NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2511853648|ref|WP_284018223|]
View 

transcriptional regulator LrhA, partial [Cronobacter turicensis]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11487634)

LysR family transcriptional regulator LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-282 0e+00

DNA-binding transcriptional repressor LrhA; Provisional


:

Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 571.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648   8 VCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLMYSNLQGVLTIGASDESADTIL 87
Cdd:PRK15092   35 VCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYSNLQGVLTIGASDDTADTIL 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  88 PYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENLDSLVLRTSPTLWYCAADYTLHKNEAVPLVMLDE 167
Cdd:PRK15092  115 PFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPALNLRTSPTLWYCAAEYVLQKGEPIPLVLLDE 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 168 PSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMMSPELRVLGTSDGLPVLPETQYMLCRNTSSKN 247
Cdd:PRK15092  195 PSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMSPDLRVLGESEGLPPLPDTEYLLCRDPNSNN 274

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 2511853648 248 EMAEIIFQAMESHYQPWRYTA-AIEGGDDTLLMQGD 282
Cdd:PRK15092  275 ELAQVIFQAMESYHNPWQYSPlSAEEGDDSLLIERD 310
 
Name Accession Description Interval E-value
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-282 0e+00

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 571.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648   8 VCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLMYSNLQGVLTIGASDESADTIL 87
Cdd:PRK15092   35 VCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYSNLQGVLTIGASDDTADTIL 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  88 PYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENLDSLVLRTSPTLWYCAADYTLHKNEAVPLVMLDE 167
Cdd:PRK15092  115 PFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPALNLRTSPTLWYCAAEYVLQKGEPIPLVLLDE 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 168 PSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMMSPELRVLGTSDGLPVLPETQYMLCRNTSSKN 247
Cdd:PRK15092  195 PSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMSPDLRVLGESEGLPPLPDTEYLLCRDPNSNN 274

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 2511853648 248 EMAEIIFQAMESHYQPWRYTA-AIEGGDDTLLMQGD 282
Cdd:PRK15092  275 ELAQVIFQAMESYHNPWQYSPlSAEEGDDSLLIERD 310
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 73-257 3.32e-92

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 270.74  E-value: 3.32e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  73 VLTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENLDSLVLRTSPTLWYCAADY 152
Cdd:cd08439     1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTVWYCAAGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 153 TLHKNEAVPLVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMMSPELRVLGTSDGLPVL 232
Cdd:cd08439    81 ILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGESEGLPPL 160

                         170       180
                  ....*....|....*....|....*
gi 2511853648 233 PETQYMLCRNTSSKNEMAEIIFQAM 257
Cdd:cd08439   161 PDTGYTLCLDPNRPSELAQAFFEAL 185
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-221 6.53e-33

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 121.13  E-value: 6.53e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSL--MYSNLQGVLTIGASDESADTILP 88
Cdd:COG0583    28 SQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELraLRGGPRGTLRIGAPPSLARYLLP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  89 YLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPE--NLDSLVLRTSPTLWYCAADYTLHKNEAvplvmld 166
Cdd:COG0583   108 PLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPdpGLVARPLGEERLVLVASPDHPLARRAP------- 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2511853648 167 epsphrdiiieqlnaanvpwrisyVASTLPAVRAAVKAGLGITARPVEMMSPELR 221
Cdd:COG0583   181 ------------------------LVNSLEALLAAVAAGLGIALLPRFLAADELA 211
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 71-221 9.40e-26

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: 100.83  E-value: 9.40e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  71 QGVLTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPEN--LDSLVLRTSPTLWYC 148
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDpgLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 149 AADYTLHKNEAV--------PLVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMMSPEL 220
Cdd:pfam03466  81 PPDHPLARGEPVsledladePLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160


                  .
gi 2511853648 221 R 221
Cdd:pfam03466 161 A 161
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 11-209 1.54e-18

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: 83.44  E-value: 1.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLM-YSN-LQGVLTIGASDESADTILP 88
Cdd:NF040786   28 TQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDrYGKeSKGVLRIGASTIPGQYLLP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  89 YLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENL---------DSLVLRTSPTLwycaADYTLHKNEA 159
Cdd:NF040786  108 ELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKrlvytpfykDRLVLITPNGT----EKYRMLKEEI 183

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 160 -------VPLVMLDEPSPHRDIIIEQLNAANVP---WRISYVASTLPAVRAAVKAGLGIT 209
Cdd:NF040786  184 siselqkEPFIMREEGSGTRKEAEKALKSLGISledLNVVASLGSTEAIKQSVEAGLGIS 243
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-60 1.37e-05

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: 45.50  E-value: 1.37e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648   1 FAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDE 60
Cdd:NF041036   18 FSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDS 77
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-92 2.14e-03

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 38.74  E-value: 2.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARhGRNKLLTEHGIQLLGYARKilrfndeacTSLMYSNLQGVLtiGASDESADTILPYL 90
Cdd:TIGR03298  28 TPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQ---------VRLLEAELLAEL--PGLAPGAPTRLTIA 95


                  ..
gi 2511853648  91 LN 92
Cdd:TIGR03298  96 VN 97
 
Name Accession Description Interval E-value
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-282 0e+00

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 571.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648   8 VCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLMYSNLQGVLTIGASDESADTIL 87
Cdd:PRK15092   35 VCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYSNLQGVLTIGASDDTADTIL 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  88 PYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENLDSLVLRTSPTLWYCAADYTLHKNEAVPLVMLDE 167
Cdd:PRK15092  115 PFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPALNLRTSPTLWYCAAEYVLQKGEPIPLVLLDE 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 168 PSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMMSPELRVLGTSDGLPVLPETQYMLCRNTSSKN 247
Cdd:PRK15092  195 PSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMSPDLRVLGESEGLPPLPDTEYLLCRDPNSNN 274

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 2511853648 248 EMAEIIFQAMESHYQPWRYTA-AIEGGDDTLLMQGD 282
Cdd:PRK15092  275 ELAQVIFQAMESYHNPWQYSPlSAEEGDDSLLIERD 310
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 73-257 3.32e-92

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 270.74  E-value: 3.32e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  73 VLTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENLDSLVLRTSPTLWYCAADY 152
Cdd:cd08439     1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTVWYCAAGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 153 TLHKNEAVPLVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMMSPELRVLGTSDGLPVL 232
Cdd:cd08439    81 ILAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGESEGLPPL 160

                         170       180
                  ....*....|....*....|....*
gi 2511853648 233 PETQYMLCRNTSSKNEMAEIIFQAM 257
Cdd:cd08439   161 PDTGYTLCLDPNRPSELAQAFFEAL 185
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
11-221 6.53e-33

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 121.13  E-value: 6.53e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSL--MYSNLQGVLTIGASDESADTILP 88
Cdd:COG0583    28 SQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELraLRGGPRGTLRIGAPPSLARYLLP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  89 YLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPE--NLDSLVLRTSPTLWYCAADYTLHKNEAvplvmld 166
Cdd:COG0583   108 PLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPdpGLVARPLGEERLVLVASPDHPLARRAP------- 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2511853648 167 epsphrdiiieqlnaanvpwrisyVASTLPAVRAAVKAGLGITARPVEMMSPELR 221
Cdd:COG0583   181 ------------------------LVNSLEALLAAVAAGLGIALLPRFLAADELA 211
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 71-221 9.40e-26

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: 100.83  E-value: 9.40e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  71 QGVLTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPEN--LDSLVLRTSPTLWYC 148
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDpgLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 149 AADYTLHKNEAV--------PLVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMMSPEL 220
Cdd:pfam03466  81 PPDHPLARGEPVsledladePLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160


                  .
gi 2511853648 221 R 221
Cdd:pfam03466 161 A 161
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 74-223 1.69e-23

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: 94.59  E-value: 1.69e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTH--QPENLDSLVLRTSPTLWYCAAD 151
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALpvDDPGLESEPLFEEPLVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 152 YTLHKNEAV--------PLVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARP----VEMMSPE 219
Cdd:cd05466    82 HPLAKRKSVtladladePLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPesavEELADGG 161


                  ....
gi 2511853648 220 LRVL 223
Cdd:cd05466   162 LVVL 165
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 11-209 1.54e-18

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: 83.44  E-value: 1.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLM-YSN-LQGVLTIGASDESADTILP 88
Cdd:NF040786   28 TQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDrYGKeSKGVLRIGASTIPGQYLLP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  89 YLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENL---------DSLVLRTSPTLwycaADYTLHKNEA 159
Cdd:NF040786  108 ELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKrlvytpfykDRLVLITPNGT----EKYRMLKEEI 183

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 160 -------VPLVMLDEPSPHRDIIIEQLNAANVP---WRISYVASTLPAVRAAVKAGLGIT 209
Cdd:NF040786  184 siselqkEPFIMREEGSGTRKEAEKALKSLGISledLNVVASLGSTEAIKQSVEAGLGIS 243
rbcR CHL00180
LysR transcriptional regulator; Provisional
 11-142 1.51e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 72.36  E-value: 1.51e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLMY-SNLQ-GVLTIGASdesaDTILP 88
Cdd:CHL00180   32 SQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDlKNLQrGTLIIGAS----QTTGT 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2511853648  89 YLLNRISSV----YPKLAIDVRVQRNPYIIEMLNQQEIDL-VVTTHQPENLDSLVLRTS 142
Cdd:CHL00180  108 YLMPRLIGLfrqrYPQINVQLQVHSTRRIAWNVANGQIDIaIVGGEVPTELKKILEITP 166
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 74-233 3.72e-13

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 66.41  E-value: 3.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVT--THQPENLDSLVLRTSPTLWYCAAD 151
Cdd:cd08412     2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTydLDLPEDIAFEPLARLPPYVWLPAD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 152 YTLHKNEAV--------PLVMLDEPsPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGIT---ARPVEMMSPE- 219
Cdd:cd08412    82 HPLAGKDEVsladlaaePLILLDLP-HSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSllnDRPYRPWSYDg 160

                         170
                  ....*....|....*.
gi 2511853648 220 --LRVLGTSDGLPVLP 233
Cdd:cd08412   161 krLVRRPLADPVPPLR 176
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
11-138 1.43e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 60.76  E-value: 1.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHG-RNKLLTEHGIQLLGYARKILR-----------FNDEActslmysnlQGVLTIGA 78
Cdd:PRK12684   29 SQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVERILQevenlkrvgkeFAAQD---------QGNLTIAT 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2511853648  79 SDESADTILPYLLNRISSVYPKLAIDVRvQRNPY-IIEMLNQQEIDLVVTTHQPENLDSLV 138
Cdd:PRK12684  100 THTQARYALPAAIKEFKKRYPKVRLSIL-QGSPTqIAEMVLHGQADLAIATEAIADYKELV 159
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 12-217 1.70e-10

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 60.55  E-value: 1.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  12 QSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEA-CTSLMYSNLQGVLTIGASDESADTILPYL 90
Cdd:PRK09906   29 QPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAkLRARKIVQEDRQLTIGFVPSAEVNLLPKV 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  91 LNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPEN--LDSLVLRTSPTLWYCAADYTLHKNEAVPLVMLD-- 166
Cdd:PRK09906  109 LPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSdeIDYLELLDEPLVVVLPVDHPLAHEKEITAAQLDgv 188

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2511853648 167 ---EPSPHR-----DIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMMS 217
Cdd:PRK09906  189 nfiSTDPAYsgslaPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCTIIPGYMNN 247
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
11-131 3.75e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 59.26  E-value: 3.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLMYSNLQGVLTIGASDESADTILPYL 90
Cdd:PRK03601   28 TQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHTSQHNELSIGASASLWECMLTPW 107

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2511853648  91 LNRISSVYPKLAIDVRV-QRNPyIIEMLNQQEIDLVVTTHQP 131
Cdd:PRK03601  108 LGRLYQNQEALQFEARIaQRQS-LVKQLHERQLDLLITTEAP 148
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 74-212 5.80e-10

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: 57.54  E-value: 5.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTT--HQPENLDSLVLRTSPTLWYCAAD 151
Cdd:cd08440     2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSepEADPDLEFEPLLRDPFVLVCPKD 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2511853648 152 YTLHKNEAV--------PLVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARP 212
Cdd:cd08440    82 HPLARRRSVtwaelagyPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLP 150
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
13-134 1.10e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 57.91  E-value: 1.10e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  13 SAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLMYSN--LQGVLTIGASDESADTILPYL 90
Cdd:PRK11716    6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGpsLSGELSLFCSVTAAYSHLPPI 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2511853648  91 LNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHqPENL 134
Cdd:PRK11716   86 LDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAK-PETL 128
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 11-209 1.10e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 57.78  E-value: 1.10e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILrfndEACTSL--MYSNLQGVLTIGASDESADTILP 88
Cdd:PRK10837   30 SQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL----EQAVEIeqLFREDNGALRIYASSTIGNYILP 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  89 YLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVV---TTHQPENL------DSLVLRTSPTLWYCAADYTLHKNEA 159
Cdd:PRK10837  106 AMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLiegPCHSPELIsepwleDELVVFAAPDSPLARGPVTLEQLAA 185

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2511853648 160 VPLVMLDEPSPHRDiIIEQLNAANVP-WRISYVASTLPAVRAAVKAGLGIT 209
Cdd:PRK10837  186 APWILRERGSGTRE-IVDYLLLSHLPrFELAMELGNSEAIKHAVRHGLGIS 235
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 11-108 1.21e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 57.93  E-value: 1.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLMYSNLQGVLTIgasdesadTILP-- 88
Cdd:PRK11139   33 TQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAKGALTV--------SLLPsf 104

                          90       100
                  ....*....|....*....|....*.
gi 2511853648  89 ---YLLNRISSV---YPklAIDVRVQ 108
Cdd:PRK11139  105 aiqWLVPRLSSFneaHP--DIDVRLK 128
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 11-138 1.63e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 57.69  E-value: 1.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRN-KLLTEHGIQLLGYARKILRfndEACT----SLMYSNLQ-GVLTIGASDESAD 84
Cdd:PRK12682   29 SQPGVSKAIIELEEELGIEIFIRHGKRlKGLTEPGKAVLDVIERILR---EVGNikriGDDFSNQDsGTLTIATTHTQAR 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2511853648  85 TILPYLLNRISSVYPKLAIDVRvQRNP-YIIEMLNQQEIDLVVTTHQPENLDSLV 138
Cdd:PRK12682  106 YVLPRVVAAFRKRYPKVNLSLH-QGSPdEIARMVISGEADIGIATESLADDPDLA 159
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 74-209 3.65e-09

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: 55.26  E-value: 3.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPE--NLDSLVLRTSPTLWYCAAD 151
Cdd:cd08415     2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDhpGLESEPLASGRAVCVLPPG 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2511853648 152 YTLHKNEAV--------PLVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGIT 209
Cdd:cd08415    82 HPLARKDVVtpadlagePLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVA 147
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 74-209 1.27e-08

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: 53.65  E-value: 1.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDL-VV--TTHQPEnL-------DSLVLrtsp 143
Cdd:cd08420     2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLgLVegPVDHPD-LivepfaeDELVL---- 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2511853648 144 tlwYCAADYTLHKNEAV--------PLVMLDEPSPHRDIIIEQLNAANVP---WRISYVASTLPAVRAAVKAGLGIT 209
Cdd:cd08420    77 ---VVPPDHPLAGRKEVtaeelaaePWILREPGSGTREVFERALAEAGLDgldLNIVMELGSTEAIKEAVEAGLGIS 150
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
11-44 1.28e-08

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 50.46  E-value: 1.28e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG 44
Cdd:pfam00126  26 SQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 11-136 1.81e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 54.28  E-value: 1.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKL-LTEHGIQLLGYARKIL-------RFNDEactslmYSNL-QGVLTIGASDE 81
Cdd:PRK12683   29 SQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLldaenlrRLAEQ------FADRdSGHLTVATTHT 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2511853648  82 SADTILPYLLNRISSVYPKLAIDVRvQRNP-YIIEMLNQQEIDLVVTThqpENLDS 136
Cdd:PRK12683  103 QARYALPKVVRQFKEVFPKVHLALR-QGSPqEIAEMLLNGEADIGIAT---EALDR 154
cbl PRK12679
HTH-type transcriptional regulator Cbl;
11-138 1.13e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 52.12  E-value: 1.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKL-LTEHGIQLLGYARKILrfnDEA-----CTSLMYSNLQGVLTIGASDESAD 84
Cdd:PRK12679   29 SQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERIL---NEAsnvrrLADLFTNDTSGVLTIATTHTQAR 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2511853648  85 TILPYLLNRISSVYPKLAIDVrVQRNPY-IIEMLNQQEIDLVVTTHQPENLDSLV 138
Cdd:PRK12679  106 YSLPEVIKAFRELFPEVRLEL-IQGTPQeIATLLQNGEADIGIASERLSNDPQLV 159
PRK12680 PRK12680
LysR family transcriptional regulator;
11-128 6.14e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 50.01  E-value: 6.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRN-KLLTEHGIQLLGYARKILrfnDEACTSLMYS-----NLQGVLTIGASDESAD 84
Cdd:PRK12680   29 TQPGLSKQLKQLEDELGFLLFVRKGRSlESVTPAGVEVIERARAVL---SEANNIRTYAanqrrESQGQLTLTTTHTQAR 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2511853648  85 TILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTT 128
Cdd:PRK12680  106 FVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVS 149
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 73-209 1.30e-06

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: 47.89  E-value: 1.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  73 VLTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEID--LVVTTHQPENLDSLVLRTSPtlwYCAA 150
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDvgFVRPPPDPPGLASRPLLREP---LVVA 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2511853648 151 ---DYTLHKNEAVPLVML-DEP---------SPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGIT 209
Cdd:cd08414    78 lpaDHPLAARESVSLADLaDEPfvlfprepgPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVA 149
PRK09791 PRK09791
LysR family transcriptional regulator;
11-135 2.37e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 47.83  E-value: 2.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKI---LRFNDEACTSLMySNLQGVLTIGASDESADTIL 87
Cdd:PRK09791   32 SQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLIleeLRAAQEDIRQRQ-GQLAGQINIGMGASIARSLM 110

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2511853648  88 PYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENLD 135
Cdd:PRK09791  111 PAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYD 158
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 11-233 5.43e-06

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 46.95  E-value: 5.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR----FNDEActSLMYSNLQGVLTIGASDESADTI 86
Cdd:PRK11151   28 SQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLRevkvLKEMA--SQQGETMSGPLHIGLIPTVGPYL 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  87 LPYLLNRISSVYPKLAIdvrvqrnpYIIEMLNQQEIDLVVTTHqpenLDSLVLRT--------------SPTLWYCAADY 152
Cdd:PRK11151  106 LPHIIPMLHQTFPKLEM--------YLHEAQTHQLLAQLDSGK----LDCAILALvkeseafievplfdEPMLLAVYEDH 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 153 TLHKNEAVP--------LVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITarpvemMSPELRVL- 223
Cdd:PRK11151  174 PWANRDRVPmsdlagekLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGIT------LLPALAVPn 247

                         250
                  ....*....|.
gi 2511853648 224 -GTSDGLPVLP 233
Cdd:PRK11151  248 eRKRDGVCYLP 258
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 74-229 7.51e-06

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 45.67  E-value: 7.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGA--SDESADtiLPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDL---VVTTHQPENLDSLVLRTSPTLWYC 148
Cdd:cd08436     2 LAIGTitSLAAVD--LPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLafvGLPERRPPGLASRELAREPLVAVV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 149 AADYTLHKNEAVPLVML-DEP-------SPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARPVEMM--SP 218
Cdd:cd08436    80 APDHPLAGRRRVALADLaDEPfvdfppgTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAarLP 159

                         170
                  ....*....|.
gi 2511853648 219 ELRVLGTSDGL 229
Cdd:cd08436   160 GLAALPLEPAP 170
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-60 1.37e-05

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: 45.50  E-value: 1.37e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648   1 FAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDE 60
Cdd:NF041036   18 FSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDS 77
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 113-209 1.37e-05

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 44.83  E-value: 1.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 113 IIEMLNQQEIDLVVTTHQP--ENLDSLVLRTSPTLWYCAADYTLHKNEAV--------PLVMLDEPSPHRDIIIEQLNAA 182
Cdd:cd08434    41 LLDDLKNGELDLALCSPVPdePDIEWIPLFTEELVLVVPKDHPLAGRDSVdlaeladePFVLLSPGFGLRPIVDELCAAA 120

                          90       100
                  ....*....|....*....|....*..
gi 2511853648 183 NVPWRISYVASTLPAVRAAVKAGLGIT 209
Cdd:cd08434   121 GFTPKIAFEGEEDSTIAGLVAAGLGVA 147
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 74-233 2.02e-05

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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 44.51  E-value: 2.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTH-------QPENLDSLVLRTSPTLW 146
Cdd:cd08423     2 LRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypvtpppDDPGLTRVPLLDDPLDL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 147 YCAADYTLHKNEAVPLVML-DEP-------SPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITarpvemMSP 218
Cdd:cd08423    82 VLPADHPLAGREEVALADLaDEPwiagcpgSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVA------LVP 155

                         170
                  ....*....|....*
gi 2511853648 219 ELRVLGTSDGLPVLP 233
Cdd:cd08423   156 RLALGARPPGVVVRP 170
cysB PRK12681
HTH-type transcriptional regulator CysB;
12-139 2.63e-05

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 44.89  E-value: 2.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  12 QSAVSQQMQRLEQLVGKELFARHGRN-KLLTEHGIQLLGYARKILRfNDEACTSLM--YSNL-QGVLTIGASDESADTIL 87
Cdd:PRK12681   30 QPGISKQVRMLEDELGIQIFARSGKHlTQVTPAGEEIIRIAREILS-KVESIKSVAgeHTWPdKGSLYIATTHTQARYAL 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2511853648  88 PYLLNRISSVYPKLAIDVRvQRNP-YIIEMLNQQEIDLVVTTHQPENLDSLVL 139
Cdd:PRK12681  109 PPVIKGFIERYPRVSLHMH-QGSPtQIAEAAAKGNADFAIATEALHLYDDLIM 160
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-231 3.61e-05

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 44.18  E-value: 3.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  12 QSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLM-YSNLQ-GVLTIGASdesaDTILPY 89
Cdd:PRK11242   29 QPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHdVADLSrGSLRLAMT----PTFTAY 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  90 ----LLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENLD-----------SLVLRTSPTLWYCAADYTL 154
Cdd:PRK11242  105 ligpLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEieaqplftetlALVVGRHHPLAARRKALTL 184

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2511853648 155 HKNEAVPLVMLDEPSPHRDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGITARP--VEMMSPELRVLGTSDGLPV 231
Cdd:PRK11242  185 DELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLATLLPaaIAREHDGLCAIPLDPPLPQ 263
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 73-141 3.65e-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: 43.74  E-value: 3.65e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2511853648  73 VLTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTT--HQPENLDSLVLRT 141
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVfpELPPGLRSQPLFE 71
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-152 4.12e-05

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 44.22  E-value: 4.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648   9 CRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACTSLMYSNLQGVLTIGASDESADTILP 88
Cdd:PRK10086   39 SLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLV 118

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2511853648  89 YLLNRISSVYPKLAIDVRVqRNPYIieMLNQQEIDLVV--TTHQPENLDSLVLRTSPTLWYCAADY 152
Cdd:PRK10086  119 PRLADFTRRYPSISLTILT-GNENV--NFQRAGIDLAIyfDDAPSAQLTHHFLMDEEILPVCSPEY 181
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 74-236 5.13e-05

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has 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: 176124  Cd Length: 198  Bit Score: 43.35  E-value: 5.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTtHQPENLDSLVLRT--SPTLW-YCAA 150
Cdd:cd08433     2 VSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALL-YGPPPIPGLSTEPllEEDLFlVGPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 151 DYTLHKNEAVPLVMLDE-----PS-PH--RDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGIT------------- 209
Cdd:cd08433    81 DAPLPRGAPVPLAELARlplilPSrGHglRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTilpasavaaevaa 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2511853648 210 ----ARPVEmmSPELR---VLGTSDGLPVLPETQ 236
Cdd:cd08433   161 grlvAAPIV--DPALTrtlSLATPRDRPLSPAAL 192
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 85-209 8.83e-05

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 42.51  E-value: 8.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  85 TILPYLLNRISSV----YPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTH--QPENLDSLVLRTSPTLWYCAADYTLHKNE 158
Cdd:cd08411    10 TIAPYLLPRLLPAlrqaYPKLRLYLREDQTERLLEKLRSGELDAALLALpvDEPGLEEEPLFDEPFLLAVPKDHPLAKRK 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2511853648 159 AVPLVMLDEPS------PH--RDIIIEQLNAANVPWRISYVASTLPAVRAAVKAGLGIT 209
Cdd:cd08411    90 SVTPEDLAGERlllleeGHclRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGIT 148
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 74-232 4.06e-04

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 40.57  E-value: 4.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASdESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQPENLD---------SLVLRTSPt 144
Cdd:cd08419     2 LRLAVV-STAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDlvaepfldnPLVVIAPP- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 145 lwycaaDYTLHKNEAVPLVML-DEP-------SPHRdIIIEQLNAAN-VPWRISYVASTLPAVRAAVKAGLGIT-----A 210
Cdd:cd08419    80 ------DHPLAGQKRIPLERLaREPfllrepgSGTR-LAMERFFAEHgVTLRVRMELGSNEAIKQAVMAGLGLSvlslhT 152

                         170       180
                  ....*....|....*....|..
gi 2511853648 211 RPVEMMSPELRVLgTSDGLPVL 232
Cdd:cd08419   153 LALELATGRLAVL-DVEGFPIR 173
leuO PRK09508
leucine transcriptional activator; Reviewed
 11-126 4.73e-04

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 41.16  E-value: 4.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRfndeactsLMYSNLQGVLTIGASDESA------- 83
Cdd:PRK09508   49 SQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQ--------LVQNELPGSGFEPESSERVfnlcics 120

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2511853648  84 --DTIL-PYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVV 126
Cdd:PRK09508  121 plDIRLtSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVI 166
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 74-247 5.32e-04

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 40.09  E-value: 5.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  74 LTIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEID--LVVTTHQPENLDSLVLRTSPTLWYCAAD 151
Cdd:cd08456     2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDlgLVSTLHEPPGIERERLLRIDGVCVLPPG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 152 YTLHKN--------EAVPLVMLDEPSPHR---DIIIEQlnaANVPWRISYVASTLPAVRAAVKAGLGIT-ARPVEMMSPE 219
Cdd:cd08456    82 HRLAVKkvltpsdlEGEPFISLARTDGTRqrvDALFEQ---AGVKRRIVVETSYAATICALVAAGVGVSvVNPLTALDYA 158

                         170       180
                  ....*....|....*....|....*...
gi 2511853648 220 LRVLGTSDGLPVLPETqYMLCRNTSSKN 247
Cdd:cd08456   159 AAGLVVRRFSPAVPFE-VSLIRPKHRPS 185
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 11-130 7.49e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 40.36  E-value: 7.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFAR-HGRnkLL-TEHGIQL--------------LGYARKILRFNdeactslmysnlQGVL 74
Cdd:PRK11013   31 SQPTVSRELARFEKVIGLKLFERvRGR--LHpTVQGLRLfeevqrsyygldriVSAAESLREFR------------QGQL 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2511853648  75 TIGASDESADTILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDLVVTTHQ 130
Cdd:PRK11013   97 SIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETL 152
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
10-128 1.15e-03

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 40.00  E-value: 1.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  10 RTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILrfnDEACTSLMYSN--LQGVLTIGASDESADTIL 87
Cdd:PRK15421   28 QTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL---PQISQALQACNepQQTRLRIAIECHSCIQWL 104

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2511853648  88 PYLLNRISSVYPKLAIDVR--VQRNPYiiEMLNQQEIDLVVTT 128
Cdd:PRK15421  105 TPALENFHKNWPQVEMDFKsgVTFDPQ--PALQQGELDLVMTS 145
PRK09986 PRK09986
LysR family transcriptional regulator;
11-212 1.51e-03

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 39.32  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILrfnDEACTSLMY-----SNLQGVLTIGASDESADT 85
Cdd:PRK09986   34 SQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLL---DNAEQSLARveqigRGEAGRIEIGIVGTALWG 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  86 ILPYLLNRISSVYPKLAIDVRVQRNPYIIEMLNQQEIDL----VVTTHQPENLDSLVLRTSPTLWYCAADYTLHKNEAVP 161
Cdd:PRK09986  111 RLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAgiwrMADLEPNPGFTSRRLHESAFAVAVPEEHPLASRSSVP 190

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2511853648 162 LVMLDE------PSPHRDIIIEQ----LNAANVPwRISYVASTLPAVRAAVKAGLGITARP 212
Cdd:PRK09986  191 LKALRNeyfitlPFVHSDWGKFLqrvcQQAGFSP-QIIRQVNEPQTVLAMVSMGIGITLLP 250
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-92 2.14e-03

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 38.74  E-value: 2.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARhGRNKLLTEHGIQLLGYARKilrfndeacTSLMYSNLQGVLtiGASDESADTILPYL 90
Cdd:TIGR03298  28 TPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQ---------VRLLEAELLAEL--PGLAPGAPTRLTIA 95


                  ..
gi 2511853648  91 LN 92
Cdd:TIGR03298  96 VN 97
PRK10341 PRK10341
transcriptional regulator TdcA;
11-103 2.55e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 38.69  E-value: 2.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR-------------FNDEACTSLMYSNLQGVltig 77
Cdd:PRK10341   34 TQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITRemknmvneingmsSEAVVDVSFGFPSLIGF---- 109

                          90       100
                  ....*....|....*....|....*.
gi 2511853648  78 asdesadTILPYLLNRISSVYPKLAI 103
Cdd:PRK10341  110 -------TFMSDMINKFKEVFPKAQV 128
PRK11482 PRK11482
DNA-binding transcriptional regulator;
11-129 2.74e-03

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 38.55  E-value: 2.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  11 TQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILrfndEACTSLMysNLQG------VLTIGASDESAD 84
Cdd:PRK11482   56 TPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGL----ESILGAL--DITGsydkqrTITIATTPSVGA 129

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2511853648  85 TILPYLLNRISSVYPKLAIdvrvqRNPYIIE---MLNQQEIDLVVTTH 129
Cdd:PRK11482  130 LVMPVIYQAIKTHYPQLLL-----RNIPISDaenQLSQFQTDLIIDTH 172
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 72-234 7.15e-03

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: 36.65  E-value: 7.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648  72 GVLTIGASDESADTILPYLLNRISSVYPKLAIDVRV-QRNPYIIEmlnqQEIDLVVTTHQPENlDSLV---LRTSPTLWY 147
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLsDRLVDLVE----EGFDLAIRIGELPD-SSLVarrLGPVRRVLV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2511853648 148 CAADYtLHKNeAVPLVmLDEPSPHRDIIIeQLNAANVPWRI-------------SYVASTLPAVRAAVKAGLGITARPVE 214
Cdd:cd08422    76 ASPAY-LARH-GTPQT-PEDLARHRCLGY-RLPGRPLRWRFrrgggevevrvrgRLVVNDGEALRAAALAGLGIALLPDF 151

                         170       180
                  ....*....|....*....|..
gi 2511853648 215 MMSPELRvlgtsDG--LPVLPE 234
Cdd:cd08422   152 LVAEDLA-----SGrlVRVLPD 168
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-55 7.86e-03

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 37.09  E-value: 7.86e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2511853648   1 FAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL 55
Cdd:PRK10094   19 FSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH