12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLsrsesitREMKNMVNEINGM 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1543042950  86 ANR-VKRVATGWEpmltiavdSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLD 157
Cdd:PRK10341   92 SSEaVVDVSFGFP--------SLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSN 156
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 125-245 3.36e-05

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: 44.13  E-value: 3.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 125 PPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASlaltatGIRTRPIGELRFVYAVAPHHPLARLPQPLSDAVMRQHR 204
Cdd:cd08417    27 PGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPP------GLRSQPLFEDRFVCVARKDHPLAGGPLTLEDYLAAPHV 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1543042950 205 AVAAADS---------ARHG---------PSMTV--NLMGGQD-VLTVPSMQAKIAAQLHGL 245
Cdd:cd08417   101 LVSPRGRghglvddalAELGlsrrvaltvPHFLAapALVAGTDlIATVPRRLAEALAERLGL 162
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 140-270 4.66e-05

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: 43.63  E-value: 4.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 140 IEALTSGEADLAI--GAVLDAaslaltatGIRTRPIGELRFVYAVAPHHPLARLPQPLSDA------VMRQH----RAVA 207
Cdd:cd08420    42 AERVLDGEIDLGLveGPVDHP--------DLIVEPFAEDELVLVVPPDHPLAGRKEVTAEElaaepwILREPgsgtREVF 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1543042950 208 AADSARHGpsmtVNLMGGQDVLTVPSMQAKIAAQLHGLGGGFLPDPMARPYIEAGHLVELKTE 270
Cdd:cd08420   114 ERALAEAG----LDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVALPVE 172
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
36-81 9.49e-05

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 43.27  E-value: 9.49e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1543042950  36 PSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNE 81
Cdd:PRK11716    5 PSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQ 50
cysB PRK12681
HTH-type transcriptional regulator CysB;
40-152 1.64e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 42.58  E-value: 1.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  40 SYRVRQIEDALDVLLFDRSARQ-ARLTEAGAELLREADRLLNEIDAVanrvKRVATGW----EPMLTIAVDSVIARDPLL 114
Cdd:PRK12681   34 SKQVRMLEDELGIQIFARSGKHlTQVTPAGEEIIRIAREILSKVESI----KSVAGEHtwpdKGSLYIATTHTQARYALP 109

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1543042950 115 DLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAI 152
Cdd:PRK12681  110 PVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAI 147
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 100-256 2.21e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 41.34  E-value: 2.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 100 LTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAvldaasLALTATGIRTRPIGELRFV 179
Cdd:cd08414     2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVR------PPPDPPGLASRPLLREPLV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 180 YAVAPHHPLARLPQ-PLSD------AVMRQHRAVAAADS-----ARHGPSMTVnlmggqdVLTVPSMQAKIAAQLHGLGG 247
Cdd:cd08414    76 VALPADHPLAARESvSLADladepfVLFPREPGPGLYDQilalcRRAGFTPRI-------VQEASDLQTLLALVAAGLGV 148


                  ....*....
gi 1543042950 248 GFLPDPMAR 256
Cdd:cd08414   149 ALVPASVAR 157
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 172-267 3.92e-04

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 5. 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: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 40.91  E-value: 3.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 172 PIG-ELRFVYAVAPHHpLARLPQPLSDAVMRQHRAVaaadsaRHGPSMTVNLM------GGQDV-------LTVPSMQAK 237
Cdd:cd08474    68 PLGpPLRMAVVASPAY-LARHGTPEHPRDLLNHRCI------RYRFPTSGALYrweferGGRELevdvegpLILNDSDLM 140

                          90       100       110
                  ....*....|....*....|....*....|
gi 1543042950 238 IAAQLHGLGGGFLPDPMARPYIEAGHLVEL 267
Cdd:cd08474   141 LDAALDGLGIAYLFEDLVAEHLASGRLVRV 170
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 101-301 5.65e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 40.41  E-value: 5.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 101 TIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASLA-LTAtgirtRPIGELRFV 179
Cdd:cd08418     3 SIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKeLIS-----EPLFESDFV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 180 YAVAPHHPLAR-------------LPQP-------LSDAVMRQH---RAVAAADSArhgpSMTVNLMGGQDVLTVpsmqa 236
Cdd:cd08418    78 VVARKDHPLQGarsleelldaswvLPGTrmgyynnLLEALRRLGynpRVAVRTDSI----VSIINLVEKADFLTI----- 148

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1543042950 237 kiaaqlhglgggfLPDPMARPYIEAGHLVELKTERKPPMGTMHCAWRVRSagKPGRALEWWLEQF 301
Cdd:cd08418   149 -------------LSRDMGRGPLDSFRLITIPVEEPLPSADYYLIYRKKS--RLTPLAEQLVELF 198
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 171-279 6.18e-04

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 8. 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: 176166  Cd Length: 197  Bit Score: 40.29  E-value: 6.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 171 RPIGELRFVYAVAPHHpLARLPQPLSDAVMRQHRAVA-AADSARHGPSMtVNLMGGQDVLTVPSMQA------KIAAqLH 243
Cdd:cd08477    65 RPLAPYRMVLCASPDY-LARHGTPTTPEDLARHECLGfSYWRARNRWRL-EGPGGEVKVPVSGRLTVnsgqalRVAA-LA 141

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1543042950 244 GLGGGFLPDPMARPYIEAGHLVELKTERKPPMGTMH 279
Cdd:cd08477   142 GLGIVLQPEALLAEDLASGRLVELLPDYLPPPRPMH 177
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 139-211 6.21e-04

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: 40.25  E-value: 6.21e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1543042950 139 TIEALTSGEADLAIGavldaaSLALTATGIRTRPIGELRFVYAVAPHHPLARLPQPLSDAVMRQHRAVAAADS 211
Cdd:cd08459    41 LEEALESGEIDLAIG------YLPDLGAGFFQQRLFRERYVCLVRKDHPRIGSTLTLEQFLAARHVVVSASGT 107
PRK12680 PRK12680
LysR family transcriptional regulator;
39-218 8.03e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 40.76  E-value: 8.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  39 LSYRVRQIEDALDVLLFDRSARQAR-LTEAGAELLREADRLL---NEIDAVANRVKRVATGwepMLTIAVDSVIARDPLL 114
Cdd:PRK12680   33 LSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLseaNNIRTYAANQRRESQG---QLTLTTTHTQARFVLP 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 115 DLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIGAVLDAASLALTATgirtrPIGELRFVYAVAPHHPLARLPQP 194
Cdd:PRK12680  110 PAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIAV-----PLYRWRRLVVVPRGHALDTPRRA 184

                         170       180
                  ....*....|....*....|....
gi 1543042950 195 LSDAVMRQHRAVAAADSARHGPSM 218
Cdd:PRK12680  185 PDMAALAEHPLISYESSTRPGSSL 208
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
13-189 1.42e-03

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 40.00  E-value: 1.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  13 LAMLQTVAAAGSFAAAARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIdavANRVKRV 92
Cdd:PRK15421    7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQI---SQALQAC 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  93 ATGWEPMLTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIgavldaASLALTATGIRTRP 172
Cdd:PRK15421   84 NEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVM------TSDILPRSGLHYSP 157

                         170
                  ....*....|....*..
gi 1543042950 173 IGELRFVYAVAPHHPLA 189
Cdd:PRK15421  158 MFDYEVRLVLAPDHPLA 174
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 141-270 1.95e-03

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: 38.79  E-value: 1.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 141 EALTSGEADLAIGAVLDAASlaltATGIRTRPIGELRFVYAVAPHHPLARLPQPLSDAVMR-----QHRAVAAADS---- 211
Cdd:cd08435    43 EGLRAGELDLAIGRLADDEQ----PPDLASEELADEPLVVVARPGHPLARRARLTLADLADypwvlPPPGTPLRQRleql 118

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1543042950 212 -ARHGPSMTVNLMGGQDVLTVPSMQAK---IAaqlhglgggFLPDPMARPYIEAGHLVELKTE 270
Cdd:cd08435   119 fAAAGLPLPRNVVETASISALLALLARsdmLA---------VLPRSVAEDELRAGVLRELPLP 172
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
28-85 2.36e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 38.97  E-value: 2.36e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1543042950  28 AARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAV 85
Cdd:PRK10632   22 AARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDV 79
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 39-82 2.56e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 38.86  E-value: 2.56e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1543042950  39 LSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEI 82
Cdd:PRK11151   32 LSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREV 75
PRK09801 PRK09801
LysR family transcriptional regulator;
28-103 2.56e-03

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 38.86  E-value: 2.56e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1543042950  28 AARELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIDAVANRVKRVATGWEPMLTIA 103
Cdd:PRK09801   26 AAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEGMIRIG 101
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 99-192 3.46e-03

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors 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. In Agrobacterium tumefaciens, 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, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 37.85  E-value: 3.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950  99 MLTIAVDSVIARDPLLDLACAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIgavldaASLALTATGIRTRPIGELRF 178
Cdd:cd08457     1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGI------ADGPLEERQGFLIETRSLPA 74

                          90
                  ....*....|....
gi 1543042950 179 VYAVAPHHPLARLP 192
Cdd:cd08457    75 VVAVPMGHPLAQLD 88
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-265 4.96e-03

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 37.50  E-value: 4.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 115 DLAcAFFALEPPTRLKLRDETLLGTIEALTSGEADLAIgaVLDAASLAltatGIRTRPIGELRFVYAVAPHHPLARLPQP 194
Cdd:cd08421    18 DLA-SFLAAHPDVRIDLEERLSADIVRAVAEGRADLGI--VAGNVDAA----GLETRPYRTDRLVVVVPRDHPLAGRASV 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1543042950 195 ------------LSDAVMRQHRAVAAADSARHGPSMTVnlmggqdvlTVPSMQAkiAAQL--HGLGGGFLPDPMARPYIE 260
Cdd:cd08421    91 afadtldhdfvgLPAGSALHTFLREAAARLGRRLRLRV---------QVSSFDA--VCRMvaAGLGIGIVPESAARRYAR 159


                  ....*
gi 1543042950 261 AGHLV 265
Cdd:cd08421   160 ALGLR 164
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 30-104 7.71e-03

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 37.52  E-value: 7.71e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1543042950  30 RELNLVPSALSYRVRQIEDALDVLLFDRSARQARLTEAGAELLREADRLLNEIdAVANRVKRvATGWEPMLTIAV 104
Cdd:PRK11139   28 EELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL-AEATRKLR-ARSAKGALTVSL 100
 
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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