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Conserved domains on  [gi|1273236942|gb|PIA68556|]
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LysR family transcriptional regulator [Pseudomonas toyotomiensis]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-294 5.99e-56

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.60  E-value: 5.99e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVH 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPL 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 163 YDDSLVLLVRGHERLRGKALLAalreqDYVATTRDTSLRGMAdetllrmglqrdpawevaymssaaalaraglgFALLPA 242
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLV-----NSLEALLAAVAAGLG--------------------------------IALLPR 203

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1273236942 243 SVADTFNSDGSLAVHVLSQ-APARSIGLLQRKPCYLSPPAQVFIALLRQQVGD 294
Cdd:COG0583   204 FLAADELAAGRLVALPLPDpPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-294 5.99e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.60  E-value: 5.99e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVH 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPL 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 163 YDDSLVLLVRGHERLRGKALLAalreqDYVATTRDTSLRGMAdetllrmglqrdpawevaymssaaalaraglgFALLPA 242
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLV-----NSLEALLAAVAAGLG--------------------------------IALLPR 203

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1273236942 243 SVADTFNSDGSLAVHVLSQ-APARSIGLLQRKPCYLSPPAQVFIALLRQQVGD 294
Cdd:COG0583   204 FLAADELAAGRLVALPLPDpPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-294 4.34e-41

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 144.33  E-value: 4.34e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   6 RQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMD---NAVH 82
Cdd:PRK11242    4 RHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEagrRAIH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEqlhLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAItsAVDDLGA--LDFQ 160
Cdd:PRK11242   84 DVAD---LSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGI--AFAPVHSpeIEAQ 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 161 PLYDDSLVLLVRGHERL--RGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGF 237
Cdd:PRK11242  159 PLFTETLALVVGRHHPLaaRRKALtLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLA 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1273236942 238 ALLPASVAdtFNSDGSLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALLRQQVGD 294
Cdd:PRK11242  239 TLLPAAIA--REHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAE 293
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-213 2.97e-38

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: 136.98  E-value: 2.97e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   1 MDisFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNA 80
Cdd:NF040786    1 MN--LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  81 VHDAHEQLHLESGSLRIAV--LPSVAIepLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALD 158
Cdd:NF040786   79 EEEFDRYGKESKGVLRIGAstIPGQYL--LPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1273236942 159 FQPLYDDSLVLLVRGHERLRGKALLAA----LREQDYVATTRDTSLRGMADETLLRMGL 213
Cdd:NF040786  157 YTPFYKDRLVLITPNGTEKYRMLKEEIsiseLQKEPFIMREEGSGTRKEAEKALKSLGI 215
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-288 1.85e-35

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: 126.87  E-value: 1.85e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVR-G 173
Cdd:cd08440     2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPkD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 174 HERLRGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSDG 252
Cdd:cd08440    82 HPLARRRSVtWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPG 161

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1273236942 253 SLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08440   162 LVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-293 5.82e-27

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://0-doi-org.brum.beds.ac.uk/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 104.68  E-value: 5.82e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  92 SGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 172 -RGHERLRGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFN 249
Cdd:pfam03466  81 pPDHPLARGEPVsLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1273236942 250 SDGSLAVHVLSQAPA-RSIGLLQRKPCYLSPPAQVFIALLRQQVG 293
Cdd:pfam03466 161 ADGRLVALPLPEPPLpRELYLVWRKGRPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-294 5.99e-56

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 181.60  E-value: 5.99e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVH 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPL 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 163 YDDSLVLLVRGHERLRGKALLAalreqDYVATTRDTSLRGMAdetllrmglqrdpawevaymssaaalaraglgFALLPA 242
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLV-----NSLEALLAAVAAGLG--------------------------------IALLPR 203

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1273236942 243 SVADTFNSDGSLAVHVLSQ-APARSIGLLQRKPCYLSPPAQVFIALLRQQVGD 294
Cdd:COG0583   204 FLAADELAAGRLVALPLPDpPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-294 4.34e-41

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 144.33  E-value: 4.34e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   6 RQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMD---NAVH 82
Cdd:PRK11242    4 RHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEagrRAIH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEqlhLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAItsAVDDLGA--LDFQ 160
Cdd:PRK11242   84 DVAD---LSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGI--AFAPVHSpeIEAQ 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 161 PLYDDSLVLLVRGHERL--RGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGF 237
Cdd:PRK11242  159 PLFTETLALVVGRHHPLaaRRKALtLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLA 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1273236942 238 ALLPASVAdtFNSDGSLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALLRQQVGD 294
Cdd:PRK11242  239 TLLPAAIA--REHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERRAE 293
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-213 2.97e-38

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: 136.98  E-value: 2.97e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   1 MDisFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNA 80
Cdd:NF040786    1 MN--LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  81 VHDAHEQLHLESGSLRIAV--LPSVAIepLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALD 158
Cdd:NF040786   79 EEEFDRYGKESKGVLRIGAstIPGQYL--LPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1273236942 159 FQPLYDDSLVLLVRGHERLRGKALLAA----LREQDYVATTRDTSLRGMADETLLRMGL 213
Cdd:NF040786  157 YTPFYKDRLVLITPNGTEKYRMLKEEIsiseLQKEPFIMREEGSGTRKEAEKALKSLGI 215
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-288 1.85e-35

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: 126.87  E-value: 1.85e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVR-G 173
Cdd:cd08440     2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPkD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 174 HERLRGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSDG 252
Cdd:cd08440    82 HPLARRRSVtWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPG 161

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1273236942 253 SLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08440   162 LVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-288 1.77e-31

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 116.55  E-value: 1.77e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV-R 172
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVpP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 173 GHERLRGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSD 251
Cdd:cd05466    81 DHPLAKRKSVtLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1273236942 252 GSLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-272 1.05e-29

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 114.74  E-value: 1.05e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   1 MDIsfRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNA 80
Cdd:PRK11151    1 MNI--RDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  81 VHDAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQ 160
Cdd:PRK11151   79 KEMASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEV 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 161 PLYDDSLVLLV-RGHE----------RLRGKALLA-----ALREQ--DY---VATTRDTSLRGMADETLLRMglqrdpaw 219
Cdd:PRK11151  159 PLFDEPMLLAVyEDHPwanrdrvpmsDLAGEKLLMledghCLRDQamGFcfeAGADEDTHFRATSLETLRNM-------- 230

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1273236942 220 eVAymssaaalarAGLGFALLPA-SVADTFNSDGSLAVHVLSQAPARSIGLLQR 272
Cdd:PRK11151  231 -VA----------AGSGITLLPAlAVPNERKRDGVCYLPCIKPEPRRTIGLVYR 273
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 6-199 6.00e-29

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 112.56  E-value: 6.00e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   6 RQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVHDAh 85
Cdd:PRK09906    4 RHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  86 EQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDD 165
Cdd:PRK09906   83 RKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDE 162

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1273236942 166 SLVLLVRGHERLR--GKALLAALREQDYVATTRDTS 199
Cdd:PRK09906  163 PLVVVLPVDHPLAheKEITAAQLDGVNFISTDPAYS 198
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-293 5.82e-27

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://0-doi-org.brum.beds.ac.uk/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 104.68  E-value: 5.82e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  92 SGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 172 -RGHERLRGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFN 249
Cdd:pfam03466  81 pPDHPLARGEPVsLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1273236942 250 SDGSLAVHVLSQAPA-RSIGLLQRKPCYLSPPAQVFIALLRQQVG 293
Cdd:pfam03466 161 ADGRLVALPLPEPPLpRELYLVWRKGRPLSPAVRAFIEFLREALA 205
cysB PRK12681
HTH-type transcriptional regulator CysB;
5-170 6.87e-24

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 99.20  E-value: 6.87e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   5 FRQLQAFVLIAEHR-SFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSV-ELTAAGQRFLEQARRLLRDMDNAVH 82
Cdd:PRK12681    3 LQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVESIKS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAvddlgALDfqpL 162
Cdd:PRK12681   83 VAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATE-----ALH---L 154


                  ....*...
gi 1273236942 163 YDDsLVLL 170
Cdd:PRK12681  155 YDD-LIML 161
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-186 3.19e-22

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 94.27  E-value: 3.19e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  21 SRAAEQVYLSQPALSYSLRKLEDALGLSLLARN-TRSVELTAAGQRFLEQARRLLRDMDNAVHDAHEQLHLESGSLRIAV 99
Cdd:PRK12684   20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIAT 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 100 LPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAI-TSAVDDLGALDFQPLYDDSLVLLV-RGHERL 177
Cdd:PRK12684  100 THTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIaTEAIADYKELVSLPCYQWNHCVVVpPDHPLL 179

                         170
                  ....*....|
gi 1273236942 178 RGKAL-LAAL 186
Cdd:PRK12684  180 ERKPLtLEDL 189
PRK09791 PRK09791
LysR family transcriptional regulator;
3-296 1.19e-21

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 92.90  E-value: 1.19e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVH 82
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGR----AGEIRQwvsaAEVDFAIT----SAVDDl 154
Cdd:PRK09791   85 DIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQlvsmINELRQ----GELDFTINtyyqGPYDH- 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 155 gALDFQPLYDDSLVLLVRGHERLRGKALLAALREQDYVATTRDTSLRGMADETLLRMGlqRDPAWEV---AYMSSAAALA 231
Cdd:PRK09791  160 -EFTFEKLLEKQFAVFCRPGHPAIGARSLKQLLDYSWTMPTPHGSYYKQLSELLDDQA--QTPQVGVvceTFSACISLVA 236

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1273236942 232 RAGLGFALLPASVADTFNSDGSLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALLRQQVGDAQ 296
Cdd:PRK09791  237 KSDFLSILPEEMGCDPLHGQGLVMLPVSEILPKATYYLIQRRDTRQTPLTASLITLFRRECGYLQ 301
rbcR CHL00180
LysR transcriptional regulator; Provisional
 1-214 1.19e-21

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 92.78  E-value: 1.19e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   1 MDISF--RQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLR--- 75
Cdd:CHL00180    1 TDLPFtlDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlce 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  76 DMDNAVHDAHeqlHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAV--DD 153
Cdd:CHL00180   81 ETCRALEDLK---NLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEvpTE 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1273236942 154 L-GALDFQPLYDDSLVLLV-RGHE-RLRGKALLAALREQDYVATTRDTSLRGMADETLLRMGLQ 214
Cdd:CHL00180  158 LkKILEITPYVEDELALIIpKSHPfAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGID 221
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 94-288 1.48e-21

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: 90.02  E-value: 1.48e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAI--TSAVDDLGALDFQPLYDDSLVLLV 171
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 172 RGHERL--RGKALLAALREQDYVATTRDTSLRGMADETLLRMGLQR-DPAWEVAYMSSAAALARAGLGFALLPASVADTF 248
Cdd:cd08435    81 RPGHPLarRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLpRNVVETASISALLALLARSDMLAVLPRSVAEDE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1273236942 249 NSDGSLAVHVLSQA-PARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08435   161 LRAGVLRELPLPLPtSRRPIGITTRRGGPLSPAARALLDAL 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.26e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.59  E-value: 1.26e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   5 FRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQ 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 95-288 3.75e-20

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: 86.05  E-value: 3.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGH 174
Cdd:cd08434     2 VRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 175 ERLRGKAL--LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPAsvADTFNSDG 252
Cdd:cd08434    82 HPLAGRDSvdLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPE--MTLLNPPG 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1273236942 253 SLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08434   160 VKKIPIKDPDAERTIGLAWLKDRYLSPAARRFKDFV 195
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 8-126 8.13e-20

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 87.59  E-value: 8.13e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   8 LQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLrdmdNAVHDAHEQ 87
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIF----DQLAEATRK 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1273236942  88 LHLES--GSLRIAVLPSVAIEPL-PRvLQEYRRRYPGIDISL 126
Cdd:PRK11139   87 LRARSakGALTVSLLPSFAIQWLvPR-LSSFNEAHPDIDVRL 127
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 5-216 1.80e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 86.64  E-value: 1.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   5 FRQLQaFVLIAEHRSF--SRAAEQVYLSQPALSYSLRKLEDALGLSLLARN-TRSVELTAAGQRFLEQARRLLRDMDNAV 81
Cdd:PRK12683    3 FQQLR-IIREAVRQNFnlTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  82 HDAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAI-TSAVDDLGALDFQ 160
Cdd:PRK12683   82 RLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIaTEALDREPDLVSF 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 161 PLYDDSLVLLV-RGHERLRGKAL-LAALREqdYVATTRDTSLRGMA--DETLLRMGLQRD 216
Cdd:PRK12683  162 PYYSWHHVVVVpKGHPLTGRENLtLEAIAE--YPIITYDQGFTGRSriDQAFAEAGLVPD 219
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 3-180 5.72e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 85.43  E-value: 5.72e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQaFVLIAEHRSF--SRAAEQVYLSQPALSYSLRKLEDALGLSLLARN-TRSVELTAAGQRFLEQARRLLRDMDN 79
Cdd:PRK12682    1 MNLQQLR-FVREAVRRNLnlTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVGN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  80 AVHDAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAI-TSAVDDLGALD 158
Cdd:PRK12682   80 IKRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIaTESLADDPDLA 159

                         170       180
                  ....*....|....*....|..
gi 1273236942 159 FQPLYDDSLVLLVRGHERLRGK 180
Cdd:PRK12682  160 TLPCYDWQHAVIVPPDHPLAQE 181
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-169 8.56e-19

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 84.10  E-value: 8.56e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  28 YLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVHDAHEQLHLESGSLRIavLPSV--AI 105
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSL--FCSVtaAY 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1273236942 106 EPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGA-LDFQPLYDDSLVL 169
Cdd:PRK11716   80 SHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPAsVAFSPIDEIPLVL 144
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-288 4.36e-17

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: 77.64  E-value: 4.36e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITS-AVDDLGALDFQPLYDDSLVLLVR 172
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGlPERRPPGLASRELAREPLVAVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 173 GHERL--RGKALLAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVAdtfNS 250
Cdd:cd08436    81 PDHPLagRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVA---AR 157

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1273236942 251 DGSLAVHVLSQAPARSIGLLQRKPcYLSPPAQVFIALL 288
Cdd:cd08436   158 LPGLAALPLEPAPRRRLYLAWSAP-PPSPAARAFLELL 194
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 95-288 4.87e-17

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: 77.60  E-value: 4.87e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGH 174
Cdd:cd08438     2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 175 ERLRGKAL--LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSDG 252
Cdd:cd08438    82 HPLAGRKTvsLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNAG 161

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1273236942 253 sLAVHVLSQAPAR-SIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08438   162 -VKVIPLTDPDLRwQLALIWRKGRYLSHAARAWLALL 197
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 94-288 4.96e-17

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: 77.60  E-value: 4.96e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV-R 172
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLpP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 173 GHeRLRGKALL--AALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNS 250
Cdd:cd08415    81 GH-PLARKDVVtpADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAG 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1273236942 251 DGsLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08415   160 AG-LVVRPFRPAIPFEFALVRPAGRPLSRLAQAFIDLL 196
PRK09986 PRK09986
LysR family transcriptional regulator;
3-211 6.92e-17

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 79.38  E-value: 6.92e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVH 82
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPL 162
Cdd:PRK09986   87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSR 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1273236942 163 yddslvllvrgheRLRGKALLAALREQDYVATTRDTSLRGMADETLLRM 211
Cdd:PRK09986  167 -------------RLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITL 202
PRK10341 PRK10341
transcriptional regulator TdcA;
6-290 1.05e-16

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 79.14  E-value: 1.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   6 RQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVHdah 85
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVN--- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  86 eQLHLESGSLRIAV---LPS-VAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDF-- 159
Cdd:PRK10341   87 -EINGMSSEAVVDVsfgFPSlIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLhv 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 160 QPLYDDSLVLLVRGHERLRGKALLAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFAL 239
Cdd:PRK10341  166 EPLFESEFVLVASKSRTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTV 245

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1273236942 240 LPASVADTFNSDGSLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALLRQ 290
Cdd:PRK10341  246 IPCDMTSPFGSNQFITIPIEETLPVAQYAAVWSKNYRIKKAASVLVELAKE 296
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-129 1.05e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 76.19  E-value: 1.05e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   8 LQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVHD-AHE 86
Cdd:PRK10086   19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDiKNQ 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1273236942  87 QLhleSGSLRIAVLPSVAIEPL-PRvLQEYRRRYPGIDISLHDG 129
Cdd:PRK10086   99 EL---SGTLTVYSRPSIAQCWLvPR-LADFTRRYPSISLTILTG 138
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 14-167 2.28e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 74.98  E-value: 2.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  14 IAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVHDAHEQLHLESG 93
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPgiDISLHdgrageIRQ------WVSAAE--VDFAI--TSAV--------DDLG 155
Cdd:PRK11074   93 QLSIAVDNIVRPDRTRQLIVDFYRHFD--DVELI------IRQevfngvWDALADgrVDIAIgaTRAIpvggrfafRDMG 164

                         170       180
                  ....*....|....*....|....*.
gi 1273236942 156 ALDF--------------QPLYDDSL 167
Cdd:PRK11074  165 MLSWacvvssdhplasmdGPLSDDEL 190
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-78 9.88e-15

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 73.30  E-value: 9.88e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1273236942   8 LQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMD 78
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-209 1.36e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 72.80  E-value: 1.36e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   1 MDISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLrdmDNA 80
Cdd:PRK10837    1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL---EQA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  81 VHDahEQL-HLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDF 159
Cdd:PRK10837   78 VEI--EQLfREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELIS 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1273236942 160 QPLYDDSLVLLVR-GHERLRGKALLAALREQDYVATTRDTSLRGMADETLL 209
Cdd:PRK10837  156 EPWLEDELVVFAApDSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLLL 206
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
6-129 1.69e-14

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 72.49  E-value: 1.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   6 RQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDmdnaVHDAH 85
Cdd:PRK10632    5 KRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHE----VQDVH 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1273236942  86 EQLH----LESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDG 129
Cdd:PRK10632   81 EQLYafnnTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTG 128
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 5-213 2.68e-14

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 72.02  E-value: 2.68e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   5 FRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNA---V 81
Cdd:PRK11233    3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAqlaV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  82 HDAHEQLhleSGSLRIAVLPSVAIEPL--PrVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDF 159
Cdd:PRK11233   83 HNVGQAL---SGQVSIGLAPGTAASSLtmP-LLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSS 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1273236942 160 QPLYDDSLvLLVRGHERLRGKALLAALREQDYVATTRDTSLRGMADETLLRMGL 213
Cdd:PRK11233  159 QPLLKEDL-FLVGTQDCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRL 211
PRK12680 PRK12680
LysR family transcriptional regulator;
3-199 4.49e-14

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 71.58  E-value: 4.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQAFVLIAEHR-SFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVE-LTAAGQRFLEQARRLLRDMDNA 80
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  81 VHDAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITS-AVDDLGALDF 159
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVStAGGEPSAGIA 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1273236942 160 QPLYD-DSLVLLVRGH--ERLRGKALLAALREQ---DYVATTRDTS 199
Cdd:PRK12680  161 VPLYRwRRLVVVPRGHalDTPRRAPDMAALAEHpliSYESSTRPGS 206
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 96-257 8.09e-14

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: 68.78  E-value: 8.09e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  96 RIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVR-GH 174
Cdd:cd08417     3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARkDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 175 ERLRGKALLAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSDGSL 254
Cdd:cd08417    83 PLAGGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGL 162


                  ...
gi 1273236942 255 AVH 257
Cdd:cd08417   163 RVL 165
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 94-288 3.43e-13

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: 67.23  E-value: 3.43e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV-R 172
Cdd:cd08433     1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGpA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 173 GHERLRGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPAS-VADTFNS 250
Cdd:cd08433    81 DAPLPRGAPVpLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASaVAAEVAA 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1273236942 251 DGSLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08433   161 GRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-215 4.66e-13

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 68.48  E-value: 4.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   1 MDISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNA 80
Cdd:PRK11013    2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  81 VHDAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQ 160
Cdd:PRK11013   82 VSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGTERT 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1273236942 161 PLYD-DSLVLLVRGHeRLRGKALLAA--LREQDYVATTRDTSLRGMADETLLRMGLQR 215
Cdd:PRK11013  162 ELLTlDEVCVLPAGH-PLAAKKVLTPddFAGENFISLSRTDSYRQLLDQLFAEHGVKR 218
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-215 5.69e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 68.12  E-value: 5.69e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVH 82
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  83 DAHEQlhlESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPL 162
Cdd:PRK15421   82 ACNEP---QQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPM 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1273236942 163 YDDSLVLLVRGHERLRGKALLaalreqdyvaTTRDtslrgMADETLLRMGLQR 215
Cdd:PRK15421  159 FDYEVRLVLAPDHPLAAKTRI----------TPED-----LASETLLIYPVQR 196
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 95-215 1.94e-12

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: 64.75  E-value: 1.94e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGH 174
Cdd:cd08456     2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPG 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1273236942 175 ERLRGKALLAA--LREQDYVATTRDTSLRGMADETLLRMGLQR 215
Cdd:cd08456    82 HRLAVKKVLTPsdLEGEPFISLARTDGTRQRVDALFEQAGVKR 124
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 93-287 3.41e-12

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: 64.47  E-value: 3.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  93 GSLRIAVLPSVAieP--LPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLL 170
Cdd:cd08411     1 GPLRLGVIPTIA--PylLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 171 VRGHERLRGKALLAA----------------LREQ-----DYVATTRDTSLRGMADETLLRMglqrdpaweVAymssaaa 229
Cdd:cd08411    79 VPKDHPLAKRKSVTPedlagerlllleeghcLRDQalelcRLAGAREQTDFEATSLETLRQM---------VA------- 142

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 230 larAGLGFALLPASVADTFNSDGSLAVHVL--SQAPARSIGLLQRKPcylSPPAQVFIAL 287
Cdd:cd08411   143 ---AGLGITLLPELAVPSEELRGDRLVVRPfaEPAPSRTIGLVWRRS---SPRAAAFEAL 196
cbl PRK12679
HTH-type transcriptional regulator Cbl;
3-216 1.33e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 64.06  E-value: 1.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   3 ISFRQLQafvLIAE----HRSFSRAAEQVYLSQPALSYSLRKLEDALGLSL-LARNTRSVELTAAGQRFLEQARRLLRDM 77
Cdd:PRK12679    1 MNFQQLK---IIREaarqDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  78 DNAVHDAHEQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSA--VDDLG 155
Cdd:PRK12679   78 SNVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASErlSNDPQ 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1273236942 156 ALDFqPLYDDSLVLLV-RGHERLRGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQRD 216
Cdd:PRK12679  158 LVAF-PWFRWHHSLLVpHDHPLTQITPLtLESIAKWPLITYRQGITGRSRIDDAFARKGLLAD 219
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-288 1.38e-11

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 62.59  E-value: 1.38e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITS----AVDDlgALDFQPLYDDSLVLL 170
Cdd:cd08427     2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVeppfPLPK--DLVWTPLVREPLVLI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 171 VrgHERLRGKALLAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVAdtfNS 250
Cdd:cd08427    80 A--PAELAGDDPRELLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAV---PL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1273236942 251 DGSLAVHVLS---QAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08427   155 PAGPRVRVLPlgdPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-288 1.45e-11

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 62.62  E-value: 1.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGA-----LDFQPLYDDSLV 168
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPpddpgLTRVPLLDDPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 169 LLVRGHERLRGKAL--LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVAD 246
Cdd:cd08423    81 LVLPADHPLAGREEvaLADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1273236942 247 TFNSDgsLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08423   161 ARPPG--VVVRPLRPPPTRRIYAAVRAGAARRPAVAAALEAL 200
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 93-287 1.66e-11

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: 62.35  E-value: 1.66e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  93 GSLRIAVLPSVA---IEPLprvLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAItsAVDDLGA--LDFQPLYDDSL 167
Cdd:cd08425     1 GSLRLAMTPTFTaylIGPL---IDRFHARYPGIALSLREMPQERIEAALADDRLDLGI--AFAPVRSpdIDAQPLFDERL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 168 VLLVRGHERLRGKAL---LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASV 244
Cdd:cd08425    76 ALVVGATHPLAQRRTaltLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAI 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1273236942 245 AdtFNSDGSLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIAL 287
Cdd:cd08425   156 A--REQPGLCAVALEPPLPGRTAALLRRKGAYRSAAARAFAAL 196
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
3-73 3.07e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.07  E-value: 3.07e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1273236942   3 ISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARnTRSVELTAAGQRFLEQARRL 73
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV 71
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 94-208 4.17e-11

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: 60.98  E-value: 4.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV-R 172
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALpA 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1273236942 173 GHERLRGKAL-LAALREQDYVATTRDTSlRGMADETL 208
Cdd:cd08414    81 DHPLAARESVsLADLADEPFVLFPREPG-PGLYDQIL 116
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 108-288 6.05e-11

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: 60.58  E-value: 6.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 108 LPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGHERL--RGKALLAA 185
Cdd:cd08420    15 LPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLagRKEVTAEE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 186 LREQDYVA-----TTRDTslrgmADETLLRMGLQRD---PAWEVAYMSSAAALARAGLGFALLPASVADTFNSDGSL-AV 256
Cdd:cd08420    95 LAAEPWILrepgsGTREV-----FERALAEAGLDGLdlnIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLvAL 169

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1273236942 257 HVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08420   170 PVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-150 1.22e-10

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 61.20  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   8 LQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDnavhDAHEQ 87
Cdd:PRK15092   16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFND----EACSS 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1273236942  88 LHLES--GSLRIAVLPSVAIEPLPRVLQEYRRRYP--GIDISLHdgRAGEIRQWVSAAEVDFAITSA 150
Cdd:PRK15092   92 LMYSNlqGVLTIGASDDTADTILPFLLNRVSSVYPklALDVRVK--RNAFMMEMLESQEVDLAVTTH 156
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
8-91 2.00e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 60.42  E-value: 2.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   8 LQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVHD-AHE 86
Cdd:PRK03601    6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEvAHT 85


                  ....*
gi 1273236942  87 QLHLE 91
Cdd:PRK03601   86 SQHNE 90
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 108-257 3.57e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 58.36  E-value: 3.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 108 LPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSaVDDLGALDF-QPLYDDSLVLLVR-GHERLRGKALLAA 185
Cdd:cd08459    15 LPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGY-LPDLGAGFFqQRLFRERYVCLVRkDHPRIGSTLTLEQ 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1273236942 186 LREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSDGSLAVH 257
Cdd:cd08459    94 FLAARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQTDLVATVPERLARLFARAGGLRIV 165
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 11-186 5.57e-10

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 59.23  E-value: 5.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  11 FVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDnAVHDAHEQLHL 90
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQ-AAQDAIAALQV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  91 E-SGSLRIA---VLPSVAIEPLprvLQEYRRRYPGIDISLhdgRAGEIRQWVSAAEVDFAITsavddlgaLDFQPLYDDS 166
Cdd:PRK14997   89 EpRGIVKLTcpvTLLHVHIGPM---LAKFMARYPDVSLQL---EATNRRVDVVGEGVDVAIR--------VRPRPFEDSD 154

                         170       180
                  ....*....|....*....|...
gi 1273236942 167 LVLLV---RGHERLRGKALLAAL 186
Cdd:PRK14997  155 LVMRVladRGHRLFASPDLIARM 177
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 94-288 8.13e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176133  Cd Length: 193  Bit Score: 57.23  E-value: 8.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV-R 172
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSpK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 173 GHERLRGkalLAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSDG 252
Cdd:cd08442    81 GHPPVSR---AEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRG 157

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1273236942 253 SLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALL 288
Cdd:cd08442   158 SVSIHPLPEPFADVTTWLVWRKDSFTAALQAFLDLL 193
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-114 4.80e-09

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 56.60  E-value: 4.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   2 DISFRQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAV 81
Cdd:PRK10082   10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNL 89

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1273236942  82 HDAHEQLHLESGSLRIAVLPSVAIEPLPRVLQE 114
Cdd:PRK10082   90 AELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQ 122
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 108-216 6.84e-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: 54.94  E-value: 6.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 108 LPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAI-TSAVDDLGALDFQPLYD-DSLVLLVRGHERLRGKAL-LA 184
Cdd:cd08413    15 LPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIaTEALDDHPDLVTLPCYRwNHCVIVPPGHPLADLGPLtLE 94

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1273236942 185 ALREqdYVATTRDTSLRGMA--DETLLRMGLQRD 216
Cdd:cd08413    95 DLAQ--YPLITYDFGFTGRSsiDRAFARAGLEPN 126
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-99 1.21e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 55.16  E-value: 1.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   6 RQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARnTRSVELTAAGQRFLEQAR--RLLRdmdnavHD 83
Cdd:PRK03635    5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARqvRLLE------AE 77

                          90
                  ....*....|....*....
gi 1273236942  84 AHEQLHLESG---SLRIAV 99
Cdd:PRK03635   78 LLGELPALDGtplTLSIAV 96
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 95-199 7.09e-08

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: 51.78  E-value: 7.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGH 174
Cdd:cd08412     2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPAD 81

                          90       100
                  ....*....|....*....|....*..
gi 1273236942 175 ERLRGKA--LLAALREQDYVATTRDTS 199
Cdd:cd08412    82 HPLAGKDevSLADLAAEPLILLDLPHS 108
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 96-256 1.71e-07

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. 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: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 50.90  E-value: 1.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  96 RIAVLPSVAIEPLPRVLQEYRRRYPGIDISL----HDGRAGEIRQwvsaAEVDFAITSAVDDLGALDFQPLYDDSLVLLV 171
Cdd:cd08467     3 TLAMPDYAEVALLPRLAPRLRERAPGLDLRLcpigDDLAERGLEQ----GTIDLAVGRFAVPPDGLVVRRLYDDGFACLV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 172 RGHERLRGKAL----LAALReqdYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADT 247
Cdd:cd08467    79 RHGHPALAQEWtlddFATLR---HVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAATDLIATVPRRVATQ 155


                  ....*....
gi 1273236942 248 FNSDGSLAV 256
Cdd:cd08467   156 VAAMLPLRV 164
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 94-214 1.87e-07

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: 50.64  E-value: 1.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAI-TSAVDDLGALDFQPLYD-DSLVLLV 171
Cdd:cd08443     1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIaTEALHDYDDLITLPCYHwNRCVVVK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1273236942 172 RGHERLRGKAL-LAALREQDYVATTRDTSLRGMADETLLRMGLQ 214
Cdd:cd08443    81 RDHPLADKQSIsIEELATYPIVTYTFGFTGRSELDTAFNRAGLT 124
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 96-289 4.13e-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: 49.66  E-value: 4.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  96 RIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDD--LGALDFQPLYDDSLVLLVRG 173
Cdd:cd08418     3 SIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEmyLKELISEPLFESDFVVVARK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 174 HERLRGKALLAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSDGS 253
Cdd:cd08418    83 DHPLQGARSLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFR 162

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1273236942 254 L-AVHVLSQAPARSIGLLQRKPCYLSPPAQVFIALLR 289
Cdd:cd08418   163 LiTIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFR 199
PRK09801 PRK09801
LysR family transcriptional regulator;
6-124 5.31e-07

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 50.42  E-value: 5.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942   6 RQLQAFVLIAEHRSFSRAAEQVYLSQPALSYSLRKLEDALGLSLLARNTRSVELTAAGQRFLEQARRLLRDMDNAVHDAH 85
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1273236942  86 EQLHLESGSLRIAVLPSVAIEPLPRVLQEYRRRYPGIDI 124
Cdd:PRK09801   89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQV 127
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 95-199 8.72e-07

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: 48.42  E-value: 8.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLG--ALDFQPLYDDSLVLLVR 172
Cdd:cd08449     2 LNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNdpPLASELLWREPMVVALP 81

                          90       100
                  ....*....|....*....|....*....
gi 1273236942 173 GHERLRGKAL--LAALREQDYVATTRDTS 199
Cdd:cd08449    82 EEHPLAGRKSltLADLRDEPFVFLRLANS 110
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-220 8.95e-07

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 48.46  E-value: 8.95e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  96 RIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAIT---SAVDDLGALDFQPLydDSLVLLVR 172
Cdd:cd08426     3 RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAfspPPEPGIRVHSRQPA--PIGAVVPP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1273236942 173 GHERLRGKA-LLAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWE 220
Cdd:cd08426    81 GHPLARQPSvTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLI 129
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 108-169 8.98e-07

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. 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: 176121  Cd Length: 199  Bit Score: 48.73  E-value: 8.98e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1273236942 108 LPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGA-LDFQPLYDDSLVL 169
Cdd:cd08430    15 LPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPArLAFLPLATSPLVF 77
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 94-192 9.00e-07

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: 48.71  E-value: 9.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPL-PRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAIT-SAVDDLGALDFQPLYDDSLVL-L 170
Cdd:cd08451     1 RLRVGFTSSAAFHPLvPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVrPPVARSDGLVLELLLEEPMLVaL 80

                          90       100
                  ....*....|....*....|...
gi 1273236942 171 VRGHERLRGKAL-LAALREQDYV 192
Cdd:cd08451    81 PAGHPLARERSIpLAALADEPFI 103
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-199 1.77e-06

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: 47.65  E-value: 1.77e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV-R 172
Cdd:cd08448     1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLpA 80

                          90       100
                  ....*....|....*....|....*....
gi 1273236942 173 GHeRLRGKAL--LAALREQDYVATTRDTS 199
Cdd:cd08448    81 GH-PLAARRRidLRELAGEPFVLFSREVS 108
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 94-189 2.97e-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: 47.12  E-value: 2.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLpSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRG 173
Cdd:cd08419     1 RLRLAVV-STAKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPP 79

                          90
                  ....*....|....*...
gi 1273236942 174 HERLRGKA--LLAALREQ 189
Cdd:cd08419    80 DHPLAGQKriPLERLARE 97
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 95-209 6.89e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 46.02  E-value: 6.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGH 174
Cdd:cd08441     2 LRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPD 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1273236942 175 ERLRGKALLAAlreQDyvattrdtslrgMADETLL 209
Cdd:cd08441    82 HPLAAKEFITP---ED------------LADETLI 101
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-200 9.33e-06

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 45.59  E-value: 9.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV-RG 173
Cdd:cd08421     2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVpRD 81

                          90       100
                  ....*....|....*....|....*....
gi 1273236942 174 HeRL--RGKALLAALREQDYVATTRDTSL 200
Cdd:cd08421    82 H-PLagRASVAFADTLDHDFVGLPAGSAL 109
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 94-242 3.94e-05

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: 43.90  E-value: 3.94e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLH----DGRAGEIRQwvsaAEVDFAITSAVDDLGALDFQPLYDDSLVL 169
Cdd:cd08450     1 VLTIGFLPGAEVQWLPEVLPILREEHPDLDVELSslfsPQLAEALMR----GKLDVAFMRPEIQSDGIDYQLLLKEPLIV 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1273236942 170 LVRGHERLRG--KALLAALREQDYVATTRDT-SLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPA 242
Cdd:cd08450    77 VLPADHRLAGreKIPPQDLAGENFISPAPTApVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPL 152
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 95-285 9.72e-05

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


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 42.48  E-value: 9.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGH 174
Cdd:cd08457     2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 175 ERLRGKALLA--ALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNSDG 252
Cdd:cd08457    82 HPLAQLDVVSpqDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPLDG 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1273236942 253 sLAVHVLSQAPARSIGLLQRKPCYLSPPAQVFI 285
Cdd:cd08457   162 -IVIRPFDTFIDAGFLVVRAANGPPSTMVDRFI 193
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-248 2.46e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 41.45  E-value: 2.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 108 LPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGherlRGKALLAALR 187
Cdd:cd08464    15 APPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYACLFDP----QQLSLSAPLT 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1273236942 188 EQDYVAT-----TRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTF 248
Cdd:cd08464    91 LEDYVARphvlvSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGTPLIATVPARLARAW 156
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-215 5.88e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 40.34  E-value: 5.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 108 LPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITS---AVDDLGAldfQPLYDDSLVLLVR-GHERLRGKALL 183
Cdd:cd08461    15 LPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTpeyAPDGLRS---RPLFEERYVCVTRrGHPLLQGPLSL 91

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1273236942 184 AALREQDY-VATTRDTSLRGMADETLLRMGLQR 215
Cdd:cd08461    92 DQFCALDHiVVSPSGGGFAGSTDEALAALGLTR 124
PBP2_Pa0477 cd08468
The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional ...
 94-218 7.96e-04

The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176157 [Multi-domain]  Cd Length: 202  Bit Score: 39.73  E-value: 7.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISL-HDGRAGEIRQwVSAAEVDFAIT-SAVDDLGALDFQPL--YDDSLVL 169
Cdd:cd08468     1 RFRFAVTDYTALAVMPRLMARLEELAPSVRLNLvHAEQKLPLDA-LLAGEIDFALGySHDDGAEPRLIEERdwWEDTYVV 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1273236942 170 LV-RGHERLRGKALLAALREQDYVATTRDTSlRGMADETLLRMGLQRDPA 218
Cdd:cd08468    80 IAsRDHPRLSRLTLDAFLAERHLVVTPWNED-RGVVDQVLEKQGLEREIA 128
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 95-251 1.31e-03

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: 39.25  E-value: 1.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  95 LRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQ--PLYDDSLVLLVR 172
Cdd:cd08416     2 LRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFEvvPLFEDDIFLAVP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 173 GHERLRGKAL--LAALREQDYVATTRDTSLRGMADETLLRMGLQRDPAWEVAYMSSAAALARAGLGFALLPASVADTFNS 250
Cdd:cd08416    82 ATSPLAASSEidLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVYED 161


                  .
gi 1273236942 251 D 251
Cdd:cd08416   162 K 162
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 94-198 4.84e-03

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: 37.48  E-value: 4.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRG 173
Cdd:cd08452     1 LLVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPK 80

                          90       100
                  ....*....|....*....|....*..
gi 1273236942 174 HERLRGKAL--LAALREQDYVATTRDT 198
Cdd:cd08452    81 QHPLASKEEitIEDLRDEPIITVAREA 107
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-174 5.92e-03

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: 37.24  E-value: 5.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942  94 SLRIAVLPSVAIEPLPRVLQEYRRRYPGIDISLHDGRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLV-R 172
Cdd:cd08447     1 SLRIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVpA 80


                  ..
gi 1273236942 173 GH 174
Cdd:cd08447    81 GH 82
PBP2_DntR_like_1 cd08460
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 160-216 6.30e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176149 [Multi-domain]  Cd Length: 200  Bit Score: 37.18  E-value: 6.30e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1273236942 160 QPLYDDSLVLLVR-GHERLRGKALLAALREQDYVATTRDTSLRGMADETLLRMGLQRD 216
Cdd:cd08460    66 QTLFRDRFVGVVRaGHPLARGPITPERYAAAPHVSVSRRGRLHGPIDDALAALGLTRR 123
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-223 6.30e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176152 [Multi-domain]  Cd Length: 203  Bit Score: 37.29  E-value: 6.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1273236942 108 LPRVLQEYRRRYPGIDISLHD-GRAGEIRQWVSAAEVDFAITSAVDDLGALDFQPLYDDSLVLLVRGHERL--RGKALLA 184
Cdd:cd08463    15 LPELVARFRREAPGARLEIHPlGPDFDYERALASGELDLVIGNWPEPPEHLHLSPLFSDEIVCLMRADHPLarRGLMTLD 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1273236942 185 ALREQDYVATTRDT-SLRGMADETLLRMGLQRDPAWEVAY 223
Cdd:cd08463    95 DYLEAPHLAPTPYSvGQRGVIDSHLARLGLKRNIVVTVPY 134
 
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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