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Conserved domains on  [gi|1774526220|gb|QGH33893|]
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LysR family transcriptional regulator [Gracilibacillus salitolerans]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444076)

LysR family transcriptional regulator, similar to Staphylococcus aureus CidR which positively up-regulates the expression of the cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|11741199

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-285 2.06e-74

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: 226.28  E-value: 2.06e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLN-DHLTADYYTFVEDNLNLVVSN 170
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPvDEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDS-TSQTFSK 249
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSiAQRLDNA 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1774526220 250 NIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd08438   161 GVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLAL 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.50e-23

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 90.14  E-value: 2.50e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   3 IKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-285 2.06e-74

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: 226.28  E-value: 2.06e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLN-DHLTADYYTFVEDNLNLVVSN 170
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPvDEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDS-TSQTFSK 249
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSiAQRLDNA 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1774526220 250 NIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd08438   161 GVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLAL 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 1.48e-65

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 205.87  E-value: 1.48e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTA-DYYTF 159
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGlVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 160 VEDNLNLVVSNQHALANQKQIqvqdlkdesfimfnqdfesrniiiqackkagfepkivseTSQIDFLEEMVATNLGVTLL 239
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1774526220 240 PDSTSQTF--SKNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAFTKEKLMQ 292
Cdd:COG0583   202 PRFLAADElaAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-288 2.34e-47

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 160.51  E-value: 2.34e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHlTADYYT-- 158
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVH-SPEIEAqp 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 159 -FVEdNLNLVVSNQHALANQ-KQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGV 236
Cdd:PRK11242  160 lFTE-TLALVVGRHHPLAARrKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLA 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1774526220 237 TLLPDSTSQTFSkNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAFTKE 288
Cdd:PRK11242  239 TLLPAAIAREHD-GLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALE 289
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-290 1.61e-42

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: 145.12  E-value: 1.61e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  90 TGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTA-DYYTFVEDNLNLVV 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGlEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 169 SNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFS 248
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1774526220 249 KN--IIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAFTKEKL 290
Cdd:pfam03466 161 ADgrLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 6-240 1.57e-31

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 118.30  E-value: 1.57e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   6 LQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEIDQI 85
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRES 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  86 RTLKTGHVRIGlptVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV-VLNDHLTADYYTFVEDNL 164
Cdd:TIGR03339  82 GALREGSLRIA---ATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSsEVVDDPRLDRVVLGNDPL 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1774526220 165 NLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLP 240
Cdd:TIGR03339 159 VAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVS 234
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.50e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 90.14  E-value: 2.50e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   3 IKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-64 9.17e-14

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 69.66  E-value: 9.17e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVL 64
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERL 64
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
2-77 9.30e-05

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 40.66  E-value: 9.30e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220    2 DIKHLQYF-LEVIKTE---NFTQAAENLYITQPALSRIVKTLESDlgvALFHRSR-------KKITLTDAGKVLHKHATK 70
Cdd:smart00347   7 GLTPTQFLvLRILYEEgplSVSELAKRLGVSPSTVTRVLDRLEKK---GLVRREPspedrrsVLVSLTEEGRELIEQLLE 83


                   ....*..
gi 1774526220   71 IADQITE 77
Cdd:smart00347  84 ARSETLA 90
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
22-88 6.13e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 39.18  E-value: 6.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  22 AENLYITQPALSRIVKTLEsDLGvaLFHRSR-------KKITLTDAGKVLHKHATKIADQITEM------EQEIDQIRTL 88
Cdd:COG1846    59 AERLGLTKSTVSRLLDRLE-EKG--LVEREPdpedrraVLVRLTEKGRALLEEARPALEALLAEllaglsEEELEALLRL 135
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-285 2.06e-74

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: 226.28  E-value: 2.06e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLN-DHLTADYYTFVEDNLNLVVSN 170
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPvDEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDS-TSQTFSK 249
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSiAQRLDNA 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1774526220 250 NIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd08438   161 GVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLAL 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 1.48e-65

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 205.87  E-value: 1.48e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTA-DYYTF 159
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGlVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 160 VEDNLNLVVSNQHALANQKQIqvqdlkdesfimfnqdfesrniiiqackkagfepkivseTSQIDFLEEMVATNLGVTLL 239
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1774526220 240 PDSTSQTF--SKNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAFTKEKLMQ 292
Cdd:COG0583   202 PRFLAADElaAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-285 5.61e-57

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: 182.03  E-value: 5.61e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTA-DYYTFVEDNLNLVVSN 170
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGlESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTF-SK 249
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELaDG 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1774526220 250 NIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLEL 196
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-288 2.34e-47

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 160.51  E-value: 2.34e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHlTADYYT-- 158
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVH-SPEIEAqp 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 159 -FVEdNLNLVVSNQHALANQ-KQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGV 236
Cdd:PRK11242  160 lFTE-TLALVVGRHHPLAARrKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLA 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1774526220 237 TLLPDSTSQTFSkNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAFTKE 288
Cdd:PRK11242  239 TLLPAAIAREHD-GLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALE 289
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-290 1.61e-42

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: 145.12  E-value: 1.61e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  90 TGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTA-DYYTFVEDNLNLVV 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGlEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 169 SNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFS 248
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1774526220 249 KN--IIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAFTKEKL 290
Cdd:pfam03466 161 ADgrLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-285 7.97e-40

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: 137.67  E-value: 7.97e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV-VLNDHLTADYYTFVEDNLNLVVSN 170
Cdd:cd08434     1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCsPVPDEPDIEWIPLFTEELVLVVPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFSKn 250
Cdd:cd08434    81 DHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTLLNPPG- 159

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1774526220 251 IIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd08434   160 VKKIPIKDPDAERTIGLAWLKDRYLSPAARRFKDF 194
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-274 2.65e-37

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: 131.09  E-value: 2.65e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTA-DYYTFVEDNLNLVVSN 170
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGlASRPLLREPLVVALPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFES--RNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFS 248
Cdd:cd08414    81 DHPLAARESVSLADLADEPFVLFPREPGPglYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQR 160

                         170       180
                  ....*....|....*....|....*.
gi 1774526220 249 KNIIRIPIVNPTIPWNLAFIWKKDPH 274
Cdd:cd08414   161 PGVVYRPLADPPPRSELALAWRRDNA 186
PRK09986 PRK09986
LysR family transcriptional regulator;
1-280 9.71e-37

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 132.54  E-value: 9.71e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRTLKTGHVRIGlptVVNSFFFSQLIT---DFHQRYPGVTFHLEE--NGSKI--IEDKVLD-GKLNCGVVVLNDHL 152
Cdd:PRK09986   87 RVEQIGRGEAGRIEIG---IVGTALWGRLRPamrHFLKENPNVEWLLRElsPSMQMaaLERRELDaGIWRMADLEPNPGF 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 153 TadYYTFVEDNLNLVVSNQHALANQKQIQVQDLKDESFIM--FNQDFESRNIIiQACKKAGFEPKIVSETSQIDFLEEMV 230
Cdd:PRK09986  164 T--SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITlpFVHSDWGKFLQ-RVCQQAGFSPQIIRQVNEPQTVLAMV 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1774526220 231 ATNLGVTLLPDSTSQTFSKNIIRIPIvNPTIPWNLAFIWKKDPHLSQINK 280
Cdd:PRK09986  241 SMGIGITLLPDSYAQIPWPGVVFRPL-KERIPADLYAVYHPDQVTPALNK 289
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-282 2.13e-36

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 132.07  E-value: 2.13e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  10 LEVIKTE-NFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEIDQIRTL 88
Cdd:CHL00180   13 LKAIATEgSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  89 KTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV------VLNDHLTADyyTFVED 162
Cdd:CHL00180   93 QRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggevptELKKILEIT--PYVED 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 163 NLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEP---KIVSETSQIDFLEEMVATNLGVTLL 239
Cdd:CHL00180  171 ELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSkrfKIEMELNSIEAIKNAVQSGLGAAFV 250

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1774526220 240 -PDSTSQTFSKNIIR-IPIVNPTIPWNLAFIWKKDPHLSQINKQF 282
Cdd:CHL00180  251 sVSAIEKELELGLLHwIKIENITIKRMLSIITNPNRYKSKASETF 295
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 6-240 1.57e-31

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 118.30  E-value: 1.57e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   6 LQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEIDQI 85
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRES 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  86 RTLKTGHVRIGlptVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV-VLNDHLTADYYTFVEDNL 164
Cdd:TIGR03339  82 GALREGSLRIA---ATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSsEVVDDPRLDRVVLGNDPL 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1774526220 165 NLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLP 240
Cdd:TIGR03339 159 VAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVS 234
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-294 1.45e-30

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 116.41  E-value: 1.45e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKI---ADQITE 77
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAIleqAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  78 MEQEIDQIRTlktgHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADYY 157
Cdd:PRK09906   81 RARKIVQEDR----QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDY 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 158 TFVEDN-LNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFES--RNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNL 234
Cdd:PRK09906  157 LELLDEpLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGslAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGL 236

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1774526220 235 GVTLLPDSTSQTFSKNIIRIPIVN--PTIpwNLAFIWKKDpHLSQINKQFIAFTKEKLMQQK 294
Cdd:PRK09906  237 GCTIIPGYMNNFNTGQVVFRPLAGnvPSI--ALLMAWKKG-EMKPALRDFIAIVQERLASVT 295
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-267 3.73e-30

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 115.55  E-value: 3.73e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRTLKTGHVRIGL-PTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNcgVVVLNDHLTADYYTF 159
Cdd:PRK11233   81 AVHNVGQALSGQVSIGLaPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLD--MAVIYEHSPVAGLSS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 160 V----EDnLNLVVSNQhalANQKQIQVQDLKDESfiMF-NQDFES-RNIIIQACKKAGFEPKIVSETSQIDFLEEMVATN 233
Cdd:PRK11233  159 QpllkED-LFLVGTQD---CPGQSVDLAAVAQMN--LFlPRDYSAvRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASG 232

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1774526220 234 LGVTLLPDSTSQTF--SKNIIRIPIVNPTIPWNLAF 267
Cdd:PRK11233  233 MGVTVLPESAARSLcgAVNGWMARITTPSMSLSLSL 268
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-273 1.36e-26

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: 103.06  E-value: 1.36e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADYYTFV--EDNLNLVVS 169
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRElaREPLVAVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 170 NQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFSk 249
Cdd:cd08436    81 PDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLP- 159

                         170       180
                  ....*....|....*....|....
gi 1774526220 250 NIIRIPIVnPTIPWNLAFIWKKDP 273
Cdd:cd08436   160 GLAALPLE-PAPRRRLYLAWSAPP 182
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-274 2.34e-26

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 102.73  E-value: 2.34e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLptvVNSFFFSQL---ITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNdHLTADYYT--FVEDNLNL 166
Cdd:cd08448     1 RLRIGF---VGSMLYRGLpriLRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSR-RLPAGLSArlLHREPFVC 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 167 VVSNQHALANQKQIQVQDLKDESFIMFNQDFESRN--IIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTS 244
Cdd:cd08448    77 CLPAGHPLAARRRIDLRELAGEPFVLFSREVSPDYydQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRSLA 156

                         170       180       190
                  ....*....|....*....|....*....|
gi 1774526220 245 QTFSKNIIRIPIVNPTIPWNLAFIWKKDPH 274
Cdd:cd08448   157 RAGLAGVRFLPLKGATQRSELYAAWKASAP 186
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-260 6.39e-26

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 103.96  E-value: 6.39e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQI---TE 77
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVkvlKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  78 MEQEidQIRTLkTGHVRIGL-PTvVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTAdy 156
Cdd:PRK11151   81 MASQ--QGETM-SGPLHIGLiPT-VGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEA-- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 157 ytFVE-----DNLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVA 231
Cdd:PRK11151  155 --FIEvplfdEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVA 232

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1774526220 232 TNLGVTLLPD--STSQTFSKNIIRIPIVNPT 260
Cdd:PRK11151  233 AGSGITLLPAlaVPNERKRDGVCYLPCIKPE 263
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-294 9.65e-26

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 103.53  E-value: 9.65e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTE-NFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKIT-LTDAGKVLHKHATKIADQITEM 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  79 EQEIDQIR-------TLKTGHV--RIGLPTVVNsfffsqlitDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV--V 147
Cdd:PRK12682   81 KRIGDDFSnqdsgtlTIATTHTqaRYVLPRVVA---------AFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAteS 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 148 LNDH---LTADYYTFvedNLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQID 224
Cdd:PRK12682  152 LADDpdlATLPCYDW---QHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSD 228

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1774526220 225 FLEEMVATNLGVTLLPD-STSQTFSKNIIRIPiVNPTIPWNLAFI-WKKDPHLSQINKQFIAFTKEKLMQQK 294
Cdd:PRK12682  229 VIKTYVRLGLGVGIVAEmAYRPDRDGDLVALP-AGHLFGPNTAWVaLKRGAYLRNYVYKFIELCAPHLSREL 299
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 93-285 4.63e-25

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: 99.16  E-value: 4.63e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  93 VRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVV-LNDHLTADYYTFVEDNLNLVVSNQ 171
Cdd:cd08412     2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYdLDLPEDIAFEPLARLPPYVWLPAD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 172 HALANQKQIQVQDLKDESFIMFNQDfESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFS--- 248
Cdd:cd08412    82 HPLAGKDEVSLADLAAEPLILLDLP-HSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRPWSydg 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1774526220 249 KNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd08412   161 KRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDF 197
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-285 3.89e-24

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 96.57  E-value: 3.89e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLptvVNSFF---FSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV----VLNDH-LTADYYTfvEDN 163
Cdd:cd08449     1 HLNIGM---VGSVLwggLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVrfadTLNDPpLASELLW--REP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 164 LNLVVSNQHALANQKQIQVQDLKDESFIMFNQDfESR--NIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPD 241
Cdd:cd08449    76 MVVALPEEHPLAGRKSLTLADLRDEPFVFLRLA-NSRfaDFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPE 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1774526220 242 STSQTFSKNIIRIPIvNPTIPWNLAFIWKKDPHLSQINKqFIAF 285
Cdd:cd08449   155 SYARLPWPGVRFIPL-KQAISADLYAVYHPDSATPVIQA-FLAL 196
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 92-282 1.01e-23

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: 95.48  E-value: 1.01e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADYYT---FVEDNLNLVV 168
Cdd:cd08437     1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSALHskiIKTQHFMIIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 169 SNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDsTSQTFS 248
Cdd:cd08437    81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTD-IAVKPD 159

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1774526220 249 KNIIRIPIV-NPTIPWNLAFIWKKDPHLSQINKQF 282
Cdd:cd08437   160 DHLVAIPLLdNEQPTFYISLAHRKDQLLTPAQKKL 194
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-256 2.40e-23

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 97.04  E-value: 2.40e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTE-NFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKIT-LTDAGKVLHKHATKI---ADQI 75
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMlldAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  76 TEMEQEI---DQIR-TLKTGHV--RIGLPTVVnsfffsqliTDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVV-- 147
Cdd:PRK12683   81 RRLAEQFadrDSGHlTVATTHTqaRYALPKVV---------RQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATea 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 148 ---LNDHLTADYYTFVEdnlNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQID 224
Cdd:PRK12683  152 ldrEPDLVSFPYYSWHH---VVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDAD 228

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1774526220 225 FLEEMVATNLGVTLLPD--------------STSQTFSKNIIRIPI 256
Cdd:PRK12683  229 VIKTYVELGMGVGIVAAmaydpqrdtglvalDTDHLFEANTTRVGL 274
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.50e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 90.14  E-value: 2.50e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   3 IKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 105-284 2.63e-23

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). 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: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 94.55  E-value: 2.63e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 105 FFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADY--YTFVEDNLNLVVSNQHALANQKQIQV 182
Cdd:cd08451    15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLvlELLLEEPMLVALPAGHPLARERSIPL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 183 QDLKDESFIMFnqdfeSRNI-------IIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFSKNIIRIP 255
Cdd:cd08451    95 AALADEPFILF-----PRPVgpglydaIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASMRQLQAPGVVYRP 169

                         170       180
                  ....*....|....*....|....*....
gi 1774526220 256 IVNPTIPWNLAFIWKKDPHlSQINKQFIA 284
Cdd:cd08451   170 LAGAPLTAPLALAYRRGER-SPAVRNFIA 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-285 2.75e-23

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: 94.48  E-value: 2.75e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV---VLNDHLTADyyTFVEDNLNLVV 168
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVegpVDHPDLIVE--PFAEDELVLVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 169 SNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEP---KIVSETSQIDFLEEMVATNLGVTLLpdstsq 245
Cdd:cd08420    79 PPDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGldlNIVMELGSTEAIKEAVEAGLGISIL------ 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1774526220 246 tfSKNIIR----------IPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd08420   153 --SRLAVRkelelgrlvaLPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEF 200
PRK10341 PRK10341
transcriptional regulator TdcA;
4-288 1.55e-22

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 94.93  E-value: 1.55e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   4 KHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEID 83
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  84 QIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGV-VVLNDHLTADYYT--FV 160
Cdd:PRK10341   90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgTLSNEMKLQDLHVepLF 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 161 EDNLNLVVSNQHALAnqKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLP 240
Cdd:PRK10341  170 ESEFVLVASKSRTCT--GTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIP 247

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1774526220 241 -DSTSQTFSKNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAFTKE 288
Cdd:PRK10341  248 cDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKE 296
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 4-192 4.44e-22

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 93.63  E-value: 4.44e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   4 KHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKiadQITEMEQEID 83
Cdd:TIGR02424   6 RHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGA---SLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  84 QIRTLKTGH---VRIG-LPTVVNSfFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADYYTF 159
Cdd:TIGR02424  83 SLSQLGEGEgptVRIGaLPTVAAR-LMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLSF 161

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1774526220 160 VE---DNLNLVVSNQHALANQKQIQVQDLKDESFIM 192
Cdd:TIGR02424 162 EHlynEPVVFVVRAGHPLLAAPSLPVASLADYPVLL 197
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-285 7.86e-22

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: 90.66  E-value: 7.86e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIG-LPTVVNSFFfSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV-VLNDHLTADYYTFVEDNLNLVVS 169
Cdd:cd08440     1 RVRVAaLPSLAATLL-PPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGsEPEADPDLEFEPLLRDPFVLVCP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 170 NQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLP-DSTSQTFS 248
Cdd:cd08440    80 KDHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPaLALPLADH 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1774526220 249 KNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd08440   160 PGLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDL 196
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-274 1.19e-21

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 92.56  E-value: 1.19e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRTLKTGHVRIglptVVNSFFFS-----QLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTAD 155
Cdd:PRK10094   82 ELQQVNDGVERQVNI----VINNLLYNpqavaQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALAN 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 156 yyTFVEDNLN-----LVVSNQHALANQKQIQVQDLKdESFIMFNQDFESRNIIIQ-ACKKAGFEPKIVSEtsqidfLEEM 229
Cdd:PRK10094  158 --TFSLDPLGsvqwrFVMAADHPLANVEEPLTEAQL-RRFPAVNIEDSARTLTKRvAWRLPGQKEIIVPD------METK 228

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1774526220 230 VATNL---GVTLLPDSTSQTF--SKNIIRIPIVNPTIPWNLAFIWKKDPH 274
Cdd:PRK10094  229 IAAHLagvGIGFLPKSLCQSMidNQQLVSRVIPTMRPPSPLSLAWRKFGS 278
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-236 5.22e-20

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 88.03  E-value: 5.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTE-NFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKIT-LTDAGkvlhKHATKIADQITEM 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAG----EEIIRIAREILSK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  79 EQEIDQIR-----------TLKTGHV--RIGLPTVvnsfffsqlITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGV 145
Cdd:PRK12681   77 VESIKSVAgehtwpdkgslYIATTHTqaRYALPPV---------IKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAI 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 146 VVLNDHLTADY-----YTFvedNLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSET 220
Cdd:PRK12681  148 ATEALHLYDDLimlpcYHW---NRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTA 224

                         250
                  ....*....|....*.
gi 1774526220 221 SQIDFLEEMVATNLGV 236
Cdd:PRK12681  225 TDADVIKTYVRLGLGV 240
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-239 2.63e-19

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 86.18  E-value: 2.63e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTE-NFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKIT-LTDAGKvlhkhatKIADQITEM 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGR-------IILASVERI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  79 EQEIDQIR--------------TLKTGHV--RIGLPTVvnsfffsqlITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLN 142
Cdd:PRK12684   74 LQEVENLKrvgkefaaqdqgnlTIATTHTqaRYALPAA---------IKEFKKRYPKVRLSILQGSPTQIAEMVLHGQAD 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 143 CGV----VVLNDHLTAdyYTFVEDNLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVS 218
Cdd:PRK12684  145 LAIateaIADYKELVS--LPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVL 222

                         250       260
                  ....*....|....*....|.
gi 1774526220 219 ETSQIDFLEEMVATNLGVTLL 239
Cdd:PRK12684  223 EAIDADVIKTYVELGLGVGIV 243
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-285 8.16e-19

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR 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 (PBP2). The PBP2 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: 176116  Cd Length: 197  Bit Score: 82.38  E-value: 8.16e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  91 GHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHlTADYYT---FVEdNLNLV 167
Cdd:cd08425     1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVR-SPDIDAqplFDE-RLALV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 168 VSNQHALANQKQ-IQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDS--TS 244
Cdd:cd08425    79 VGATHPLAQRRTaLTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAiaRE 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1774526220 245 QTfskNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIAF 285
Cdd:cd08425   159 QP---GLCAVALEPPLPGRTAALLRRKGAYRSAAARAFAAL 196
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-242 4.21e-18

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: 80.65  E-value: 4.21e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  91 GHVRIG-LPTVVnSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHlTADYYTFV--EDNLNLV 167
Cdd:cd08411     1 GPLRLGvIPTIA-PYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVD-EPGLEEEPlfDEPFLLA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 168 VSNQHALANQKQIQVQDLKDESFIM------FnqdfesRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPD 241
Cdd:cd08411    79 VPKDHPLAKRKSVTPEDLAGERLLLleeghcL------RDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPE 152


                  .
gi 1774526220 242 S 242
Cdd:cd08411   153 L 153
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 93-284 7.32e-18

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: 79.91  E-value: 7.32e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  93 VRIG-LPTVVNSFFfSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVL-NDH--LTADyyTFVEDNLNLVV 168
Cdd:cd08415     2 LRIAaLPALALSLL-PRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLpLDHpgLESE--PLASGRAVCVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 169 SNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLL-PDSTSQTF 247
Cdd:cd08415    79 PPGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVdPLTAAGYA 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1774526220 248 SKNIIRIPIVnPTIPWNLAFIWKKDPHLSQINKQFIA 284
Cdd:cd08415   159 GAGLVVRPFR-PAIPFEFALVRPAGRPLSRLAQAFID 194
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 92-259 5.36e-17

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and 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 (PBP2). The PBP2 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: 176108  Cd Length: 199  Bit Score: 77.39  E-value: 5.36e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGL--PTVVNSFffSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLND-HLTADYYTF--VEDNLNL 166
Cdd:cd08416     1 RLRLGSlySLTVNTV--PRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEgLNDPDFEVVplFEDDIFL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 167 VVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQT 246
Cdd:cd08416    79 AVPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADV 158

                         170
                  ....*....|...
gi 1774526220 247 FSKNIIRIPIVNP 259
Cdd:cd08416   159 YEDKVQLIPLAEP 171
PRK09791 PRK09791
LysR family transcriptional regulator;
3-126 5.53e-17

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 79.42  E-value: 5.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   3 IKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEI 82
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1774526220  83 DQIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEE 126
Cdd:PRK09791   87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIME 130
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-246 3.99e-16

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 77.16  E-value: 3.99e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTE-NFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKIT-LTDAGKVLHKHATKIADQITEM 78
Cdd:PRK12679    1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  79 EQEIDQ-------IRTLKTGHV--RIGLPTVvnsfffsqlITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV--- 146
Cdd:PRK12679   81 RRLADLftndtsgVLTIATTHTqaRYSLPEV---------IKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIAser 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 147 VLNDHLTADYYTFVEDNlNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFL 226
Cdd:PRK12679  152 LSNDPQLVAFPWFRWHH-SLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVI 230

                         250       260
                  ....*....|....*....|
gi 1774526220 227 EEMVATNLGVTLLPDSTSQT 246
Cdd:PRK12679  231 KTYVALGLGIGLVAEQSSGE 250
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 105-283 6.06e-16

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 74.46  E-value: 6.06e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 105 FFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV---VLNDHLTADyyTFVEDNLNLVVSNQHALANQKQIQ 181
Cdd:cd08452    14 FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLhppIQHTALHIE--TVQSSPCVLALPKQHPLASKEEIT 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 182 VQDLKDESFIMFnqdfeSRNI-------IIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFSKNIIRI 254
Cdd:cd08452    92 IEDLRDEPIITV-----AREAwptlydeIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSAKKLFNLEVAYR 166

                         170       180
                  ....*....|....*....|....*....
gi 1774526220 255 PIVNPTIPWNLAFIWKKDPHlSQINKQFI 283
Cdd:cd08452   167 KIDQINLNAEWSIAYRKDNH-NPLLKHFI 194
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-276 9.62e-16

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: 73.78  E-value: 9.62e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADYYTFV-EDNLNLVVSN 170
Cdd:cd08433     1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLlEEDLFLVGPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDS--TSQTFS 248
Cdd:cd08433    81 DAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASavAAEVAA 160

                         170       180
                  ....*....|....*....|....*...
gi 1774526220 249 KNIIRIPIVNPTIPWNLAFIWKKDPHLS 276
Cdd:cd08433   161 GRLVAAPIVDPALTRTLSLATPRDRPLS 188
PRK09801 PRK09801
LysR family transcriptional regulator;
4-157 3.17e-15

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 74.69  E-value: 3.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   4 KHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEID 83
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1774526220  84 QIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKI--IEDKV-LDgklncgvVVLNDHLtADYY 157
Cdd:PRK09801   89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIdlVQDNIdLD-------IRINDEI-PDYY 157
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-249 4.88e-15

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 73.90  E-value: 4.88e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRTLKtghVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNcgVVVLNDHLTAD---YY 157
Cdd:PRK15421   82 ACNEPQQTR---LRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELD--LVMTSDILPRSglhYS 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 158 TFVEDNLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIdFLEEMVATNLGVT 237
Cdd:PRK15421  157 PMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTL-LLIQMVAARMGIA 235

                         250
                  ....*....|..
gi 1774526220 238 LLPDSTSQTFSK 249
Cdd:PRK15421  236 ALPHWVVESFER 247
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-192 9.17e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 72.80  E-value: 9.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   3 IKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEI 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  83 DQirtlKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTaDYYT--FV 160
Cdd:PRK10837   85 RE----DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSP-ELISepWL 159

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1774526220 161 EDNLNLVVSNQHALAnQKQIQVQDLKDESFIM 192
Cdd:PRK10837  160 EDELVVFAAPDSPLA-RGPVTLEQLAAAPWIL 190
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 16-120 1.07e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 72.57  E-value: 1.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  16 ENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEIdqIRTLKTGHVRI 95
Cdd:PRK11139   21 LSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAKGALTV 98

                          90       100
                  ....*....|....*....|....*...
gi 1774526220  96 GLPTvvnSFFFSQL---ITDFHQRYPGV 120
Cdd:PRK11139   99 SLLP---SFAIQWLvprLSSFNEAHPDI 123
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-64 9.17e-14

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 69.66  E-value: 9.17e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVL 64
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERL 64
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 7-124 1.03e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 69.97  E-value: 1.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   7 QYFLEVI----KTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEI 82
Cdd:PRK11074    4 EYSLEVVdavaRTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQC 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1774526220  83 DQIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHL 124
Cdd:PRK11074   84 QQVANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELII 125
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-131 2.16e-13

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 69.25  E-value: 2.16e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQ 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1774526220  81 EIDQIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKI 131
Cdd:PRK14997   82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRV 132
PRK12680 PRK12680
LysR family transcriptional regulator;
1-263 6.52e-13

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 68.11  E-value: 6.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTE-NFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKI-TLTDAGkvlhkhaTKIADQITEM 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAG-------VEVIERARAV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  79 EQEIDQIRTLKTGHVR--IGLPTVVNS-----FFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVL--- 148
Cdd:PRK12680   74 LSEANNIRTYAANQRResQGQLTLTTThtqarFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTagg 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 149 --NDHLTADYYTFvedNLNLVVSNQHALAN-QKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDF 225
Cdd:PRK12680  154 epSAGIAVPLYRW---RRLVVVPRGHALDTpRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADL 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1774526220 226 LEEMVATNLGVTLLPDSTSQTFSKNIIRIPIVNPT---IPW 263
Cdd:PRK12680  231 IKTYVRAGLGVGLLAEMAVNANDEDLRAWPAPAPIaecIAW 271
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 93-285 1.41e-12

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: 65.22  E-value: 1.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  93 VRIGLPTVVNsFFFSQLITDFHQRYPGVTFHLEE-NGSKIIE---DKVLDgklncgVVVLN---DHLTADYYTFVEDNLN 165
Cdd:cd08419     2 LRLAVVSTAK-YFAPRLLGAFCRRHPGVEVSLRVgNREQVLErlaDNEDD------LAIMGrppEDLDLVAEPFLDNPLV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 166 LVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQ 245
Cdd:cd08419    75 VIAPPDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1774526220 246 TFSKN-------IIRIPIVNptiPWNLafIWKKDPHLSQINKQFIAF 285
Cdd:cd08419   155 LELATgrlavldVEGFPIRR---QWYV--VHRKGKRLSPAAQAFLDF 196
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-103 1.92e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 66.15  E-value: 1.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   2 DIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRkKITLTDAGKVLHKHATKIAdqitemEQE 81
Cdd:PRK13348    3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGR-PCRPTPAGQRLLRHLRQVA------LLE 75

                          90       100
                  ....*....|....*....|...
gi 1774526220  82 IDQIRTLKTGHV-RIGLPTVVNS 103
Cdd:PRK13348   76 ADLLSTLPAERGsPPTLAIAVNA 98
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-240 2.44e-12

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: 64.64  E-value: 2.44e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 105 FFSQLITDFHQRYPGVTFHLE-ENGSKIIEDkVLDGKLNCGVVV-------LNDHLTADYytfvedNLNLVVSNQHALAN 176
Cdd:cd08426    14 LLPSLIARFRQRYPGVFFTVDvASTADVLEA-VLSGEADIGLAFspppepgIRVHSRQPA------PIGAVVPPGHPLAR 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1774526220 177 QKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLP 240
Cdd:cd08426    87 QPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLT 150
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-124 4.02e-12

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 65.41  E-value: 4.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   6 LQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLhKHATKiaDQITEMEQEIDQI 85
Cdd:PRK10086   19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRV-FWALK--SSLDTLNQEILDI 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1774526220  86 RTLKTGhvriGLPTVVNSFFFSQL-----ITDFHQRYPGVTFHL 124
Cdd:PRK10086   96 KNQELS----GTLTVYSRPSIAQCwlvprLADFTRRYPSISLTI 135
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-134 9.68e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 64.02  E-value: 9.68e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRkKITLTDAGKVLHKHatkiADQITEMEQ 80
Cdd:PRK03635    2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRLLRH----ARQVRLLEA 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1774526220  81 EI-DQIRTLKTGHVRigLPTVVN----SFFFSQLITDFHQRyPGVTFHLeengskIIED 134
Cdd:PRK03635   77 ELlGELPALDGTPLT--LSIAVNadslATWFLPALAPVLAR-SGVLLDL------VVED 126
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 94-284 1.09e-11

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 62.82  E-value: 1.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  94 RIG-LPTVVNSFFfSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTA-DYYTFVEDNLNLVVSNQ 171
Cdd:cd08456     3 RIAvLPALSQSFL-PRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGiERERLLRIDGVCVLPPG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 172 HALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFSKNI 251
Cdd:cd08456    82 HRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAAAG 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1774526220 252 IRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIA 284
Cdd:cd08456   162 LVVRRFSPAVPFEVSLIRPKHRPSSALVAAFSA 194
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-241 1.49e-11

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 62.23  E-value: 1.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIG-LPTVVNSFFfSQLITDFHQRYPGVTFHLEEngskiIE-----DKVLDGKLNCGVVV------LNDHLTADYYTF 159
Cdd:cd08423     1 TLRVGaFPTAAAALL-PPALAALRARHPGLEVRLRE-----AEppeslDALRAGELDLAVVFdypvtpPPDDPGLTRVPL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 160 VEDNLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLL 239
Cdd:cd08423    75 LDDPLDLVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALV 154


                  ..
gi 1774526220 240 PD 241
Cdd:cd08423   155 PR 156
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-124 2.36e-11

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 63.24  E-value: 2.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   3 IKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEI 82
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1774526220  83 DQIRTLKTGHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHL 124
Cdd:PRK10632   84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL 125
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-242 2.93e-11

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: 61.38  E-value: 2.93e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTA-DYYTFVEDNLNLVVSN 170
Cdd:cd08421     1 HVRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGlETRPYRTDRLVVVVPR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDS 242
Cdd:cd08421    81 DHPLAGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPES 152
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 94-284 3.55e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 61.24  E-value: 3.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  94 RIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV---VLNDHLtaDYYTFVEDNLNLVVSN 170
Cdd:cd08450     3 TIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMrpeIQSDGI--DYQLLLKEPLIVVLPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 171 QHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQA-CKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFSK 249
Cdd:cd08450    81 DHRLAGREKIPPQDLAGENFISPAPTAPVLQQVIENyAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLLPP 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1774526220 250 NIIRIPIVN--PTIpwNLAFIWKKDpHLSQINKQFIA 284
Cdd:cd08450   161 SVVARPLSGetPTI--DLVMGYNKA-NTSPLLKRFLS 194
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 92-283 2.07e-10

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: 58.90  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADYYTF---VEDNLNLVV 168
Cdd:cd08418     1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISeplFESDFVVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 169 SNQHALANQKQIqvQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFS 248
Cdd:cd08418    81 RKDHPLQGARSL--EELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPL 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1774526220 249 K--NIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFI 283
Cdd:cd08418   159 DsfRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLV 195
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-86 2.62e-10

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 60.07  E-value: 2.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   1 MDIKHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHkhaTKIADQITEMEQ 80
Cdd:PRK10082   11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFH---SQIRHLLQQLES 87


                  ....*.
gi 1774526220  81 EIDQIR 86
Cdd:PRK10082   88 NLAELR 93
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-241 4.74e-10

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 59.06  E-value: 4.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  26 YITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEIDQIRTLKTGHVRI-GLPTVVNSF 104
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfCSVTAAYSH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 105 FFsQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADyYTFVE-DNLNLVV------SNQHALANQ 177
Cdd:PRK11716   82 LP-PILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPAS-VAFSPiDEIPLVLiapalpCPVRQQLSQ 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1774526220 178 KQIqvqDLKDESFIMFNQDFeSRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPD 241
Cdd:PRK11716  160 EKP---DWSRIPFILPEHGP-ARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALGCGVGLLPE 219
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 87-239 4.88e-10

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: 58.02  E-value: 4.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  87 TLKTGHV--RIGLPTVvnsfffsqlITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV--VLNDH---LTADYYTF 159
Cdd:cd08413     3 TIATTHTqaRYVLPPV---------IAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIAteALDDHpdlVTLPCYRW 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 160 vedNLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLL 239
Cdd:cd08413    74 ---NHCVIVPPGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGII 150
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-259 7.16e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 58.85  E-value: 7.16e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220   4 KHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLH---KHATKIADQITEMEQ 80
Cdd:PRK11013    7 RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFeevQRSYYGLDRIVSAAE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  81 EIDQIRtlkTGHVRIG-LPTvvnsffFSQ-----LITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGvvvLNDHLTA 154
Cdd:PRK11013   87 SLREFR---QGQLSIAcLPV------FSQsllpgLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLG---LTETLHT 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 155 DYYTFVEDNLNL----VVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMV 230
Cdd:PRK11013  155 PAGTERTELLTLdevcVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMV 234

                         250       260
                  ....*....|....*....|....*....
gi 1774526220 231 ATNLGVTllpdstsqtfskniiripIVNP 259
Cdd:PRK11013  235 RAGVGVS------------------IVNP 245
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 108-272 3.48e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 55.36  E-value: 3.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 108 QLITDFHQRYPGVTFHLEeNGSKIIE-DKVLDGKLNCGVvvlndhltADYYTFVED---------NLNLVVSNQHALANQ 177
Cdd:cd08446    18 RLLRAFLTARPDVTVSLH-NMTKDEQiEALRAGRIHIGF--------GRFYPVEPDiavenvaqeRLYLAVPKSHPLAAR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 178 KQIQVQDLKDESFIMFNQdfESR----NIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFSKNIIR 253
Cdd:cd08446    89 PAVSLADLRNEPLILFPR--GGRpsfaDEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVAALRWPGVVF 166

                         170
                  ....*....|....*....
gi 1774526220 254 IPIVNPTIPWNLAFIWKKD 272
Cdd:cd08446   167 RPLADAEAKVPLSCIYRKD 185
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 109-286 4.29e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 55.45  E-value: 4.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 109 LITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVV--LNDHLTA--DYYTFVEDNLNLVVSNQHALANQKQIQVQD 184
Cdd:cd08453    18 LVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIppPGASAPPalAYRPLLSEPLVLAVPAAWAAEGGAPLALAA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 185 LKDESFIMFnqdfeSRNI------IIQAC-KKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFSKNIIRIPIV 257
Cdd:cd08453    98 VAAEPLVIF-----PRRIapafhdAVTGYyRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASLRNLARPGVVYRELA 172

                         170       180
                  ....*....|....*....|....*....
gi 1774526220 258 NPTIPWNLAFIWKKDPhLSQINKQFIAFT 286
Cdd:cd08453   173 DPAPVLETGLVWRRDD-ASPVLARFLDLV 200
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-272 4.52e-09

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 55.35  E-value: 4.52e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  93 VRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLN-DHLTADYYTFVEDNLNLVVSNQ 171
Cdd:cd08447     2 LRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPfARPGLETRPLVREPLVAAVPAG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 172 HALANQKQIQVQDLKDESFIMFNQdFESR---NIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTFS 248
Cdd:cd08447    82 HPLAGAERLTLEDLDGQPFIMYSP-TEARyfhDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASASRLRF 160

                         170       180
                  ....*....|....*....|....*
gi 1774526220 249 KNIIRIPIVNPT-IPWNLAFIWKKD 272
Cdd:cd08447   161 EGVVFRPLDLPRdVPVELHLAWRRD 185
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-284 1.83e-08

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: 53.43  E-value: 1.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADYYTFV---EDNLNLVV 168
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEelaDEPLVVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 169 SNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFE-PKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTF 247
Cdd:cd08435    81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPlPRNVVETASISALLALLARSDMLAVLPRSVAEDE 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1774526220 248 --SKNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFIA 284
Cdd:cd08435   161 lrAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLD 199
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-272 2.20e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 52.96  E-value: 2.20e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIG-LPTVVNSFFfSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVV---LNDHLTADYYTFVEDNLNLV 167
Cdd:cd08427     1 RLRLGaIATVLTGLL-PRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVeppFPLPKDLVWTPLVREPLVLI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 168 VSNQHALANQKQIqvqdLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDS-TSQT 246
Cdd:cd08427    80 APAELAGDDPREL----LATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIaVPLP 155

                         170       180
                  ....*....|....*....|....*.
gi 1774526220 247 FSKNIIRIPIVNPTIPWNLAFIWKKD 272
Cdd:cd08427   156 AGPRVRVLPLGDPAFSRRVGLLWRRS 181
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 108-286 2.63e-08

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: 52.99  E-value: 2.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 108 QLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNcGVVVLNDHLTADYYTFV--EDNLNLVVSNQHALAnqkqIQVQDL 185
Cdd:cd08442    17 PLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLD-GAFVAGPVEHPRLEQEPvfQEELVLVSPKGHPPV----SRAEDL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 186 KDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQTF--SKNIIRIPIVNPTIPW 263
Cdd:cd08442    92 AGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLqgRGSVSIHPLPEPFADV 171

                         170       180
                  ....*....|....*....|...
gi 1774526220 264 NLAFIWKKDPHLSQInKQFIAFT 286
Cdd:cd08442   172 TTWLVWRKDSFTAAL-QAFLDLL 193
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 87-236 8.50e-08

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: 51.41  E-value: 8.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  87 TLKTGHV--RIGLPTVvnsfffsqlITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLNDHLTADYYTF--VED 162
Cdd:cd08443     3 YVATTHTqaRYVLPPV---------IKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLITLpcYHW 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1774526220 163 NLNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGV 236
Cdd:cd08443    74 NRCVVVKRDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGV 147
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 166-241 1.92e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 50.26  E-value: 1.92e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1774526220 166 LVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPD 241
Cdd:cd08441    76 LVVAPDHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPN 151
PBP2_NocR cd08458
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the ...
 105-283 2.86e-07

The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. 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, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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: 176147  Cd Length: 196  Bit Score: 50.09  E-value: 2.86e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 105 FFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVV-VLNDHLTADYYTFVEDNLNLVVSNQHALANQKQIQVQ 183
Cdd:cd08458    14 FMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGISiLAGDYPGLTTEPVPSFRAVCLLPPGHRLEDKETVHAT 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 184 DLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLL-PDSTSQTFSKNIIRIPIVnPTIP 262
Cdd:cd08458    94 DLEGESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRGMGVGIVdPFTADYYSANPVIQRSFD-PVVP 172

                         170       180
                  ....*....|....*....|.
gi 1774526220 263 WNLAFIWKKDPHLSQINKQFI 283
Cdd:cd08458   173 YHFAIVLPTDSPPPRLVSEFR 193
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 87-255 2.71e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl 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: 176135  Cd Length: 198  Bit Score: 47.11  E-value: 2.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  87 TLKTGHV--RIGLPTVVNSFffsqlitdfHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVvlNDHLTAD-------YY 157
Cdd:cd08444     3 TIATTHTqaRYALPWVVQAF---------KEQFPNVHLVLHQGSPEEIASMLANGQADIGIA--TEALENHpelvsfpYY 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 158 TFVEdnlNLVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVT 237
Cdd:cd08444    72 DWHH---HIIVPVGHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIG 148

                         170       180
                  ....*....|....*....|..
gi 1774526220 238 LLpdsTSQTFSK----NIIRIP 255
Cdd:cd08444   149 IV---AEMAFEGqrdtNLIKLD 167
nhaR PRK11062
transcriptional activator NhaR; Provisional
 5-78 3.55e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 44.61  E-value: 3.55e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1774526220   5 HLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEM 78
Cdd:PRK11062    8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEM 81
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 92-269 7.31e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 42.97  E-value: 7.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  92 HVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVLnDHLTADYY--TFVEDNLNLVVS 169
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVF-PELPPGLRsqPLFEDRFVCVAR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 170 NQHALAnQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVA-TNLgVTLLPDSTSQTFS 248
Cdd:cd08417    80 KDHPLA-GGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAgTDL-IATVPRRLAEALA 157

                         170       180
                  ....*....|....*....|....*
gi 1774526220 249 KN----IIRIPIVNPTIPWNLafIW 269
Cdd:cd08417   158 ERlglrVLPLPFELPPFTVSL--YW 180
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
2-77 9.30e-05

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 40.66  E-value: 9.30e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220    2 DIKHLQYF-LEVIKTE---NFTQAAENLYITQPALSRIVKTLESDlgvALFHRSR-------KKITLTDAGKVLHKHATK 70
Cdd:smart00347   7 GLTPTQFLvLRILYEEgplSVSELAKRLGVSPSTVTRVLDRLEKK---GLVRREPspedrrsVLVSLTEEGRELIEQLLE 83


                   ....*..
gi 1774526220   71 IADQITE 77
Cdd:smart00347  84 ARSETLA 90
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 94-283 1.50e-04

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: 42.09  E-value: 1.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  94 RIG-LPTVVNSFFfSQLITDFHQRYPGVTFHLEENGSKIIEDKVLDGKLNCGVVVL-------NDHLTADYYTFVednln 165
Cdd:cd08457     3 RIAaMPALANGFL-PRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGpleerqgFLIETRSLPAVV----- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220 166 lVVSNQHALANQKQIQVQDLKDESFIMFNQDFESRNIIIQACKKAGFEPKIVSETSQIDFLEEMVATNLGVTLLPDSTSQ 245
Cdd:cd08457    77 -AVPMGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAI 155

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1774526220 246 TFSKNIIRIPIVNPTIPWNLAFIWKKDPHLSQINKQFI 283
Cdd:cd08457   156 GLPLDGIVIRPFDTFIDAGFLVVRAANGPPSTMVDRFI 193
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-82 3.01e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 41.58  E-value: 3.01e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1774526220   4 KHLQYFLEVIKTENFTQAAENLYITQPALSRIVKTLESDLGVALFHRSRKKITLTDAGKVLHKHATKIADQITEMEQEI 82
Cdd:PRK15243    7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQEI 85
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
22-88 6.13e-04

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 39.18  E-value: 6.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774526220  22 AENLYITQPALSRIVKTLEsDLGvaLFHRSR-------KKITLTDAGKVLHKHATKIADQITEM------EQEIDQIRTL 88
Cdd:COG1846    59 AERLGLTKSTVSRLLDRLE-EKG--LVEREPdpedrraVLVRLTEKGRALLEEARPALEALLAEllaglsEEELEALLRL 135
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-125 1.04e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 39.35  E-value: 1.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1774526220  91 GHVRIGLPTVVNSFFFSQLITDFHQRYPGVTFHLE 125
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELV 35
 
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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