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Conserved domains on  [gi|575844639|gb|ETY75792|]
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hypothetical protein LFAB_00150 [Lactiplantibacillus fabifermentans T30PCM01]

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_Sec_metab super family cl49002
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-268 2.77e-43

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.


The actual alignment was detected with superfamily member NF040786:

Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 149.69  E-value: 2.77e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   3 NLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQLEQT 82
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  83 FVR---PVQATLKVAATSVLSL-IAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAAlnsDQVATYQTRYa 156
Cdd:NF040786  82 FDRygkESKGVLRIGASTIPGQyLLPELLKKFKEKypNVRFKLMISDSIKVIELLLEGEVDIGFTG---TKLEKKRLVY- 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 157 vMPLATDAVYLVANRQNSLSQRTQ--VTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQS---ILRVPQHATVAQMI 231
Cdd:NF040786 158 -TPFYKDRLVLITPNGTEKYRMLKeeISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEDlnvVASLGSTEAIKQSV 236

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 575844639 232 QNGMGIGLLSQYWLQSAAD--KLTILPVADFPVEREIYL 268
Cdd:NF040786 237 EAGLGISVISELAAEKEVErgRVLIFPIPGLPKNRDFYL 275
 
Name Accession Description Interval E-value
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-268 2.77e-43

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: 149.69  E-value: 2.77e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   3 NLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQLEQT 82
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  83 FVR---PVQATLKVAATSVLSL-IAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAAlnsDQVATYQTRYa 156
Cdd:NF040786  82 FDRygkESKGVLRIGASTIPGQyLLPELLKKFKEKypNVRFKLMISDSIKVIELLLEGEVDIGFTG---TKLEKKRLVY- 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 157 vMPLATDAVYLVANRQNSLSQRTQ--VTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQS---ILRVPQHATVAQMI 231
Cdd:NF040786 158 -TPFYKDRLVLITPNGTEKYRMLKeeISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEDlnvVASLGSTEAIKQSV 236

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 575844639 232 QNGMGIGLLSQYWLQSAAD--KLTILPVADFPVEREIYL 268
Cdd:NF040786 237 EAGLGISVISELAAEKEVErgRVLIFPIPGLPKNRDFYL 275
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-290 5.70e-36

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 129.60  E-value: 5.70e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   3 NLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQLEQT 82
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  83 ---FVRPVQATLKVAAT-SVLSLIAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDqvatyQTRYA 156
Cdd:COG0583   82 lraLRGGPRGTLRIGAPpSLARYLLPPLLARFRARhpGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-----DPGLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 157 VMPLATDAVYLVANRQNSLSQRTQVtpkdlqqqvfvmreagsgtatlltkflrgqqikaqsilrVPQHATVAQMIQNGMG 236
Cdd:COG0583  157 ARPLGEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLG 197

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 575844639 237 IGLLSQYWLQS--AADKLTILPVADFPVEREIYLLAPQATDQ---LRAFASLVTELLTA 290
Cdd:COG0583  198 IALLPRFLAADelAAGRLVALPLPDPPPPRPLYLVWRRRRHLspaVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-291 3.05e-27

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: 105.06  E-value: 3.05e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   90 TLKVAATSVLSL-IAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDQvatyqTRYAVMPLATDAVY 166
Cdd:pfam03466   3 RLRIGAPPTLASyLLPPLLARFRERypDVELELTEGNSEELLDLLLEGELDLAIRRGPPDD-----PGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  167 LVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYWLQ 246
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 575844639  247 S--AADKLTILPVADFPVEREIYLLAPQATDQLRAFASLVTELLTAA 291
Cdd:pfam03466 158 RelADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 90-287 1.27e-25

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: 100.75  E-value: 1.27e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  90 TLKVAATSVLSL-IAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDQvatyqTRYAVMPLATDAVY 166
Cdd:cd05466    1 TLRIGASPSIAAyLLPPLLAAFRQRypGVELSLVEGGSSELLEALLEGELDLAIVALPVDD-----PGLESEPLFEEPLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 167 LVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYWLQ 246
Cdd:cd05466   76 LVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 575844639 247 SAAD-KLTILPVADFPVEREIYLLAPQATDQLRAFASLVTEL 287
Cdd:cd05466  156 ELADgGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 2-269 3.23e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 68.56  E-value: 3.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   2 VNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLlrFD--GQRYRATADGAIVLSYAAKIFQLTDQL 79
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQL--FDrvGKRLVVNEHGRLLYPRALALLEQAVEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  80 EQTFVRPVQAtLKVAATSVL-SLIAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCAL---AALNSDQVATyqt 153
Cdd:PRK10837  81 EQLFREDNGA-LRIYASSTIgNYILPAMIARYRRDypQLPLELSVGNSQDVINAVLDFRVDIGLiegPCHSPELISE--- 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 154 ryavmPLATDAVYLVANRQNSLSQRtQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQN 233
Cdd:PRK10837 157 -----PWLEDELVVFAAPDSPLARG-PVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRH 230

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 575844639 234 GMGIGLLSQYWL--QSAADKLTILPVADFPVEREIYLL 269
Cdd:PRK10837 231 GLGISCLSRRVIadQLQAGTLVEVAVPLPRLMRTLYRI 268
 
Name Accession Description Interval E-value
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-268 2.77e-43

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: 149.69  E-value: 2.77e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   3 NLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQLEQT 82
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  83 FVR---PVQATLKVAATSVLSL-IAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAAlnsDQVATYQTRYa 156
Cdd:NF040786  82 FDRygkESKGVLRIGASTIPGQyLLPELLKKFKEKypNVRFKLMISDSIKVIELLLEGEVDIGFTG---TKLEKKRLVY- 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 157 vMPLATDAVYLVANRQNSLSQRTQ--VTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQS---ILRVPQHATVAQMI 231
Cdd:NF040786 158 -TPFYKDRLVLITPNGTEKYRMLKeeISISELQKEPFIMREEGSGTRKEAEKALKSLGISLEDlnvVASLGSTEAIKQSV 236

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 575844639 232 QNGMGIGLLSQYWLQSAAD--KLTILPVADFPVEREIYL 268
Cdd:NF040786 237 EAGLGISVISELAAEKEVErgRVLIFPIPGLPKNRDFYL 275
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-290 5.70e-36

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 129.60  E-value: 5.70e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   3 NLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQLEQT 82
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  83 ---FVRPVQATLKVAAT-SVLSLIAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDqvatyQTRYA 156
Cdd:COG0583   82 lraLRGGPRGTLRIGAPpSLARYLLPPLLARFRARhpGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-----DPGLV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 157 VMPLATDAVYLVANRQNSLSQRTQVtpkdlqqqvfvmreagsgtatlltkflrgqqikaqsilrVPQHATVAQMIQNGMG 236
Cdd:COG0583  157 ARPLGEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLG 197

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 575844639 237 IGLLSQYWLQS--AADKLTILPVADFPVEREIYLLAPQATDQ---LRAFASLVTELLTA 290
Cdd:COG0583  198 IALLPRFLAADelAAGRLVALPLPDPPPPRPLYLVWRRRRHLspaVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-291 3.05e-27

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: 105.06  E-value: 3.05e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   90 TLKVAATSVLSL-IAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDQvatyqTRYAVMPLATDAVY 166
Cdd:pfam03466   3 RLRIGAPPTLASyLLPPLLARFRERypDVELELTEGNSEELLDLLLEGELDLAIRRGPPDD-----PGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  167 LVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYWLQ 246
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 575844639  247 S--AADKLTILPVADFPVEREIYLLAPQATDQLRAFASLVTELLTAA 291
Cdd:pfam03466 158 RelADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 90-287 1.27e-25

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: 100.75  E-value: 1.27e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  90 TLKVAATSVLSL-IAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDQvatyqTRYAVMPLATDAVY 166
Cdd:cd05466    1 TLRIGASPSIAAyLLPPLLAAFRQRypGVELSLVEGGSSELLEALLEGELDLAIVALPVDD-----PGLESEPLFEEPLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 167 LVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYWLQ 246
Cdd:cd05466   76 LVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 575844639 247 SAAD-KLTILPVADFPVEREIYLLAPQATDQLRAFASLVTEL 287
Cdd:cd05466  156 ELADgGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 90-272 5.24e-20

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: 85.64  E-value: 5.24e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  90 TLKVAATSVLSLIAPQMYAAVHQ--TGAELYLNISNSTGALDSLAAGGVDCALAALNSDQVATYQTRYAVMPLAtdavyL 167
Cdd:cd08419    1 RLRLAVVSTAKYFAPRLLGAFCRrhPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLV-----V 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 168 VANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYWLQS 247
Cdd:cd08419   76 IAPPDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLAL 155

                        170       180
                 ....*....|....*....|....*..
gi 575844639 248 --AADKLTILPVADFPVEREIYLLAPQ 272
Cdd:cd08419  156 elATGRLAVLDVEGFPIRRQWYVVHRK 182
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 90-287 1.42e-19

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: 84.47  E-value: 1.42e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  90 TLKVAATSVL-SLIAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCAL--AALNSDQVAtyqtryaVMPLATDA 164
Cdd:cd08420    1 TLRIGASTTIgEYLLPRLLARFRKRypEVRVSLTIGNTEEIAERVLDGEIDLGLveGPVDHPDLI-------VEPFAEDE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 165 VYLVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQI---KAQSILRVPQHATVAQMIQNGMGIGLLS 241
Cdd:cd08420   74 LVLVVPPDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLdglDLNIVMELGSTEAIKEAVEAGLGISILS 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 575844639 242 QYWLQS--AADKLTILPVADFPVEREIYLLAPQATDQLRAFASLVTEL 287
Cdd:cd08420  154 RLAVRKelELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 3.55e-14

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 65.87  E-value: 3.55e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 575844639    4 LKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADG 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 2-269 3.23e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 68.56  E-value: 3.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   2 VNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLlrFD--GQRYRATADGAIVLSYAAKIFQLTDQL 79
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQL--FDrvGKRLVVNEHGRLLYPRALALLEQAVEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  80 EQTFVRPVQAtLKVAATSVL-SLIAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCAL---AALNSDQVATyqt 153
Cdd:PRK10837  81 EQLFREDNGA-LRIYASSTIgNYILPAMIARYRRDypQLPLELSVGNSQDVINAVLDFRVDIGLiegPCHSPELISE--- 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 154 ryavmPLATDAVYLVANRQNSLSQRtQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQN 233
Cdd:PRK10837 157 -----PWLEDELVVFAAPDSPLARG-PVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRH 230

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 575844639 234 GMGIGLLSQYWL--QSAADKLTILPVADFPVEREIYLL 269
Cdd:PRK10837 231 GLGISCLSRRVIadQLQAGTLVEVAVPLPRLMRTLYRI 268
PBP_like pfam12727
PBP superfamily domain; This family belongs to the periplasmic binding domain superfamily. It ...
 104-287 1.93e-11

PBP superfamily domain; This family belongs to the periplasmic binding domain superfamily. It is often associated with a helix-turn-helix domain.


Pssm-ID: 463683 [Multi-domain]  Cd Length: 192  Bit Score: 61.82  E-value: 1.93e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  104 PQMYAAVHQTGaelylnisnSTGALDSLAAGGVDCALAALNSDQVATYQTRY----------AVMPLATDAVYLVANRQN 173
Cdd:pfam12727   9 PGVRLAVAYVG---------SLGGLAALRRGEAHIAGIHLLDPETGEYNLPFlrrllpgipvVLINLAYREQGLVVAPGN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  174 SLSQRTqvtPKDLQQQ--VFVMREAGSGTATLLTKFLRGQQIKAQSI----LRVPQHATVAQMIQNGM---GIGllsqyw 244
Cdd:pfam12727  80 PKGITG---WEDLARPglRFVNRQRGSGTRVLLDELLRKAGIDPSDIngydREERSHLAVAAAVASGRadaGLG------ 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 575844639  245 LQSAADKLTILpvaDF-PVEREIY-LLAPQATDQLRAFASLVTEL 287
Cdd:pfam12727 151 IEAAARALGGL---DFiPLARERYdLVIPKEALDDPAVQALLEVL 192
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 89-269 3.39e-11

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: 61.39  E-value: 3.39e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  89 ATLKVAATSVLsliaPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDQvatyqTRYAVMPLATDAVY 166
Cdd:cd08440    5 AALPSLAATLL----PPVLAAFRRRhpGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEAD-----PDLEFEPLLRDPFV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 167 LVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQY-WL 245
Cdd:cd08440   76 LVCPKDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALaLP 155

                        170       180
                 ....*....|....*....|....
gi 575844639 246 QSAADKLTILPVADFPVEREIYLL 269
Cdd:cd08440  156 LADHPGLVARPLTEPVVTRTVGLI 179
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 90-287 5.33e-10

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: 57.96  E-value: 5.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  90 TLKVAATSVLSL-IAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDQVATyqtryAVMPLATDAVY 166
Cdd:cd08415    1 TLRIAALPALALsLLPRAIARFRARhpDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGL-----ESEPLASGRAV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 167 LVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYWLQ 246
Cdd:cd08415   76 CVLPPGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAA 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 575844639 247 S-AADKLTILPVADfPVEREIYLLAPQATDQLRAFASLVTEL 287
Cdd:cd08415  156 GyAGAGLVVRPFRP-AIPFEFALVRPAGRPLSRLAQAFIDLL 196
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 90-284 1.47e-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: 56.36  E-value: 1.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  90 TLKVAAT-SVLSLIAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCALAALNSDQvatyqTRYAVMPLATDAVY 166
Cdd:cd08414    1 RLRIGFVgSALYGLLPRLLRRFRARypDVELELREMTTAEQLEALRAGRLDVGFVRPPPDP-----PGLASRPLLREPLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 167 LVANRQNSLSQRTQVTPKDLQQQVFVM--REAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYW 244
Cdd:cd08414   76 VALPADHPLAARESVSLADLADEPFVLfpREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASV 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 575844639 245 LQSAADKLTILPVADFPVEREIYLL--APQATDQLRAFASLV 284
Cdd:cd08414  156 ARLQRPGVVYRPLADPPPRSELALAwrRDNASPALRAFLELA 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-247 5.85e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 56.18  E-value: 5.85e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   1 MVNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQLE 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  81 QTFVRPVQATLKVA--ATSVLSLIAPQMYA-AVHQTGAELYLNISNSTGALDSLAAGGVDCalaALNSDQVATYQTRYAv 157
Cdd:PRK15421  81 QACNEPQQTRLRIAieCHSCIQWLTPALENfHKNWPQVEMDFKSGVTFDPQPALQQGELDL---VMTSDILPRSGLHYS- 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 158 mPLATDAVYLVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIkAQSILRVPQHATVAQMIQNGMGI 237
Cdd:PRK15421 157 -PMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGV-SPSLKSVDNTLLLIQMVAARMGI 234

                        250
                 ....*....|
gi 575844639 238 GLLSQYWLQS 247
Cdd:PRK15421 235 AALPHWVVES 244
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-78 1.52e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 54.64  E-value: 1.52e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 575844639   4 LKALQTfvqVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQ 78
Cdd:CHL00180  10 LRILKA---IATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEE 81
PRK10341 PRK10341
transcriptional regulator TdcA;
5-256 7.33e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 52.94  E-value: 7.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   5 KALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQLEQTFV 84
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  85 RPVQATLKVAATSVLSLIAPQMYAAVHQTGAELYLNISNS------TGALDSLAAGGVDCALAALnSDQVATYQtrYAVM 158
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSmyeaqlSSFLPAIRDGRLDFAIGTL-SNEMKLQD--LHVE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 159 PLATDAVYLVANRQNSLSQRTqvTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNgmgig 238
Cdd:PRK10341 167 PLFESEFVLVASKSRTCTGTT--TLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLN----- 239

                        250
                 ....*....|....*...
gi 575844639 239 llsqywlqsaADKLTILP 256
Cdd:PRK10341 240 ----------ADFLTVIP 247
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 128-281 1.04e-07

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: 51.00  E-value: 1.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 128 LDSLAAGGVDCALAALnsdqVATYQTrYAVMPLATDAVYLVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKF 207
Cdd:cd08434   42 LDDLKNGELDLALCSP----VPDEPD-IEWIPLFTEELVLVVPKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDEL 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 208 LRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSqYWLQSAADKLTILPVADFPVEREIYL-------LAPqATDQLRAF 280
Cdd:cd08434  117 CAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILP-EMTLLNPPGVKKIPIKDPDAERTIGLawlkdryLSP-AARRFKDF 194


                 .
gi 575844639 281 A 281
Cdd:cd08434  195 V 195
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 104-268 2.00e-07

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: 50.22  E-value: 2.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 104 PQMYAAVHQTGAELYLNIS-NSTGAL-DSLAAGGVDCALAALNsdqVATYQTRyaVMPLATDAVYLVANRQNSLSQRTQV 181
Cdd:cd08411   17 PRLLPALRQAYPKLRLYLReDQTERLlEKLRSGELDAALLALP---VDEPGLE--EEPLFDEPFLLAVPKDHPLAKRKSV 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 182 TPKDLQQQVFVMREAGSGtatlltkfLRGQQIKAQSILRVPQHA--------TVAQMIQNGMGIGLLSQ-YWLQ--SAAD 250
Cdd:cd08411   92 TPEDLAGERLLLLEEGHC--------LRDQALELCRLAGAREQTdfeatsleTLRQMVAAGLGITLLPElAVPSeeLRGD 163

                        170
                 ....*....|....*...
gi 575844639 251 KLTILPVADFPVEREIYL 268
Cdd:cd08411  164 RLVVRPFAEPAPSRTIGL 181
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 124-271 2.69e-07

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: 50.02  E-value: 2.69e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 124 STGALDSLAAGGVDCALaaLNSDQvATYQTRYAVMPLATDAVYLVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATL 203
Cdd:cd08437   38 SAELLEQLLQGDLDIAL--LGSLT-PLENSALHSKIIKTQHFMIIVSKDHPLAKAKKVNFADLKKENFILLNEHFVHPKA 114

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 575844639 204 LTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYWLQSaADKLTILPVADFP--------VEREIYLLAP 271
Cdd:cd08437  115 FDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKP-DDHLVAIPLLDNEqptfyislAHRKDQLLTP 189
YvgK COG1910
Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism];
111-270 2.82e-07

Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism];


Pssm-ID: 441514 [Multi-domain]  Cd Length: 328  Bit Score: 51.16  E-value: 2.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 111 HQTGAELYLNISN--STGALDSLAAGGVDCALAALNSDQVATYQTRY-AVMPLATDAVyLVAnrqnsLSQRTQ---VTP- 183
Cdd:COG1910  115 EKRESGAGLASSYvgSLGGLEALARGEADIAGIHLLDEETGEYNIPYvRRYLPGRPAV-LIN-----LARREQgliVAKg 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 184 --------KDLQQQ--VFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQ----HATVAQMIQNGM---GIGllsqywLQ 246
Cdd:COG1910  189 npkgikglEDLARPdlRFVNRQKGSGTRVLLDELLRRLGIDPEDINGYEReeytHLAVAAAVASGEadvGLG------IE 262

                        170       180
                 ....*....|....*....|....*
gi 575844639 247 SAADKLTIlpvaDF-PVEREIYLLA 270
Cdd:COG1910  263 AAARAFGL----DFiPLAEERYDLV 283
PRK09986 PRK09986
LysR family transcriptional regulator;
2-240 3.16e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 50.88  E-value: 3.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   2 VNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRyratadgaIVLSYAAKIF-----QLT 76
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRS--------VVLTHAGKILmeesrRLL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  77 DQLEQTFVRPVQATLKVAATSVLSLIAPQMYAAVHQTGAELYLNISNSTGALDSLAAGGVDCALAALNSD-----QVATY 151
Cdd:PRK09986  79 DNAEQSLARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDagiwrMADLE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 152 QTR-YAVMPLATDAVYLVANRQNSLSQRTQVTPKDLQQQVFV-MREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQ 229
Cdd:PRK09986 159 PNPgFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFItLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLA 238

                        250
                 ....*....|.
gi 575844639 230 MIQNGMGIGLL 240
Cdd:PRK09986 239 MVSMGIGITLL 249
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 4-140 4.48e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 50.15  E-value: 4.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   4 LKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQLEQTF 83
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 575844639  84 VRPVQATLK-------VAATSVLSLIAPQMYAavHQTGAELYLNISNSTGALDSLAAGGVDCAL 140
Cdd:PRK09906  83 RKIVQEDRQltigfvpSAEVNLLPKVLPMFRL--RHPDTLIELVSLITTQQEEKLRRGELDVGF 144
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-79 7.02e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 49.77  E-value: 7.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   1 MVNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDF-QTKLLRfdGQRYRATADGAIVLSYAAKIFQLTDQL 79
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVgQVLLVR--TQPCRPTEAGQRLLRHARQVRLLEAEL 78
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-81 1.06e-06

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 49.42  E-value: 1.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   1 MVNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQ----LT 76
Cdd:PRK10094   1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSwlesMP 80


                 ....*
gi 575844639  77 DQLEQ 81
Cdd:PRK10094  81 SELQQ 85
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 131-281 1.79e-06

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: 47.55  E-value: 1.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 131 LAAGGVDCALAALNSDQvatyqTRYAVMPLATDAVYLVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGtatlLTKFLRG 210
Cdd:cd08438   45 VLNGELDVGITVLPVDE-----EEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLADLADEPFILFNEDFA----LHDRIID 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 211 QQIKA----QSILRVPQHATVAQMIQNGMGIGLLSQYWLQS-AADKLTILPVADFPVE--------REIYLlaPQATDQL 277
Cdd:cd08438  116 ACQQAgftpNIAARSSQWDFIAELVAAGLGVALLPRSIAQRlDNAGVKVIPLTDPDLRwqlaliwrKGRYL--SHAARAW 193


                 ....
gi 575844639 278 RAFA 281
Cdd:cd08438  194 LALL 197
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-136 3.25e-06

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 47.66  E-value: 3.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   1 MVNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQrYRATADGAIVLSYAAKIFQLTDQLE 80
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQVALLEADLL 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  81 QTF----VRPVQATLKVAATSVLSLIAPQMYAAVHQTGAELYLNISNSTGALDSLAAGGV 136
Cdd:PRK13348  80 STLpaerGSPPTLAIAVNADSLATWFLPALAAVLAGERILLELIVDDQDHTFALLERGEV 139
nhaR PRK11062
transcriptional activator NhaR; Provisional
 2-76 3.59e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 47.70  E-value: 3.59e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 575844639   2 VNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLT 76
Cdd:PRK11062   4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLS 78
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
3-96 4.19e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 47.28  E-value: 4.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   3 NLKALQTFVQVAQIG-SYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRA-TADGAIVLSYAAKIFQLTDQLE 80
Cdd:PRK12684   2 NLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGlTEPGRIILASVERILQEVENLK 81

                         90
                 ....*....|....*....
gi 575844639  81 QT---FVRPVQATLKVAAT 96
Cdd:PRK12684  82 RVgkeFAAQDQGNLTIATT 100
PRK14498 PRK14498
putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing ...
 124-284 8.72e-06

putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional


Pssm-ID: 237732 [Multi-domain]  Cd Length: 633  Bit Score: 47.13  E-value: 8.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 124 STGALDSLAAGGVDCALAALNSDQVATYQTRYAVMPLATDAVYLVanrqnSLSQRTQ--VTPKDLQQQV----------- 190
Cdd:PRK14498 450 SMGGLMALKRGEADIAGIHLLDPETGEYNIPYIKKYLLGEDAVLV-----KGYRREQglVVRKGNPKGIegiedlvrkdv 524

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 191 -FVMREAGSGTATLLTKFLRGQQIKAQSI----LRVPQHATVAQMIQNG---MGIGLLsqywlqSAADKLTIlpvaDF-P 261
Cdd:PRK14498 525 rFVNRQRGSGTRILLDYHLKELAIDPERIngydREEKTHMAVAAAVAQGradAGLGIR------AAAKALGL----DFiP 594

                        170       180
                 ....*....|....*....|....*..
gi 575844639 262 VEREIY-LLAPQA---TDQLRAFASLV 284
Cdd:PRK14498 595 LAEEEYdLLIPKErleKPAVRAFLEAL 621
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 4-234 8.76e-06

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 46.49  E-value: 8.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   4 LKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQltdQLE--Q 81
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQ---DLEagR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  82 TFVRPVQ----ATLKVAATSVLS--LIAPQMyAAVHQtgaeLYLNISNSTGAL------DSLAAGGVDCALA---ALNSD 146
Cdd:PRK11242  80 RAIHDVAdlsrGSLRLAMTPTFTayLIGPLI-DAFHA----RYPGITLTIREMsqerieALLADDELDVGIAfapVHSPE 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 147 QVATyqtryavmPLATDAVYLVANRQNSL-SQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHA 225
Cdd:PRK11242 155 IEAQ--------PLFTETLALVVGRHHPLaARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSIS 226


                 ....*....
gi 575844639 226 TVAQMIQNG 234
Cdd:PRK11242 227 AVLEIVRRG 235
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-292 9.01e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.52  E-value: 9.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   1 MVNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGaivlsyaakiFQLTDQLE 80
Cdd:PRK11013   3 AVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQG----------LRLFEEVQ 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  81 QTFV---RPV----------QATLKVAATSVLS-LIAPQMYAAVHQTGAELYLNISNSTGAL--DSLAAGGVDCALAALN 144
Cdd:PRK11013  73 RSYYgldRIVsaaeslrefrQGQLSIACLPVFSqSLLPGLCQPFLARYPDVSLNIVPQESPLleEWLSAQRHDLGLTETL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 145 SDQVATYQTryavmPLATDAVYLVANRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQH 224
Cdd:PRK11013 153 HTPAGTERT-----ELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSA 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 225 ATVAQMIQNGMGIGL---LSQywLQSAADKLTILPVA-DF--------PVEREIYLLAPQATDQLRAFASLVTELLTAAL 292
Cdd:PRK11013 228 ASVCAMVRAGVGVSIvnpLTA--LDYAGSGLVVRRFSiSVpftvslirPLHRPASALVDAFSEHLQQQAPALVTRLAAIL 305
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-160 2.27e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 45.14  E-value: 2.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   1 MVNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQL- 79
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVh 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  80 EQTFV---RPVqATLKVAATSVLS--LIAPqMYAAVHQTGAELYLNISNSTGALDsLAAGGVDCALAALNSDQVATYQTR 154
Cdd:PRK10632  81 EQLYAfnnTPI-GTLRIGCSSTMAqnVLAG-LTAKMLKEYPGLSVNLVTGIPAPD-LIADGLDVVIRVGALQDSSLFSRR 157


                 ....*.
gi 575844639 155 YAVMPL 160
Cdd:PRK10632 158 LGAMPM 163
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-287 8.78e-05

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 42.56  E-value: 8.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  94 AATSVLSLIAPQMYAAVHQTGAELYLNIS--NSTGALDSLAAGGVDcalAALNSDQVATYQTRYAVMPLATDAVYLVANR 171
Cdd:cd08427    6 AIATVLTGLLPRALARLRRRHPDLEVHIVpgLSAELLARVDAGELD---AAIVVEPPFPLPKDLVWTPLVREPLVLIAPA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 172 QnslsqrtqVTPKD----LQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQY--WL 245
Cdd:cd08427   83 E--------LAGDDprelLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIavPL 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 575844639 246 QSAADkLTILPVADFPVEREIYLLAPQATDQLRAFASLVTEL 287
Cdd:cd08427  155 PAGPR-VRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 3-96 1.50e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 42.67  E-value: 1.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   3 NLKALQtFVQVAQIGSYSL--AAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRY-RATADGAIVLSYAAKIFQLTDQL 79
Cdd:PRK12682   2 NLQQLR-FVREAVRRNLNLteAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNI 80

                         90       100
                 ....*....|....*....|
gi 575844639  80 EQT---FVRPVQATLKVAAT 96
Cdd:PRK12682  81 KRIgddFSNQDSGTLTIATT 100
PBP2_phosphate_like_1 cd13653
Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 ...
 88-280 3.08e-04

Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 periplasmic binding fold superfamily; This subfamily contains uncharacterized phosphate binding domains found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts 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. The PstS proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270371 [Multi-domain]  Cd Length: 240  Bit Score: 41.40  E-value: 3.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  88 QATLKVAATSVLSLIAPQMYAAVHQTGAELYLNIS--NSTGALDSLAAGGVDCALA--ALNSDQVATYQTRYAVmPLATD 163
Cdd:cd13653    1 SGTITISGSTTVAPLAEALAEAFMEKHPGVRIEVQggGSGTGIKALIEGTADIGMAsrPLKAEEKAAASGLVEH-VIALD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 164 AVYLVANRQN-----SLSQRT-----------QVTPKDLQQQVFVmREAGSGT-ATLLTKFLRGQQIKAQSIlRVPQHAT 226
Cdd:cd13653   80 GIAIIVNPDNpvknlTLEQLRdifsgkitnwkEVGGPDGPIVVIS-REEGSGTrETFEELVLGKKDFAKNAV-VVPSNGA 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 575844639 227 VAQMI-QNGMGIGLLSQYWLQSAADK-LTILPVA---------DFPVEREIYLLAP-QATDQLRAF 280
Cdd:cd13653  158 VVQAVaKNPNAIGYVSLGYVDDSKVKaLSVDGVAptpeniksgKYPLSRPLYLYTKgEPSGLVKAF 223
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 2-139 4.50e-04

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 41.21  E-value: 4.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   2 VNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIFQLTDQlEQ 81
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ-AQ 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 575844639  82 TFVRPV------QATLKVAATSVLSLIAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDCA 139
Cdd:PRK11233  80 LAVHNVgqalsgQVSIGLAPGTAASSLTMPLLQAVRAEfpGIVLYLHENSGATLNEKLMNGQLDMA 145
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 95-288 6.40e-04

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: 39.89  E-value: 6.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  95 ATSVLSLIAPQMYAAVHQT--GAELYLNISNSTGALDSLAAGGVDcalAALNSDQVAtyQTRYAVMPLATDAVYLVANRQ 172
Cdd:cd08433    7 PPSAASVLAVPLLRAVRRRypGIRLRIVEGLSGHLLEWLLNGRLD---LALLYGPPP--IPGLSTEPLLEEDLFLVGPAD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 173 NSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLLSQYWL--QSAAD 250
Cdd:cd08433   82 APLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVaaEVAAG 161

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 575844639 251 KLTILPVADFPVEREIYLLAPQATDQLRAfASLVTELL 288
Cdd:cd08433  162 RLVAAPIVDPALTRTLSLATPRDRPLSPA-ALAVRDLL 198
PBP_like_2 pfam12849
PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
 86-253 1.75e-03

PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.


Pssm-ID: 432831 [Multi-domain]  Cd Length: 267  Bit Score: 39.07  E-value: 1.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   86 PVQATLKVA-ATSVLSLIAPQMYA-AVHQTGAELYLNISNSTGALDSLAAGGVDCAL--AALNSDQVATYQTR----YAV 157
Cdd:pfam12849   7 PTVGTILIAgSSTQAPGLLDLAEAfEKKYPGAKVKVTSVGSGEGIKALLNGDVDVALvsRPLTEEEFEAFGANgaggLVE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  158 MPLATDAVYLVANRQNSLsqrTQVTPKDL-----------------QQQVFVMREAGSGTATLLTKFLRGQQIKAQSILR 220
Cdd:pfam12849  87 VPVAYDGIAIVVNKDNPA---NILTVEALkkifsgkitnwndggpdGPIKFVSRGDNSGTTELFSTHLKEKGPWGAAGIG 163

                         170       180       190
                  ....*....|....*....|....*....|....
gi 575844639  221 VPQHATVAQMIQN-GMGIGLLSQYWLQSAADKLT 253
Cdd:pfam12849 164 AAGSPGVASVVAGpGAIGYVEVSYALANLGYTLA 197
PRK09801 PRK09801
LysR family transcriptional regulator;
5-86 1.80e-03

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 39.25  E-value: 1.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   5 KALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRFDGQRYRATADGAIVLSYAAKIF----QLTDQLE 80
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILtqyqRLVDDVT 88


                 ....*.
gi 575844639  81 QTFVRP 86
Cdd:PRK09801  89 QIKTRP 94
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 1-142 1.99e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 39.15  E-value: 1.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639   1 MVNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLLRfdgQRYRA---TADGAIVLSYAAKIF-QLT 76
Cdd:PRK11074   1 MWSEYSLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFE---RRHRDvelTPAGEWFVKEARSVIkKMQ 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 575844639  77 DQLEQTfvRPV----QATLKVA------ATSVLSLIApQMYAavHQTGAELYLNISNSTGALDSLAAGGVDCALAA 142
Cdd:PRK11074  78 ETRRQC--QQVangwRGQLSIAvdnivrPDRTRQLIV-DFYR--HFDDVELIIRQEVFNGVWDALADGRVDIAIGA 148
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 123-287 3.20e-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: 37.89  E-value: 3.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 123 NSTGALDSLAAGGVDCALAALNSDqVATYQTRyavmPLATDAVYLVANRQNSLSQRTQVTPKDLQQQVFVmreaGSGTAT 202
Cdd:cd08421   37 LSADIVRAVAEGRADLGIVAGNVD-AAGLETR----PYRTDRLVVVVPRDHPLAGRASVAFADTLDHDFV----GLPAGS 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639 203 LLTKFLR------GQQIKAQsiLRVPQHATVAQMIQNGMGIGLL--SQYWLQSAADKLTILPVADFPVEREIYLLApQAT 274
Cdd:cd08421  108 ALHTFLReaaarlGRRLRLR--VQVSSFDAVCRMVAAGLGIGIVpeSAARRYARALGLRVVPLDDAWARRRLLLCV-RSF 184

                        170
                 ....*....|....
gi 575844639 275 DQLRAFA-SLVTEL 287
Cdd:cd08421  185 DALPPAArALVDHL 198
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 90-240 3.74e-03

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 37.85  E-value: 3.74e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844639  90 TLKVAATSVLSL-IAPQMYAAVHQTGAELYLNIS--NSTGALDSLAAGGVDCALAA--LNSDQVATYQTRyavmplATDA 164
Cdd:cd08457    1 TLRIAAMPALANgFLPRFLAAFLRLRPNLHLSLMglSSSQVLEAVASGRADLGIADgpLEERQGFLIETR------SLPA 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 575844639 165 VYLVaNRQNSLSQRTQVTPKDLQQQVFVMREAGSGTATLLTKFLRGQQIKAQSILRVPQHATVAQMIQNGMGIGLL 240
Cdd:cd08457   75 VVAV-PMGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAII 149
PRK09791 PRK09791
LysR family transcriptional regulator;
2-48 4.00e-03

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 38.20  E-value: 4.00e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 575844639   2 VNLKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKL 48
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQL 51
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-55 6.11e-03

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 37.67  E-value: 6.11e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 575844639   4 LKALQTFVQVAQIGSYSLAAQQLHLSQPTVSVHIKALETDFQTKLL-RF--------DGQR 55
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFvRShrkvelteEGKR 76
 
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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