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Conserved domains on  [gi|518211809|ref|WP_019382017|]
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MULTISPECIES: LysR family transcriptional regulator [Cytobacillus]

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 ...
 92-288 1.44e-79

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: 239.38  E-value: 1.44e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVG-ITVLPVDEEEFDSQPLCNEPLVAVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYS 251
Cdd:cd08438   80 RGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDN 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518211809 252 QDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd08438  160 AGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLAL 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.60e-26

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 98.23  E-value: 2.60e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809    3 IRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGK 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 ...
 92-288 1.44e-79

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: 239.38  E-value: 1.44e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVG-ITVLPVDEEEFDSQPLCNEPLVAVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYS 251
Cdd:cd08438   80 RGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDN 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518211809 252 QDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd08438  160 AGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLAL 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 7.61e-65

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 203.94  E-value: 7.61e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTL 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIIN 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLA-IRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 161 VLKDPLMLIVHREHPLASNSEVhfsqlanepfilyrkdftlydliieecsksgfhpnivCESSqkDFLLGMVEGKLGITM 240
Cdd:COG0583  160 LGEERLVLVASPDHPLARRAPL-------------------------------------VNSL--EALLAAVAAGLGIAL 200

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 518211809 241 LPSKICQN-IYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIA 287
Cdd:COG0583  201 LPRFLAADeLAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLD 248
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-288 8.20e-50

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: 164.00  E-value: 8.20e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   90 SGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQgSSFEIINVLKDPLMLI 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDD-PGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  170 VHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQN- 248
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARe 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 518211809  249 IYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEF 199
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-288 4.06e-49

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 164.74  E-value: 4.06e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKV---LDAFKN 77
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAlqdLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  78 ltlELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFE 157
Cdd:PRK11242  81 ---AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVG-IAFAPVHSPEIE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 158 IINVLKDPLMLIVHREHPLASNSE-VHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVE-GK 235
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRrGR 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 518211809 236 LGiTMLPSKICQNiySQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:PRK11242 237 LA-TLLPAAIARE--HDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIEL 286
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-286 5.98e-42

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 146.22  E-value: 5.98e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTL 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAqGSSFEIIN 160
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLE-KKRLVYTP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 161 VLKDPLMLIVHREHPLASN--SEVHFSQLANEPFIL------YRKDFTLYdLIIEECSKSGFhpNIVCESSQKDFLLGMV 232
Cdd:NF040786 160 FYKDRLVLITPNGTEKYRMlkEEISISELQKEPFIMreegsgTRKEAEKA-LKSLGISLEDL--NVVASLGSTEAIKQSV 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 518211809 233 EGKLGITMLpSKIC--QNIYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFI 286
Cdd:NF040786 237 EAGLGISVI-SELAaeKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFL 291
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 6-288 6.80e-32

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: 119.45  E-value: 6.80e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809    6 LEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLELTDV 85
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRES 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   86 TELKSGEIKIGippIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQgSSFEIINVLKDP 165
Cdd:TIGR03339  82 GALREGSLRIA---ATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDD-PRLDRVVLGNDP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  166 LMLIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKI 245
Cdd:TIGR03339 158 LVAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAE 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 518211809  246 CQNiySQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:TIGR03339 238 VGR--DPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLEL 278
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.60e-26

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 98.23  E-value: 2.60e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809    3 IRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-71 1.06e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 66.92  E-value: 1.06e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   2 DIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRsSKQLELTDAGKAVLINAKKV 71
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV 71
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
22-72 9.54e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 35.56  E-value: 9.54e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 518211809  22 SQTLHVTQPSISKAIKNLEgELGVpLFYRSSKQLELTDAGKAVlinAKKVL 72
Cdd:COG1321   31 AERLGVSPPSVTEMLKKLE-EKGL-VEYEPYGGITLTEEGREL---ALRIV 76
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-288 1.44e-79

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: 239.38  E-value: 1.44e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVG-ITVLPVDEEEFDSQPLCNEPLVAVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYS 251
Cdd:cd08438   80 RGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDN 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518211809 252 QDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd08438  160 AGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLAL 196
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-287 7.61e-65

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 203.94  E-value: 7.61e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTL 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIIN 160
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLA-IRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 161 VLKDPLMLIVHREHPLASNSEVhfsqlanepfilyrkdftlydliieecsksgfhpnivCESSqkDFLLGMVEGKLGITM 240
Cdd:COG0583  160 LGEERLVLVASPDHPLARRAPL-------------------------------------VNSL--EALLAAVAAGLGIAL 200

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 518211809 241 LPSKICQN-IYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIA 287
Cdd:COG0583  201 LPRFLAADeLAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLD 248
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-288 1.35e-61

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: 193.59  E-value: 1.35e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLA-IVALPVDDPGLESEPLFEEPLVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYS 251
Cdd:cd05466   80 PDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELAD 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518211809 252 QDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd05466  160 GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLEL 196
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-288 8.20e-50

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: 164.00  E-value: 8.20e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   90 SGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQgSSFEIINVLKDPLMLI 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDD-PGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  170 VHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQN- 248
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARe 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 518211809  249 IYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEF 199
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-288 4.06e-49

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 164.74  E-value: 4.06e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKV---LDAFKN 77
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAlqdLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  78 ltlELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFE 157
Cdd:PRK11242  81 ---AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVG-IAFAPVHSPEIE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 158 IINVLKDPLMLIVHREHPLASNSE-VHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVE-GK 235
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRrGR 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 518211809 236 LGiTMLPSKICQNiySQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:PRK11242 237 LA-TLLPAAIARE--HDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIEL 286
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-287 1.70e-43

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: 147.30  E-value: 1.70e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLiCTVPAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd08434    1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLAL-CSPVPDEPDIEWIPLFTEELVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKIcqNIYS 251
Cdd:cd08434   80 KDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMT--LLNP 157

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 518211809 252 QDLVVLPISESAINLELGMIWKKEKYLSFAVREFIA 287
Cdd:cd08434  158 PGVKKIPIKDPDAERTIGLAWLKDRYLSPAARRFKD 193
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-288 1.10e-42

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: 145.34  E-value: 1.10e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIcTVPAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFV-RPPPDPPGLASRPLLREPLVVALP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFILYRKDF--TLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKIcQNI 249
Cdd:cd08414   80 ADHPLAARESVSLADLADEPFVLFPREPgpGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASV-ARL 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 518211809 250 YSQDLVVLPISESAINLELGMIWKKEKyLSFAVREFIAC 288
Cdd:cd08414  159 QRPGVVYRPLADPPPRSELALAWRRDN-ASPALRAFLEL 196
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-286 5.98e-42

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 146.22  E-value: 5.98e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTL 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAqGSSFEIIN 160
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLE-KKRLVYTP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 161 VLKDPLMLIVHREHPLASN--SEVHFSQLANEPFIL------YRKDFTLYdLIIEECSKSGFhpNIVCESSQKDFLLGMV 232
Cdd:NF040786 160 FYKDRLVLITPNGTEKYRMlkEEISISELQKEPFIMreegsgTRKEAEKA-LKSLGISLEDL--NVVASLGSTEAIKQSV 236

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 518211809 233 EGKLGITMLpSKIC--QNIYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFI 286
Cdd:NF040786 237 EAGLGISVI-SELAaeKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFL 291
PRK09986 PRK09986
LysR family transcriptional regulator;
1-272 4.07e-40

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 141.40  E-value: 4.07e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNltl 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQ--- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGE---IKIGippIVGAAFFSQLI---SQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLI-CTVPAQG 153
Cdd:PRK09986  84 SLARVEQIGRGEagrIEIG---IVGTALWGRLRpamRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWrMADLEPN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 154 SSFEIINVLKDPLMLIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEE-CSKSGFHPNIVCESSQKDFLLGMV 232
Cdd:PRK09986 161 PGFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRvCQQAGFSPQIIRQVNEPQTVLAMV 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 518211809 233 EGKLGITMLPSKiCQNIYSQDLVVLPISEsAINLELGMIW 272
Cdd:PRK09986 241 SMGIGITLLPDS-YAQIPWPGVVFRPLKE-RIPADLYAVY 278
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-293 3.87e-38

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 136.44  E-value: 3.87e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTL 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSgEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIcTVPAQGSSFEIIN 160
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFM-RHPVYSDEIDYLE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 161 VLKDPLMLIVHREHPLASNSEVHFSQLANEPFILYRKDF--TLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGI 238
Cdd:PRK09906 159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYsgSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGC 238

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 518211809 239 TMLPSKIcQNIYSQDLVVLPISESAINLELGMIWKKEKyLSFAVREFIACSESYL 293
Cdd:PRK09906 239 TIIPGYM-NNFNTGQVVFRPLAGNVPSIALLMAWKKGE-MKPALRDFIAIVQERL 291
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 101-286 5.41e-34

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: 122.61  E-value: 5.41e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 101 VGAAFFSQL---ISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIcTVPAQGSSFEIINVLKDPLMLIVHREHPLA 177
Cdd:cd08452    7 VGAAIYEFLppiVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFL-HPPIQHTALHIETVQSSPCVLALPKQHPLA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 178 SNSEVHFSQLANEPFILYRKDF--TLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKIcQNIYSQDLV 255
Cdd:cd08452   86 SKEEITIEDLRDEPIITVAREAwpTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSA-KKLFNLEVA 164

                        170       180       190
                 ....*....|....*....|....*....|.
gi 518211809 256 VLPISESAINLELGMIWKKEKyLSFAVREFI 286
Cdd:cd08452  165 YRKIDQINLNAEWSIAYRKDN-HNPLLKHFI 194
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-243 1.17e-33

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 124.76  E-value: 1.17e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTL 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPaQGSSFEIIN 160
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVK-ESEAFIEVP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 161 VLKDPLMLIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITM 240
Cdd:PRK11151 160 LFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITL 239


                 ...
gi 518211809 241 LPS 243
Cdd:PRK11151 240 LPA 242
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 6-288 6.80e-32

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: 119.45  E-value: 6.80e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809    6 LEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLELTDV 85
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRES 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   86 TELKSGEIKIGippIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQgSSFEIINVLKDP 165
Cdd:TIGR03339  82 GALREGSLRIA---ATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDD-PRLDRVVLGNDP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  166 LMLIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKI 245
Cdd:TIGR03339 158 LVAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAE 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 518211809  246 CQNiySQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:TIGR03339 238 VGR--DPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLEL 278
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-288 6.93e-29

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: 109.15  E-value: 6.93e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  93 IKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIINVLKDPLMLIVHR 172
Cdd:cd08440    2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFG-IGSEPEADPDLEFEPLLRDPFVLVCPK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 173 EHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYSQ 252
Cdd:cd08440   81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHP 160

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 518211809 253 DLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd08440  161 GLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDL 196
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 105-288 1.79e-28

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: 108.03  E-value: 1.79e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 105 FFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQGSSFEIINVLKDPLMLIVHREHPLASNSEVHF 184
Cdd:cd08451   15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLLEEPMLVALPAGHPLARERSIPL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 185 SQLANEPFILYRKDF--TLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKIcQNIYSQDLVVLPISES 262
Cdd:cd08451   95 AALADEPFILFPRPVgpGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASM-RQLQAPGVVYRPLAGA 173

                        170       180
                 ....*....|....*....|....*.
gi 518211809 263 AINLELGMIWKKEKyLSFAVREFIAC 288
Cdd:cd08451  174 PLTAPLALAYRRGE-RSPAVRNFIAL 198
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-258 7.35e-28

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 109.31  E-value: 7.35e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQH-LSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLE-LTDAGKAVLINAKKVL---DAF 75
Cdd:PRK12682   1 MNLQQLRFVREAVRRnLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILrevGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  76 KNLTLELTDVtelKSGEIKIG---------IPPIVgAAFfsqlisqyKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLI 146
Cdd:PRK12682  81 KRIGDDFSNQ---DSGTLTIAtthtqaryvLPRVV-AAF--------RKRYPKVNLSLHQGSPDEIARMVISGEADIGIA 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 147 CTVPAQGSSFEIINVLKDPLMLIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKD 226
Cdd:PRK12682 149 TESLADDPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSD 228

                        250       260       270
                 ....*....|....*....|....*....|..
gi 518211809 227 FLLGMVEGKLGITMLPSKICQNIYSQDLVVLP 258
Cdd:PRK12682 229 VIKTYVRLGLGVGIVAEMAYRPDRDGDLVALP 260
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 2.60e-26

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 98.23  E-value: 2.60e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809    3 IRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-285 2.34e-25

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 102.41  E-value: 2.34e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   3 IRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLEL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  83 TDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLI-CTVPAQ-GSSFEIIN 160
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVgGEVPTElKKILEITP 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 161 VLKDPLMLIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPN---IVCESSQKDFLLGMVEGKLG 237
Cdd:CHL00180 167 YVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKrfkIEMELNSIEAIKNAVQSGLG 246

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 518211809 238 ITML-PSKICQNIYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREF 285
Cdd:CHL00180 247 AAFVsVSAIEKELELGLLHWIKIENITIKRMLSIITNPNRYKSKASETF 295
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-238 1.21e-24

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 100.82  E-value: 1.21e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVA-QHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQL-ELTDAGKAVLINAKKVLDAFKNL 78
Cdd:PRK12684   1 MNLHQLRFVREAVrQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  79 TLELTDVTELKSGEIKIG---------IPPIvgaaffsqlISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTv 149
Cdd:PRK12684  81 KRVGKEFAAQDQGNLTIAtthtqaryaLPAA---------IKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLA-IAT- 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 150 paqgssfEIINVLKDPLML---------IVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVC 220
Cdd:PRK12684 150 -------EAIADYKELVSLpcyqwnhcvVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVL 222

                        250
                 ....*....|....*...
gi 518211809 221 ESSQKDFLLGMVEGKLGI 238
Cdd:PRK12684 223 EAIDADVIKTYVELGLGV 240
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 4-194 2.75e-24

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: 99.40  E-value: 2.75e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809    4 RHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLELT 83
Cdd:TIGR02424   6 RHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVASLS 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   84 DVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIgLICTVPA----QGSSFEii 159
Cdd:TIGR02424  86 QLGEGEGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDL-VVGRLGApetmQGLSFE-- 162

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 518211809  160 NVLKDPLMLIVHREHPLASNSEVHFSQLANEPFIL 194
Cdd:TIGR02424 163 HLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLL 197
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 92-285 3.66e-24

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: 96.63  E-value: 3.66e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTV-PAQGSSFEIINVLKDPLMLIV 170
Cdd:cd08437    1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLtPLENSALHSKIIKTQHFMIIV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 171 HREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNiy 250
Cdd:cd08437   81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKP-- 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 518211809 251 SQDLVVLPISES-AINLELGMIWKKEKYLSFAVREF 285
Cdd:cd08437  159 DDHLVAIPLLDNeQPTFYISLAHRKDQLLTPAQKKL 194
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-287 1.65e-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: 95.25  E-value: 1.65e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTvPAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEG-PVDHPDLIVEPFAEDELVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFIL------YRKDFtlyDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSK- 244
Cdd:cd08420   80 PDHPLAGRKEVTAEELAAEPWILrepgsgTREVF---ERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLa 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 518211809 245 ICQNIYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIA 287
Cdd:cd08420  157 VRKELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLE 199
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-286 2.62e-23

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: 94.53  E-value: 2.62e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICT--VPaQGSSFEIINVLkdPLMLI 169
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDldLP-EDIAFEPLARL--PPYVW 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 170 VHREHPLASNSEVHFSQLANEPFILYRKDFTlYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNi 249
Cdd:cd08412   78 LPADHPLAGKDEVSLADLAAEPLILLDLPHS-REYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRP- 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 518211809 250 YSQD---LVVLPISESAINLELGMIWKKEKYLSFAVREFI 286
Cdd:cd08412  156 WSYDgkrLVRRPLADPVPPLRLGLAWRRGARLTRAARAFV 195
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-272 3.74e-23

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: 93.82  E-value: 3.74e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  93 IKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIC---TVPAQGSSFEIInvlKDPLMLI 169
Cdd:cd08436    2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGlpeRRPPGLASRELA---REPLVAV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 170 VHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNi 249
Cdd:cd08436   79 VAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAAR- 157

                        170       180
                 ....*....|....*....|...
gi 518211809 250 ySQDLVVLPISESAINlELGMIW 272
Cdd:cd08436  158 -LPGLAALPLEPAPRR-RLYLAW 178
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-274 5.70e-23

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: 93.74  E-value: 5.70e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  91 GEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTvPAQGSSFEIINVLKDPLMLIV 170
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLAL-PVDEPGLEEEPLFDEPFLLAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 171 HREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLP-----SKI 245
Cdd:cd08411   80 PKDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPelavpSEE 159

                        170       180
                 ....*....|....*....|....*....
gi 518211809 246 CQniySQDLVVLPISESAINLELGMIWKK 274
Cdd:cd08411  160 LR---GDRLVVRPFAEPAPSRTIGLVWRR 185
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-287 1.13e-22

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: 92.72  E-value: 1.13e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIppiVGAAFFSQL---ISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICT--VPAQgssFEIINVLKDPL 166
Cdd:cd08448    1 RLRIGF---VGSMLYRGLpriLRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSrrLPAG---LSARLLHREPF 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 167 MLIVHREHPLASNSEVHFSQLANEPFILYRKDFT--LYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSK 244
Cdd:cd08448   75 VCCLPAGHPLAARRRIDLRELAGEPFVLFSREVSpdYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRS 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 518211809 245 ICQnIYSQDLVVLPISESAINLELGMIWKKEKYlSFAVREFIA 287
Cdd:cd08448  155 LAR-AGLAGVRFLPLKGATQRSELYAAWKASAP-NPALQAFLA 195
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-257 2.82e-22

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 94.49  E-value: 2.82e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVA-QHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQL-ELTDAGKAVLINAKKVLDAFKNL 78
Cdd:PRK12679   1 MNFQQLKIIREAArQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLlGMTEPGKALLVIAERILNEASNV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  79 TlELTDV-TELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLictvpaqgSSFE 157
Cdd:PRK12679  81 R-RLADLfTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGI--------ASER 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 158 IINvlkDPLM-----------LIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKD 226
Cdd:PRK12679 152 LSN---DPQLvafpwfrwhhsLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSD 228

                        250       260       270
                 ....*....|....*....|....*....|.
gi 518211809 227 FLLGMVEGKLGITMLPSKICQNIYSQDLVVL 257
Cdd:PRK12679 229 VIKTYVALGLGIGLVAEQSSGEQEESNLIRL 259
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-296 6.54e-22

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 92.83  E-value: 6.54e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   3 IRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAfknlTLEL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ----AVEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  83 TDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLI---CTVPaqgssfEII 159
Cdd:PRK10837  81 EQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIegpCHSP------ELI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 160 NV--LKDPLMLIVHREHPLASNsEVHFSQLANEPFILYRK--------DFTLYDLIieecskSGFHpnIVCESSQKDFLL 229
Cdd:PRK10837 155 SEpwLEDELVVFAAPDSPLARG-PVTLEQLAAAPWILRERgsgtreivDYLLLSHL------PRFE--LAMELGNSEAIK 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 518211809 230 GMVEGKLGITMLPSK-ICQNIYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIacseSYLENG 296
Cdd:PRK10837 226 HAVRHGLGISCLSRRvIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFL----SYCQEA 289
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-243 1.27e-21

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 92.41  E-value: 1.27e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVA-QHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLE-LTDAGKAVLINAKKVLDAFKNL 78
Cdd:PRK12683   1 MNFQQLRIIREAVrQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  79 TLELTDVTELKSGEIKIG---------IPPIVgaaffsqliSQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTv 149
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVAtthtqaryaLPKVV---------RQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIG-IAT- 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 150 PAQGSSFEIINVlkdPL-----MLIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQ 224
Cdd:PRK12683 150 EALDREPDLVSF---PYyswhhVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALD 226

                        250
                 ....*....|....*....
gi 518211809 225 KDFLLGMVEGKLGITMLPS 243
Cdd:PRK12683 227 ADVIKTYVELGMGVGIVAA 245
PRK10341 PRK10341
transcriptional regulator TdcA;
4-292 5.04e-20

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 88.00  E-value: 5.04e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   4 RHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLELT 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  84 DVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDiglictvpaqgssFEIINVLK 163
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLD-------------FAIGTLSN 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 164 DPLMLIVHREhPLASNSEVHFS-------------QLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLG 230
Cdd:PRK10341 157 EMKLQDLHVE-PLFESEFVLVAsksrtctgtttleSLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYN 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 518211809 231 MVEGKLGITMLPSKICQNIYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIACSESY 292
Cdd:PRK10341 236 LVLNADFLTVIPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKEY 297
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-288 1.13e-19

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: 84.54  E-value: 1.13e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIcTVPAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd08415    1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLA-SLPLDHPGLESEPLASGRAVCVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYS 251
Cdd:cd08415   80 PGHPLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAG 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518211809 252 QDLVVLPISEsAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd08415  160 AGLVVRPFRP-AIPFEFALVRPAGRPLSRLAQAFIDL 195
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 13-127 3.85e-19

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 85.28  E-value: 3.85e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  13 AQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAfknltleLTDVTE--LKS 90
Cdd:PRK11139  18 ARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQ-------LAEATRklRAR 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 518211809  91 GEIK---IGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEV 127
Cdd:PRK11139  91 SAKGaltVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAV 130
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-261 7.54e-19

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 84.95  E-value: 7.54e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQH-LSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQL-ELTDAGKAVLINAKKVL---DAF 75
Cdd:PRK12681   1 MKLQQLRYIVEVVNHnLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILskvESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  76 KNLTLELTDVtelKSGEIKIG---------IPPIvgaaffsqlISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlI 146
Cdd:PRK12681  81 KSVAGEHTWP---DKGSLYIAtthtqaryaLPPV---------IKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFA-I 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 147 CTvpaqgssfEIINVLKDPLML---------IVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPN 217
Cdd:PRK12681 148 AT--------EALHLYDDLIMLpcyhwnrsvVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPR 219

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 518211809 218 IVCESSQKDFLLGMVEGKLGITMLPSKICQNIYSQDLVVLPISE 261
Cdd:PRK12681 220 IVFTATDADVIKTYVRLGLGVGVIASMAVDPVADPDLVAIDASH 263
PRK09791 PRK09791
LysR family transcriptional regulator;
3-262 9.84e-19

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 84.43  E-value: 9.84e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   3 IRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLEL 82
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  83 TDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIglicTVPA--QGS-----S 155
Cdd:PRK09791  87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDF----TINTyyQGPydhefT 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 156 FEiiNVLKDPLMLIVHREHPLASNSEVhfSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNI--VCES--------SQK 225
Cdd:PRK09791 163 FE--KLLEKQFAVFCRPGHPAIGARSL--KQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVgvVCETfsacislvAKS 238

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 518211809 226 DFLlgmvegklgiTMLPSK-ICQNIYSQDLVVLPISES 262
Cdd:PRK09791 239 DFL----------SILPEEmGCDPLHGQGLVMLPVSEI 266
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-287 2.03e-18

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: 81.22  E-value: 2.03e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  91 GEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIINVLKDPLMLIV 170
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLG-IAFAPVRSPDIDAQPLFDERLALVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 171 HREHPLA-SNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMV-EGKLGiTMLPSKICQN 248
Cdd:cd08425   80 GATHPLAqRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVrRGRLA-TILPDAIARE 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 518211809 249 iySQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIA 287
Cdd:cd08425  159 --QPGLCAVALEPPLPGRTAALLRRKGAYRSAAARAFAA 195
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-256 2.50e-18

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 83.53  E-value: 2.50e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLdafKNLTL 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL---PQISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTV-PAQGSSFEii 159
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDIlPRSGLHYS-- 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 160 NVLKDPLMLIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIvcESSQKDFLL-GMVEGKLGI 238
Cdd:PRK15421 157 PMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSL--KSVDNTLLLiQMVAARMGI 234

                        250
                 ....*....|....*...
gi 518211809 239 TMLPSKICQNIYSQDLVV 256
Cdd:PRK15421 235 AALPHWVVESFERQGLVV 252
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-287 4.07e-18

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: 80.64  E-value: 4.07e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 109 LISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIINVLKDPLMLIVHREHPLASNSEVHFSQLA 188
Cdd:cd08421   18 DLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLG-IVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAFADTL 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 189 NEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQ-NIYSQDLVVLPISESAINLE 267
Cdd:cd08421   97 DHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARrYARALGLRVVPLDDAWARRR 176

                        170       180
                 ....*....|....*....|
gi 518211809 268 LGMIWKKEKYLSFAVREFIA 287
Cdd:cd08421  177 LLLCVRSFDALPPAARALVD 196
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-262 4.78e-18

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: 80.39  E-value: 4.78e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIppiVGAAF---FSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQGSSfEIINVL--KDPL 166
Cdd:cd08449    1 HLNIGM---VGSVLwggLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDP-PLASELlwREPM 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 167 MLIVHREHPLASNSEVHFSQLANEPFI-LYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKI 245
Cdd:cd08449   77 VVALPEEHPLAGRKSLTLADLRDEPFVfLRLANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESY 156

                        170
                 ....*....|....*..
gi 518211809 246 cQNIYSQDLVVLPISES 262
Cdd:cd08449  157 -ARLPWPGVRFIPLKQA 172
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 95-283 1.18e-17

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: 79.18  E-value: 1.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  95 IGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIC-TVPAQGSSFEIInvLKDPLMLIVHRE 173
Cdd:cd08433    4 VGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYgPPPIPGLSTEPL--LEEDLFLVGPAD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 174 HPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLP-SKICQNIYSQ 252
Cdd:cd08433   82 APLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPaSAVAAEVAAG 161

                        170       180       190
                 ....*....|....*....|....*....|.
gi 518211809 253 DLVVLPISESAINLELGMIWKKEKYLSFAVR 283
Cdd:cd08433  162 RLVAAPIVDPALTRTLSLATPRDRPLSPAAL 192
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-243 1.18e-16

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: 76.48  E-value: 1.18e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLI----CTVPAQGSSFEIINVLKDPLM 167
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypVTPPPDDPGLTRVPLLDDPLD 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 518211809 168 LIVHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPS 243
Cdd:cd08423   81 LVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR 156
PRK12680 PRK12680
LysR family transcriptional regulator;
1-258 1.26e-16

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 78.90  E-value: 1.26e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQ-HLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLE-LTDAGKAVLINAKKVLDAFKNL 78
Cdd:PRK12680   1 MTLTQLRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  79 TLELTDVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQGSSFEI 158
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 159 INVLKDPLMLIVHREHPLASNSEV-HFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLG 237
Cdd:PRK12680 161 VPLYRWRRLVVVPRGHALDTPRRApDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLG 240

                        250       260
                 ....*....|....*....|.
gi 518211809 238 ITMLpSKICQNIYSQDLVVLP 258
Cdd:PRK12680 241 VGLL-AEMAVNANDEDLRAWP 260
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-242 1.67e-15

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 75.10  E-value: 1.67e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTL 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGEIKIGIPPIVGAAFFS-QLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIC-TVPAQGSSFei 158
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLAPGTAASSLTmPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYeHSPVAGLSS-- 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 159 INVLKDPLMLIVHREHPlasNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGI 238
Cdd:PRK11233 159 QPLLKEDLFLVGTQDCP---GQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGV 235


                 ....
gi 518211809 239 TMLP 242
Cdd:PRK11233 236 TVLP 239
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-275 1.79e-15

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: 73.06  E-value: 1.79e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  93 IKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQgSSFEIINVLKDPLMLIVHR 172
Cdd:cd08447    2 LRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFAR-PGLETRPLVREPLVAAVPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 173 EHPLASNSEVHFSQLANEPFILY--RKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIY 250
Cdd:cd08447   81 GHPLAGAERLTLEDLDGQPFIMYspTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASASRLRF 160

                        170       180
                 ....*....|....*....|....*.
gi 518211809 251 SqDLVVLPIS-ESAINLELGMIWKKE 275
Cdd:cd08447  161 E-GVVFRPLDlPRDVPVELHLAWRRD 185
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-276 2.17e-15

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 74.84  E-value: 2.17e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTL 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  81 ELTDVTELKSGEIKIGI------PPIVGaaffsQLISQYKEKFPLIEIKLtevgTKKIKKGV------DDGTLDIGLICT 148
Cdd:PRK10094  82 ELQQVNDGVERQVNIVInnllynPQAVA-----QLLAWLNERYPFTQFHI----SRQIYMGVwdsllyEGFSLAIGVTGT 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 149 VPAQgSSFEIinvlkDPL-----MLIVHREHPLASNSEVhfsqLANEpfiLYRKdftlYDLI-IEECSK----------S 212
Cdd:PRK10094 153 EALA-NTFSL-----DPLgsvqwRFVMAADHPLANVEEP----LTEA---QLRR----FPAVnIEDSARtltkrvawrlP 215

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 518211809 213 GFHPNIVCESSQKdfLLGMVEGkLGITMLPSKICQN-IYSQDLVVLPISESAINLELGMIWKKEK 276
Cdd:PRK10094 216 GQKEIIVPDMETK--IAAHLAG-VGIGFLPKSLCQSmIDNQQLVSRVIPTMRPPSPLSLAWRKFG 277
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 108-276 5.94e-15

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: 71.99  E-value: 5.94e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 108 QLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICT-VPAQGSSFEIINVLKDPLMLIVHREHPLASNSEVHFSQ 186
Cdd:cd08416   17 RIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATpEGLNDPDFEVVPLFEDDIFLAVPATSPLAASSEIDLRD 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 187 LANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKIcQNIYSQDLVVLPISES-AIN 265
Cdd:cd08416   97 LKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRI-ADVYEDKVQLIPLAEPyQIR 175

                        170
                 ....*....|.
gi 518211809 266 LELGMIWKKEK 276
Cdd:cd08416  176 QTIGLVFLRSR 186
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-285 6.35e-15

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: 71.57  E-value: 6.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 103 AAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLiCTVPAQGSSFEIINVLKDPLMLIVHREHPLASNSEV 182
Cdd:cd08426   12 AELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGL-AFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 183 HFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPS-KICQNIYSQDLVVLPISE 261
Cdd:cd08426   91 TLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTElAVRREIRRGQLVAVPLAD 170

                        170       180
                 ....*....|....*....|....*
gi 518211809 262 -SAINLELGMIWKKEKYLSFAVREF 285
Cdd:cd08426  171 pHMNHRQLELQTRAGRQLPAAASAF 195
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-288 7.16e-15

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: 71.54  E-value: 7.16e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  91 GEIKIGIppiVGAAFFS---QLISQYKEKFPLIEIKLTEVgTKKIK-KGVDDGTLDIGLICTVPAQgSSFEIINVLKDPL 166
Cdd:cd08446    1 GELDVGY---FGSAILDtvpRLLRAFLTARPDVTVSLHNM-TKDEQiEALRAGRIHIGFGRFYPVE-PDIAVENVAQERL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 167 MLIVHREHPLASNSEVHFSQLANEPFILY----RKDFTlyDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLP 242
Cdd:cd08446   76 YLAVPKSHPLAARPAVSLADLRNEPLILFprggRPSFA--DEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVP 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518211809 243 SKICqNIYSQDLVVLPISESAINLELGMIWKKEKYlSFAVREFIAC 288
Cdd:cd08446  154 ESVA-ALRWPGVVFRPLADAEAKVPLSCIYRKDDR-SPILRAFLDV 197
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-125 1.67e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 71.77  E-value: 1.67e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  26 HVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLELTDVTELKSGEIKIGIPpiVGAA- 104
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCS--VTAAy 79

                         90       100
                 ....*....|....*....|..
gi 518211809 105 -FFSQLISQYKEKFPLIEIKLT 125
Cdd:PRK11716  80 sHLPPILDRFRAEHPLVEIKLT 101
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-178 5.90e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 70.74  E-value: 5.90e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   6 LEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLELTDV 85
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  86 TELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLT-EVgtkkiKKGV----DDGTLD--IGLICTVPAqGSSFEI 158
Cdd:PRK11074  87 ANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRqEV-----FNGVwdalADGRVDiaIGATRAIPV-GGRFAF 160

                        170       180
                 ....*....|....*....|....
gi 518211809 159 invlKDPLML----IVHREHPLAS 178
Cdd:PRK11074 161 ----RDMGMLswacVVSSDHPLAS 180
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 114-288 1.91e-13

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: 67.60  E-value: 1.91e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 114 KEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIcTVPAQG--SSFEIINVLKDPLMLIVHREHPLASNSEVhfsqLANEP 191
Cdd:cd08427   23 RRRHPDLEVHIVPGLSAELLARVDAGELDAAIV-VEPPFPlpKDLVWTPLVREPLVLIAPAELAGDDPREL----LATQP 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 192 FILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYSQDLVVLPISESAINLELGMI 271
Cdd:cd08427   98 FIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPAGPRVRVLPLGDPAFSRRVGLL 177

                        170
                 ....*....|....*..
gi 518211809 272 WKKEKYLSFAVREFIAC 288
Cdd:cd08427  178 WRRSSPRSRLIQALLEA 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-124 2.17e-13

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 69.26  E-value: 2.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   6 LEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDafkNLTLELTDV 85
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD---TLNQEILDI 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 518211809  86 --TELkSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKL 124
Cdd:PRK10086  96 knQEL-SGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTI 135
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 101-274 3.62e-13

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: 67.00  E-value: 3.62e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 101 VGAAFFSQL---ISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIctVPAQGS----SFEIINVLKDPLMLIVHRE 173
Cdd:cd08453    7 VSTADYSVLpelVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIV--IPPPGAsappALAYRPLLSEPLVLAVPAA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 174 HPLASNSEVHFSQLANEPFILYRKDF--TLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICqNIYS 251
Cdd:cd08453   85 WAAEGGAPLALAAVAAEPLVIFPRRIapAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASLR-NLAR 163

                        170       180
                 ....*....|....*....|...
gi 518211809 252 QDLVVLPISESAINLELGMIWKK 274
Cdd:cd08453  164 PGVVYRELADPAPVLETGLVWRR 186
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 101-264 7.18e-13

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 66.10  E-value: 7.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 101 VGAAFFSQL---ISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIG---LICTVPAqgssFEIINVLKDPLMLIVHREH 174
Cdd:cd08445    8 VPSTLYGLLpelIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGfgrLRIEDPA----IRRIVLREEPLVVALPAGH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 175 PLA-SNSEVHFSQLANEPFILY----RKDFTlyDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKIcQNI 249
Cdd:cd08445   84 PLAqEKAPLTLAQLADEPLILYpaspRPSFA--DQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPASV-QRL 160

                        170
                 ....*....|....*
gi 518211809 250 YSQDLVVLPISESAI 264
Cdd:cd08445  161 RRDDVVYRPLLDPDA 175
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-71 1.06e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 66.92  E-value: 1.06e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   2 DIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRsSKQLELTDAGKAVLINAKKV 71
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV 71
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 95-287 7.07e-12

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: 63.16  E-value: 7.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  95 IGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLIcTVPAQGSSFEIINVLKDPLMLIVHREH 174
Cdd:cd08450    4 IGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFM-RPEIQSDGIDYQLLLKEPLIVVLPADH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 175 PLASNSEVHFSQLANEPFILY-RKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKIcQNIYSQD 253
Cdd:cd08450   83 RLAGREKIPPQDLAGENFISPaPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYA-NNLLPPS 161

                        170       180       190
                 ....*....|....*....|....*....|....
gi 518211809 254 LVVLPISESAINLELGMIWKKEKyLSFAVREFIA 287
Cdd:cd08450  162 VVARPLSGETPTIDLVMGYNKAN-TSPLLKRFLS 194
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 93-288 3.77e-11

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 61.13  E-value: 3.77e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  93 IKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEvGTKKI-KKGVDDGTLD--IGLIcTVPAQGSSFEIINVLKDPLMLI 169
Cdd:cd08435    2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVE-GTSDElLEGLRAGELDlaIGRL-ADDEQPPDLASEELADEPLVVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 170 VHREHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFH-PNIVCESSQKDFLLGMVEGKLGITMLPSKICQN 248
Cdd:cd08435   80 ARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPlPRNVVETASISALLALLARSDMLAVLPRSVAED 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 518211809 249 -IYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd08435  160 eLRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDA 200
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 93-286 1.21e-09

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: 56.73  E-value: 1.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  93 IKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIINVLKDPLMLIVHR 172
Cdd:cd08457    2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLG-IADGPLEERQGFLIETRSLPAVVAVPM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 173 EHPLASNSEVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITML-PSKICQniYS 251
Cdd:cd08457   81 GHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIdPATAIG--LP 158

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 518211809 252 QDLVVLPISESAINLELGMIWKKEKYLSFAVREFI 286
Cdd:cd08457  159 LDGIVIRPFDTFIDAGFLVVRAANGPPSTMVDRFI 193
PRK09801 PRK09801
LysR family transcriptional regulator;
4-150 1.73e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 57.74  E-value: 1.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   4 RHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLELT 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518211809  84 DVTELKSGEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLtEVGTKKIKKGVDDGTLDIGLICTVP 150
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHF-ELFDRQIDLVQDNIDLDIRINDEIP 154
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 110-260 7.39e-09

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: 54.43  E-value: 7.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 110 ISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSfeiiNVLKDPLM-----LIVHREHPLASNSEVHF 184
Cdd:cd08444   19 VQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIG-IATEALENHP----ELVSFPYYdwhhhIIVPVGHPLESITPLTI 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 518211809 185 SQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYSQDLVVLPIS 260
Cdd:cd08444   94 ETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRDTNLIKLDTS 169
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 110-261 8.40e-09

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: 54.55  E-value: 8.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 110 ISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTvPAQGSSFEIINVlkdPL-----MLIVHREHPLASNSEVHF 184
Cdd:cd08413   19 IAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIA-IAT-EALDDHPDLVTL---PCyrwnhCVIVPPGHPLADLGPLTL 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518211809 185 SQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYSQDLVVLPISE 261
Cdd:cd08413   94 EDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGLGVGIIAEMAYDPQRDADLVALDAGH 170
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 110-261 2.46e-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: 52.95  E-value: 2.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 110 ISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTvpaqgssfEIINVLKDPLML---------IVHREHPLASNS 180
Cdd:cd08443   19 IKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFA-IAT--------EALHDYDDLITLpcyhwnrcvVVKRDHPLADKQ 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 181 EVHFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNIYSQDLVVLPIS 260
Cdd:cd08443   90 SISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDDPDLVIRDAR 169


                 .
gi 518211809 261 E 261
Cdd:cd08443  170 D 170
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-288 2.75e-08

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: 52.81  E-value: 2.75e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVpAQGSSFEIINVLKDPLMLIVH 171
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTL-HEPPGIERERLLRIDGVCVLP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 172 REHPLASNSEVHFSQLANEPFI-LYRKDFT--LYDLIIEEcskSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQN 248
Cdd:cd08456   80 PGHRLAVKKVLTPSDLEGEPFIsLARTDGTrqRVDALFEQ---AGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALD 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 518211809 249 IYSQDLVVLPIsESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd08456  157 YAAAGLVVRRF-SPAVPFEVSLIRPKHRPSSALVAAFSAC 195
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-96 7.16e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 52.84  E-value: 7.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   3 IRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLEL 82
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                         90
                 ....*....|....
gi 518211809  83 TDVTELKSGEIKIG 96
Cdd:PRK10632  84 YAFNNTPIGTLRIG 97
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
17-267 9.09e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 52.36  E-value: 9.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  17 SFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDAFKNLTLELTDVTELKSGEIKIG 96
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRKIKIA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  97 IPPIVGAAFFSQLISQYKEKFP-LIEIKLTEVGTKKIKKGVDDGTLdiglictvpaqgsSFEIINVLKDP---LMLIVHR 172
Cdd:PRK10082 107 AAHSLSLGLLPSIISQMPPLFTwAIEAIDVDEAVDKLREGQSDCIF-------------SFHDEDLLEAPfdhIRLFESQ 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 173 EHPLASNSEvHFSQLANE-----PFILYRKDFTLYDLI---IEECSKSGFHPNIVceSSQKDFLLGMVEGKLGITMLPS- 243
Cdd:PRK10082 174 LFPVCASDE-HGEALFNLaqphfPLLNYSRNSYMGRLInrtLTRHSELSFSTFFV--SSMSELLKQVALDGCGIAWLPEy 250

                        250       260
                 ....*....|....*....|....
gi 518211809 244 KICQNIYSQDLVVLPISESAINLE 267
Cdd:PRK10082 251 AIQQEIRSGQLVVLNRDELVIPIQ 274
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 92-288 1.58e-07

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: 50.81  E-value: 1.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  92 EIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGlICTVPAQGSSFEIIN--VLKDPLMLI 169
Cdd:cd08418    1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFA-IGTLPDEMYLKELISepLFESDFVVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 170 VHREHPLASNSEvhFSQLANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSK-ICQN 248
Cdd:cd08418   80 ARKDHPLQGARS--LEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDmGRGP 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 518211809 249 IYSQDLVVLPISESAINLELGMIWKKEKYLSFAVREFIAC 288
Cdd:cd08418  158 LDSFRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVEL 197
PBP2_ClcR cd08485
The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved ...
 91-245 5.83e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold; In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. 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: 176174 [Multi-domain]  Cd Length: 198  Bit Score: 48.92  E-value: 5.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  91 GEIKIGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTVPAQgSSFEIINVLKDPLMLIV 170
Cdd:cd08485    1 GELRVAYFGTVVLHTLPLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGRFYPYQ-EGVVVRNVTNERLFLGA 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518211809 171 HREHPLASNSEVHFSQLANEPFILYRKDF--TLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKI 245
Cdd:cd08485   80 QKSRARSFGEQVHCSALRNEPLILFPREGrpSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAGVGVTIVPETV 156
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-65 6.89e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 49.63  E-value: 6.89e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVL 65
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLL 65
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 105-285 1.72e-06

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: 47.50  E-value: 1.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 105 FFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIgLICTVPAQGSSFEIINVLKDPLMLIVHREHPLASNSEVHF 184
Cdd:cd08419   13 FAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDL-AIMGRPPEDLDLVAEPFLDNPLVVIAPPDHPLAGQKRIPL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 185 SQLANEPFIL------YRkdftlydLIIEE-CSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLP-SKICQNIYSQDLVV 256
Cdd:cd08419   92 ERLAREPFLLrepgsgTR-------LAMERfFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSlHTLALELATGRLAV 164

                        170       180
                 ....*....|....*....|....*....
gi 518211809 257 LPISESAINLELGMIWKKEKYLSFAVREF 285
Cdd:cd08419  165 LDVEGFPIRRQWYVVHRKGKRLSPAAQAF 193
nhaR PRK11062
transcriptional activator NhaR; Provisional
 5-85 1.19e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 45.77  E-value: 1.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   5 HLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVLDafknLTLELTD 84
Cdd:PRK11062   8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFT----LSQEMLD 83


                 .
gi 518211809  85 V 85
Cdd:PRK11062  84 I 84
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 108-287 2.23e-05

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: 44.14  E-value: 2.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 108 QLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIGLICTvPAQGSSFEIINVLKDPLMLIVHREHPLASNSEvhfsQL 187
Cdd:cd08442   17 PLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAG-PVEHPRLEQEPVFQEELVLVSPKGHPPVSRAE----DL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 188 ANEPFILYRKDFTLYDLIIEECSKSGFHPNIVCESSQKDFLLGMVEGKLGITMLPSKICQNI-YSQDLVVLPISESAINL 266
Cdd:cd08442   92 AGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLqGRGSVSIHPLPEPFADV 171

                        170       180
                 ....*....|....*....|.
gi 518211809 267 ELGMIWKKEKYLSfAVREFIA 287
Cdd:cd08442  172 TTWLVWRKDSFTA-ALQAFLD 191
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 95-272 2.68e-04

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 41.05  E-value: 2.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809  95 IGIPPIVGAAFFSQLISQYKEKFPLIEIKLTEVGTKKIKKGVDDGTLDIgLICTVPAQGSSFEIINVLKDPLMLIVHREH 174
Cdd:cd08417    4 IAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDL-AIGVFPELPPGLRSQPLFEDRFVCVARKDH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809 175 PLAsNSEVHFSQLANEPFILY---RKDFTLYDLIIEEcskSGFHPNIVCESSQkdFL--LGMVEGKLGITMLPSKICQNI 249
Cdd:cd08417   83 PLA-GGPLTLEDYLAAPHVLVsprGRGHGLVDDALAE---LGLSRRVALTVPH--FLaaPALVAGTDLIATVPRRLAEAL 156

                        170       180
                 ....*....|....*....|....
gi 518211809 250 -YSQDLVVLPISESAINLELGMIW 272
Cdd:cd08417  157 aERLGLRVLPLPFELPPFTVSLYW 180
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-61 4.07e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 41.13  E-value: 4.07e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 518211809   4 RHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAG 61
Cdd:PRK11013   7 RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQG 64
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-98 2.47e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.86  E-value: 2.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518211809   1 MDIRHLEYFAEVAQHLSFTKASQTLHVTQPSISKAIKNLEGELGVPLFYRSSKQLELTDAGKAVLINAKKVL----DAFK 76
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILrfndEACS 90

                         90       100
                 ....*....|....*....|..
gi 518211809  77 NLTLELTDvtelksGEIKIGIP 98
Cdd:PRK15092  91 SLMYSNLQ------GVLTIGAS 106
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
22-72 9.54e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 35.56  E-value: 9.54e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 518211809  22 SQTLHVTQPSISKAIKNLEgELGVpLFYRSSKQLELTDAGKAVlinAKKVL 72
Cdd:COG1321   31 AERLGVSPPSVTEMLKKLE-EKGL-VEYEPYGGITLTEEGREL---ALRIV 76
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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