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Conserved domains on  [gi|1419384359|gb|RBA23193|]
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Transcriptional regulator [Herminiimonas fonticola]

Protein Classification

hydrogen peroxide-inducible genes activator( domain architecture ID 10444038)

hydrogen peroxide-inducible genes activator OxyR is a lysR-type transcriptional regulator that regulates transcription in response to a low level of cellular H2O2

CATH:  1.10.10.10
Gene Ontology:  GO:0003700|GO:0003677
PubMed:  25931525|19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-296 1.47e-96

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: 283.65  E-value: 1.47e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  91 GPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVP 170
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEmsrfstSGDGIARTFEGSSLETIRHMVASGIGITVLPQAS 250
Cdd:cd08411    81 KDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRL------AGAREQTDFEATSLETLRQMVAAGLGITLLPELA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1419384359 251 VPDMNATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08411   155 VPSEELRGDRLVVRPFAEPAPSRTIGLVWRRSSPRAAAFEALAELI 200
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 7.32e-19

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.58  E-value: 7.32e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1419384359   3 LTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-296 1.47e-96

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: 283.65  E-value: 1.47e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  91 GPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVP 170
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEmsrfstSGDGIARTFEGSSLETIRHMVASGIGITVLPQAS 250
Cdd:cd08411    81 KDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRL------AGAREQTDFEATSLETLRQMVAAGLGITLLPELA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1419384359 251 VPDMNATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08411   155 VPSEELRGDRLVVRPFAEPAPSRTIGLVWRRSSPRAAAFEALAELI 200
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-280 8.63e-96

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 285.39  E-value: 8.63e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPV 160
Cdd:PRK11151   81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 161 YDEPFVVAVPKSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCpemsrFSTSGDGIARtFEGSSLETIRHMVASG 240
Cdd:PRK11151  161 FDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFC-----FEAGADEDTH-FRATSLETLRNMVAAG 234

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1419384359 241 IGITVLPQASVPDMNATDGmLRYIPFVQPGPSRRVVLVWR 280
Cdd:PRK11151  235 SGITLLPALAVPNERKRDG-VCYLPCIKPEPRRTIGLVYR 273
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-298 4.28e-70

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 218.20  E-value: 4.28e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPV 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 161 YDEPFVVAVPKSHPWAKRSSVTtddlksetmlllgnghcfrdqvlevcpemsrfstsgdgiartfegSSLETIRHMVASG 240
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLV---------------------------------------------NSLEALLAAVAAG 195

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1419384359 241 IGITVLPQASVPDMNAtDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQALLS 298
Cdd:COG0583   196 LGIALLPRFLAADELA-AGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-297 1.67e-48

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 160.92  E-value: 1.67e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  91 GPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVP 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEMsrfstsGDGIARTFEGSSLETIRHMVASGIGITVLPQAS 250
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAA------GLRPRVVLEVNSLEALLQLVAAGLGIALLPRSA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1419384359 251 VPDMNAtDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQALL 297
Cdd:pfam03466 156 VARELA-DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-297 2.63e-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: 137.36  E-value: 2.63e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPV 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 161 YDEPFVVAVPKSHPWAKRSSVTTD--DLKSETMLLLGNGHCFRDQVLEVCPEMsRFSTSGDGIARTFEgsSLETIRHMVA 238
Cdd:NF040786  161 YKDRLVLITPNGTEKYRMLKEEISisELQKEPFIMREEGSGTRKEAEKALKSL-GISLEDLNVVASLG--STEAIKQSVE 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1419384359 239 SGIGITVLPQASVPDMNAtDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQALL 297
Cdd:NF040786  238 AGLGISVISELAAEKEVE-RGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVK 295
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 7.32e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.58  E-value: 7.32e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1419384359   3 LTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
4-82 8.58e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 61.57  E-value: 8.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   4 TE-LKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERvLEQT--AAIKE 80
Cdd:PRK03601    3 TElLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAET-LMNTwqAAKKE 81


                  ..
gi 1419384359  81 IA 82
Cdd:PRK03601   82 VA 83
 
Name Accession Description Interval E-value
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-296 1.47e-96

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: 283.65  E-value: 1.47e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  91 GPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVP 170
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEmsrfstSGDGIARTFEGSSLETIRHMVASGIGITVLPQAS 250
Cdd:cd08411    81 KDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRL------AGAREQTDFEATSLETLRQMVAAGLGITLLPELA 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1419384359 251 VPDMNATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08411   155 VPSEELRGDRLVVRPFAEPAPSRTIGLVWRRSSPRAAAFEALAELI 200
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-280 8.63e-96

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 285.39  E-value: 8.63e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPV 160
Cdd:PRK11151   81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 161 YDEPFVVAVPKSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCpemsrFSTSGDGIARtFEGSSLETIRHMVASG 240
Cdd:PRK11151  161 FDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFC-----FEAGADEDTH-FRATSLETLRNMVAAG 234

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1419384359 241 IGITVLPQASVPDMNATDGmLRYIPFVQPGPSRRVVLVWR 280
Cdd:PRK11151  235 SGITLLPALAVPNERKRDG-VCYLPCIKPEPRRTIGLVYR 273
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-298 4.28e-70

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 218.20  E-value: 4.28e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPV 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 161 YDEPFVVAVPKSHPWAKRSSVTtddlksetmlllgnghcfrdqvlevcpemsrfstsgdgiartfegSSLETIRHMVASG 240
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPLV---------------------------------------------NSLEALLAAVAAG 195

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1419384359 241 IGITVLPQASVPDMNAtDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQALLS 298
Cdd:COG0583   196 LGIALLPRFLAADELA-AGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-296 1.14e-50

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: 166.24  E-value: 1.14e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd05466     3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 174 PWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCpemsrfSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQASVPD 253
Cdd:cd05466    83 PLAKRKSVTLADLADEPLILFERGSGLRRLLDRAF------AEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1419384359 254 MNATDgmLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd05466   157 LADGG--LVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-297 1.67e-48

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 160.92  E-value: 1.67e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  91 GPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVP 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEMsrfstsGDGIARTFEGSSLETIRHMVASGIGITVLPQAS 250
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAA------GLRPRVVLEVNSLEALLQLVAAGLGIALLPRSA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1419384359 251 VPDMNAtDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQALL 297
Cdd:pfam03466 156 VARELA-DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-297 2.63e-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: 137.36  E-value: 2.63e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPV 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 161 YDEPFVVAVPKSHPWAKRSSVTTD--DLKSETMLLLGNGHCFRDQVLEVCPEMsRFSTSGDGIARTFEgsSLETIRHMVA 238
Cdd:NF040786  161 YKDRLVLITPNGTEKYRMLKEEISisELQKEPFIMREEGSGTRKEAEKALKSL-GISLEDLNVVASLG--STEAIKQSVE 237

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1419384359 239 SGIGITVLPQASVPDMNAtDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQALL 297
Cdd:NF040786  238 AGLGISVISELAAEKEVE-RGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVK 295
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-288 1.84e-36

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: 129.55  E-value: 1.84e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKS 172
Cdd:cd08414     2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPAD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 173 HPWAKRSSVTTDDLKSETMLLL--GNGHCFRDQVLEVCPEmsrfstSGDGIARTFEGSSLETIRHMVASGIGITVLPqAS 250
Cdd:cd08414    82 HPLAARESVSLADLADEPFVLFprEPGPGLYDQILALCRR------AGFTPRIVQEASDLQTLLALVAAGLGVALVP-AS 154

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1419384359 251 VPDMNATDgmLRYIPFVQPGPSRRVVLVWRKSFTRGVA 288
Cdd:cd08414   155 VARLQRPG--VVYRPLADPPPRSELALAWRRDNASPAL 190
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-288 1.03e-33

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 125.07  E-value: 1.03e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPV 160
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 161 YDEPFVVAVPKSHPWA-KRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEMsrfstsgdGIAR--TFEGSSLETIRHMV 237
Cdd:PRK11242  161 FTETLALVVGRHHPLAaRRKALTLDELADEPLVLLSAEFATREQIDRYFRRH--------GVTPrvAIEANSISAVLEIV 232

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1419384359 238 ASGIGITVLPQASVpdmnATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVA 288
Cdd:PRK11242  233 RRGRLATLLPAAIA----REHDGLCAIPLDPPLPQRTAALLRRKGAYRSAA 279
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-186 4.15e-30

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 115.84  E-value: 4.15e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREK-HFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEI-SMTPLGVQIVAQAERVLEQTAAI 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  79 KEIAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAI----VALpfpDQG 154
Cdd:PRK12684   81 KRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIateaIAD---YKE 157

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1419384359 155 LLVQPVYDEPFVVAVPKSHPWAKRSSVTTDDL 186
Cdd:PRK12684  158 LVSLPCYQWNHCVVVPPDHPLLERKPLTLEDL 189
rbcR CHL00180
LysR transcriptional regulator; Provisional
 2-242 1.42e-29

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 114.35  E-value: 1.42e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   2 TLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVL----EQTAA 77
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILalceETCRA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  78 IKEIAKQNKDPLVgpfrLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPD--QGL 155
Cdd:CHL00180   86 LEDLKNLQRGTLI----IGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTelKKI 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 156 L-VQPVYDEPFVVAVPKSHPWAKRSSVTTDDLKSETMLLLGNGHCFR---DQVL-EVCPEMSRFSTSgdgiartFEGSSL 230
Cdd:CHL00180  162 LeITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRkviDNILiQNGIDSKRFKIE-------MELNSI 234

                         250
                  ....*....|..
gi 1419384359 231 ETIRHMVASGIG 242
Cdd:CHL00180  235 EAIKNAVQSGLG 246
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-189 1.49e-29

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 114.32  E-value: 1.49e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREK-HFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEI-SMTPLGVQIVAQAERVLEQTAAI 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  79 KEIAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVA---LPFPDqgL 155
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATeslADDPD--L 158

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1419384359 156 LVQPVYDEPFVVAVPKSHPWAKRSSVTTDDLKSE 189
Cdd:PRK12682  159 ATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEY 192
PRK09986 PRK09986
LysR family transcriptional regulator;
3-247 1.96e-29

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 113.66  E-value: 1.96e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   3 LTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQT----AAI 78
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAeqslARV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  79 KEIAKQNKdplvGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAI--VALPFPDQGLL 156
Cdd:PRK09986   89 EQIGRGEA----GRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFT 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 157 VQPVYDEPFVVAVPKSHPWAKRSSVTTDDLKSETMLLLGNGHC-FRDQVLEVCPEMSrFSTSgdgIARtfEGSSLETIRH 235
Cdd:PRK09986  165 SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSdWGKFLQRVCQQAG-FSPQ---IIR--QVNEPQTVLA 238

                         250
                  ....*....|..
gi 1419384359 236 MVASGIGITVLP 247
Cdd:PRK09986  239 MVSMGIGITLLP 250
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 94-282 2.17e-29

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: 111.09  E-value: 2.17e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd08434     3 RLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 174 PWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEMSrFSTSgdgIArtFEGSSLETIRHMVASGIGITVLPQASVPD 253
Cdd:cd08434    83 PLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAG-FTPK---IA--FEGEEDSTIAGLVAAGLGVAILPEMTLLN 156

                         170       180
                  ....*....|....*....|....*....
gi 1419384359 254 MNATdgmlRYIPFVQPGPSRRVVLVWRKS 282
Cdd:cd08434   157 PPGV----KKIPIKDPDAERTIGLAWLKD 181
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-186 4.44e-29

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 113.45  E-value: 4.44e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREK-HFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEIS-MTPLGVQIVAQAERVLEQTAAI 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  79 KEIAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIV--ALP-FPDqgL 155
Cdd:PRK12681   81 KSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIAteALHlYDD--L 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1419384359 156 LVQPVYDEPFVVAVPKSHPWAKRSSVTTDDL 186
Cdd:PRK12681  159 IMLPCYHWNRSVVVPPDHPLAKKKKLTIEEL 189
PRK12680 PRK12680
LysR family transcriptional regulator;
1-271 6.77e-28

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 110.48  E-value: 6.77e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVA-REKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEI-SMTPLGVQIVAQAERVLEQTAAI 78
Cdd:PRK12680    1 MTLTQLRYLVAIAdAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  79 KEIAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIV--ALPFPDQGLL 156
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVstAGGEPSAGIA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 157 VqPVYDEPFVVAVPKSHPWAKRSsvTTDDLksetmlllgnghcfrdQVLEVCPEMSRFSTS--GDGIARTFEGSSLET-- 232
Cdd:PRK12680  161 V-PLYRWRRLVVVPRGHALDTPR--RAPDM----------------AALAEHPLISYESSTrpGSSLQRAFAQLGLEPsi 221

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1419384359 233 ---------IRHMVASGIGITVLPQASVpdmNATDGMLRYIPFVQPGP 271
Cdd:PRK12680  222 altaldadlIKTYVRAGLGVGLLAEMAV---NANDEDLRAWPAPAPIA 266
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-296 8.75e-28

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: 106.84  E-value: 8.75e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 100 TIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAKRS 179
Cdd:cd08440     9 SLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 180 SVTTDDLKSETMLLLGNGHCFRDQVLEVcpemsrFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQASVPDMNATDg 259
Cdd:cd08440    89 SVTWAELAGYPLIALGRGSGVRALIDRA------LAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPG- 161

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1419384359 260 mLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08440   162 -LVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 94-291 1.37e-27

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: 106.42  E-value: 1.37e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd08420     3 RIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 174 PWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVcpeMSRFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQASVPD 253
Cdd:cd08420    83 PLAGRKEVTAEELAAEPWILREPGSGTREVFERA---LAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRK 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1419384359 254 MNAtDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEE 291
Cdd:cd08420   160 ELE-LGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEA 196
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-186 7.46e-26

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 104.35  E-value: 7.46e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREK-HFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEIS-MTPLGVQIVAQAERVLEQTAAI 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  79 KEIAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIV--AL-PFPDqgL 155
Cdd:PRK12683   81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIAteALdREPD--L 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1419384359 156 LVQPVYDEPFVVAVPKSHPWAKRSSVTTDDL 186
Cdd:PRK12683  159 VSFPYYSWHHVVVVPKGHPLTGRENLTLEAI 189
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-282 9.77e-26

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 101.14  E-value: 9.77e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  92 PFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPD-QGLLVQPVYDEPFVVAVP 170
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRpPGLASRELAREPLVAVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEMsrfstsgdGIART--FEGSSLETIRHMVASGIGITVLPQ 248
Cdd:cd08436    81 PDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAA--------GVRRRvaFEVSDVDLLLDLVARGLGVALLPA 152

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1419384359 249 ASVPDMnatdGMLRYIPfVQPGPSRRVVLVWRKS 282
Cdd:cd08436   153 SVAARL----PGLAALP-LEPAPRRRLYLAWSAP 181
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 94-281 1.03e-25

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: 101.09  E-value: 1.03e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd08438     3 RLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 174 PWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCpEMSRFStsgdgIARTFEGSSLETIRHMVASGIGITVLPQASVPD 253
Cdd:cd08438    83 PLAGRKTVSLADLADEPFILFNEDFALHDRIIDAC-QQAGFT-----PNIAARSSQWDFIAELVAAGLGVALLPRSIAQR 156

                         170       180
                  ....*....|....*....|....*...
gi 1419384359 254 MNATDgmLRYIPFVQPGPSRRVVLVWRK 281
Cdd:cd08438   157 LDNAG--VKVIPLTDPDLRWQLALIWRK 182
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-281 4.35e-24

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 99.46  E-value: 4.35e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQ-NKDPLVgpFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQP 159
Cdd:PRK09906   81 RARKiVQEDRQ--LTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 160 VYDEPFVVAVPKSHPWAKRSSVTTDDLKSETMLLLGNGHcfrDQVLEvcPEMSRFSTSGDGIARTFE-GSSLETIRHMVA 238
Cdd:PRK09906  159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAY---SGSLA--PIIKAWFAQHNSQPNIVQvATNILVTMNLVG 233

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1419384359 239 SGIGITVLPqASVPDMNATDGMLRyiPFVQPGPSRRVVLVWRK 281
Cdd:PRK09906  234 MGLGCTIIP-GYMNNFNTGQVVFR--PLAGNVPSIALLMAWKK 273
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 92-285 1.91e-23

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: 94.98  E-value: 1.91e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  92 PFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPK 171
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 172 SHPWAKRSSvttdDLKSETMLLLGNGHCFRDQVlevcpeMSRFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQASV 251
Cdd:cd08442    81 GHPPVSRAE----DLAGSTLLAFRAGCSYRRRL------EDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVL 150

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1419384359 252 PDMNATDGmLRYIPFVQPGPSRRVVLVWRK-SFTR 285
Cdd:cd08442   151 DSLQGRGS-VSIHPLPEPFADVTTWLVWRKdSFTA 184
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 94-296 2.89e-23

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: 94.58  E-value: 2.89e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd08433     3 SVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 174 PWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVcpemsrFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQASVPD 253
Cdd:cd08433    83 PLPRGAPVPLAELARLPLILPSRGHGLRRLVDEA------AARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1419384359 254 MnATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08433   157 E-VAAGRLVAAPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 94-296 4.53e-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: 88.87  E-value: 4.53e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALP--FPDQGLLVQPVYDEPFVVAVPK 171
Cdd:cd08435     3 RVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLAddEQPPDLASEELADEPLVVVARP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 172 SHPWAKRSSVTTDDLKSETMLLLGNGHCFRdQVLEvcpemSRFSTSGDGIAR-TFEGSSLETIRHMVASGIGITVLPQaS 250
Cdd:cd08435    83 GHPLARRARLTLADLADYPWVLPPPGTPLR-QRLE-----QLFAAAGLPLPRnVVETASISALLALLARSDMLAVLPR-S 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1419384359 251 VPDMNATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08435   156 VAEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-296 5.36e-21

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: 88.40  E-value: 5.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  92 PFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALP-FPDQGLLV-QPVYDEPFVVAV 169
Cdd:cd08427     1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPpFPLPKDLVwTPLVREPLVLIA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 170 PKSHPWAkrssvttDDLksetmlllgnghcfrdQVLEVCPEMsRFSTS---GDGIAR-----------TFEGSSLETIRH 235
Cdd:cd08427    81 PAELAGD-------DPR----------------ELLATQPFI-RYDRSawgGRLVDRflrrqgirvreVMELDSLEAIAA 136

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1419384359 236 MVASGIGITVLPQASVPDMNATDgmLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08427   137 MVAQGLGVAIVPDIAVPLPAGPR--VRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-296 5.49e-21

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: 88.81  E-value: 5.49e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  92 PFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIV-----ALPFPDQGLLVQPVYDEPFV 166
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypvTPPPDDPGLTRVPLLDDPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 167 VAVPKSHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVC------PEMsrfstsgdgiarTFEGSSLETIRHMVASG 240
Cdd:cd08423    81 LVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACraagftPRI------------AHEADDYATVLALVAAG 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1419384359 241 IGITVLPQASVPDMNATdgmLRYIPFVQPgPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08423   149 LGVALVPRLALGARPPG---VVVRPLRPP-PTRRIYAAVRAGAARRPAVAAALEAL 200
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-294 3.07e-20

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: 86.44  E-value: 3.07e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  92 PFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAI---VALPfpdQGLLVQPVYDEPFVVA 168
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALtydLDLP---EDIAFEPLARLPPYVW 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 169 VPKSHPWAKRSSVTTDDLKSETMLLLGNGHCfRDQVLEVCpemSRFSTSGDGIARTfegSSLETIRHMVASGIGITVLPQ 248
Cdd:cd08412    78 LPADHPLAGKDEVSLADLAAEPLILLDLPHS-REYFLSLF---AAAGLTPRIAYRT---SSFEAVRSLVANGLGYSLLND 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1419384359 249 ASVPDMNATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQ 294
Cdd:cd08412   151 RPYRPWSYDGKRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVD 196
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 105-281 2.60e-19

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: 84.15  E-value: 2.60e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 105 LLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFP-DQGLLVQPVYDEPFVVAVPKSHPWAKRSSVTT 183
Cdd:cd08451    15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVArSDGLVLELLLEEPMLVALPAGHPLARERSIPL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 184 DDLKSETMLL----LGNGhcFRDQVLEVCpemsrfSTSGDGIARTFEGSSLETIRHMVASGIGITVLPqASVPDMNAtDG 259
Cdd:cd08451    95 AALADEPFILfprpVGPG--LYDAIIAAC------RRAGFTPRIGQEAPQMASAINLVAAGLGVSIVP-ASMRQLQA-PG 164

                         170       180
                  ....*....|....*....|..
gi 1419384359 260 mLRYIPFVQPGPSRRVVLVWRK 281
Cdd:cd08451   165 -VVYRPLAGAPLTAPLALAYRR 185
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 7.32e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.58  E-value: 7.32e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1419384359   3 LTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 94-296 1.59e-17

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176128  Cd Length: 198  Bit Score: 79.30  E-value: 1.59e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIV--ALPFPDQGLLVQPVYDEPFVVAVPK 171
Cdd:cd08437     3 RFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLgsLTPLENSALHSKIIKTQHFMIIVSK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 172 SHPWAKRSSVTTDDLKSETMLLLGNG----HCFRDqvleVCpemSRFSTSGDGIARTFEgssLETIRHMVASGIGITVLP 247
Cdd:cd08437    83 DHPLAKAKKVNFADLKKENFILLNEHfvhpKAFDS----LC---QQANFQPNIVYRTND---IHILKSMVRENVGIGFLT 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1419384359 248 QASV-PDMNatdgmLRYIPFV-QPGPSRRVVLVWRKSFTRGVAIEEVRQAL 296
Cdd:cd08437   153 DIAVkPDDH-----LVAIPLLdNEQPTFYISLAHRKDQLLTPAQKKLLDLL 198
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-282 4.59e-16

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: 74.99  E-value: 4.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 105 LLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAKRSSVTTD 184
Cdd:cd08447    14 FLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAERLTLE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 185 DLKSETMLLlgnghcfrdqvlevcpemsrFSTSG-----DGIARTFEG-----------SSLETIRHMVASGIGITVLPq 248
Cdd:cd08447    94 DLDGQPFIM--------------------YSPTEaryfhDLVVRLFASagvqpryvqylSQIHTMLALVRAGLGVALVP- 152

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1419384359 249 ASVPDMNATDGMLRYIPFVQPGPSrRVVLVWRKS 282
Cdd:cd08447   153 ASASRLRFEGVVFRPLDLPRDVPV-ELHLAWRRD 185
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 93-281 7.29e-16

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: 74.70  E-value: 7.29e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALP--FPDQGLLVQPVYDEPFVVAVP 170
Cdd:cd08418     2 VSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPdeMYLKELISEPLFESDFVVVAR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVttDDLKSETMLLLGNGHCFRDQVLEVCPemsRFSTSGDGIARTfegSSLETIRHMVASGIGITVLPQAS 250
Cdd:cd08418    82 KDHPLQGARSL--EELLDASWVLPGTRMGYYNNLLEALR---RLGYNPRVAVRT---DSIVSIINLVEKADFLTILSRDM 153

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1419384359 251 VPDMNATDGmLRYIPFVQPGPSRRVVLVWRK 281
Cdd:cd08418   154 GRGPLDSFR-LITIPVEEPLPSADYYLIYRK 183
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-186 1.25e-15

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 76.00  E-value: 1.25e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAR-EKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLF-ERGGSEISMTPLGVQIVAQAERVLEQTAAI 78
Cdd:PRK12679    1 MNFQQLKIIREAARqDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASNV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  79 KEIAKQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQ 158
Cdd:PRK12679   81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVA 160

                         170       180
                  ....*....|....*....|....*....
gi 1419384359 159 -PVYDEPFVVAVPKSHPWAKRSSVTTDDL 186
Cdd:PRK12679  161 fPWFRWHHSLLVPHDHPLTQITPLTLESI 189
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-288 1.94e-15

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: 73.52  E-value: 1.94e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  91 GPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVP 170
Cdd:cd08425     1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWA-KRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEMsrfstsgdGIAR--TFEGSSLETIRHMVASGIGITVLP 247
Cdd:cd08425    81 ATHPLAqRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQ--------GIKPriAIEANSISAVLEVVRRGRLATILP 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1419384359 248 QASVpdmnATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVA 288
Cdd:cd08425   153 DAIA----REQPGLCAVALEPPLPGRTAALLRRKGAYRSAA 189
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-282 8.22e-15

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 71.53  E-value: 8.22e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 106 LPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAKRSSVTTDD 185
Cdd:cd08448    15 LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRIDLRE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 186 LKSETMLLLGNGHC--FRDQVLEVCpemsrfstsgdgIARTFEGSSLETIRH------MVASGIGITVLPQA-SVPDMNA 256
Cdd:cd08448    95 LAGEPFVLFSREVSpdYYDQIIALC------------MDAGFHPKIRHEVRHwltvvaLVAAGMGVALVPRSlARAGLAG 162

                         170       180
                  ....*....|....*....|....*.
gi 1419384359 257 TdgmlRYIPFVQPGPSRRVVLVWRKS 282
Cdd:cd08448   163 V----RFLPLKGATQRSELYAAWKAS 184
PRK09791 PRK09791
LysR family transcriptional regulator;
3-181 1.11e-14

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 73.26  E-value: 1.11e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   3 LTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKEIA 82
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  83 KQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAI-VALPFP-DQGLLVQPV 160
Cdd:PRK09791   87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTInTYYQGPyDHEFTFEKL 166

                         170       180
                  ....*....|....*....|.
gi 1419384359 161 YDEPFVVAVPKSHPWAKRSSV 181
Cdd:PRK09791  167 LEKQFAVFCRPGHPAIGARSL 187
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 94-269 1.27e-14

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: 71.05  E-value: 1.27e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd08415     3 RIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 174 PWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCpemsrfstSGDGIAR--TFEGSSLETIRHMVASGIGITVLPQASV 251
Cdd:cd08415    83 PLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAF--------ERAGVEPriVIETQLSHTACALVAAGLGVAIVDPLTA 154

                         170
                  ....*....|....*...
gi 1419384359 252 PDMNATDgmLRYIPFVQP 269
Cdd:cd08415   155 AGYAGAG--LVVRPFRPA 170
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 93-247 1.84e-14

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: 70.84  E-value: 1.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALP--FPDQGLLVQPVYDEPFVVAVP 170
Cdd:cd08416     2 LRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPegLNDPDFEVVPLFEDDIFLAVP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVTTDDLKSETMLLLGNGhcfrdqvlevcpemsrFSTSGDGiARTFEGSSLE-----------TIRHMVAS 239
Cdd:cd08416    82 ATSPLAASSEIDLRDLKDEKFVTLSEG----------------FATYRGF-DEAFEIAGFEpnvvmrvndifSLMSMVSG 144


                  ....*...
gi 1419384359 240 GIGITVLP 247
Cdd:cd08416   145 GVGYALLP 152
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 94-282 2.18e-14

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 70.61  E-value: 2.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTiAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd08419     3 RLAVVST-AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 174 PWAKRSSVTTDDLKSETMLL--LGNG------HCFRDQVLEVCPEMsrfstsgdgiartfEGSSLETIRHMVASGIGITV 245
Cdd:cd08419    82 PLAGQKRIPLERLAREPFLLrePGSGtrlameRFFAEHGVTLRVRM--------------ELGSNEAIKQAVMAGLGLSV 147

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1419384359 246 LPQASVPdMNATDGMLRYIPfVQPGPSRRV-VLVWRKS 282
Cdd:cd08419   148 LSLHTLA-LELATGRLAVLD-VEGFPIRRQwYVVHRKG 183
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 94-281 2.64e-14

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 70.47  E-value: 2.64e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQ---GLLVQPVYDEPFVVAVP 170
Cdd:cd08453     3 SLAFVSTADYSVLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASappALAYRPLLSEPLVLAVP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 171 KSHPWAKRSSVTTDDLKSETMLLLGN--GHCFRDQVlevcpeMSRFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQ 248
Cdd:cd08453    83 AAWAAEGGAPLALAAVAAEPLVIFPRriAPAFHDAV------TGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPA 156

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1419384359 249 aSVPDMNATDgmLRYIPFVQPGPSRRVVLVWRK 281
Cdd:cd08453   157 -SLRNLARPG--VVYRELADPAPVLETGLVWRR 186
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 93-299 5.29e-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: 69.55  E-value: 5.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKS 172
Cdd:cd08417     2 FRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 173 HPWAKRsSVTTDDLKSE---TMLLLGNGHCFRDQVLEvcpemsrfstsGDGIART--FEGSSLETIRHMVASGIGITVLP 247
Cdd:cd08417    82 HPLAGG-PLTLEDYLAAphvLVSPRGRGHGLVDDALA-----------ELGLSRRvaLTVPHFLAAPALVAGTDLIATVP 149

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1419384359 248 qASVPDMNATDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQALLSC 299
Cdd:cd08417   150 -RRLAEALAERLGLRVLPLPFELPPFTVSLYWHPRRDRDPAHRWLRELIAEL 200
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 105-281 5.32e-14

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: 69.45  E-value: 5.32e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 105 LLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAKRSSVTTD 184
Cdd:cd08452    14 FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 185 DLKSETMLLLGNG--HCFRDQVLEVCpEMSRFSTSgdgIARtfEGSSLETIRHMVASGIGITVLPqASVPDMNATDgmLR 262
Cdd:cd08452    94 DLRDEPIITVAREawPTLYDEIIQLC-EQAGFRPK---IVQ--EATEYQTVIGLVSAGIGVTFVP-SSAKKLFNLE--VA 164

                         170
                  ....*....|....*....
gi 1419384359 263 YIPFVQPGPSRRVVLVWRK 281
Cdd:cd08452   165 YRKIDQINLNAEWSIAYRK 183
PRK10341 PRK10341
transcriptional regulator TdcA;
12-283 5.63e-14

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 71.05  E-value: 5.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  12 VAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVL-EQTAAIKEIAKQNKDPLV 90
Cdd:PRK10341   18 VIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITrEMKNMVNEINGMSSEAVV 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  91 gPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVAL--PFPDQGLLVQPVYDEPFVVA 168
Cdd:PRK10341   98 -DVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLsnEMKLQDLHVEPLFESEFVLV 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 169 VPKSHPWAKrsSVTTDDLKSETMLLLGNGHCFRDQVLEVcpeMSRFSTSGDGIARTfegSSLETIRHMVASGIGITVLPQ 248
Cdd:PRK10341  177 ASKSRTCTG--TTTLESLKNEQWVLPQTNMGYYSELLTT---LQRNGISIENIVKT---DSVVTIYNLVLNADFLTVIPC 248

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1419384359 249 asvpDMNAT--DGMLRYIPFVQPGPSRRVVLVWRKSF 283
Cdd:PRK10341  249 ----DMTSPfgSNQFITIPIEETLPVAQYAAVWSKNY 281
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-280 5.84e-14

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: 69.09  E-value: 5.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 106 LPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAKRSSVTTDD 185
Cdd:cd08421    15 LPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAFAD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 186 LKSETMLLLGNGHCFRDQVLEVCPEMSRFstsgdgIARTFEGSSLETIRHMVASGIGITVLPQASVPDMNATDGmLRYIP 265
Cdd:cd08421    95 TLDHDFVGLPAGSALHTFLREAAARLGRR------LRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALG-LRVVP 167

                         170
                  ....*....|....*
gi 1419384359 266 FVQPGPSRRVVLVWR 280
Cdd:cd08421   168 LDDAWARRRLLLCVR 182
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-262 1.04e-13

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 70.48  E-value: 1.04e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGIIY-TIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQP 159
Cdd:PRK11233   81 AVHNVGQALSGQVSIGLAPgTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 160 VYDEPFVVAVPKSHPwakRSSVTTDDLKSETMLLLGNGHCFRDQVLEVcpeMSRFSTSGDGIArtfEGSSLETIRHMVAS 239
Cdd:PRK11233  161 LLKEDLFLVGTQDCP---GQSVDLAAVAQMNLFLPRDYSAVRLRVDEA---FSLRRLTAKVIG---EIESIATLTAAIAS 231

                         250       260
                  ....*....|....*....|....*
gi 1419384359 240 GIGITVLPQASVPDM-NATDG-MLR 262
Cdd:PRK11233  232 GMGVTVLPESAARSLcGAVNGwMAR 256
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-193 1.51e-13

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 70.05  E-value: 1.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   3 LTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQtaaIKEIA 82
Cdd:PRK15421    4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQ---ISQAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  83 KQNKDPLVGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYD 162
Cdd:PRK15421   81 QACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFD 160

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1419384359 163 EPFVVAVPKSHPWAKRSSVTTDDLKSETMLL 193
Cdd:PRK15421  161 YEVRLVLAPDHPLAAKTRITPEDLASETLLI 191
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-246 3.13e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 68.56  E-value: 3.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE 80
Cdd:PRK10837    3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKdplvGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPV 160
Cdd:PRK10837   83 LFREDN----GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPW 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 161 YDEPFVVAVPKSHPWAKRsSVTTDDLKSETMLLLGNGHCFRDQVLEVC-PEMSRFSTSgdgiartFEGSSLETIRHMVAS 239
Cdd:PRK10837  159 LEDELVVFAAPDSPLARG-PVTLEQLAAAPWILRERGSGTREIVDYLLlSHLPRFELA-------MELGNSEAIKHAVRH 230


                  ....*..
gi 1419384359 240 GIGITVL 246
Cdd:PRK10837  231 GLGISCL 237
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 94-272 8.62e-12

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: 63.06  E-value: 8.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALP--FPDQGLLVQPVYDEPFVVAVPK 171
Cdd:cd08449     3 NIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFAdtLNDPPLASELLWREPMVVALPE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 172 SHPWAKRSSVTTDDLKSETMLLLGNGHC-FRDQVLEVCPEmSRFSTSgdgIARTFEGSSleTIRHMVASGIGITVLPQaS 250
Cdd:cd08449    83 EHPLAGRKSLTLADLRDEPFVFLRLANSrFADFLINCCLQ-AGFTPQ---ITQEVVEPQ--TLMALVAAGFGVALVPE-S 155

                         170       180
                  ....*....|....*....|..
gi 1419384359 251 VPDMNATDgmLRYIPFVQPGPS 272
Cdd:cd08449   156 YARLPWPG--VRFIPLKQAISA 175
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 92-251 1.08e-11

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: 62.89  E-value: 1.08e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  92 PFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPK 171
Cdd:cd08457     1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPM 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 172 SHPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVcpemsrFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQASV 251
Cdd:cd08457    81 GHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVA------LGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATA 154
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 105-281 7.91e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176136  Cd Length: 203  Bit Score: 60.32  E-value: 7.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 105 LLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAK-RSSVTT 183
Cdd:cd08445    15 LLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRRIVLREEPLVVALPAGHPLAQeKAPLTL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 184 DDLKSETMLLLGNGH--CFRDQVLEVcpemsrFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPqASVPDMNATDgmL 261
Cdd:cd08445    95 AQLADEPLILYPASPrpSFADQVLSL------FRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVP-ASVQRLRRDD--V 165

                         170       180
                  ....*....|....*....|
gi 1419384359 262 RYIPFVQPGPSRRVVLVWRK 281
Cdd:cd08445   166 VYRPLLDPDATSPIIMSVRA 185
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
4-82 8.58e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 61.57  E-value: 8.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   4 TE-LKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERvLEQT--AAIKE 80
Cdd:PRK03601    3 TElLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAET-LMNTwqAAKKE 81


                  ..
gi 1419384359  81 IA 82
Cdd:PRK03601   82 VA 83
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-149 1.81e-10

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 60.22  E-value: 1.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  25 CFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKEIAKQNKDPLVGPFRLGIIYTIAPY 104
Cdd:PRK11716    1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1419384359 105 LLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALP 149
Cdd:PRK11716   81 HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKP 125
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 93-247 1.95e-10

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: 59.31  E-value: 1.95e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKS 172
Cdd:cd08450     2 LTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPAD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1419384359 173 HPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEvcpemSRFSTSGDGIARTFEGSSLETIRHMVASGIGITVLP 247
Cdd:cd08450    82 HRLAGREKIPPQDLAGENFISPAPTAPVLQQVIE-----NYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLP 151
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-185 2.07e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 60.34  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   6 LKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKEIAKQN 85
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  86 KDPLVGPFRlgiiytIApylLPPLVKAmiDRVPQMPLVLQENFT-VKLL----------EQLRQGEIDAAI---VALP-- 149
Cdd:PRK11074   87 ANGWRGQLS------IA---VDNIVRP--DRTRQLIVDFYRHFDdVELIirqevfngvwDALADGRVDIAIgatRAIPvg 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1419384359 150 ----FPDQGLLvqpvyDEPFVVAvpKSHPWAKRSSVTTDD 185
Cdd:PRK11074  156 grfaFRDMGML-----SWACVVS--SDHPLASMDGPLSDD 188
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 104-189 4.72e-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: 4.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 104 YLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAkRSSVTT 183
Cdd:cd08459    13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRI-GSTLTL 91


                  ....*.
gi 1419384359 184 DDLKSE 189
Cdd:cd08459    92 EQFLAA 97
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 90-281 4.91e-10

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 58.06  E-value: 4.91e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  90 VGPFRLGIIYTIapyllPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAV 169
Cdd:cd08446     5 VGYFGSAILDTV-----PRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 170 PKSHPWAKRSSVTTDDLKSETMLLLGNGH--CFRDQVLEVC------PEMSRfstsgdgiartfEGSSLETIRHMVASGI 241
Cdd:cd08446    80 PKSHPLAARPAVSLADLRNEPLILFPRGGrpSFADEVLGLFrragvePRVAQ------------EVEDVVAALALVAAGF 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1419384359 242 GITVLPqASV-----PDmnatdgmLRYIPFVQPGPSRRVVLVWRK 281
Cdd:cd08446   148 GVCIVP-ESVaalrwPG-------VVFRPLADAEAKVPLSCIYRK 184
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 93-186 1.17e-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: 56.86  E-value: 1.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIV--ALPFPDQgLLVQPVYDEPFVVAVP 170
Cdd:cd08413     2 LTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIAteALDDHPD-LVTLPCYRWNHCVIVP 80

                          90
                  ....*....|....*.
gi 1419384359 171 KSHPWAKRSSVTTDDL 186
Cdd:cd08413    81 PGHPLADLGPLTLEDL 96
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 106-247 1.71e-09

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: 56.42  E-value: 1.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 106 LPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAKRSSVTTDD 185
Cdd:cd08441    15 LMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPED 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 186 LKSETMLllgnghcfrdqVLEVCPEM----SRFSTSGdGIA----RTFEGSSLetIRHMVASGIGITVLP 247
Cdd:cd08441    95 LADETLI-----------TYPVERERldvfRHFLQPA-GIEpkrrRTVELTLM--ILQLVASGRGVAALP 150
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 3-171 2.05e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 57.55  E-value: 2.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   3 LTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKE-- 80
Cdd:PRK11139    8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRkl 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLvgpfrlgiiyTI-------APYLLPPLVKaMIDRVPQMPLVLQenfTVKLLEQLRQGEIDAAIVALPFPDQ 153
Cdd:PRK11139   88 RARSAKGAL----------TVsllpsfaIQWLVPRLSS-FNEAHPDIDVRLK---AVDRLEDFLRDDVDVAIRYGRGNWP 153

                         170
                  ....*....|....*....
gi 1419384359 154 GLLVQPVYDEPFV-VAVPK 171
Cdd:PRK11139  154 GLRVEKLLDEYLLpVCSPA 172
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-274 8.70e-09

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: 54.62  E-value: 8.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd08426     3 RVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 174 PWAKRSSVTTDDLKSETMLLLGNGHCFRdQVLEVCpemsrFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQASVPD 253
Cdd:cd08426    83 PLARQPSVTLAQLAGYPLALPPPSFSLR-QILDAA-----FARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRR 156

                         170       180
                  ....*....|....*....|.
gi 1419384359 254 MNATdGMLRYIPFVQPGPSRR 274
Cdd:cd08426   157 EIRR-GQLVAVPLADPHMNHR 176
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 93-248 1.32e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 54.18  E-value: 1.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKS 172
Cdd:cd08466     2 FNIAANETLDLLLLPRLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 173 HPwakrssvttddlksetmllLGNGHCFRDQVLE---VCPEMSRF-STSGDGIARTF--------EGSSLETIRHMVASG 240
Cdd:cd08466    82 HP-------------------RIQGSLSLEQYLAekhVVLSLRRGnLSALDLLTEEVlpqrniayEVSSLLSMLAVVSQT 142


                  ....*...
gi 1419384359 241 IGITVLPQ 248
Cdd:cd08466   143 DLIAIAPR 150
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-160 4.00e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 53.44  E-value: 4.00e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   5 ELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSeISMTPLGvqivaqaERVLEQTAAIK----E 80
Cdd:PRK13348    6 QLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAG-------QRLLRHLRQVAlleaD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  81 IAKQNKDPLVGPFRLGII---YTIAPYLLPPLVKAMIDRVPQMPLVLQ-ENFTVKLleqLRQGEIDAAIVALPFPDQGLL 156
Cdd:PRK13348   78 LLSTLPAERGSPPTLAIAvnaDSLATWFLPALAAVLAGERILLELIVDdQDHTFAL---LERGEVVGCVSTQPKPMRGCL 154


                  ....
gi 1419384359 157 VQPV 160
Cdd:PRK13348  155 AEPL 158
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 94-246 2.25e-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: 50.25  E-value: 2.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQ-PVYDEPFVVAVPKS 172
Cdd:cd08443     3 YVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLITlPCYHWNRCVVVKRD 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1419384359 173 HPWAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVcpemsrFSTSGDGIARTFEGSSLETIRHMVASGIGITVL 246
Cdd:cd08443    83 HPLADKQSISIEELATYPIVTYTFGFTGRSELDTA------FNRAGLTPNIVLTATDADVIKTYVRLGLGVGVI 150
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
11-163 5.90e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 50.00  E-value: 5.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  11 AVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQ-TAAIKEIAKQNkdpL 89
Cdd:PRK10086   24 VAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTlNQEILDIKNQE---L 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1419384359  90 VGPFrlgIIY---TIAPYLLPPLVKAMIDRVPQMPL-VLQENFTVklleQLRQGEIDAAIVALPFPDQGLLVQPVYDE 163
Cdd:PRK10086  101 SGTL---TVYsrpSIAQCWLVPRLADFTRRYPSISLtILTGNENV----NFQRAGIDLAIYFDDAPSAQLTHHFLMDE 171
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 94-246 6.25e-07

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: 48.95  E-value: 6.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  94 RLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSH 173
Cdd:cd08456     3 RIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPGH 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1419384359 174 PWAKRSSVTTDDLKSETMLLLGNGHCFR---DQVLE---VCPEMsrfstsgdgiarTFEGSSLETIRHMVASGIGITVL 246
Cdd:cd08456    83 RLAVKKVLTPSDLEGEPFISLARTDGTRqrvDALFEqagVKRRI------------VVETSYAATICALVAAGVGVSVV 149
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-73 1.05e-06

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 49.42  E-value: 1.05e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1419384359   6 LKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLE 73
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-185 3.33e-06

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: 46.92  E-value: 3.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQE-NFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPK 171
Cdd:cd08463     2 FRIAAPDYLNALFLPELVARFRREAPGARLEIHPlGPDFDYERALASGELDLVIGNWPEPPEHLHLSPLFSDEIVCLMRA 81

                          90
                  ....*....|....
gi 1419384359 172 SHPWAKRSSVTTDD 185
Cdd:cd08463    82 DHPLARRGLMTLDD 95
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
16-159 1.54e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 45.82  E-value: 1.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  16 KHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKEIAKQNKDPLVGPFRL 95
Cdd:PRK10082   26 RNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDYAQRKIKI 105

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1419384359  96 GIIYTIAPYLLPPLVKAMidrVPQMPLVLQENFTVKLLEQLRQGEIDaaiVALPFPDQGLLVQP 159
Cdd:PRK10082  106 AAAHSLSLGLLPSIISQM---PPLFTWAIEAIDVDEAVDKLREGQSD---CIFSFHDEDLLEAP 163
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-299 3.06e-05

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: 44.19  E-value: 3.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 105 LLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAKRsSVTTD 184
Cdd:cd08461    14 ILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEERYVCVTRRGHPLLQG-PLSLD 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 185 DLksetmlllgnghCFRDQVLeVCPEMSRFSTSGD------GIAR--TFEGSSLETIRHMVASGIGITVLPQASVPDmna 256
Cdd:cd08461    93 QF------------CALDHIV-VSPSGGGFAGSTDealaalGLTRnvVLSVPSFLVVPEILAATDMVAFVPSRLVPN--- 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1419384359 257 tDGMLRYIPFVQPGPSRRVVLVWRKSFTRGVAIEEVRQALLSC 299
Cdd:cd08461   157 -LEGLQEVELPLEPPGFDVVMAWHERTHRDPAHRWLRELLAAA 198
leuO PRK09508
leucine transcriptional activator; Reviewed
 11-285 4.23e-05

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 44.63  E-value: 4.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  11 AVAREKHFGHAAEACFVAQPTLSVAIKKLE----DELgvtlFERGGSEISMTPLGVQI---VAQAERVLeqtaaikeiak 83
Cdd:PRK09508   32 AVMQEQNITRAAHNLGMSQPAVSNAVARLKvmfnDEL----FVRYGRGIQPTARARQLfgpVRQALQLV----------- 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  84 QNKDPLVG--P------FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGL 155
Cdd:PRK09508   97 QNELPGSGfePesservFNLCICSPLDIRLTSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEF 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 156 LVQPVYDEPFVVAVPKSHPwAKRSSVTTDDLKSE--TMLLLGNGHCFRDQVLEVcPEMSRFstsgdgIArtFEGSSLETI 233
Cdd:PRK09508  177 TSVPLFKDELVLVASKNHP-RIKGPITEEQLYNEqhAVVSLDRFASFSQPWYDT-VDKQAS------IA--YQGTALSSV 246

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1419384359 234 RHMVASGIGITVLPQASVPDMNATDGmLRYIPFVQPGPSRRVVLVWRKSFTR 285
Cdd:PRK09508  247 LNVVSQTHLVAIAPRWLAEEFAESLE-LQILPLPLKNNSRTCYLSWHESAGR 297
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-159 1.09e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.22  E-value: 1.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  11 AVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERgGSEISMTPLGVQIVAQAERV--LEQTAAikeiakQNKDP 88
Cdd:PRK03635   12 AVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQVrlLEAELL------GELPA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  89 LVG-PFRLGIIY---TIAPYLLPPLvkamiDRVPQMPLVL------QENFTvklLEQLRQGEIDAAIVALPFPDQGLLVQ 158
Cdd:PRK03635   85 LDGtPLTLSIAVnadSLATWFLPAL-----APVLARSGVLldlvveDQDHT---AELLRRGEVVGAVTTEPQPVQGCRVD 156


                  .
gi 1419384359 159 P 159
Cdd:PRK03635  157 P 157
PBP2_NocR cd08458
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the ...
 93-262 2.95e-04

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


Pssm-ID: 176147  Cd Length: 196  Bit Score: 41.23  E-value: 2.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKS 172
Cdd:cd08458     2 LRVACYTAPALSFMSGVIQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGISILAGDYPGLTTEPVPSFRAVCLLPPG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 173 HPWAKRSSVTTDDLKSETMLLLGnghcfRDQVLEVCPEMSrFSTSGDGIARTFEGSSLETIRHMVASGIGITVLPQASVP 252
Cdd:cd08458    82 HRLEDKETVHATDLEGESLICLS-----PVSLLRMQTDAA-LDSCGVHCNRRIESSLALNLCDLVSRGMGVGIVDPFTAD 155

                         170
                  ....*....|
gi 1419384359 253 DMNATDGMLR 262
Cdd:cd08458   156 YYSANPVIQR 165
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-277 3.00e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 41.90  E-value: 3.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   1 MTLTELKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVL-EQTAAIK 79
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLvEAQAAQD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  80 EIAKQNKDPLvGPFRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQEnfTVKLLEQLRQGeIDAAIVALPFP--DQGLLV 157
Cdd:PRK14997   82 AIAALQVEPR-GIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEA--TNRRVDVVGEG-VDVAIRVRPRPfeDSDLVM 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 158 QPVYDEPF-VVAVPKSHPWAKRSSVTTdDLKSETMLLLGNG-HCFRDQVLEvcPEMSRFSTSgdgIARTFEGSSLETIRH 235
Cdd:PRK14997  158 RVLADRGHrLFASPDLIARMGIPSAPA-ELSHWPGLSLASGkHIHRWELYG--PQGARAEVH---FTPRMITTDMLALRE 231

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1419384359 236 MVASGIGITVLPQASVPDMNATDGMLRYIPFVQPG--------PSRRVVL 277
Cdd:PRK14997  232 AAMAGVGLVQLPVLMVKEQLAAGELVAVLEEWEPRrevihavfPSRRGLL 281
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 105-185 3.72e-04

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: 40.88  E-value: 3.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359 105 LLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHPWAKRsSVTTD 184
Cdd:cd08467    14 LLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDGLVVRRLYDDGFACLVRHGHPALAQ-EWTLD 92


                  .
gi 1419384359 185 D 185
Cdd:cd08467    93 D 93
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 6-145 9.40e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 40.40  E-value: 9.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359   6 LKYIVAVAREKHFGHAAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVL----EQTAAIKei 81
Cdd:PRK15092   16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILrfndEACSSLM-- 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1419384359  82 akqnKDPLVGPFRLG----IIYTIAPYLL-------PPLvkAMIDRVPQMPLvlqenftvkLLEQLRQGEIDAAI 145
Cdd:PRK15092   94 ----YSNLQGVLTIGasddTADTILPFLLnrvssvyPKL--ALDVRVKRNAF---------MMEMLESQEVDLAV 153
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 21-245 1.25e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 39.98  E-value: 1.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  21 AAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERV---LEQTAAIKEIAKQNKDplvGPFRLGI 97
Cdd:PRK11013   24 AARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRIVSAAESLREFRQ---GQLSIAC 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  98 IYTIAPYLLPPLVKAMIDRVPQMPL--VLQENftvKLLEQ-LRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKSHP 174
Cdd:PRK11013  101 LPVFSQSLLPGLCQPFLARYPDVSLniVPQES---PLLEEwLSAQRHDLGLTETLHTPAGTERTELLTLDEVCVLPAGHP 177

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1419384359 175 WAKRSSVTTDDLKSETMLLLGNGHCFRDQVLEVCPEMsrfstsgdGIAR--TFEGSSLETIRHMVASGIGITV 245
Cdd:PRK11013  178 LAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEH--------GVKRrmVVETHSAASVCAMVRAGVGVSI 242
nhaR PRK11062
transcriptional activator NhaR; Provisional
 21-142 1.87e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.22  E-value: 1.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  21 AAEACFVAQPTLSVAIKKLEDELGVTLFERGGSEISMTPLGVQIVAQAERVLEQTAAIKEIAKQNKDPLVgPFRLGiiyt 100
Cdd:PRK11062   24 AAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEMLDIVNYRKESNL-LFDVG---- 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1419384359 101 IAPYLLPPLV-KAMIDRVP---QMPLVLQENFTVKLLEQLRQGEID 142
Cdd:PRK11062   99 VADALSKRLVsRVLLTAVPedeSIHLRCFESTHEMLLEQLSQHKLD 144
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-166 2.23e-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: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 38.37  E-value: 2.23e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFV 166
Cdd:cd08464     2 FRIGLSDDVESWLAPPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYA 75
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 99-186 4.71e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176135  Cd Length: 198  Bit Score: 37.48  E-value: 4.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  99 YTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIV--ALPFPDQgLLVQPVYDEPFVVAVPKSHPWA 176
Cdd:cd08444     8 HTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIAteALENHPE-LVSFPYYDWHHHIIVPVGHPLE 86

                          90
                  ....*....|
gi 1419384359 177 KRSSVTTDDL 186
Cdd:cd08444    87 SITPLTIETI 96
PBP2_ToxR cd08465
The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates ...
 93-173 8.91e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. 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: 176154  Cd Length: 200  Bit Score: 36.90  E-value: 8.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1419384359  93 FRLGIIYTIAPYLLPPLVKAMIDRVPQMPLVLQENFTVKLLEQLRQGEIDAAIVALPFPDQGLLVQPVYDEPFVVAVPKS 172
Cdd:cd08465     2 FRLAMSDYGARLVLPALMRQLRAEAPGIDLAVSQASREAMLAQVADGEIDLALGVFPELPEELHAETLFEERFVCLADRA 81


                  .
gi 1419384359 173 H 173
Cdd:cd08465    82 T 82
 
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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