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Conserved domains on  [gi|1564868385|gb|RXS08106|]
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LysR family transcriptional regulator [Staphylococcus saprophyticus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444076)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-287 9.92e-87

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: 257.49  E-value: 9.92e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNK 171
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 172 EHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLDSS 251
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1564868385 252 -FSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFM 287
Cdd:cd08438   161 gVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 6.87e-21

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.59  E-value: 6.87e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1564868385   3 IKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-287 9.92e-87

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: 257.49  E-value: 9.92e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNK 171
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 172 EHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLDSS 251
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1564868385 252 -FSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFM 287
Cdd:cd08438   161 gVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 1.01e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 193.16  E-value: 1.01e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 161 YQEDLKLVLNKEHHLANEAHVdmsmlkdedfilfnedfylndkiieaaknagfipntiskISQWNFIENLLNAHLGVSIL 240
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1564868385 241 PENIV--HLLDSSFSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFMKERL 291
Cdd:COG0583   202 PRFLAadELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-291 7.47e-41

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: 140.50  E-value: 7.47e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  90 TGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVL 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 170 NKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIV--HL 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVarEL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1564868385 248 LDSSFSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFMKERL 291
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-193 1.58e-40

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: 142.37  E-value: 1.58e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSLLGLETGHISIGLSAVmnMNQFI--NILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSV 158
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTI--PGQYLlpELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYT 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1564868385 159 TLYQEDLKLVLNKEHHLANEAH--VDMSMLKDEDFIL 193
Cdd:NF040786  159 PFYKDRLVLITPNGTEKYRMLKeeISISELQKEPFIM 195
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-291 4.43e-31

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 117.56  E-value: 4.43e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKeiLTLYN-DVP 79
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDAR--AILEQaEKA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  80 KEINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVT 159
Cdd:PRK09906   79 KLRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 160 LYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGV 237
Cdd:PRK09906  159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYsgSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGC 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1564868385 238 SILPENIVHLLDSSFSNKTLEDPGMRWELGVIWKKDKyLSHATKQWIDFMKERL 291
Cdd:PRK09906  239 TIIPGYMNNFNTGQVVFRPLAGNVPSIALLMAWKKGE-MKPALRDFIAIVQERL 291
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 6.87e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.59  E-value: 6.87e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1564868385   3 IKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 32-73 3.79e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 47.24  E-value: 3.79e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1564868385  32 ISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILT 73
Cdd:PRK11074   33 VSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK 74
 
Name Accession Description Interval E-value
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-287 9.92e-87

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: 257.49  E-value: 9.92e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNK 171
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 172 EHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLDSS 251
Cdd:cd08438    81 GHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNA 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1564868385 252 -FSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFM 287
Cdd:cd08438   161 gVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 1.01e-60

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 193.16  E-value: 1.01e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 161 YQEDLKLVLNKEHHLANEAHVdmsmlkdedfilfnedfylndkiieaaknagfipntiskISQWNFIENLLNAHLGVSIL 240
Cdd:COG0583   161 GEERLVLVASPDHPLARRAPL---------------------------------------VNSLEALLAAVAAGLGIALL 201

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1564868385 241 PENIV--HLLDSSFSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFMKERL 291
Cdd:COG0583   202 PRFLAadELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREAL 254
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-287 1.03e-59

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: 188.58  E-value: 1.03e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNK 171
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 172 EHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLL-DS 250
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELaDG 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1564868385 251 SFSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFM 287
Cdd:cd05466   161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-291 7.47e-41

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: 140.50  E-value: 7.47e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  90 TGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVL 169
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 170 NKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIV--HL 247
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVarEL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1564868385 248 LDSSFSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFMKERL 291
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-193 1.58e-40

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: 142.37  E-value: 1.58e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSLLGLETGHISIGLSAVmnMNQFI--NILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSV 158
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTI--PGQYLlpELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYT 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1564868385 159 TLYQEDLKLVLNKEHHLANEAH--VDMSMLKDEDFIL 193
Cdd:NF040786  159 PFYKDRLVLITPNGTEKYRMLKeeISISELQKEPFIM 195
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-287 3.01e-36

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: 128.42  E-value: 3.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGlsavmnmnqFINILG---------EFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQ 162
Cdd:cd08434     1 TVRLG---------FLHSLGtslvpdlirAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFT 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 163 EDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPE 242
Cdd:cd08434    72 EELVLVVPKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPE 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1564868385 243 niVHLLDSSFSNK-TLEDPGMRWELGVIWKKDKYLSHATKQWIDFM 287
Cdd:cd08434   152 --MTLLNPPGVKKiPIKDPDAERTIGLAWLKDRYLSPAARRFKDFV 195
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-291 4.43e-31

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 117.56  E-value: 4.43e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKeiLTLYN-DVP 79
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDAR--AILEQaEKA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  80 KEINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVT 159
Cdd:PRK09906   79 KLRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 160 LYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGV 237
Cdd:PRK09906  159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYsgSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGC 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1564868385 238 SILPENIVHLLDSSFSNKTLEDPGMRWELGVIWKKDKyLSHATKQWIDFMKERL 291
Cdd:PRK09906  239 TIIPGYMNNFNTGQVVFRPLAGNVPSIALLMAWKKGE-MKPALRDFIAIVQERL 291
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-273 7.10e-31

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: 114.14  E-value: 7.10e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNK 171
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 172 EHHLANEAHVDMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLD 249
Cdd:cd08414    81 DHPLAARESVSLADLADEPFVLFPREPgpGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVARLQR 160

                         170       180
                  ....*....|....*....|....
gi 1564868385 250 SSFSNKTLEDPGMRWELGVIWKKD 273
Cdd:cd08414   161 PGVVYRPLADPPPRSELALAWRRD 184
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-291 1.12e-30

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 116.59  E-value: 1.12e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSLLGLETGHISIGLSAVMnMNQFINILGE-FHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVT 159
Cdd:PRK11242   81 AIHDVADLSRGSLRLAMTPTF-TAYLIGPLIDaFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 160 LYQEDLKLVLNKEHHLANEAH-VDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIP------NTISKIsqwnfIENLLN 232
Cdd:PRK11242  160 LFTETLALVVGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPrvaieaNSISAV-----LEIVRR 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1564868385 233 AHLGvSILPENIVHlLDSSFSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFMKERL 291
Cdd:PRK11242  235 GRLA-TLLPAAIAR-EHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIELALERR 291
PRK09986 PRK09986
LysR family transcriptional regulator;
1-242 3.24e-28

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 109.81  E-value: 3.24e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGI--TTLPVDQSIFHSV 158
Cdd:PRK09986   87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFTSR 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 159 TLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFIL--FNE-DFYLNdkIIEAAKNAGFIPNTISKISQWNFIENLLNAHL 235
Cdd:PRK09986  167 RLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITlpFVHsDWGKF--LQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGI 244


                  ....*..
gi 1564868385 236 GVSILPE 242
Cdd:PRK09986  245 GITLLPD 251
rbcR CHL00180
LysR transcriptional regulator; Provisional
 12-195 1.53e-24

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 100.09  E-value: 1.53e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  12 VVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPKEINSLLGLETG 91
Cdd:CHL00180   16 IATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKNLQRG 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGIT--TLPVDQSIFHSVTLYQED-LKLV 168
Cdd:CHL00180   96 TLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTELKKILEITPYVEDeLALI 175

                         170       180
                  ....*....|....*....|....*..
gi 1564868385 169 LNKEHHLANEAHVDMSMLKDEDFILFN 195
Cdd:CHL00180  176 IPKSHPFAKLKKIQKEDLYRLNFITLD 202
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-251 4.02e-22

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 93.59  E-value: 4.02e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSLLGLETGHISIGL---SAVMNMNqfINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDI----------GITT 147
Cdd:PRK11233   81 AVHNVGQALSGQVSIGLapgTAASSLT--MPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMaviyehspvaGLSS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 148 LPvdqsifhsvtLYQEDLKLVLNkehHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFI 227
Cdd:PRK11233  159 QP----------LLKEDLFLVGT---QDCPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATL 225

                         250       260
                  ....*....|....*....|....
gi 1564868385 228 ENLLNAHLGVSILPENIVHLLDSS 251
Cdd:PRK11233  226 TAAIASGMGVTVLPESAARSLCGA 249
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 92-273 9.67e-22

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: 90.31  E-value: 9.67e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFI-NILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSI-FHSVTLYQEDLKLVL 169
Cdd:cd08451     1 RLRVGFTSSAAFHPLVpGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDgLVLELLLEEPMLVAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 170 NKEHHLANEAHVDMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHL 247
Cdd:cd08451    81 PAGHPLARERSIPLAALADEPFILFPRPVgpGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPASMRQL 160

                         170       180
                  ....*....|....*....|....*.
gi 1564868385 248 LDSSFSNKTLEDPGMRWELGVIWKKD 273
Cdd:cd08451   161 QAPGVVYRPLAGAPLTAPLALAYRRG 186
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 6.87e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.59  E-value: 6.87e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1564868385   3 IKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-242 7.22e-21

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 90.09  E-value: 7.22e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILtlyNDVP- 79
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVL---REVKv 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  80 -KEINSLLGLE-TGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHS 157
Cdd:PRK11151   78 lKEMASQQGETmSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 158 VTLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGV 237
Cdd:PRK11151  158 VPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGI 237


                  ....*
gi 1564868385 238 SILPE 242
Cdd:PRK11151  238 TLLPA 242
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-244 2.14e-20

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: 86.56  E-value: 2.14e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGL-SAVMNMnQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSI--FHSVTLYQEDLKLV 168
Cdd:cd08449     1 HLNIGMvGSVLWG-GLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDppLASELLWREPMVVA 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1564868385 169 LNKEHHLANEAHVDMSMLKDEDFILFN-EDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENI 244
Cdd:cd08449    80 LPEEHPLAGRKSLTLADLRDEPFVFLRlANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESY 156
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 92-287 2.19e-19

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: 83.70  E-value: 2.19e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNK 171
Cdd:cd08452     1 LLVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 172 EHHLANEAHVDMSMLKDEDFILFNEDFY--LNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLD 249
Cdd:cd08452    81 QHPLASKEEITIEDLRDEPIITVAREAWptLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSAKKLFN 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1564868385 250 SSFSNKTLEDPGMRWELGVIWKKDKyLSHATKQWIDFM 287
Cdd:cd08452   161 LEVAYRKIDQINLNAEWSIAYRKDN-HNPLLKHFIHIS 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-240 3.50e-18

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 82.72  E-value: 3.50e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQK-GMTNASKHLFIAQPTISKAIKDLEQELDMTLFDR-SKRQLVLTDAGsifykkcKEILTLYNDV 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPG-------RIILASVERI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  79 PKEINSL--LGLE-----TGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTlpvd 151
Cdd:PRK12684   74 LQEVENLkrVGKEfaaqdQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAT---- 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 152 QSIFHS---VTL--YQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNF 226
Cdd:PRK12684  150 EAIADYkelVSLpcYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADV 229

                         250
                  ....*....|....
gi 1564868385 227 IENLLNAHLGVSIL 240
Cdd:PRK12684  230 IKTYVELGLGVGIV 243
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-286 3.36e-17

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: 77.95  E-value: 3.36e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKD 188
Cdd:cd08440    18 VLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWAELAG 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 189 EDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLDSS-FSNKTLEDPGMRWELG 267
Cdd:cd08440    98 YPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPgLVARPLTEPVVTRTVG 177

                         170
                  ....*....|....*....
gi 1564868385 268 VIWKKDKYLSHATKQWIDF 286
Cdd:cd08440   178 LIRRRGRSLSPAAQAFLDL 196
PRK09791 PRK09791
LysR family transcriptional regulator;
3-177 3.66e-17

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 79.81  E-value: 3.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   3 IKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPKEI 82
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  83 NSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVEngGKMIET--QLINDEIDIGITTL---PVDQSIFHS 157
Cdd:PRK09791   87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIME--GQLVSMinELRQGELDFTINTYyqgPYDHEFTFE 164

                         170       180
                  ....*....|....*....|
gi 1564868385 158 vTLYQEDLKLVLNKEHHLAN 177
Cdd:PRK09791  165 -KLLEKQFAVFCRPGHPAIG 183
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-273 6.72e-17

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: 76.92  E-value: 6.72e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNK 171
Cdd:cd08448     1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 172 EHHLANEAHVDMSMLKDEDFILFNEDF--YLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVH--L 247
Cdd:cd08448    81 GHPLAARRRIDLRELAGEPFVLFSREVspDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPRSLARagL 160

                         170       180
                  ....*....|....*....|....*.
gi 1564868385 248 LDSSFSnkTLEDPGMRWELGVIWKKD 273
Cdd:cd08448   161 AGVRFL--PLKGATQRSELYAAWKAS 184
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 92-287 8.02e-17

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


Pssm-ID: 176128  Cd Length: 198  Bit Score: 76.99  E-value: 8.02e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIG--ITTLPVDQSIFHSVTLYQEDLKLVL 169
Cdd:cd08437     1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIAllGSLTPLENSALHSKIIKTQHFMIIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 170 NKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLD 249
Cdd:cd08437    81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKPDD 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1564868385 250 SSFSNKTLEDPGMRWELGVIWKKDKYLSHATKQWIDFM 287
Cdd:cd08437   161 HLVAIPLLDNEQPTFYISLAHRKDQLLTPAQKKLLDLL 198
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 109-272 1.82e-16

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: 76.02  E-value: 1.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKD 188
Cdd:cd08411    19 LLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDLAG 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 189 EDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPE---NIVHLLDSSFSNKTLEDPGMRWE 265
Cdd:cd08411    99 ERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPElavPSEELRGDRLVVRPFAEPAPSRT 178


                  ....*..
gi 1564868385 266 LGVIWKK 272
Cdd:cd08411   179 IGLVWRR 185
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-155 2.62e-16

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 77.49  E-value: 2.62e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   3 IKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPKEI 82
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1564868385  83 NSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENggkMIETQLINDEIDIGITTLPV-DQSIF 155
Cdd:PRK10632   84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTG---IPAPDLIADGLDVVIRVGALqDSSLF 154
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-216 4.04e-16

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 77.01  E-value: 4.04e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQK-GMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRS-KRQLVLTDAGSIFYKKCKEILTLYNDV 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  79 PKEINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSI-FHS 157
Cdd:PRK12683   81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPdLVS 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1564868385 158 VTLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPN 216
Cdd:PRK12683  161 FPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPD 219
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-242 3.16e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 74.26  E-value: 3.16e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQK-GMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRS-KRQLVLTDAGSIFYKKCKEILTLYNDV 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  79 PKEINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQsifHS- 157
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLAD---DPd 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 158 -VTL--YQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAH 234
Cdd:PRK12682  158 lATLpcYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLG 237


                  ....*...
gi 1564868385 235 LGVSILPE 242
Cdd:PRK12682  238 LGVGIVAE 245
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 109-286 7.99e-15

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: 71.37  E-value: 7.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSL-VENGGKMIEtQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLK 187
Cdd:cd08420    18 LLARFRKRYPEVRVSLtIGNTEEIAE-RVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 188 DEDFILfnedfylndKIIEAA-KNAGFIPNTISKISQWNFIENLLNA---HLGVSILPENIV--HLLDSSFSNKTLEDPG 261
Cdd:cd08420    97 AEPWILrepg-sgtrEVFERAlAEAGLDGLDLNIVMELGSTEAIKEAveaGLGISILSRLAVrkELELGRLVALPVEGLR 175

                         170       180
                  ....*....|....*....|....*
gi 1564868385 262 MRWELGVIWKKDKYLSHATKQWIDF 286
Cdd:cd08420   176 LTRPFSLIYHKDKYLSPAAEAFLEF 200
PRK10341 PRK10341
transcriptional regulator TdcA;
4-289 9.45e-15

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 72.97  E-value: 9.45e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   4 KHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPKEIN 83
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  84 SLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSlvenggkMIETQL------IND-EIDIGITTLPVDQSI-- 154
Cdd:PRK10341   90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVS-------MYEAQLssflpaIRDgRLDFAIGTLSNEMKLqd 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 155 FHSVTLYQEDLKLVLNKEHhlANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENL-LNA 233
Cdd:PRK10341  163 LHVEPLFESEFVLVASKSR--TCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLvLNA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1564868385 234 HLGVSILPENIVHLLDSSFSNKTLED--PGMRWELgvIWKKDKYLSHATKQWIDFMKE 289
Cdd:PRK10341  241 DFLTVIPCDMTSPFGSNQFITIPIEEtlPVAQYAA--VWSKNYRIKKAASVLVELAKE 296
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-270 5.95e-13

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 66.09  E-value: 5.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 110 LGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQ-SIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKD 188
Cdd:cd08436    19 LARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRpPGLASRELAREPLVAVVAPDHPLAGRRRVALADLAD 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 189 EDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENI------VHLLDSSfsnktledPGM 262
Cdd:cd08436    99 EPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVaarlpgLAALPLE--------PAP 170


                  ....*...
gi 1564868385 263 RWELGVIW 270
Cdd:cd08436   171 RRRLYLAW 178
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 92-279 2.47e-12

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: 64.54  E-value: 2.47e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGL----SAVMnmnqFINILGEFHQKYPNVTYSLVEN-GGKMIEtQLINDEIDIGITTLPVDQSIFHSVTLYQEDLK 166
Cdd:cd08433     1 RVSVGLppsaASVL----AVPLLRAVRRRYPGIRLRIVEGlSGHLLE-WLLNGRLDLALLYGPPPIPGLSTEPLLEEDLF 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 167 LVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVH 246
Cdd:cd08433    76 LVGPADAPLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVA 155

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1564868385 247 --LLDSSFSNKTLEDPGMRWELGVIWKKDKYLSHA 279
Cdd:cd08433   156 aeVAAGRLVAAPIVDPALTRTLSLATPRDRPLSPA 190
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-242 3.67e-12

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 65.60  E-value: 3.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQK-GMTNASKHLFIAQPTISKAIKDLEQELDMTLF-DRSKRQLVLTDAGSIFYKKCKEILTLYNDV 78
Cdd:PRK12679    1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASNV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  79 PKEINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITT-LPVDQSIFHS 157
Cdd:PRK12679   81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASeRLSNDPQLVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 158 VTLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGV 237
Cdd:PRK12679  161 FPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGI 240


                  ....*
gi 1564868385 238 SILPE 242
Cdd:PRK12679  241 GLVAE 245
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-149 1.32e-11

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 63.86  E-value: 1.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1564868385  81 EINSLLGLETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLvENGGKMIEtqLINDEIDIGITTLP 149
Cdd:PRK14997   82 AIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL-EATNRRVD--VVGEGVDVAIRVRP 147
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-273 1.95e-11

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: 61.89  E-value: 1.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 108 NILGEFHQKYPNVTYSLVEnggkMIETQ----LINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDM 183
Cdd:cd08447    17 RLLAAARAALPDVDLVLRE----MVTTDqieaLESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAERLTL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 184 SMLKDEDFILF--NEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLldsSFSN---KTLE 258
Cdd:cd08447    93 EDLDGQPFIMYspTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPASASRL---RFEGvvfRPLD 169

                         170
                  ....*....|....*.
gi 1564868385 259 DP-GMRWELGVIWKKD 273
Cdd:cd08447   170 LPrDVPVELHLAWRRD 185
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 113-281 5.90e-11

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 60.42  E-value: 5.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 113 FHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLA-NEAHVDMSMLKDEDF 191
Cdd:cd08425    23 FHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPLAqRRTALTLDDLAAEPL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 192 ILFNEDFYLNDKIIEAAKNAGFIP------NTISKIsqwnfIENLLNAHLGvSILPENIVHlldssfsnktlEDPGMRwE 265
Cdd:cd08425   103 ALLSPDFATRQHIDRYFQKQGIKPriaieaNSISAV-----LEVVRRGRLA-TILPDAIAR-----------EQPGLC-A 164

                         170       180
                  ....*....|....*....|....*..
gi 1564868385 266 LGVI-----------WKKDKYLSHATK 281
Cdd:cd08425   165 VALEpplpgrtaallRRKGAYRSAAAR 191
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 109-287 1.17e-10

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: 59.48  E-value: 1.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGIT---TLPVDqsiFHSVTLYQEDLKLVLNKEHHLANEAHVDMSM 185
Cdd:cd08412    18 LLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTydlDLPED---IAFEPLARLPPYVWLPADHPLAGKDEVSLAD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 186 LKDEDFILFNEDFyLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVH--LLD-SSFSNKTLEDPGM 262
Cdd:cd08412    95 LAAEPLILLDLPH-SREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRpwSYDgKRLVRRPLADPVP 173

                         170       180
                  ....*....|....*....|....*
gi 1564868385 263 RWELGVIWKKDKYLSHATKQWIDFM 287
Cdd:cd08412   174 PLRLGLAWRRGARLTRAARAFVDFA 198
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 9-193 3.59e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 59.32  E-value: 3.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   9 FVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILtlynDVPKEINSLLGL 88
Cdd:PRK10837   11 FAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL----EQAVEIEQLFRE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  89 ETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSL-VENGGKMIETqLINDEIDIGITTLPVdqsifHSVTL----YQE 163
Cdd:PRK10837   87 DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELsVGNSQDVINA-VLDFRVDIGLIEGPC-----HSPELisepWLE 160

                         170       180       190
                  ....*....|....*....|....*....|
gi 1564868385 164 DLKLVLNKEHHLANEAHVDMSMLKDEDFIL 193
Cdd:PRK10837  161 DELVVFAAPDSPLARGPVTLEQLAAAPWIL 190
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-245 1.40e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 58.11  E-value: 1.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIfykkckeILTLYNDVPK 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEI-------LLQLANQVLP 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSLLGL----ETGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLveNGGKMIETQ--LINDEIDIGITTLPVDQSI 154
Cdd:PRK15421   75 QISQALQAcnepQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDF--KSGVTFDPQpaLQQGELDLVMTSDILPRSG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 155 FHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIEnLLNAH 234
Cdd:PRK15421  153 LHYSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQ-MVAAR 231

                         250
                  ....*....|.
gi 1564868385 235 LGVSILPENIV 245
Cdd:PRK15421  232 MGIAALPHWVV 242
PRK09801 PRK09801
LysR family transcriptional regulator;
4-145 4.06e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 56.58  E-value: 4.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   4 KHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPKEIN 83
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1564868385  84 SLLGLETGHISIGLSAVMNMNQFINILGEFHQKYP--NVTYSLVENggkmiETQLINDEIDIGI 145
Cdd:PRK09801   89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPelQVHFELFDR-----QIDLVQDNIDLDI 147
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 92-251 4.09e-09

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: 55.43  E-value: 4.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLP---VDQSiFHSVTLYQEDLKLV 168
Cdd:cd08416     1 RLRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPeglNDPD-FEVVPLFEDDIFLA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 169 LNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLL 248
Cdd:cd08416    80 VPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVY 159


                  ...
gi 1564868385 249 DSS 251
Cdd:cd08416   160 EDK 162
PRK12680 PRK12680
LysR family transcriptional regulator;
1-250 5.29e-09

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 56.17  E-value: 5.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQK-GMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQL-VLTDAGSIFYKKCKEILTLYNDV 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  79 -------PKEINSLLGLETGHisiglsavmNMNQFI--NILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGI-TTL 148
Cdd:PRK12680   81 rtyaanqRRESQGQLTLTTTH---------TQARFVlpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvSTA 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 149 PVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHV-DMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFI 227
Cdd:PRK12680  152 GGEPSAGIAVPLYRWRRLVVVPRGHALDTPRRApDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLI 231

                         250       260
                  ....*....|....*....|...
gi 1564868385 228 ENLLNAHLGVSILPENIVHLLDS 250
Cdd:PRK12680  232 KTYVRAGLGVGLLAEMAVNANDE 254
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-242 1.28e-08

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 53.76  E-value: 1.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 110 LGEFHQKYPNVTYSLVEnggkmIET-----QLINDEIDIGITT------LPVDQSiFHSVTLYQEDLKLVLNKEHHLANE 178
Cdd:cd08423    19 LAALRARHPGLEVRLRE-----AEPpesldALRAGELDLAVVFdypvtpPPDDPG-LTRVPLLDDPLDLVLPADHPLAGR 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1564868385 179 AHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPE 242
Cdd:cd08423    93 EEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR 156
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-120 1.78e-08

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 54.46  E-value: 1.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  19 TNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPKEInsLLGLETGHISIGLS 98
Cdd:PRK11139   24 TRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL--RARSAKGALTVSLL 101

                          90       100
                  ....*....|....*....|..
gi 1564868385  99 AVMNMNQFINILGEFHQKYPNV 120
Cdd:PRK11139  102 PSFAIQWLVPRLSSFNEAHPDI 123
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-286 1.82e-08

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 53.29  E-value: 1.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 103 MNQFI-NILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTlYQED-LKLVLNKEHHLANEAH 180
Cdd:cd08421    11 IVEFLpEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRP-YRTDrLVVVVPRDHPLAGRAS 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 181 VDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLDSSFSNKT--LE 258
Cdd:cd08421    90 VAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPESAARRYARALGLRVvpLD 169

                         170       180
                  ....*....|....*....|....*...
gi 1564868385 259 DPGMRWELGVIWKKDKYLSHATKQWIDF 286
Cdd:cd08421   170 DAWARRRLLLCVRSFDALPPAARALVDH 197
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 109-287 1.98e-08

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 52.99  E-value: 1.98e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSLVEN-GGKMIEtQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHhlanEAHVDMSMLK 187
Cdd:cd08442    18 LLAAYHARYPKVDLSLSTGtTGALIQ-AVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGH----PPVSRAEDLA 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 188 DEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLDSSFSNKTLEDPG-MRWEL 266
Cdd:cd08442    93 GSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSVSIHPLPEpFADVT 172

                         170       180
                  ....*....|....*....|..
gi 1564868385 267 GV-IWKKDkYLSHATKQWIDFM 287
Cdd:cd08442   173 TWlVWRKD-SFTAALQAFLDLL 193
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-177 2.55e-08

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 54.04  E-value: 2.55e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPK 80
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  81 EINSL-LGLETgHISIGLSAVMNMNQFI-NILGEFHQKYPNVTYSLVENGGKMIETQLINDE--IDIGIT-TLPVDQSiF 155
Cdd:PRK10094   82 ELQQVnDGVER-QVNIVINNLLYNPQAVaQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGfsLAIGVTgTEALANT-F 159

                         170       180
                  ....*....|....*....|..
gi 1564868385 156 HSVTLYQEDLKLVLNKEHHLAN 177
Cdd:PRK10094  160 SLDPLGSVQWRFVMAADHPLAN 181
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 92-290 5.78e-08

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: 51.97  E-value: 5.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGLS---AVMNMNQFINilgEFHQKYPNVTYSLVEngGKMIET--QLINDEIDIGITTLPVDQSI--FHSVTLYQED 164
Cdd:cd08418     1 KVSIGVSsliAHTLMPAVIN---RFKEQFPDVQISIYE--GQLSSLlpELRDGRLDFAIGTLPDEMYLkeLISEPLFESD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 165 LKLVLNKEHHLANEAhvDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENI 244
Cdd:cd08418    76 FVVVARKDHPLQGAR--SLEELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDM 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1564868385 245 VHLLDSSFSNKTL--EDPGMRWELGVIWKKDKYLSHATKQWIDFMKER 290
Cdd:cd08418   154 GRGPLDSFRLITIpvEEPLPSADYYLIYRKKSRLTPLAEQLVELFRRY 201
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-192 1.31e-07

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 51.92  E-value: 1.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   4 KHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGsifykkckeiLTLYNDVPKein 83
Cdd:PRK11013    7 RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQG----------LRLFEEVQR--- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  84 SLLGLE-------------TGHISIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPV 150
Cdd:PRK11013   74 SYYGLDrivsaaeslrefrQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLH 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1564868385 151 DQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFI 192
Cdd:PRK11013  154 TPAGTERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFI 195
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-216 2.40e-07

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 51.05  E-value: 2.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385   1 MDIKHMKYFVEVVDQK-GMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLV-LTDAGsifykkcKEILTLYNDV 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAG-------EEIIRIAREI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  79 PKEINSLLGL-------ETGHISIGLSAVMNMNQFINILGEFHQKYPNVtySL-VENGGKM-IETQLINDEIDIGITTLP 149
Cdd:PRK12681   74 LSKVESIKSVagehtwpDKGSLYIATTHTQARYALPPVIKGFIERYPRV--SLhMHQGSPTqIAEAAAKGNADFAIATEA 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 150 vdQSIFHSVTL---YQEDLKLVLNKEHHLANEAHVDMSMLKDEDFILFNEDFYLNDKIIEAAKNAGFIPN 216
Cdd:PRK12681  152 --LHLYDDLIMlpcYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPR 219
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 97-287 2.62e-07

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: 49.81  E-value: 2.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  97 LSAVMNMNQFI-NILGEFHQKYPNVTYSL-VENGGKMIEtQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHH 174
Cdd:cd08419     4 LAVVSTAKYFApRLLGAFCRRHPGVEVSLrVGNREQVLE-RLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDHP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 175 LANEAHVDMSMLKDEDFIL---------FNEDFYlndkiieaaKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIV 245
Cdd:cd08419    83 LAGQKRIPLERLAREPFLLrepgsgtrlAMERFF---------AEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTL 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1564868385 246 HLLDSSFSNKTLEDPGM----RWElgVIWKKDKYLSHATKQWIDFM 287
Cdd:cd08419   154 ALELATGRLAVLDVEGFpirrQWY--VVHRKGKRLSPAAQAFLDFL 197
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 113-240 4.99e-07

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 49.34  E-value: 4.99e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 113 FHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFI 192
Cdd:cd08456    22 FLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPGHRLAVKKVLTPSDLEGEPFI 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1564868385 193 LFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSIL 240
Cdd:cd08456   102 SLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVV 149
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 113-285 1.17e-06

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: 47.94  E-value: 1.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 113 FHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDFI 192
Cdd:cd08415    22 FRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHPLARKDVVTPADLAGEPLI 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 193 LFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSIlpenIVHLLDSSFSNKTLE----DPGMRWELGV 268
Cdd:cd08415   102 SLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAI----VDPLTAAGYAGAGLVvrpfRPAIPFEFAL 177

                         170
                  ....*....|....*..
gi 1564868385 269 IWKKDKYLSHATKQWID 285
Cdd:cd08415   178 VRPAGRPLSRLAQAFID 194
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-247 1.34e-06

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


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 48.05  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSLvENGGKMIETQLIND-EIDIGITTL-PVDQSIfHSVTLYQEDLKLVLNKEHHLANEAHVDMSML 186
Cdd:cd08446    19 LLRAFLTARPDVTVSL-HNMTKDEQIEALRAgRIHIGFGRFyPVEPDI-AVENVAQERLYLAVPKSHPLAARPAVSLADL 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1564868385 187 KDEDFILF-NEDF-YLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHL 247
Cdd:cd08446    97 RNEPLILFpRGGRpSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPESVAAL 159
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 109-185 2.94e-06

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: 46.82  E-value: 2.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEA--------- 179
Cdd:cd08417    18 LLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGPltledylaa 97


                  ....*..
gi 1564868385 180 -HVDMSM 185
Cdd:cd08417    98 pHVLVSP 104
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 32-73 3.79e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 47.24  E-value: 3.79e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1564868385  32 ISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILT 73
Cdd:PRK11074   33 VSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIK 74
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 94-248 6.70e-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: 45.83  E-value: 6.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  94 SIGLSAVMNMNQFINILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEH 173
Cdd:cd08450     3 TIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADH 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1564868385 174 HLANEAHVDMSMLKDEDFILFNEDF-YLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLL 248
Cdd:cd08450    83 RLAGREKIPPQDLAGENFISPAPTApVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLL 158
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-149 6.77e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 46.35  E-value: 6.77e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  31 TISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPKEINSLLGLETGHISIGLSAVMNMNQFINIL 110
Cdd:PRK11716    7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSHLPPIL 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1564868385 111 GEFHQKYPNVTYSLvENG--GKMIEtQLINDEIDIGITTLP 149
Cdd:PRK11716   87 DRFRAEHPLVEIKL-TTGdaADAVE-KVQSGEADLAIAAKP 125
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-285 1.71e-05

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: 44.57  E-value: 1.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  92 HISIGlsAVMNMNQFI--NILGEFHQKYPNVTYSLVENGGKMIETQLINDEID--IGITTLPVDQSIFHSVTLYQEDLKL 167
Cdd:cd08435     1 TVRVG--AVPAAAPVLlpPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDlaIGRLADDEQPPDLASEELADEPLVV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 168 VLNKEHHLANEAHVDMSMLKDEDFILfnedfylndkiieaaknagfiPNTISKISQWnfIENLLNAHlGVSiLPENIVH- 246
Cdd:cd08435    79 VARPGHPLARRARLTLADLADYPWVL---------------------PPPGTPLRQR--LEQLFAAA-GLP-LPRNVVEt 133

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1564868385 247 --------LLDSS-----FSNKTLED--------------PGMRWELGVIWKKDKYLSHATKQWID 285
Cdd:cd08435   134 asisallaLLARSdmlavLPRSVAEDelragvlrelplplPTSRRPIGITTRRGGPLSPAARALLD 199
nhaR PRK11062
transcriptional activator NhaR; Provisional
 5-66 2.22e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 45.00  E-value: 2.22e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1564868385   5 HMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYK 66
Cdd:PRK11062    8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFR 69
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 112-216 4.11e-05

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 43.38  E-value: 4.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 112 EFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSI-FHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKDED 190
Cdd:cd08413    21 AFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPdLVTLPCYRWNHCVIVPPGHPLADLGPLTLEDLAQYP 100

                          90       100
                  ....*....|....*....|....*.
gi 1564868385 191 FILFNEDFYLNDKIIEAAKNAGFIPN 216
Cdd:cd08413   101 LITYDFGFTGRSSIDRAFARAGLEPN 126
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-82 9.42e-05

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 43.12  E-value: 9.42e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1564868385   4 KHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEILTLYNDVPKEI 82
Cdd:PRK15243    7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQEI 85
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 113-242 3.39e-04

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


Pssm-ID: 176135  Cd Length: 198  Bit Score: 40.95  E-value: 3.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 113 FHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSI-FHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKDEDF 191
Cdd:cd08444    22 FKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPeLVSFPYYDWHHHIIVPVGHPLESITPLTIETIAKWPI 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1564868385 192 ILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPE 242
Cdd:cd08444   102 ITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMGIGIVAE 152
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 112-261 4.08e-04

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


Pssm-ID: 176136  Cd Length: 203  Bit Score: 40.67  E-value: 4.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 112 EFHQKYPNVTYSLVEnggkMIETQLIN----DEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAH-VDMSML 186
Cdd:cd08445    22 RFRQAAPDVEIELIE----MTTVQQIEalkeGRIDVGFGRLRIEDPAIRRIVLREEPLVVALPAGHPLAQEKApLTLAQL 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1564868385 187 KDEDFILFNEDFYLN--DKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPENIVHLLDSSFSNKTLEDPG 261
Cdd:cd08445    98 ADEPLILYPASPRPSfaDQVLSLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPASVQRLRRDDVVYRPLLDPD 174
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-287 8.01e-04

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 39.60  E-value: 8.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSL-VENGGKMIEtQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLK 187
Cdd:cd08426    18 LIARFRQRYPGVFFTVdVASTADVLE-AVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSVTLAQLA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 188 DEDFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSILPE-NIVHLLDSS-FSNKTLEDPGMRW- 264
Cdd:cd08426    97 GYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTElAVRREIRRGqLVAVPLADPHMNHr 176

                         170       180
                  ....*....|....*....|...
gi 1564868385 265 ELGVIWKKDKYLSHATKQWIDFM 287
Cdd:cd08426   177 QLELQTRAGRQLPAAASAFLQLL 199
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 109-192 1.15e-03

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: 39.09  E-value: 1.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSLVenGGKMIETQ--LINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSML 186
Cdd:cd08441    18 VLDQFRERWPDVELDLS--SGFHFDPLpaLLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPEDL 95


                  ....*.
gi 1564868385 187 KDEDFI 192
Cdd:cd08441    96 ADETLI 101
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
27-72 1.19e-03

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 39.65  E-value: 1.19e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1564868385  27 IAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCKEIL 72
Cdd:PRK10082   37 VSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLL 82
leuO PRK09508
leucine transcriptional activator; Reviewed
 109-199 3.39e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 38.47  E-value: 3.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 109 ILGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEH----------HLANE 178
Cdd:PRK09508  130 IYNRIEQIAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFTSVPLFKDELVLVASKNHprikgpiteeQLYNE 209

                          90       100
                  ....*....|....*....|.
gi 1564868385 179 AHVDMSMlkdEDFILFNEDFY 199
Cdd:PRK09508  210 QHAVVSL---DRFASFSQPWY 227
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
21-118 3.51e-03

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 38.44  E-value: 3.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385  21 ASKHLFIAQPTISKAIKDLEQELDMTLFDRSKRQLVLTDAGSIFYKKCK--------EILTLYNdvpKEINSLLGLETgH 92
Cdd:PRK10086   34 AADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKssldtlnqEILDIKN---QELSGTLTVYS-R 109

                          90       100
                  ....*....|....*....|....*.
gi 1564868385  93 ISIGLSAVMNMnqfiniLGEFHQKYP 118
Cdd:PRK10086  110 PSIAQCWLVPR------LADFTRRYP 129
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-78 5.75e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 37.64  E-value: 5.75e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1564868385   2 DIKHMKYFVEVVDQKGMTNASKHLFIAQPTISKAIKDLEQELDMTLFDRSkRQLVLTDAGSIFYKKCKEILTLYNDV 78
Cdd:PRK13348    3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADL 78
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 110-240 7.40e-03

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: 36.70  E-value: 7.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1564868385 110 LGEFHQKYPNVTYSLVENGGKMIETQLINDEIDIGITTLPVDQSIFHSVTLYQEDLKLVLNKEHHLANEAHVDMSMLKDE 189
Cdd:cd08457    19 LAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHPLAQLDVVSPQDLAGE 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1564868385 190 DFILFNEDFYLNDKIIEAAKNAGFIPNTISKISQWNFIENLLNAHLGVSIL 240
Cdd:cd08457    99 RIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAII 149
 
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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