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Conserved domains on  [gi|547305109|ref|WP_022037261|]
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LysR family transcriptional regulator [Mediterraneibacter gnavus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-276 2.64e-52

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.59  E-value: 2.64e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   2 LDFR-METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL----RSALETMRNDEN 76
Cdd:COG0583    1 MDLRqLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLleraRRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  77 TLkKRMQESLKGkkVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYET 156
Cdd:COG0583   81 EL-RALRGGPRG--TLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 157 RIYKAEEYIAVASADHTFEnsvhslkdltserllirehgsgtrailtktlalknmsvkdfRHLVEIENIHTIVTLLKEDC 236
Cdd:COG0583  158 RPLGEERLVLVASPDHPLA-----------------------------------------RRAPLVNSLEALLAAVAAGL 196

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 547305109 237 GISFLYKAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKD 276
Cdd:COG0583  197 GIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRR 236
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-276 2.64e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.59  E-value: 2.64e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   2 LDFR-METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL----RSALETMRNDEN 76
Cdd:COG0583    1 MDLRqLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLleraRRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  77 TLkKRMQESLKGkkVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYET 156
Cdd:COG0583   81 EL-RALRGGPRG--TLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 157 RIYKAEEYIAVASADHTFEnsvhslkdltserllirehgsgtrailtktlalknmsvkdfRHLVEIENIHTIVTLLKEDC 236
Cdd:COG0583  158 RPLGEERLVLVASPDHPLA-----------------------------------------RRAPLVNSLEALLAAVAAGL 196

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 547305109 237 GISFLYKAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKD 276
Cdd:COG0583  197 GIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRR 236
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-276 7.50e-46

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: 156.24  E-value: 7.50e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   5 RMETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL-RSALETMRNDENTLKKRMQ 83
Cdd:NF040786   5 QLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLyEYAKEMLDLWEKLEEEFDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  84 ESLKGKKVLTFGVTMTIGEYaIVPA-LSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDH-YETRIYKA 161
Cdd:NF040786  85 YGKESKGVLRIGASTIPGQY-LLPElLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRlVYTPFYKD 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 162 EeyIAVASADHTFENSVH----SLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLLKEDCG 237
Cdd:NF040786 164 R--LVLITPNGTEKYRMLkeeiSISELQKEPFIMREEGSGTRKEAEKALKSLGISLEDLNVVASLGSTEAIKQSVEAGLG 241

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 547305109 238 ISFLYKAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKD 276
Cdd:NF040786 242 ISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKN 280
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-280 8.07e-40

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: 137.62  E-value: 8.07e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASAD 171
Cdd:cd08420    2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 172 HTF-ENSVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLLKEDCGISFLYKAAVEQEL 250
Cdd:cd08420   82 HPLaGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKEL 161

                        170       180       190
                 ....*....|....*....|....*....|
gi 547305109 251 KKGTLVQIPLSDFMVMHDFTFLWNKDSVFS 280
Cdd:cd08420  162 ELGRLVALPVEGLRLTRPFSLIYHKDKYLS 191
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-277 1.17e-29

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: 111.61  E-value: 1.17e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASAD 171
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  172 HTFENSVH-SLKDLTSERLLIREHGSGTRAILTKTLALKNMSVkdfRHLVEIENIHTIVTLLKEDCGISFLYKAAVEQEL 250
Cdd:pfam03466  84 HPLARGEPvSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRP---RVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180
                  ....*....|....*....|....*..
gi 547305109  251 KKGTLVQIPLSDFMVMHDFTFLWNKDS 277
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGR 187
rbcR CHL00180
LysR transcriptional regulator; Provisional
 11-290 2.79e-28

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 110.49  E-value: 2.79e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  11 TVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGE--------ILRSALETMR--NDENTLKk 80
Cdd:CHL00180  15 AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllrygnrILALCEETCRalEDLKNLQ- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  81 rmqeslKGKkvLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYET---R 157
Cdd:CHL00180  94 ------RGT--LIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKIleiT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 158 IYKAEEYIAVASADHTFENSVHSLK-DLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLLKEDC 236
Cdd:CHL00180 166 PYVEDELALIIPKSHPFAKLKKIQKeDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQSGL 245

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 547305109 237 GISFLYKAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKDSVFSQEYESIFHEL 290
Cdd:CHL00180 246 GAAFVSVSAIEKELELGLLHWIKIENITIKRMLSIITNPNRYKSKASETFYNEI 299
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 6-263 4.77e-27

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: 107.13  E-value: 4.77e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   6 METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILRSALETMRNDENTLKKRMQeS 85
Cdd:NF041036   6 LKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELK-S 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  86 LKGKKVLTFGVTMTIGEYAIVPALSRFVKTHPDM-DFHIRYGNTQTLLTYLCEGTIDFAIVEgYFSGDHYET-RIYK--A 161
Cdd:NF041036  85 FKGRQRLSICCTPTFGMAHLPGVLNRFMLRNADVvDLKFLFHSPAQALEGIQNKEFDLAIIE-HCADLDLGRfHTYPlpQ 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 162 EEYIAVASADHTFENSVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLLKEDCGISFL 241
Cdd:NF041036 164 DELVFVSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLDDFRRVVVSDDLRLTIQTVLDGGGISFV 243

                        250       260
                 ....*....|....*....|..
gi 547305109 242 YKAAVEQELKKGTLVQIPLSDF 263
Cdd:NF041036 244 SRSLVCEYLKNGQLREHYVEGF 265
HTH_metalloreg NF033788
metalloregulator ArsR/SmtB family transcription factor; Transcriptional repressors that sense ...
 22-41 7.24e-03

metalloregulator ArsR/SmtB family transcription factor; Transcriptional repressors that sense toxic heavy metals such as arsenic or cadmium, and are released from DNA so that resistance factors will be expressed, include ArsR, SmtB, ZiaR, CadC, CadX, KmtR, etc. However, some members of this family, including the sporulation delaying system autorepressor SdpR and its family (see NF033789), may lack metal-binding cites and instead regulate other cellular processes.


Pssm-ID: 411368 [Multi-domain]  Cd Length: 76  Bit Score: 34.74  E-value: 7.24e-03
                         10        20
                 ....*....|....*....|
gi 547305109  22 AEHLNLTQPAVSQHIKHLEK 41
Cdd:NF033788  31 AEALGLSQSAVSQHLKVLRD 50
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-276 2.64e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 171.59  E-value: 2.64e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   2 LDFR-METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL----RSALETMRNDEN 76
Cdd:COG0583    1 MDLRqLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLleraRRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  77 TLkKRMQESLKGkkVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYET 156
Cdd:COG0583   81 EL-RALRGGPRG--TLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 157 RIYKAEEYIAVASADHTFEnsvhslkdltserllirehgsgtrailtktlalknmsvkdfRHLVEIENIHTIVTLLKEDC 236
Cdd:COG0583  158 RPLGEERLVLVASPDHPLA-----------------------------------------RRAPLVNSLEALLAAVAAGL 196

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 547305109 237 GISFLYKAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKD 276
Cdd:COG0583  197 GIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRR 236
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 5-276 7.50e-46

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: 156.24  E-value: 7.50e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   5 RMETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL-RSALETMRNDENTLKKRMQ 83
Cdd:NF040786   5 QLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLyEYAKEMLDLWEKLEEEFDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  84 ESLKGKKVLTFGVTMTIGEYaIVPA-LSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDH-YETRIYKA 161
Cdd:NF040786  85 YGKESKGVLRIGASTIPGQY-LLPElLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRlVYTPFYKD 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 162 EeyIAVASADHTFENSVH----SLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLLKEDCG 237
Cdd:NF040786 164 R--LVLITPNGTEKYRMLkeeiSISELQKEPFIMREEGSGTRKEAEKALKSLGISLEDLNVVASLGSTEAIKQSVEAGLG 241

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 547305109 238 ISFLYKAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKD 276
Cdd:NF040786 242 ISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKN 280
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-280 8.07e-40

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: 137.62  E-value: 8.07e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASAD 171
Cdd:cd08420    2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 172 HTF-ENSVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLLKEDCGISFLYKAAVEQEL 250
Cdd:cd08420   82 HPLaGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKEL 161

                        170       180       190
                 ....*....|....*....|....*....|
gi 547305109 251 KKGTLVQIPLSDFMVMHDFTFLWNKDSVFS 280
Cdd:cd08420  162 ELGRLVALPVEGLRLTRPFSLIYHKDKYLS 191
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-280 4.62e-31

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: 115.00  E-value: 4.62e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASAD 171
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 172 HTFEN-SVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSvkdFRHLVEIENIHTIVTLLKEDCGISFLYKAAVeQEL 250
Cdd:cd05466   82 HPLAKrKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFT---PNIALEVDSLEAIKALVAAGLGIALLPESAV-EEL 157

                        170       180       190
                 ....*....|....*....|....*....|
gi 547305109 251 KKGTLVQIPLSDFMVMHDFTFLWNKDSVFS 280
Cdd:cd05466  158 ADGGLVVLPLEDPPLSRTIGLVWRKGRYLS 187
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-277 1.17e-29

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: 111.61  E-value: 1.17e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASAD 171
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  172 HTFENSVH-SLKDLTSERLLIREHGSGTRAILTKTLALKNMSVkdfRHLVEIENIHTIVTLLKEDCGISFLYKAAVEQEL 250
Cdd:pfam03466  84 HPLARGEPvSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRP---RVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180
                  ....*....|....*....|....*..
gi 547305109  251 KKGTLVQIPLSDFMVMHDFTFLWNKDS 277
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGR 187
rbcR CHL00180
LysR transcriptional regulator; Provisional
 11-290 2.79e-28

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 110.49  E-value: 2.79e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  11 TVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGE--------ILRSALETMR--NDENTLKk 80
Cdd:CHL00180  15 AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGElllrygnrILALCEETCRalEDLKNLQ- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  81 rmqeslKGKkvLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYET---R 157
Cdd:CHL00180  94 ------RGT--LIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKIleiT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 158 IYKAEEYIAVASADHTFENSVHSLK-DLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLLKEDC 236
Cdd:CHL00180 166 PYVEDELALIIPKSHPFAKLKKIQKeDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQSGL 245

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 547305109 237 GISFLYKAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKDSVFSQEYESIFHEL 290
Cdd:CHL00180 246 GAAFVSVSAIEKELELGLLHWIKIENITIKRMLSIITNPNRYKSKASETFYNEI 299
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 6-263 4.77e-27

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: 107.13  E-value: 4.77e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   6 METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILRSALETMRNDENTLKKRMQeS 85
Cdd:NF041036   6 LKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELK-S 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  86 LKGKKVLTFGVTMTIGEYAIVPALSRFVKTHPDM-DFHIRYGNTQTLLTYLCEGTIDFAIVEgYFSGDHYET-RIYK--A 161
Cdd:NF041036  85 FKGRQRLSICCTPTFGMAHLPGVLNRFMLRNADVvDLKFLFHSPAQALEGIQNKEFDLAIIE-HCADLDLGRfHTYPlpQ 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 162 EEYIAVASADHTFENSVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLLKEDCGISFL 241
Cdd:NF041036 164 DELVFVSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLDDFRRVVVSDDLRLTIQTVLDGGGISFV 243

                        250       260
                 ....*....|....*....|..
gi 547305109 242 YKAAVEQELKKGTLVQIPLSDF 263
Cdd:NF041036 244 SRSLVCEYLKNGQLREHYVEGF 265
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 6-260 5.21e-22

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 93.21  E-value: 5.21e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   6 METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL----RSALETMRNDENTLKkr 81
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLypraLALLEQAVEIEQLFR-- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  82 mqeslKGKKVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKA 161
Cdd:PRK10837  86 -----EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 162 EEYIAVASADHTFENSVHSLKDLTSERLLIREHGSGTRAILTKTLaLKNMSvkDFRHLVEIENIHTIVTLLKEDCGISFL 241
Cdd:PRK10837 161 DELVVFAAPDSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLL-LSHLP--RFELAMELGNSEAIKHAVRHGLGISCL 237

                        250
                 ....*....|....*....
gi 547305109 242 YKAAVEQELKKGTLVQIPL 260
Cdd:PRK10837 238 SRRVIADQLQAGTLVEVAV 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-62 1.25e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.20  E-value: 1.25e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 547305109    5 RMETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGE 62
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 11-291 1.14e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 86.97  E-value: 1.14e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  11 TVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKL-RLTPAGEILRSALETMRNDENTLkKRMQESLKGK 89
Cdd:PRK12682  12 AVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNI-KRIGDDFSNQ 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  90 KV--LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGyfSGDHYET----RIYKAEE 163
Cdd:PRK12682  91 DSgtLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATE--SLADDPDlatlPCYDWQH 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 164 YIAVASaDHTF-ENSVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEIENIHTIVTLlkeDCGISFLY 242
Cdd:PRK12682 169 AVIVPP-DHPLaQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRL---GLGVGIVA 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 547305109 243 KAAVEQElKKGTLVQIPlsdfmVMHDF----TFLWNKDSVFSQEYESIFHELC 291
Cdd:PRK12682 245 EMAYRPD-RDGDLVALP-----AGHLFgpntAWVALKRGAYLRNYVYKFIELC 291
PRK09986 PRK09986
LysR family transcriptional regulator;
2-144 6.85e-19

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 84.39  E-value: 6.85e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   2 LDFRM-ETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILrsaLETMR----NDEN 76
Cdd:PRK09986   7 IDLKLlRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKIL---MEESRrlldNAEQ 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 547305109  77 TLKKRMQESLKGKKVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI 144
Cdd:PRK09986  84 SLARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGI 151
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
5-185 2.09e-17

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 80.43  E-value: 2.09e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   5 RMETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILRSALE-TMRN-DENTLKKRM 82
Cdd:PRK10086  18 KLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKsSLDTlNQEILDIKN 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  83 QEsLKGKkvLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQ-TLLTYlcegTIDFAIvegYFSGDHYE--TRIY 159
Cdd:PRK10086  98 QE-LSGT--LTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENvNFQRA----GIDLAI---YFDDAPSAqlTHHF 167

                        170       180       190
                 ....*....|....*....|....*....|.
gi 547305109 160 KAEEYIA-VASAD----HTFENSVHSLKDLT 185
Cdd:PRK10086 168 LMDEEILpVCSPEyaerHALTGNPDNLRHCT 198
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
6-144 3.01e-17

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 79.68  E-value: 3.01e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   6 METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILRSALETMRNDENTLKKRMQES 85
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHT 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 547305109  86 LKGKKvLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI 144
Cdd:PRK03601  86 SQHNE-LSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLI 143
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 9-172 8.34e-17

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 78.66  E-value: 8.34e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   9 FLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEI-LRSALETMRNDENTlKKRMQESLK 87
Cdd:PRK09906   9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVfLQDARAILEQAEKA-KLRARKIVQ 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  88 GKKVLTFGVtMTIGEYAIVP-ALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIA 166
Cdd:PRK09906  88 EDRQLTIGF-VPSAEVNLLPkVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDEPLVV 166


                 ....*.
gi 547305109 167 VASADH 172
Cdd:PRK09906 167 VLPVDH 172
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
15-144 7.37e-16

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 76.17  E-value: 7.37e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  15 DMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLR-LTPAG-EILRSALETMRNDENTLKKRMQESLKGKKVL 92
Cdd:PRK12684  16 NFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGrIILASVERILQEVENLKRVGKEFAAQDQGNL 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 547305109  93 TFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI 144
Cdd:PRK12684  96 TIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 16-190 8.27e-16

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 76.04  E-value: 8.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  16 MNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL----RSALETMRndENTLKKRmqeSLKGKKV 91
Cdd:PRK11139  21 LSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYfldiREIFDQLA--EATRKLR---ARSAKGA 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRygnTQTLLTYLCEGTIDFAIvegYFSGDHY---ETRIYKAEEYIAVA 168
Cdd:PRK11139  96 LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLK---AVDRLEDFLRDDVDVAI---RYGRGNWpglRVEKLLDEYLLPVC 169

                        170       180
                 ....*....|....*....|...
gi 547305109 169 S-ADHTFENSVHSLKDLTSERLL 190
Cdd:PRK11139 170 SpALLNGGKPLKTPEDLARHTLL 192
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 11-144 8.47e-16

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 75.85  E-value: 8.47e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  11 TVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLR-LTPAGEILRSALETMRNDENTLKKRMQE-SLKG 88
Cdd:PRK12683  12 AVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQfADRD 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 547305109  89 KKVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI 144
Cdd:PRK12683  92 SGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGI 147
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 9-144 1.95e-15

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 74.99  E-value: 1.95e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   9 FLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEI-LRSA------LETMR---NDENTL 78
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVyLRYArralqdLEAGRraiHDVADL 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 547305109  79 KkrmqeslKGKkvLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI 144
Cdd:PRK11242  89 S-------RGS--LRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGI 145
PRK10341 PRK10341
transcriptional regulator TdcA;
9-276 7.79e-15

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 73.36  E-value: 7.79e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   9 FLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILRSALETMRND-ENTLKKRMQESLK 87
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREmKNMVNEINGMSSE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  88 GKKVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIveGYFSGD------HYETrIYKA 161
Cdd:PRK10341  95 AVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAI--GTLSNEmklqdlHVEP-LFES 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 162 eEYIAVASADHTFENSVhSLKDLTSERLLIREHGSGTRAILTKTLAlknmsvkdfRHLVEIENI---HTIVTLLKEDCGI 238
Cdd:PRK10341 172 -EFVLVASKSRTCTGTT-TLESLKNEQWVLPQTNMGYYSELLTTLQ---------RNGISIENIvktDSVVTIYNLVLNA 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 547305109 239 SFL--YKAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKD 276
Cdd:PRK10341 241 DFLtvIPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKN 280
cysB PRK12681
HTH-type transcriptional regulator CysB;
12-144 1.17e-14

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 73.01  E-value: 1.17e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  12 VCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKL-RLTPAGE-ILRSALETMRNDENtLKKRMQE-SLKG 88
Cdd:PRK12681  13 VNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEeIIRIAREILSKVES-IKSVAGEhTWPD 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 547305109  89 KKVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI 144
Cdd:PRK12681  92 KGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAI 147
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 92-266 4.00e-14

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: 69.46  E-value: 4.00e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTiGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVeGYFSgDHYETRIYK--AEEYIAVAS 169
Cdd:cd08419    2 LRLAVVST-AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIM-GRPP-EDLDLVAEPflDNPLVVIAP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 170 ADHTFEN-SVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSvkdFRHLVEIENIHTIVTLLKEDCGISFLYKAAVEQ 248
Cdd:cd08419   79 PDHPLAGqKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVT---LRVRMELGSNEAIKQAVMAGLGLSVLSLHTLAL 155

                        170
                 ....*....|....*...
gi 547305109 249 ELKKGTLVQIPLSDFMVM 266
Cdd:cd08419  156 ELATGRLAVLDVEGFPIR 173
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 91-281 5.05e-13

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: 66.61  E-value: 5.05e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  91 VLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIveGYFSGDHYeTRIYKAE-----EYI 165
Cdd:cd08418    1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAI--GTLPDEMY-LKELISEplfesDFV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 166 AVASADHTFENSvHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVkdfRHLVEIENIHTIVTLLKEDCGISFLYKAA 245
Cdd:cd08418   78 VVARKDHPLQGA-RSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNP---RVAVRTDSIVSIINLVEKADFLTILSRDM 153

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 547305109 246 VEQELKKGTLVQIPLSDFMVMHDFTFLWNKDSVFSQ 281
Cdd:cd08418  154 GRGPLDSFRLITIPVEEPLPSADYYLIYRKKSRLTP 189
PRK12680 PRK12680
LysR family transcriptional regulator;
15-145 6.56e-12

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 65.03  E-value: 6.56e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  15 DMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLR-LTPAG-EIL---RSALETMRNDENTLKKRMQESlKGK 89
Cdd:PRK12680  16 ELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGvEVIeraRAVLSEANNIRTYAANQRRES-QGQ 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 547305109  90 kvLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIV 145
Cdd:PRK12680  95 --LTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIV 148
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-78 7.50e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 64.61  E-value: 7.50e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 547305109   1 MLDFR-METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDkKKLRLTPAGEILRSALETMRNDENTL 78
Cdd:PRK13348   1 MLDYKqLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADL 78
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 94-280 9.33e-12

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: 62.55  E-value: 9.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  94 FGVTMTIGEYaIVPAL-SRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVeGYFS-GDHYETRIYKAEEYIAVASAD 171
Cdd:cd08434    4 LGFLHSLGTS-LVPDLiRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALC-SPVPdEPDIEWIPLFTEELVLVVPKD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 172 HTF--ENSVHsLKDLTSERLLIREHGSGTRAILTKTLALKNmsvkdFRHLV--EIENIHTIVTLLKEDCGISFLYKAAVE 247
Cdd:cd08434   82 HPLagRDSVD-LAELADEPFVLLSPGFGLRPIVDELCAAAG-----FTPKIafEGEEDSTIAGLVAAGLGVAILPEMTLL 155

                        170       180       190
                 ....*....|....*....|....*....|...
gi 547305109 248 QELKkgtLVQIPLSDFMVMHDFTFLWNKDSVFS 280
Cdd:cd08434  156 NPPG---VKKIPIKDPDAERTIGLAWLKDRYLS 185
PRK09791 PRK09791
LysR family transcriptional regulator;
21-184 1.09e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 64.01  E-value: 1.09e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  21 AAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGE-ILRSA---LETMRNDENTLKKRMQEsLKGkkVLTFGV 96
Cdd:PRK09791  25 ASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGEsFYQHAsliLEELRAAQEDIRQRQGQ-LAG--QINIGM 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  97 TMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIvEGYFSG--DH---YETRIYKaeEYIAVASAD 171
Cdd:PRK09791 102 GASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTI-NTYYQGpyDHeftFEKLLEK--QFAVFCRPG 178

                        170
                 ....*....|...
gi 547305109 172 HTFENSVhSLKDL 184
Cdd:PRK09791 179 HPAIGAR-SLKQL 190
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 91-280 2.51e-11

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: 61.52  E-value: 2.51e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  91 VLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI----VEGYFSGDHYEtRIYKaEEYIA 166
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrlaDDEQPPDLASE-ELAD-EPLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 167 VASADH-TFENSVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKdfRHLVEIENIHTIVTLLKEDCGISFLYKAA 245
Cdd:cd08435   79 VARPGHpLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLP--RNVVETASISALLALLARSDMLAVLPRSV 156

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 547305109 246 VEQELKKGTLVQIPLSDFMVMHDFTFLWNKDSVFS 280
Cdd:cd08435  157 AEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLS 191
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 18-195 9.88e-11

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 61.20  E-value: 9.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  18 FTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILRSALETMRNDENTLKKrMQeSLKGKKV---LTF 94
Cdd:PRK11151  18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE-MA-SQQGETMsgpLHI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  95 GVTMTIGEY---AIVPALSRfvkTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIV----EgyfSGDHYETRIYKAEEYIAV 167
Cdd:PRK11151  96 GLIPTVGPYllpHIIPMLHQ---TFPKLEMYLHEAQTHQLLAQLDSGKLDCAILalvkE---SEAFIEVPLFDEPMLLAV 169

                        170       180
                 ....*....|....*....|....*....
gi 547305109 168 aSADHTFENSVH-SLKDLTSERLLIREHG 195
Cdd:PRK11151 170 -YEDHPWANRDRvPMSDLAGEKLLMLEDG 197
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-117 2.03e-10

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 60.17  E-value: 2.03e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   1 MLDFR-METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDkKKLRLTPAGEILRSALETMRNDENTLK 79
Cdd:PRK03635   1 MLDYKqLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVRLLEAELL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 547305109  80 KRMQESLKGKkvltfgVTMTIgeyAI---------VPALSRFVKTHP 117
Cdd:PRK03635  80 GELPALDGTP------LTLSI---AVnadslatwfLPALAPVLARSG 117
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 2-144 2.43e-10

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 60.04  E-value: 2.43e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   2 LDFrMETFLTVCnDMN-FTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAG-EILRSALETMR-NDENTL 78
Cdd:PRK15092  13 LDL-LRTFVAVA-DLNtFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGiQLLGYARKILRfNDEACS 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 547305109  79 kKRMQESLKGkkVLTFGVTmtiGEYA--IVP-ALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI 144
Cdd:PRK15092  91 -SLMYSNLQG--VLTIGAS---DDTAdtILPfLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV 153
cbl PRK12679
HTH-type transcriptional regulator Cbl;
15-152 2.84e-10

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 59.82  E-value: 2.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  15 DMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLR-LTPAGEILRSALETMRNDENTLkKRMQESLKGKK--V 91
Cdd:PRK12679  16 DYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNV-RRLADLFTNDTsgV 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGD 152
Cdd:PRK12679  95 LTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSND 155
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-290 3.10e-10

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 59.68  E-value: 3.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   9 FLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEI----LRSALETMRNDENTLKKRMQE 84
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIfhsqIRHLLQQLESNLAELRGGSDY 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  85 SLKGKKV-----LTFGVTMTIgeYAIVPALSRFVKTHPDMDFHI---RYGNTQTLLTYLcegtiDFAIVEGYFsgDHyeT 156
Cdd:PRK10082  99 AQRKIKIaaahsLSLGLLPSI--ISQMPPLFTWAIEAIDVDEAVdklREGQSDCIFSFH-----DEDLLEAPF--DH--I 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 157 RIYKAEEYIAVASADHTfensvHSLKDLTSER--LLIREHGSGTRAILTKTLALKN-MSVKDFRhlveienIHTIVTLLK 233
Cdd:PRK10082 168 RLFESQLFPVCASDEHG-----EALFNLAQPHfpLLNYSRNSYMGRLINRTLTRHSeLSFSTFF-------VSSMSELLK 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 547305109 234 E----DCGISFLYKAAVEQELKKGTLVQIPlSDFMVMHDFTFLWNKDSVFSQEYESIFHEL 290
Cdd:PRK10082 236 QvaldGCGIAWLPEYAIQQEIRSGQLVVLN-RDELVIPIQAYAYRMNTRMNPVAERFWREL 295
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 107-277 4.26e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 58.00  E-value: 4.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 107 PALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASADHTfenSVHSLKDLTS 186
Cdd:cd08442   17 PLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHP---PVSRAEDLAG 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 187 ERLLIREHGSGTRAILTKTLALKNMSVKdfrHLVEIENIHTIVTLLKEDCGISFLYKAAVEQELKKGTLVQIPLSDFMVM 266
Cdd:cd08442   94 STLLAFRAGCSYRRRLEDWLAEEGVSPG---KIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSIHPLPEPFAD 170

                        170
                 ....*....|.
gi 547305109 267 HDFTFLWNKDS 277
Cdd:cd08442  171 VTTWLVWRKDS 181
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 92-262 4.45e-10

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: 57.92  E-value: 4.45e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYET-RIYKaEEYIAVASA 170
Cdd:cd08411    3 LRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEePLFD-EPFLLAVPK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 171 DHT-FENSVHSLKDLTSERLLIREHGSGTRAIltkTLALKNMsvKDFRHLVEIE--NIHTIVTLLKEDCGISFLYKAAVE 247
Cdd:cd08411   82 DHPlAKRKSVTPEDLAGERLLLLEEGHCLRDQ---ALELCRL--AGAREQTDFEatSLETLRQMVAAGLGITLLPELAVP 156

                        170
                 ....*....|....*.
gi 547305109 248 QELKKGTLVQI-PLSD 262
Cdd:cd08411  157 SEELRGDRLVVrPFAE 172
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-64 8.19e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 58.66  E-value: 8.19e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 547305109   1 MLDFRM-ETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL 64
Cdd:PRK10094   1 MFDPETlRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHL 65
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-262 5.50e-09

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: 54.91  E-value: 5.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASAD 171
Cdd:cd08433    2 VSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPAD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 172 HTFE--NSVhSLKDLTSERLLIREHGSGTRAILTKTLALKNM--SVKdfrhlVEIENIHTIVTLLKEDCGISFLYKAAVE 247
Cdd:cd08433   82 APLPrgAPV-PLAELARLPLILPSRGHGLRRLVDEAAARAGLtlNVV-----VEIDSVATLKALVAAGLGYTILPASAVA 155

                        170
                 ....*....|....*
gi 547305109 248 QELKKGTLVQIPLSD 262
Cdd:cd08433  156 AEVAAGRLVAAPIVD 170
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-277 7.55e-09

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: 54.44  E-value: 7.55e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  91 VLTFGVTMTIGeYAIVP-ALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVAS 169
Cdd:cd08414    1 RLRIGFVGSAL-YGLLPrLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 170 ADHTF--ENSVhSLKDLTSERLLI--REHGSGTRAILTKTLAlknmsvkdfRHLV------EIENIHTIVTLLKEDCGIS 239
Cdd:cd08414   80 ADHPLaaRESV-SLADLADEPFVLfpREPGPGLYDQILALCR---------RAGFtprivqEASDLQTLLALVAAGLGVA 149

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 547305109 240 FLykAAVEQELKKGTLVQIPLSDFMVMHDFTFLWNKDS 277
Cdd:cd08414  150 LV--PASVARLQRPGVVYRPLADPPPRSELALAWRRDN 185
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
6-262 1.50e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 55.02  E-value: 1.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   6 METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL-----------RSALETMRND 74
Cdd:PRK15421   7 LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILlqlanqvlpqiSQALQACNEP 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  75 ENTlkkRMQESLKGKKVLTFgvtmtigeyaIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYF--SGD 152
Cdd:PRK15421  87 QQT---RLRIAIECHSCIQW----------LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILprSGL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 153 HYeTRIYKAEEYIAVAsADHTFENSVH-SLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKdfrhLVEIENIHTIVTL 231
Cdd:PRK15421 154 HY-SPMFDYEVRLVLA-PDHPLAAKTRiTPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPS----LKSVDNTLLLIQM 227

                        250       260       270
                 ....*....|....*....|....*....|.
gi 547305109 232 LKEDCGISFLYKAAVEQELKKGTLVQIPLSD 262
Cdd:PRK15421 228 VAARMGIAALPHWVVESFERQGLVVTKTLGE 258
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-262 1.72e-08

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: 53.37  E-value: 1.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIV-------EGyfsgdhYETRIYKAEEY 164
Cdd:cd08436    2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVglperrpPG------LASRELAREPL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 165 IAVASADHTFENSVH-SLKDLTSERLLIREHGSGTRAILTKTLA---LKnmsvkdfRHLV-EIENIHTIVTLLKEDCGIS 239
Cdd:cd08436   76 VAVVAPDHPLAGRRRvALADLADEPFVDFPPGTGARRQVDRAFAaagVR-------RRVAfEVSDVDLLLDLVARGLGVA 148

                        170       180
                 ....*....|....*....|...
gi 547305109 240 FLYKAAVEQelkKGTLVQIPLSD 262
Cdd:cd08436  149 LLPASVAAR---LPGLAALPLEP 168
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-262 1.54e-07

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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 50.77  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 109 LSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVegyFSGDH---YETRIYKAEEYIAVASADHTF--ENSVhSLKD 183
Cdd:cd08426   19 IARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLA---FSPPPepgIRVHSRQPAPIGAVVPPGHPLarQPSV-TLAQ 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 184 LTSERLLIREHGSGTRAILTKTLALKNMSVkdfrHLVEIEN-IHTIVTLLKEDCGISFLYKAAVEQELKKGTLVQIPLSD 262
Cdd:cd08426   95 LAGYPLALPPPSFSLRQILDAAFARAGVQL----EPVLISNsIETLKQLVAAGGGISLLTELAVRREIRRGQLVAVPLAD 170
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-126 2.85e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 50.59  E-value: 2.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  31 AVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILRS-ALETMrNDENTLKKRM---QESLKGKKVLTFGVTMTigeYAIV 106
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPfAQQTL-LQWQQLRHTLdqqGPSLSGELSLFCSVTAA---YSHL 82

                         90       100
                 ....*....|....*....|.
gi 547305109 107 PA-LSRFVKTHPDMDFHIRYG 126
Cdd:PRK11716  83 PPiLDRFRAEHPLVEIKLTTG 103
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-278 3.86e-07

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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 49.49  E-value: 3.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 107 PALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI-VEGYFSGD-HYETRIYKAEEYIAVASADHTfensVHSLKDL 184
Cdd:cd08427   17 RALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIvVEPPFPLPkDLVWTPLVREPLVLIAPAELA----GDDPREL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 185 TSERLLIR-EHGSGTRAILTKTLALKNMSVKDFrhlVEIENIHTIVTLLKEDCGISFLYKAAVEQELKKGtLVQIPLSDF 263
Cdd:cd08427   93 LATQPFIRyDRSAWGGRLVDRFLRRQGIRVREV---MELDSLEAIAAMVAQGLGVAIVPDIAVPLPAGPR-VRVLPLGDP 168

                        170
                 ....*....|....*
gi 547305109 264 MVMHDFTFLWNKDSV 278
Cdd:cd08427  169 AFSRRVGLLWRRSSP 183
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-262 4.09e-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: 49.45  E-value: 4.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 107 PALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIveGYFSGDHYE---TRIYKaEEYIAVASADHTFEN--SVhSL 181
Cdd:cd08440   17 PVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGI--GSEPEADPDlefEPLLR-DPFVLVCPKDHPLARrrSV-TW 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 182 KDLTSERLLIREHGSGTRAILTKTLALKNMsvkDFRHLVEIENIHTIVTLLKEDCGISFLYKAAVEQELKKGtLVQIPLS 261
Cdd:cd08440   93 AELAGYPLIALGRGSGVRALIDRALAAAGL---TLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPG-LVARPLT 168


                 .
gi 547305109 262 D 262
Cdd:cd08440  169 E 169
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 93-201 1.13e-06

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: 48.34  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  93 TFGVTMT-IGEYAIVPALSRFVKTH-PDMDFHIRYGNTQTLLTYLCEGTIDFAIveGYF---SGDHYETRIYKaEEYIAV 167
Cdd:cd08459    1 TFRIAMSdIGEMYFLPRLLAALREVaPGVRIETVRLPVDELEEALESGEIDLAI--GYLpdlGAGFFQQRLFR-ERYVCL 77

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 547305109 168 ASADHTFENSVHSLKDLTSER-LLIREHGSGTRAI 201
Cdd:cd08459   78 VRKDHPRIGSTLTLEQFLAARhVVVSASGTGHGLV 112
PRK09801 PRK09801
LysR family transcriptional regulator;
6-258 1.39e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.88  E-value: 1.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   6 METFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGE-ILRSALETMRNDENTLKKRMQE 84
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQrCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  85 SLKGKKVLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTylcEGTIDFAIVEGYFSGDHYETRIYKAEEY 164
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLV---QDNIDLDIRINDEIPDYYIAHLLTKNKR 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 165 IAVASADHTFENSV-HSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEiENIHTIVTLLKEDCGISFLYK 243
Cdd:PRK09801 168 ILCAAPEYLQKYPQpQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSS-NSGEIVLQWALEGKGIMLRSE 246

                        250
                 ....*....|....*
gi 547305109 244 AAVEQELKKGTLVQI 258
Cdd:PRK09801 247 WDVLPFLESGKLVQV 261
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 105-272 3.87e-05

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: 43.63  E-value: 3.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 105 IVP-ALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFS---GDHYETRIYKAeeYIAVASADHTFENSVHS 180
Cdd:cd08457   14 FLPrFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEerqGFLIETRSLPA--VVAVPMGHPLAQLDVVS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 181 LKDLTSERLLIREHGSGTRAILTKtlALKNMSVKDfRHLVEIENIHTIVTLLKEDCGISFLYKAAVEQELKKGtLVQIPL 260
Cdd:cd08457   92 PQDLAGERIITLENGYLFRMRVEV--ALGKIGVKR-RPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPLDG-IVIRPF 167

                        170
                 ....*....|..
gi 547305109 261 SDFMvmhDFTFL 272
Cdd:cd08457  168 DTFI---DAGFL 176
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 92-280 4.12e-05

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. 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: 176128  Cd Length: 198  Bit Score: 43.48  E-value: 4.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEG--YFSGDHYETRIYKAEEYIAVAS 169
Cdd:cd08437    2 LRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSltPLENSALHSKIIKTQHFMIIVS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 170 ADHTF-ENSVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMSVKDFRHLVEienIHTIVTLLKEDCGISFLYKAAVEQ 248
Cdd:cd08437   82 KDHPLaKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTND---IHILKSMVRENVGIGFLTDIAVKP 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 547305109 249 ElkkGTLVQIPLSDfmvMHDFTFLWN----KDSVFS 280
Cdd:cd08437  159 D---DHLVAIPLLD---NEQPTFYISlahrKDQLLT 188
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 5-64 4.98e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.90  E-value: 4.98e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   5 RMETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL 64
Cdd:PRK11233   5 RLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKIL 64
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 91-280 5.15e-05

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. 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: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 43.31  E-value: 5.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  91 VLTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASA 170
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 171 DHTF--ENSVhSLKDLTSERLLirehgsgtraILTKTLALKNMSVKDFRHL-------VEIENIHTIVTLLKEDCGISFL 241
Cdd:cd08438   81 GHPLagRKTV-SLADLADEPFI----------LFNEDFALHDRIIDACQQAgftpniaARSSQWDFIAELVAAGLGVALL 149

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 547305109 242 YKAAVeQELKKGTLVQIPLSDFMVMHDFTFLWNKDSVFS 280
Cdd:cd08438  150 PRSIA-QRLDNAGVKVIPLTDPDLRWQLALIWRKGRYLS 187
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 18-71 7.02e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 43.39  E-value: 7.02e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 547305109  18 FTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEIL----RSALETM 71
Cdd:PRK11074  19 FSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFvkeaRSVIKKM 76
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 93-201 1.81e-04

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: 41.82  E-value: 1.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  93 TFGVTMT-IGEYAIVPALSRFVKTH-PDMDFHIRYGNTQTLLTYLCEGTIDFAI-VEGYFSGDHYETRIYKaEEYIAVAS 169
Cdd:cd08417    1 TFRIAASdYLEALLLPPLLARLRQEaPGVRLRFVPLDRDDLEEALESGEIDLAIgVFPELPPGLRSQPLFE-DRFVCVAR 79

                         90       100       110
                 ....*....|....*....|....*....|...
gi 547305109 170 ADHTFENSVHSLKDLTSER-LLIREHGSGTRAI 201
Cdd:cd08417   80 KDHPLAGGPLTLEDYLAAPhVLVSPRGRGHGLV 112
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 92-144 2.11e-04

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176134  Cd Length: 198  Bit Score: 41.39  E-value: 2.11e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAI 144
Cdd:cd08443    2 LYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAI 54
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-239 3.14e-04

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: 41.01  E-value: 3.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASAD 171
Cdd:cd08415    2 LRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPG 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 547305109 172 HTF-ENSVHSLKDLTSERLLIREHGSGTRAILTKTLA---LKNMSVkdfrhlVEIENIHTIVTLLKEDCGIS 239
Cdd:cd08415   82 HPLaRKDVVTPADLAGEPLISLGRGDPLRQRVDAAFEragVEPRIV------IETQLSHTACALVAAGLGVA 147
PBP2_Pa0477 cd08468
The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional ...
 102-212 6.23e-04

The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. 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. 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: 176157 [Multi-domain]  Cd Length: 202  Bit Score: 40.11  E-value: 6.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 102 EYAIVPALSRFVKTH-PDMDFHIRYGNTQTLLTYLCEGTIDFAIveGYFSGDHYETR-----IYKAEEYIAVASADHTfE 175
Cdd:cd08468   11 ALAVMPRLMARLEELaPSVRLNLVHAEQKLPLDALLAGEIDFAL--GYSHDDGAEPRlieerDWWEDTYVVIASRDHP-R 87

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 547305109 176 NSVHSLKDLTSERLLIREHGSGTRAILTKTLALKNMS 212
Cdd:cd08468   88 LSRLTLDAFLAERHLVVTPWNEDRGVVDQVLEKQGLE 124
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-144 8.95e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 40.36  E-value: 8.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109   9 FLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEILRSALETMRNDENTLKK---RMQES 85
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDaiaALQVE 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 547305109  86 LKGKKVLTFGVTMTigEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLtyLCEGtIDFAI 144
Cdd:PRK14997  90 PRGIVKLTCPVTLL--HVHIGPMLAKFMARYPDVSLQLEATNRRVDV--VGEG-VDVAI 143
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-187 1.12e-03

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 39.45  E-value: 1.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASAD 171
Cdd:cd08412    2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPAD 81

                         90
                 ....*....|....*..
gi 547305109 172 HTF-ENSVHSLKDLTSE 187
Cdd:cd08412   82 HPLaGKDEVSLADLAAE 98
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 7-66 2.60e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 38.82  E-value: 2.60e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 547305109   7 ETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAG-----EILRS 66
Cdd:PRK11013  10 EIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlrlfeEVQRS 74
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 92-145 2.84e-03

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB 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 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 37.99  E-value: 2.84e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 547305109  92 LTFGVTMTIGEYAIVPALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIV 145
Cdd:cd08413    2 LTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIA 55
leuO PRK09508
leucine transcriptional activator; Reviewed
 1-50 3.25e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 38.47  E-value: 3.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 547305109   1 MLDFRMET-FLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIR 50
Cdd:PRK09508  21 MVDLNLLTvFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVR 71
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 91-174 3.76e-03

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: 37.70  E-value: 3.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109  91 VLTFGVTMTIGEyAIVPA-LSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGyfSGDHYETRIYKAEEYIAVAS 169
Cdd:cd08439    1 TLRIGCPDDYAD-TILPFlLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITH--PPPGASATILRRSPTVWYCA 77


                 ....*
gi 547305109 170 ADHTF 174
Cdd:cd08439   78 AGYIL 82
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-262 4.41e-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: 4.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 104 AIV----PALSRFVKTHPDMDFHIRYGNTQTLLTYLCEGTIDFAIVEGYFSGDHYETRIYKAEEYIAVASADHTFENSVH 179
Cdd:cd08421   10 AIVeflpEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRAS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547305109 180 -SLKDL-----------TSERLLIREHGsgtrAILTKTLALKnMSVKDF---RHLVEienihtivtllkEDCGISFLYKA 244
Cdd:cd08421   90 vAFADTldhdfvglpagSALHTFLREAA----ARLGRRLRLR-VQVSSFdavCRMVA------------AGLGIGIVPES 152

                        170
                 ....*....|....*...
gi 547305109 245 AVEQELKKGTLVQIPLSD 262
Cdd:cd08421  153 AARRYARALGLRVVPLDD 170
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
5-63 5.78e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 37.82  E-value: 5.78e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 547305109   5 RMETFLTVCNDMNFTHAAEHLNLTQPAVSQHIKHLEKTYGTELFIRDKKKLRLTPAGEI 63
Cdd:PRK10632   6 RMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRI 64
HTH_metalloreg NF033788
metalloregulator ArsR/SmtB family transcription factor; Transcriptional repressors that sense ...
 22-41 7.24e-03

metalloregulator ArsR/SmtB family transcription factor; Transcriptional repressors that sense toxic heavy metals such as arsenic or cadmium, and are released from DNA so that resistance factors will be expressed, include ArsR, SmtB, ZiaR, CadC, CadX, KmtR, etc. However, some members of this family, including the sporulation delaying system autorepressor SdpR and its family (see NF033789), may lack metal-binding cites and instead regulate other cellular processes.


Pssm-ID: 411368 [Multi-domain]  Cd Length: 76  Bit Score: 34.74  E-value: 7.24e-03
                         10        20
                 ....*....|....*....|
gi 547305109  22 AEHLNLTQPAVSQHIKHLEK 41
Cdd:NF033788  31 AEALGLSQSAVSQHLKVLRD 50
 
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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