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Conserved domains on  [gi|1242555517|gb|ATA76323|]
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DNA-binding transcriptional regulator OxyR [Capnocytophaga canimorsus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11151 super family cl32649
DNA-binding transcriptional regulator OxyR; Provisional
 1-274 1.52e-70

DNA-binding transcriptional regulator OxyR; Provisional


The actual alignment was detected with superfamily member PRK11151:

Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 221.06  E-value: 1.52e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPL 160
Cdd:PRK11151   81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 161 FYEPFVAYIPENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFqiKSGSFETLIRLSNEGLGMT 240
Cdd:PRK11151  161 FDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHF--RATSLETLRNMVAAGSGIT 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1242555517 241 LLPYLHSLELSEKQLQHIRHFNEPQPAREISLVY 274
Cdd:PRK11151  239 LLPALAVPNERKRDGVCYLPCIKPEPRRTIGLVY 272
 
Name Accession Description Interval E-value
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-274 1.52e-70

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 221.06  E-value: 1.52e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPL 160
Cdd:PRK11151   81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 161 FYEPFVAYIPENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFqiKSGSFETLIRLSNEGLGMT 240
Cdd:PRK11151  161 FDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHF--RATSLETLRNMVAAGSGIT 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1242555517 241 LLPYLHSLELSEKQLQHIRHFNEPQPAREISLVY 274
Cdd:PRK11151  239 LLPALAVPNERKRDGVCYLPCIKPEPRRTIGLVY 272
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-291 4.84e-69

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: 213.54  E-value: 4.84e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  91 GEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIP 170
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 171 ENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFQikSGSFETLIRLSNEGLGMTLLP--YLHSL 248
Cdd:cd08411    81 KDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFE--ATSLETLRQMVAAGLGITLLPelAVPSE 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1242555517 249 ELSEKQLqHIRHFNEPQPAREISLVYHKNELKAQMINALHEVI 291
Cdd:cd08411   159 ELRGDRL-VVRPFAEPAPSRTIGLVWRRSSPRAAAFEALAELI 200
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-296 3.01e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 190.46  E-value: 3.01e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 161 FYEPFVAYIPENHWLCKSNKInsedlqideilmledghcfkntvlnlcgqkqatqkrgfqikSGSFETLIRLSNEGLGMT 240
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIA 199

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1242555517 241 LLP-YLHSLELSEKQLqHIRHFNEPQPAREISLVYHKNELKAQMINALHEVISGVIR 296
Cdd:COG0583   200 LLPrFLAADELAAGRL-VALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-291 1.57e-32

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: 119.70  E-value: 1.57e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  91 GEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIP 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 171 ENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFQIksGSFETLIRLSNEGLGMTLLP-YLHSLE 249
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEV--NSLEALLQLVAAGLGIALLPrSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1242555517 250 LSEKQLQhIRHFNEPQPAREISLVYHKNELKAQMINALHEVI 291
Cdd:pfam03466 160 LADGRLV-ALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-277 1.78e-32

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: 121.96  E-value: 1.78e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPL 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 161 FYEPFVAYIPENHwlcKSNKINSEDLQIDEI-----LMLEDGhcfkntvlnlCGQKQATQKrgfQIKS------------ 223
Cdd:NF040786  161 YKDRLVLITPNGT---EKYRMLKEEISISELqkepfIMREEG----------SGTRKEAEK---ALKSlgisledlnvva 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1242555517 224 --GSFETLIRLSNEGLGMTLLPYLHSLElsEKQLQHIRHFNEP--QPAREISLVYHKN 277
Cdd:NF040786  225 slGSTEAIKQSVEAGLGISVISELAAEK--EVERGRVLIFPIPglPKNRDFYLVYNKN 280
 
Name Accession Description Interval E-value
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-274 1.52e-70

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 221.06  E-value: 1.52e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPL 160
Cdd:PRK11151   81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 161 FYEPFVAYIPENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFqiKSGSFETLIRLSNEGLGMT 240
Cdd:PRK11151  161 FDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHF--RATSLETLRNMVAAGSGIT 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1242555517 241 LLPYLHSLELSEKQLQHIRHFNEPQPAREISLVY 274
Cdd:PRK11151  239 LLPALAVPNERKRDGVCYLPCIKPEPRRTIGLVY 272
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-291 4.84e-69

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: 213.54  E-value: 4.84e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  91 GEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIP 170
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 171 ENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFQikSGSFETLIRLSNEGLGMTLLP--YLHSL 248
Cdd:cd08411    81 KDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFE--ATSLETLRQMVAAGLGITLLPelAVPSE 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1242555517 249 ELSEKQLqHIRHFNEPQPAREISLVYHKNELKAQMINALHEVI 291
Cdd:cd08411   159 ELRGDRL-VVRPFAEPAPSRTIGLVWRRSSPRAAAFEALAELI 200
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-296 3.01e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 190.46  E-value: 3.01e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 161 FYEPFVAYIPENHWLCKSNKInsedlqideilmledghcfkntvlnlcgqkqatqkrgfqikSGSFETLIRLSNEGLGMT 240
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL-----------------------------------------VNSLEALLAAVAAGLGIA 199

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1242555517 241 LLP-YLHSLELSEKQLqHIRHFNEPQPAREISLVYHKNELKAQMINALHEVISGVIR 296
Cdd:COG0583   200 LLPrFLAADELAAGRL-VALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-291 3.55e-36

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: 128.87  E-value: 3.55e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPE 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 172 NHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCgqkqatQKRGFQ----IKSGSFETLIRLSNEGLGMTLLPYLHS 247
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAF------AEAGFTpniaLEVDSLEAIKALVAAGLGIALLPESAV 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1242555517 248 LELSEKQLqHIRHFNEPQPAREISLVYHKNELKAQMINALHEVI 291
Cdd:cd05466   155 EELADGGL-VVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-291 1.57e-32

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: 119.70  E-value: 1.57e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  91 GEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIP 170
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 171 ENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFQIksGSFETLIRLSNEGLGMTLLP-YLHSLE 249
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEV--NSLEALLQLVAAGLGIALLPrSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1242555517 250 LSEKQLQhIRHFNEPQPAREISLVYHKNELKAQMINALHEVI 291
Cdd:pfam03466 160 LADGRLV-ALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-277 1.78e-32

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: 121.96  E-value: 1.78e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPL 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 161 FYEPFVAYIPENHwlcKSNKINSEDLQIDEI-----LMLEDGhcfkntvlnlCGQKQATQKrgfQIKS------------ 223
Cdd:NF040786  161 YKDRLVLITPNGT---EKYRMLKEEISISELqkepfIMREEG----------SGTRKEAEK---ALKSlgisledlnvva 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1242555517 224 --GSFETLIRLSNEGLGMTLLPYLHSLElsEKQLQHIRHFNEP--QPAREISLVYHKN 277
Cdd:NF040786  225 slGSTEAIKQSVEAGLGISVISELAAEK--EVERGRVLIFPIPglPKNRDFYLVYNKN 280
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-187 4.71e-26

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 104.85  E-value: 4.71e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESER--- 77
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKakl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  78 MQDIVAQEKgfigGEFRLGIIPTVSPTLLPLFLKNFikKYSKVDLKIEEQ---HTQQaLTNIENGSLDAAILATPLENAN 154
Cdd:PRK09906   81 RARKIVQED----RQLTIGFVPSAEVNLLPKVLPMF--RLRHPDTLIELVsliTTQQ-EEKLRRGELDVGFMRHPVYSDE 153

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1242555517 155 FIEKPLFYEPFVAYIPENHWLCKSNKINSEDLQ 187
Cdd:PRK09906  154 IDYLELLDEPLVVVLPVDHPLAHEKEITAAQLD 186
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-164 2.92e-22

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 94.25  E-value: 2.92e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPL 160
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160


                  ....
gi 1242555517 161 FYEP 164
Cdd:PRK11242  161 FTET 164
PRK09986 PRK09986
LysR family transcriptional regulator;
6-243 1.01e-20

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 90.17  E-value: 1.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   6 LEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESE----RMQDI 81
Cdd:PRK09986   12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEqslaRVEQI 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  82 VAQEKGFIggefRLGIIPT-VSPTLLPLfLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAI--LATPLENANFIEK 158
Cdd:PRK09986   92 GRGEAGRI----EIGIVGTaLWGRLRPA-MRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFTSR 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 159 PLFYEPFVAYIPENHWLCKSNKINSEDLQIDEILMLEDGHC-FKNTVLNLCgqkqatQKRGF--QIKSGSFE--TLIRLS 233
Cdd:PRK09986  167 RLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSdWGKFLQRVC------QQAGFspQIIRQVNEpqTVLAMV 240

                         250
                  ....*....|
gi 1242555517 234 NEGLGMTLLP 243
Cdd:PRK09986  241 SMGIGITLLP 250
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-186 3.73e-20

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 88.51  E-value: 3.73e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQ-NFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQ-ITKIGEQIVKQAQIIVNESERM 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  79 QDIVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEK 158
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLAT 160

                         170       180
                  ....*....|....*....|....*....
gi 1242555517 159 PLFYE-PFVAYIPENHWLCKSNKINSEDL 186
Cdd:PRK12682  161 LPCYDwQHAVIVPPDHPLAQEERITLEDL 189
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 94-277 8.48e-20

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 85.28  E-value: 8.48e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPENH 173
Cdd:cd08434     3 RLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 174 WLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCgqkqatQKRGFQIKSgSFE-----TLIRLSNEGLGMTLLPYLHSL 248
Cdd:cd08434    83 PLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELC------AAAGFTPKI-AFEgeedsTIAGLVAAGLGVAILPEMTLL 155

                         170       180
                  ....*....|....*....|....*....
gi 1242555517 249 ELSEKQLQHIRhfnEPQPAREISLVYHKN 277
Cdd:cd08434   156 NPPGVKKIPIK---DPDAERTIGLAWLKD 181
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.87e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.12  E-value: 1.87e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   3 ITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12680 PRK12680
LysR family transcriptional regulator;
1-175 3.38e-19

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 86.21  E-value: 3.38e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQ-NFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQ-ITKIGEQIVKQAQIIVNESERM 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  79 QDIVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATP-LENANFIE 157
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAgGEPSAGIA 160

                         170
                  ....*....|....*...
gi 1242555517 158 KPLFYEPFVAYIPENHWL 175
Cdd:PRK12680  161 VPLYRWRRLVVVPRGHAL 178
rbcR CHL00180
LysR transcriptional regulator; Provisional
 2-186 3.96e-19

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 85.84  E-value: 3.96e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   2 TITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQDI 81
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  82 VAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAIL--ATPLENANFIE-K 158
Cdd:CHL00180   86 LEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTELKKILEiT 165

                         170       180
                  ....*....|....*....|....*...
gi 1242555517 159 PLFYEPFVAYIPENHWLCKSNKINSEDL 186
Cdd:CHL00180  166 PYVEDELALIIPKSHPFAKLKKIQKEDL 193
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-277 3.49e-18

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: 81.06  E-value: 3.49e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEqHTQQALTN-IENGSLDAAILATPLENANFIEKPLFYEPFVAYIP 170
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVE-YGGKKVEQaVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 171 ENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCgqkqatQKRGFQIK----SGSFETLIRLSNEGLGMTLLPYLH 246
Cdd:cd08438    80 RGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDAC------QQAGFTPNiaarSSQWDFIAELVAAGLGVALLPRSI 153

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1242555517 247 SLELSEKQLqHIRHFNEPQPAREISLVYHKN 277
Cdd:cd08438   154 AQRLDNAGV-KVIPLTDPDLRWQLALIWRKG 183
PRK09791 PRK09791
LysR family transcriptional regulator;
5-173 2.03e-16

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 78.27  E-value: 2.03e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   5 QLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQDIVAQ 84
Cdd:PRK09791    9 QIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRQ 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  85 EKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAI---LATPLENANFIEKpLF 161
Cdd:PRK09791   89 RQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntyYQGPYDHEFTFEK-LL 167

                         170
                  ....*....|..
gi 1242555517 162 YEPFVAYIPENH 173
Cdd:PRK09791  168 EKQFAVFCRPGH 179
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-278 8.49e-16

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: 74.47  E-value: 8.49e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPE 171
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 172 NHWLCKSNKINSEDLQiDEILML---EDGHCFKNTVLNLCGQkqatqkRGFQIK----SGSFETLIRLSNEGLGMTLLPy 244
Cdd:cd08414    81 DHPLAARESVSLADLA-DEPFVLfprEPGPGLYDQILALCRR------AGFTPRivqeASDLQTLLALVAAGLGVALVP- 152

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1242555517 245 lHSLelseKQLQH----IRHFNEPQPAREISLVYHKNE 278
Cdd:cd08414   153 -ASV----ARLQRpgvvYRPLADPPPRSELALAWRRDN 185
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-148 2.53e-15

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 75.01  E-value: 2.53e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVA-QYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQ-ITKIGEQIVKQAQIIVNESERM 78
Cdd:PRK12684    1 MNLHQLRFVREAVrQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1242555517  79 Q----DIVAQEKgfigGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAIlAT 148
Cdd:PRK12684   81 KrvgkEFAAQDQ----GNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI-AT 149
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-186 9.54e-15

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 73.39  E-value: 9.54e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQ-NFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPI-QITKIGEQIVKQAQIIVnesERM 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREIL---SKV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  79 QDI--VAQEkgFIG---GEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLE-N 152
Cdd:PRK12681   78 ESIksVAGE--HTWpdkGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATEALHlY 155

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1242555517 153 ANFIEKPLFYEPFVAYIPENHWLCKSNKINSEDL 186
Cdd:PRK12681  156 DDLIMLPCYHWNRSVVVPPDHPLAKKKKLTIEEL 189
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
25-149 3.99e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 71.00  E-value: 3.99e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  25 CHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQDIVAQEKGFIGGEFRLGIIPTVSPT 104
Cdd:PRK11716    1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1242555517 105 LLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATP 149
Cdd:PRK11716   81 HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKP 125
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-290 1.07e-11

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 62.98  E-value: 1.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLEN--ANFIEKPLFYEPFVAyi 169
Cdd:cd08427     1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPlpKDLVWTPLVREPLVL-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 170 penhwlcksnkINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQAT---QKRGFQIKSG----SFETLIRLSNEGLGMTLL 242
Cdd:cd08427    79 -----------IAPAELAGDDPRELLATQPFIRYDRSAWGGRLVDrflRRQGIRVREVmeldSLEAIAAMVAQGLGVAIV 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1242555517 243 PYLHSLELSEKQLQHIRhFNEPQPAREISLVYHKNELKAQMINALHEV 290
Cdd:cd08427   148 PDIAVPLPAGPRVRVLP-LGDPAFSRRVGLLWRRSSPRSRLIQALLEA 194
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-186 2.63e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 63.14  E-value: 2.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVL-AVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRS-KKPIQITKIGEQIVKQAQIIVNESERM 78
Cdd:PRK12683    1 MNFQQLRIIReAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  79 QDIVAQEKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLEN-ANFIE 157
Cdd:PRK12683   81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDRePDLVS 160

                         170       180
                  ....*....|....*....|....*....
gi 1242555517 158 KPLFYEPFVAYIPENHWLCKSNKINSEDL 186
Cdd:PRK12683  161 FPYYSWHHVVVVPKGHPLTGRENLTLEAI 189
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-276 9.47e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 61.75  E-value: 9.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  10 LAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQDIVAQEKGfi 89
Cdd:PRK10094   11 IAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVND-- 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  90 GGEFRLGIIPT---VSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILAT---PLENaNFIEKPLFYE 163
Cdd:PRK10094   89 GVERQVNIVINnllYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTgteALAN-TFSLDPLGSV 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 164 PFVAYIPENHWLCKSNKINSED-LQIDEILMLEDG--HCFKNTVLNLCGQKqatqkrgfQIKSGSFETLIRLSNEGLGMT 240
Cdd:PRK10094  168 QWRFVMAADHPLANVEEPLTEAqLRRFPAVNIEDSarTLTKRVAWRLPGQK--------EIIVPDMETKIAAHLAGVGIG 239

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1242555517 241 LLP------YLHSLELSEKQLQHIRHfnePQPareISLVYHK 276
Cdd:PRK10094  240 FLPkslcqsMIDNQQLVSRVIPTMRP---PSP---LSLAWRK 275
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-277 1.02e-10

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: 59.85  E-value: 1.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPENH 173
Cdd:cd08440     3 RVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 174 WLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFQIksGSFETLIRLSNEGLGMTLLPYLHSLELSEK 253
Cdd:cd08440    83 PLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEV--SHMSTALGMVAAGLGVAVLPALALPLADHP 160

                         170       180
                  ....*....|....*....|....
gi 1242555517 254 QLQHIRhFNEPQPAREISLVYHKN 277
Cdd:cd08440   161 GLVARP-LTEPVVTRTVGLIRRRG 183
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 92-279 2.42e-10

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: 58.88  E-value: 2.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAIL--ATPLENANFIEKPLFYEPFVAYI 169
Cdd:cd08437     1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLgsLTPLENSALHSKIIKTQHFMIIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 170 PENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFqiKSGSFETLIRLSNEGLGMTLLpylhsLE 249
Cdd:cd08437    81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVY--RTNDIHILKSMVRENVGIGFL-----TD 153

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1242555517 250 LSEKQLQHIRHF---NEPQPAREISLVYHKNEL 279
Cdd:cd08437   154 IAVKPDDHLVAIpllDNEQPTFYISLAHRKDQL 186
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-193 2.90e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 57.33  E-value: 2.90e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   3 ITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQA-QIIVNESERMQDI 81
Cdd:PRK15421    4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLAnQVLPQISQALQAC 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  82 VAQEKgfigGEFRLGI-----IPTVSPTllplfLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFI 156
Cdd:PRK15421   84 NEPQQ----TRLRIAIechscIQWLTPA-----LENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLH 154

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1242555517 157 EKPLF-YEPFVAYIPEnHWLCKSNKINSEDLQIDEILM 193
Cdd:PRK15421  155 YSPMFdYEVRLVLAPD-HPLAAKTRITPEDLASETLLI 191
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-145 5.08e-09

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 56.55  E-value: 5.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  10 LAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQI---VKQAQIIVNESerMQDIVAQEk 86
Cdd:PRK10086   23 EVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVfwaLKSSLDTLNQE--ILDIKNQE- 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1242555517  87 gfIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIeeqHTQQALTNIENGSLDAAI 145
Cdd:PRK10086  100 --LSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTI---LTGNENVNFQRAGIDLAI 153
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 93-276 9.86e-09

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: 54.15  E-value: 9.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  93 FRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPEN 172
Cdd:cd08442     2 LRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 173 HwlckSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGQKQATQKRGFQIksGSFETLIRLSNEGLGMTLLP--YLHSLEL 250
Cdd:cd08442    82 H----PPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEF--GSYHAILGCVAAGMGIALLPrsVLDSLQG 155

                         170       180
                  ....*....|....*....|....*...
gi 1242555517 251 SEKqlqhIRHFNEPQPAREIS--LVYHK 276
Cdd:cd08442   156 RGS----VSIHPLPEPFADVTtwLVWRK 179
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 94-274 1.07e-08

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: 54.14  E-value: 1.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEE---QHTQQALtniENGSLDAAILATPLENANFIEKPLFYEPFVAYIP 170
Cdd:cd08433     3 SVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEglsGHLLEWL---LNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 171 ENHWLCKSNKINSEDLQiDEILML-EDGHCFKNTVLNLCGQKQATQKRGFQIksGSFETLIRLSNEGLGMTLLPYLHSLE 249
Cdd:cd08433    80 ADAPLPRGAPVPLAELA-RLPLILpSRGHGLRRLVDEAAARAGLTLNVVVEI--DSVATLKALVAAGLGYTILPASAVAA 156

                         170       180
                  ....*....|....*....|....*
gi 1242555517 250 LSEKQLQHIRHFNEPQPAREISLVY 274
Cdd:cd08433   157 EVAAGRLVAAPIVDPALTRTLSLAT 181
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 105-290 1.40e-08

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: 53.72  E-value: 1.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 105 LLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLEN-ANFIEKPLFYEPFVAYIPENHWLCKSNKINS 183
Cdd:cd08451    15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARsDGLVLELLLEEPMLVALPAGHPLARERSIPL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 184 EDLQiDEILML---EDGHCFKNTVLnlcgqkQATQKRGFQIKSGsFE-----TLIRLSNEGLGMTLLPylhsleLSEKQL 255
Cdd:cd08451    95 AALA-DEPFILfprPVGPGLYDAII------AACRRAGFTPRIG-QEapqmaSAINLVAAGLGVSIVP------ASMRQL 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1242555517 256 Q----HIRHFNEPQPAREISLVYHKNELKAQMINALHEV 290
Cdd:cd08451   161 QapgvVYRPLAGAPLTAPLALAYRRGERSPAVRNFIALV 199
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 94-242 2.11e-08

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: 53.26  E-value: 2.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPENH 173
Cdd:cd08457     3 RIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGH 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1242555517 174 WLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCGqkQATQKRGFQIKSGSFETLIRLSNEGLGMTLL 242
Cdd:cd08457    83 PLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALG--KIGVKRRPIIEVNLSHTALSLVREGLGIAII 149
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 105-277 2.52e-08

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: 53.26  E-value: 2.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 105 LLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPENHWLCKSNKINSE 184
Cdd:cd08420    14 LLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 185 DLQIDEILMLEDGHCFKNTV---LNLCGQKQATQKRGFQIksGSFETLIRLSNEGLGMTLLPYLhSL--ELSEKQLQHIR 259
Cdd:cd08420    94 ELAAEPWILREPGSGTREVFeraLAEAGLDGLDLNIVMEL--GSTEAIKEAVEAGLGISILSRL-AVrkELELGRLVALP 170

                         170
                  ....*....|....*...
gi 1242555517 260 hFNEPQPAREISLVYHKN 277
Cdd:cd08420   171 -VEGLRLTRPFSLIYHKD 187
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-164 3.85e-08

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 53.92  E-value: 3.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGIIP-TVSPTL-LPLfLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAIL--ATPLENANFI 156
Cdd:PRK11233   81 AVHNVGQALSGQVSIGLAPgTAASSLtMPL-LQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIyeHSPVAGLSSQ 159


                  ....*...
gi 1242555517 157 ekPLFYEP 164
Cdd:PRK11233  160 --PLLKED 165
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 95-288 4.58e-08

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: 52.50  E-value: 4.58e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  95 LGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPENHW 174
Cdd:cd08452     4 IGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 175 LCKSNKINSEDLQIDEILML--EDGHCFKNTVLNLCgqkqatQKRGFQIK----SGSFETLIRLSNEGLGMTLLPylHSL 248
Cdd:cd08452    84 LASKEEITIEDLRDEPIITVarEAWPTLYDEIIQLC------EQAGFRPKivqeATEYQTVIGLVSAGIGVTFVP--SSA 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1242555517 249 ELSEKQLQHIRHFNEPQPAREISLVYHKNELKAQMINALH 288
Cdd:cd08452   156 KKLFNLEVAYRKIDQINLNAEWSIAYRKDNHNPLLKHFIH 195
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
10-161 2.92e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 51.21  E-value: 2.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  10 LAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESE------RMQDIVA 83
Cdd:PRK10082   20 LTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLEsnlaelRGGSDYA 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  84 QEKGFIGG--EFRLGIIPTVSPTLLPLFlknfikkyskvDLKIEEQHTQQALTNIENGSLDAA-------ILATPLENAN 154
Cdd:PRK10082  100 QRKIKIAAahSLSLGLLPSIISQMPPLF-----------TWAIEAIDVDEAVDKLREGQSDCIfsfhdedLLEAPFDHIR 168


                  ....*..
gi 1242555517 155 FIEKPLF 161
Cdd:PRK10082  169 LFESQLF 175
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 11-145 4.46e-07

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 50.61  E-value: 4.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  11 AVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNE----SERMQDivAQEK 86
Cdd:PRK11139   16 AAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQlaeaTRKLRA--RSAK 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1242555517  87 GfiggefRLGIipTVSPT-----LLPLfLKNFIKKYSKVDLKIEeqhTQQALTNIENGSLDAAI 145
Cdd:PRK11139   94 G------ALTV--SLLPSfaiqwLVPR-LSSFNEAHPDIDVRLK---AVDRLEDFLRDDVDVAI 145
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 2-187 5.35e-07

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 50.38  E-value: 5.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   2 TITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQI-------IVNE 74
Cdd:PRK11013    5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRsyygldrIVSA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  75 SERMQDivaqekgFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKI--------EEQHTQQ----ALTniENGSLD 142
Cdd:PRK11013   85 AESLRE-------FRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIvpqespllEEWLSAQrhdlGLT--ETLHTP 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1242555517 143 AAILATPLENANfiekplfyepFVAYIPENHWLCKSNKINSEDLQ 187
Cdd:PRK11013  156 AGTERTELLTLD----------EVCVLPAGHPLAAKKVLTPDDFA 190
PRK10341 PRK10341
transcriptional regulator TdcA;
5-166 5.59e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 50.25  E-value: 5.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   5 QLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQDIVAQ 84
Cdd:PRK10341   11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEING 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  85 EKGFIGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAI--LATPLENANFIEKPLFY 162
Cdd:PRK10341   91 MSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVEPLFE 170


                  ....
gi 1242555517 163 EPFV 166
Cdd:PRK10341  171 SEFV 174
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-149 9.40e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 49.58  E-value: 9.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   5 QLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSkKPIQITKIGEQIVKQA-QIIVNESERMQDIVA 83
Cdd:PRK13348    6 QLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLrQVALLEADLLSTLPA 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1242555517  84 QEKGfiggefrlgiIPTVS--------PTLLPLFLKNFIKKYS-KVDLKIEEQ-HTQQALtniENGSLDAAILATP 149
Cdd:PRK13348   85 ERGS----------PPTLAiavnadslATWFLPALAAVLAGERiLLELIVDDQdHTFALL---ERGEVVGCVSTQP 147
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-186 9.68e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 49.42  E-value: 9.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVA-QYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIF-DRSKKPIQITKIGEQIVKQAQIIVNES--- 75
Cdd:PRK12679    1 MNFQQLKIIREAArQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEAsnv 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  76 ERMQDIVAQEKgfiGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLEN-AN 154
Cdd:PRK12679   81 RRLADLFTNDT---SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNdPQ 157

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1242555517 155 FIEKPLFYEPFVAYIPENHWLCKSNKINSEDL 186
Cdd:PRK12679  158 LVAFPWFRWHHSLLVPHDHPLTQITPLTLESI 189
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-84 1.25e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.17  E-value: 1.25e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1242555517   6 LEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNeseRMQDIVAQ 84
Cdd:PRK11074    7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK---KMQETRRQ 82
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-245 1.78e-06

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 47.59  E-value: 1.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAIL-----ATPLENANFIEKPLFYEPFV 166
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdypvTPPPDDPGLTRVPLLDDPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 167 AYIPENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCgqkqatQKRGFQIK----SGSFETLIRLSNEGLGMTLL 242
Cdd:cd08423    81 LVLPADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRAC------RAAGFTPRiaheADDYATVLALVAAGLGVALV 154


                  ...
gi 1242555517 243 PYL 245
Cdd:cd08423   155 PRL 157
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 93-187 2.37e-06

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: 47.37  E-value: 2.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  93 FRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPEN 172
Cdd:cd08450     2 LTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPAD 81

                          90
                  ....*....|....*
gi 1242555517 173 HWLCKSNKINSEDLQ 187
Cdd:cd08450    82 HRLAGREKIPPQDLA 96
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-160 2.91e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 48.06  E-value: 2.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTITQLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQD 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLgiipTVSPTLLPL----FLKNFIKKYSKVDLKIEEQHTQqalTNIENGSLDAAILA--TPLENAN 154
Cdd:PRK14997   82 AIAALQVEPRGIVKL----TCPVTLLHVhigpMLAKFMARYPDVSLQLEATNRR---VDVVGEGVDVAIRVrpRPFEDSD 154


                  ....*.
gi 1242555517 155 FIEKPL 160
Cdd:PRK14997  155 LVMRVL 160
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-273 3.50e-06

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 46.83  E-value: 3.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  93 FRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLE-NANFIEKPLFYEPFVAYIPE 171
Cdd:cd08436     2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERrPPGLASRELAREPLVAVVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 172 NHWLCKSNKINSEDLQiDEILM-LEDGHCFKNTVLNLCGQKQATQKRGFQIksGSFETLIRLSNEGLGMTLLPylhslEL 250
Cdd:cd08436    82 DHPLAGRRRVALADLA-DEPFVdFPPGTGARRQVDRAFAAAGVRRRVAFEV--SDVDLLLDLVARGLGVALLP-----AS 153

                         170       180
                  ....*....|....*....|....
gi 1242555517 251 SEKQLQHIRHFN-EPQPAREISLV 273
Cdd:cd08436   154 VAARLPGLAALPlEPAPRRRLYLA 177
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-243 3.73e-06

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: 46.77  E-value: 3.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAI---LATPLENAnFIekPLFYEPFVAY 168
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALtydLDLPEDIA-FE--PLARLPPYVW 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1242555517 169 IPENHWLCKSNKINSEDLQIDEILMLEDGHCfKNTVLNLCGQKQATQKRGFqiKSGSFETLIRLSNEGLGMTLLP 243
Cdd:cd08412    78 LPADHPLAGKDEVSLADLAAEPLILLDLPHS-REYFLSLFAAAGLTPRIAY--RTSSFEAVRSLVANGLGYSLLN 149
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 92-291 3.88e-06

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: 46.96  E-value: 3.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLE--NANFIEKPLFYEPFVAYI 169
Cdd:cd08418     1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEmyLKELISEPLFESDFVVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 170 PENHWLCKSNKInsEDLQIDEILMLEDGHCFKNTVLNLCgQKQATQKRgFQIKSGSFETLIRLSNEGLGMTLLPYLHSLE 249
Cdd:cd08418    81 RKDHPLQGARSL--EELLDASWVLPGTRMGYYNNLLEAL-RRLGYNPR-VAVRTDSIVSIINLVEKADFLTILSRDMGRG 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1242555517 250 LSEK-QLQHIRhFNEPQPAREISLVYHKNELKAQMINALHEVI 291
Cdd:cd08418   157 PLDSfRLITIP-VEEPLPSADYYLIYRKKSRLTPLAEQLVELF 198
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 94-250 6.85e-06

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


Pssm-ID: 176111  Cd Length: 197  Bit Score: 45.96  E-value: 6.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPtLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPENH 173
Cdd:cd08419     3 RLAVVSTAKY-FAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 174 WLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCgqkqatQKRGFQIKsgsfetlIRL---SNE--------GLGMTLL 242
Cdd:cd08419    82 PLAGQKRIPLERLAREPFLLREPGSGTRLAMERFF------AEHGVTLR-------VRMelgSNEaikqavmaGLGLSVL 148


                  ....*...
gi 1242555517 243 PyLHSLEL 250
Cdd:cd08419   149 S-LHTLAL 155
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 11-206 1.12e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.17  E-value: 1.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  11 AVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVneseRMQDIVAQEKGF-- 88
Cdd:PRK15092   21 AVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL----RFNDEACSSLMYsn 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  89 IGGEFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAIlaTPLENANFIEKPLFYEPfvay 168
Cdd:PRK15092   97 LQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV--TTHRPSSFPALNLRTSP---- 170

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1242555517 169 ipeNHWLCKSNKInsedLQIDE---ILMLEDGHCFKNTVLN 206
Cdd:PRK15092  171 ---TLWYCAAEYV----LQKGEpipLVLLDEPSPFRDMALA 204
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-159 2.74e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 45.06  E-value: 2.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   1 MTIT--QLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERM 78
Cdd:PRK10837    1 MHITlrQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  79 QDIVAQEKGFIggefRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEK 158
Cdd:PRK10837   81 EQLFREDNGAL----RIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISE 156


                  .
gi 1242555517 159 P 159
Cdd:PRK10837  157 P 157
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-193 1.01e-04

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: 42.63  E-value: 1.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPENH 173
Cdd:cd08447     3 RIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGH 82

                          90       100
                  ....*....|....*....|
gi 1242555517 174 WLCKSNKINSEDLQIDEILM 193
Cdd:cd08447    83 PLAGAERLTLEDLDGQPFIM 102
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-291 1.06e-04

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: 42.41  E-value: 1.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAiLATPLENANFIEKPLFYE-PFVAYIP 170
Cdd:cd08456     1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLG-LVSTLHEPPGIERERLLRiDGVCVLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 171 ENHWLCKSNKINSEDLQIDEILMLEDGHCFKNTVLNLCgqKQATQKRGFQIKSGSFETLIRLSNEGLGMTLLPYLHSLEL 250
Cdd:cd08456    80 PGHRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALF--EQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDY 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1242555517 251 SEKQLQhIRHFnEPQPAREISLVYHKNELKAQMINALHEVI 291
Cdd:cd08456   158 AAAGLV-VRRF-SPAVPFEVSLIRPKHRPSSALVAAFSACL 196
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-149 1.12e-04

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 43.22  E-value: 1.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   5 QLEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSkKPIQITKIGEQIVKQAQiivneseRMQ----D 80
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHAR-------QVRlleaE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  81 IVAQEKGFIGGEFRLGI-----------IPTVSPTL--LPLFLknfikkyskvDLKIEEQ-HTQQALtniENGSLDAAIL 146
Cdd:PRK03635   78 LLGELPALDGTPLTLSIavnadslatwfLPALAPVLarSGVLL----------DLVVEDQdHTAELL---RRGEVVGAVT 144


                  ...
gi 1242555517 147 ATP 149
Cdd:PRK03635  145 TEP 147
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 94-278 1.17e-04

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: 42.35  E-value: 1.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLEN---ANFIEKPLFYEPFVAYIP 170
Cdd:cd08453     3 SLAFVSTADYSVLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGAsapPALAYRPLLSEPLVLAVP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 171 ENHWLCKSNKINSEDLqIDEILMLEDGH---CFKNTVLNL---CGQKQATQKRGFQIksgsfETLIRLSNEGLGMTLLPY 244
Cdd:cd08453    83 AAWAAEGGAPLALAAV-AAEPLVIFPRRiapAFHDAVTGYyraAGQTPRIAQEAIQM-----QTIISLVSAGMGVALVPA 156

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1242555517 245 lhslelSEKQLQHI----RHFNEPQPAREISLVYHKNE 278
Cdd:cd08453   157 ------SLRNLARPgvvyRELADPAPVLETGLVWRRDD 188
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 94-243 1.87e-04

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: 41.87  E-value: 1.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAIL--ATPLENANFIEKPLFYEPFVAYIPE 171
Cdd:cd08449     3 NIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVrfADTLNDPPLASELLWREPMVVALPE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1242555517 172 NHWLCKSNKINSEDLQIDEILMLEDGHC-FKNTVLNLCgqkqatQKRGF--QIKSGSFE--TLIRLSNEGLGMTLLP 243
Cdd:cd08449    83 EHPLAGRKSLTLADLRDEPFVFLRLANSrFADFLINCC------LQAGFtpQITQEVVEpqTLMALVAAGFGVALVP 153
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
10-73 3.10e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 41.54  E-value: 3.10e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1242555517  10 LAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVN 73
Cdd:PRK03601   10 LEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMN 73
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 94-187 5.12e-04

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: 40.24  E-value: 5.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPENH 173
Cdd:cd08415     3 RIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGH 82

                          90
                  ....*....|....
gi 1242555517 174 WLCKSNKINSEDLQ 187
Cdd:cd08415    83 PLARKDVVTPADLA 96
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 105-192 5.38e-04

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: 40.24  E-value: 5.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517 105 LLPLfLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLF-YEPfVAYIPENHWLCKSNKINS 183
Cdd:cd08441    15 LMPV-LDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFdYEV-VLVVAPDHPLAAKEFITP 92


                  ....*....
gi 1242555517 184 EDLqIDEIL 192
Cdd:cd08441    93 EDL-ADETL 100
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-243 7.85e-04

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: 39.94  E-value: 7.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPE 171
Cdd:cd08448     1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1242555517 172 NHWLCKSNKINSEDLQIDEILML--EDGHCFKNTVLNLCgqkqatQKRGF--QIKSGS--FETLIRLSNEGLGMTLLP 243
Cdd:cd08448    81 GHPLAARRRIDLRELAGEPFVLFsrEVSPDYYDQIIALC------MDAGFhpKIRHEVrhWLTVVALVAAGMGVALVP 152
PRK09801 PRK09801
LysR family transcriptional regulator;
6-96 9.93e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 40.40  E-value: 9.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517   6 LEYVLAVAQYQNFTSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQDIVAQE 85
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90
                  ....*....|.
gi 1242555517  86 KGFIGGEFRLG 96
Cdd:PRK09801   91 KTRPEGMIRIG 101
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 93-243 1.24e-03

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176108  Cd Length: 199  Bit Score: 39.25  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  93 FRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATP--LENANFIEKPLFYEPFVAYIP 170
Cdd:cd08416     2 LRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPegLNDPDFEVVPLFEDDIFLAVP 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1242555517 171 ENHWLCKSNKINSEDLQIDEILMLEDGHCFKNtvlnlcGQKQATQKRGFQ----IKSGSFETLIRLSNEGLGMTLLP 243
Cdd:cd08416    82 ATSPLAASSEIDLRDLKDEKFVTLSEGFATYR------GFDEAFEIAGFEpnvvMRVNDIFSLMSMVSGGVGYALLP 152
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 92-173 2.60e-03

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: 38.35  E-value: 2.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  92 EFRLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAILATPLENANFIEKPLFYEPFVAYIPE 171
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80


                  ..
gi 1242555517 172 NH 173
Cdd:cd08417    81 DH 82
nhaR PRK11062
transcriptional activator NhaR; Provisional
 19-82 3.98e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 38.45  E-value: 3.98e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1242555517  19 TSASEKCHVTQPTLSMQIQKLEEELGALIFDRSKKPIQITKIGEQIVKQAQIIVNESERMQDIV 82
Cdd:PRK11062   22 VGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEMLDIV 85
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 94-187 4.94e-03

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: 37.64  E-value: 4.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1242555517  94 RLGIIPTVSPTLLPLFLKNFIKKYSKVDLKIEEQHTQQALTNIENGSLDAAI--LATPLENANFIEKPLFYEPFVAYIPE 171
Cdd:cd08435     3 RVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVARP 82

                          90
                  ....*....|....*.
gi 1242555517 172 NHWLCKSNKINSEDLQ 187
Cdd:cd08435    83 GHPLARRARLTLADLA 98
 
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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