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Conserved domains on  [gi|1167872373|ref|WP_080170093|]
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MULTISPECIES: LysR family transcriptional regulator [Salmonella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 8.61e-58

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 186.23  E-value: 8.61e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQ-DAEPGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQL 159
Cdd:COG0583    81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 160 GEQSLALVASPllqdadftqpdqhipcsfiinepqcvfrqlfESTLRQRRITLEntielwSIESIKQCVAANLGISFLPR 239
Cdd:COG0583   161 GEERLVLVASP-------------------------------DHPLARRAPLVN------SLEALLAAVAAGLGIALLPR 203

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1167872373 240 FTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCMEACFT 291
Cdd:COG0583   204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 8.61e-58

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 186.23  E-value: 8.61e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQ-DAEPGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQL 159
Cdd:COG0583    81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 160 GEQSLALVASPllqdadftqpdqhipcsfiinepqcvfrqlfESTLRQRRITLEntielwSIESIKQCVAANLGISFLPR 239
Cdd:COG0583   161 GEERLVLVASP-------------------------------DHPLARRAPLVN------SLEALLAAVAAGLGIALLPR 203

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1167872373 240 FTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCMEACFT 291
Cdd:COG0583   204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-286 3.55e-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: 141.66  E-value: 3.55e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  90 GELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVAS 169
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 170 P--LLQDADFTQPDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVERELS 247
Cdd:pfam03466  82 PdhPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1167872373 248 TGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCM 286
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-284 1.76e-38

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 137.36  E-value: 1.76e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQD-AEPGGELRVAT----GETLLaykmPQVLQRFKLRAPNVKLSL-QSLNCYVIrDALLNDEVDLGVFYRVGNDDAL 154
Cdd:NF040786   81 EFDRYgKESKGVLRIGAstipGQYLL----PELLKKFKEKYPNVRFKLmISDSIKVI-ELLLEGEVDIGFTGTKLEKKRL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 155 TMQQLGEQSLALVASPLLqdADFTQPDQHIPCSFIINEPqcvF---------RQLFESTLRQRRITLE--NTI-ELWSIE 222
Cdd:NF040786  156 VYTPFYKDRLVLITPNGT--EKYRMLKEEISISELQKEP---FimreegsgtRKEAEKALKSLGISLEdlNVVaSLGSTE 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1167872373 223 SIKQCVAANLGISFLPRFTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQ 284
Cdd:NF040786  231 AIKQSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQ 292
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-286 3.38e-38

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: 133.49  E-value: 3.38e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVASP 170
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 171 --LLQDADFTQPDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVErELST 248
Cdd:cd05466    81 dhPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELAD 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1167872373 249 GQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCM 286
Cdd:cd05466   160 GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-288 8.83e-25

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 100.92  E-value: 8.83e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   3 LRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIREAA 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  83 RQDaepGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQ 162
Cdd:PRK10837   85 RED---NGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLED 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 163 SLALVASP---LLQdADFTQpDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPR 239
Cdd:PRK10837  162 ELVVFAAPdspLAR-GPVTL-EQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLGISCLSR 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1167872373 240 FTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQ-CMEA 288
Cdd:PRK10837  240 RVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSyCQEA 289
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-292 2.75e-20

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 88.64  E-value: 2.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKlmphiheltrVMESIRE 80
Cdd:NF041036    1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEM----------VLEKARR 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQDAEPGGELRVATGETLL----------AYkMPQVLQRFKLRAPNV-------KLSLQSLncyvirDALLNDEVDLG 143
Cdd:NF041036   71 ILDIEDSLMDELKSFKGRQRLsicctptfgmAH-LPGVLNRFMLRNADVvdlkflfHSPAQAL------EGIQNKEFDLA 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 144 VFYRVGNDDALTMQQ--LGEQSLALVASPLLqdaDFTQPDQHI----PCSFIINEPQCVFRQLFESTLRQRRITLEN--- 214
Cdd:NF041036  144 IIEHCADLDLGRFHTypLPQDELVFVSAPSL---GLPTPNVTLerllELCLITRRDGCSSRDLLRRNLAEQGRDLDDfrr 220

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1167872373 215 TIELWSIESIKQCVAANLGISFLPRFTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCMEACFTV 292
Cdd:NF041036  221 VVVSDDLRLTIQTVLDGGGISFVSRSLVCEYLKNGQLREHYVEGFPHVRCRTVVARKCRENDPLLSAFMACLFKVFDD 298
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 1-95 8.97e-07

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 49.53  E-value: 8.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLErefslqlfEKIGRRMCL-------TTEGKKLMPHIhELTR 73
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALE--------ERLGQPLLVrtqpcraTEAGQRLLRHA-RQVR 71

                          90       100
                  ....*....|....*....|..
gi 1167872373  74 VMESIREAARQDAEPGGELRVA 95
Cdd:TIGR03298  72 LLEAELLAELPGLAPGAPTRLT 93
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 8.61e-58

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 186.23  E-value: 8.61e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQ-DAEPGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQL 159
Cdd:COG0583    81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 160 GEQSLALVASPllqdadftqpdqhipcsfiinepqcvfrqlfESTLRQRRITLEntielwSIESIKQCVAANLGISFLPR 239
Cdd:COG0583   161 GEERLVLVASP-------------------------------DHPLARRAPLVN------SLEALLAAVAAGLGIALLPR 203

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1167872373 240 FTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCMEACFT 291
Cdd:COG0583   204 FLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-286 3.55e-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: 141.66  E-value: 3.55e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  90 GELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVAS 169
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 170 P--LLQDADFTQPDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVERELS 247
Cdd:pfam03466  82 PdhPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1167872373 248 TGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCM 286
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-284 1.76e-38

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 137.36  E-value: 1.76e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQD-AEPGGELRVAT----GETLLaykmPQVLQRFKLRAPNVKLSL-QSLNCYVIrDALLNDEVDLGVFYRVGNDDAL 154
Cdd:NF040786   81 EFDRYgKESKGVLRIGAstipGQYLL----PELLKKFKEKYPNVRFKLmISDSIKVI-ELLLEGEVDIGFTGTKLEKKRL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 155 TMQQLGEQSLALVASPLLqdADFTQPDQHIPCSFIINEPqcvF---------RQLFESTLRQRRITLE--NTI-ELWSIE 222
Cdd:NF040786  156 VYTPFYKDRLVLITPNGT--EKYRMLKEEISISELQKEP---FimreegsgtRKEAEKALKSLGISLEdlNVVaSLGSTE 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1167872373 223 SIKQCVAANLGISFLPRFTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQ 284
Cdd:NF040786  231 AIKQSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQ 292
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-286 3.38e-38

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: 133.49  E-value: 3.38e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVASP 170
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 171 --LLQDADFTQPDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVErELST 248
Cdd:cd05466    81 dhPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVE-ELAD 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1167872373 249 GQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCM 286
Cdd:cd05466   160 GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 91-284 2.55e-29

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: 110.66  E-value: 2.55e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVfyrVG---NDDALTMQQLGEQSLALV 167
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL---VEgpvDHPDLIVEPFAEDELVLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 168 AS---PLLQDADFTQPD-QHIPcsFIINEPQCVFRQLFESTLRQRRITLEN---TIELWSIESIKQCVAANLGISFLPRF 240
Cdd:cd08420    78 VPpdhPLAGRKEVTAEElAAEP--WILREPGSGTREVFERALAEAGLDGLDlniVMELGSTEAIKEAVEAGLGISILSRL 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1167872373 241 TVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQ 284
Cdd:cd08420   156 AVRKELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLE 199
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-288 8.83e-25

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 100.92  E-value: 8.83e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   3 LRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIREAA 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  83 RQDaepGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQ 162
Cdd:PRK10837   85 RED---NGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLED 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 163 SLALVASP---LLQdADFTQpDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPR 239
Cdd:PRK10837  162 ELVVFAAPdspLAR-GPVTL-EQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLGISCLSR 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1167872373 240 FTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQ-CMEA 288
Cdd:PRK10837  240 RVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSyCQEA 289
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 91-284 8.93e-25

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: 98.35  E-value: 8.93e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVA---TGEtllaYKMPQVLQRFKLRAPNVKLSLQSLNcyviRDALL----NDEVDLGVFYRVGNDDALTMQQLGEQS 163
Cdd:cd08419     1 RLRLAvvsTAK----YFAPRLLGAFCRRHPGVEVSLRVGN----REQVLerlaDNEDDLAIMGRPPEDLDLVAEPFLDNP 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 164 LALVAS---PLLQDADFTQPD-QHIPcsFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPR 239
Cdd:cd08419    73 LVVIAPpdhPLAGQKRIPLERlAREP--FLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSL 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1167872373 240 FTVERELSTGQLKELPF-GAPSLSIMALcAHHAGKAVSPAMQIFMQ 284
Cdd:cd08419   151 HTLALELATGRLAVLDVeGFPIRRQWYV-VHRKGKRLSPAAQAFLD 195
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-251 1.07e-22

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 95.47  E-value: 1.07e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   3 LRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMEsirEAA 82
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCE---ETC 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  83 R-----QDAEpGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVfyrVGND------ 151
Cdd:CHL00180   84 RaledlKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI---VGGEvptelk 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 152 DALTMQQLGEQSLALVASPL--------LQDADFTQPDqhipcsFIINEPQCVFRQLFESTLRQRRI---TLENTIELWS 220
Cdd:CHL00180  160 KILEITPYVEDELALIIPKShpfaklkkIQKEDLYRLN------FITLDSNSTIRKVIDNILIQNGIdskRFKIEMELNS 233

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1167872373 221 IESIKQCVAANLGISFLPRFTVERELSTGQL 251
Cdd:CHL00180  234 IEAIKNAVQSGLGAAFVSVSAIEKELELGLL 264
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-292 2.75e-20

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 88.64  E-value: 2.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKlmphiheltrVMESIRE 80
Cdd:NF041036    1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEM----------VLEKARR 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQDAEPGGELRVATGETLL----------AYkMPQVLQRFKLRAPNV-------KLSLQSLncyvirDALLNDEVDLG 143
Cdd:NF041036   71 ILDIEDSLMDELKSFKGRQRLsicctptfgmAH-LPGVLNRFMLRNADVvdlkflfHSPAQAL------EGIQNKEFDLA 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 144 VFYRVGNDDALTMQQ--LGEQSLALVASPLLqdaDFTQPDQHI----PCSFIINEPQCVFRQLFESTLRQRRITLEN--- 214
Cdd:NF041036  144 IIEHCADLDLGRFHTypLPQDELVFVSAPSL---GLPTPNVTLerllELCLITRRDGCSSRDLLRRNLAEQGRDLDDfrr 220

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1167872373 215 TIELWSIESIKQCVAANLGISFLPRFTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCMEACFTV 292
Cdd:NF041036  221 VVVSDDLRLTIQTVLDGGGISFVSRSLVCEYLKNGQLREHYVEGFPHVRCRTVVARKCRENDPLLSAFMACLFKVFDD 298
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-172 1.24e-17

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 81.04  E-value: 1.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  17 SFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHE-LTRVMESIREAARQDAEpgGELRVA 95
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREiFDQLAEATRKLRARSAK--GALTVS 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1167872373  96 TGETLLA-YKMPQvLQRFKLRAPNVKLSLQSLNcyviRDA-LLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVASPLL 172
Cdd:PRK11139  100 LLPSFAIqWLVPR-LSSFNEAHPDIDVRLKAVD----RLEdFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPVCSPAL 173
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-144 1.88e-17

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 80.79  E-value: 1.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFL-RASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTE-GKKLMPHIHELTRVMESI 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNFNLtEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEpGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  79 R----EAARQDAepgGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV 144
Cdd:PRK12684   81 KrvgkEFAAQDQ---GNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 21-144 1.80e-16

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 78.16  E-value: 1.80e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  21 ASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMC-LTTEGKKLMPHIHELTRVMESIREAARQDAE-PGGELRVATGE 98
Cdd:PRK12683   22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADrDSGHLTVATTH 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1167872373  99 TLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV 144
Cdd:PRK12683  102 TQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGI 147
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-284 4.05e-16

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 75.04  E-value: 4.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV-FYRVGNDD----ALTMQQLG----- 160
Cdd:cd08426     1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLaFSPPPEPGirvhSRQPAPIGavvpp 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 161 EQSLALVASPLLqdadftqpDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRF 240
Cdd:cd08426    81 GHPLARQPSVTL--------AQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTEL 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1167872373 241 TVERELSTGQLKELPFGAPSLSIMA--LCAhHAGKAVSPAMQIFMQ 284
Cdd:cd08426   153 AVRREIRRGQLVAVPLADPHMNHRQleLQT-RAGRQLPAAASAFLQ 197
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-224 4.37e-16

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 76.92  E-value: 4.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPH----IHELT---R 73
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYarraLQDLEagrR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  74 VMESIREAARqdaepgGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV-FYRVGNDD 152
Cdd:PRK11242   81 AIHDVADLSR------GSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIaFAPVHSPE 154

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1167872373 153 aLTMQQLGEQSLALVAS---PLLQDADFTQPDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESI 224
Cdd:PRK11242  155 -IEAQPLFTETLALVVGrhhPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAV 228
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 4.22e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 68.18  E-value: 4.22e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   3 LRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 21-234 1.67e-14

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 72.33  E-value: 1.67e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  21 ASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMC-LTTEGKKLMPHIHELTRVMESIREAARQDAEP-GGELRVATGE 98
Cdd:PRK12682   22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNIKRIGDDFSNQdSGTLTIATTH 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  99 TLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLG-VFYRVGNDDALTMQQLGEQSLALV---ASPLLQD 174
Cdd:PRK12682  102 TQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGiATESLADDPDLATLPCYDWQHAVIvppDHPLAQE 181

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1167872373 175 ADFTQPDqhipcsfIINEPQCVFRQLFESTLRQRRI----TLENTIELWSIES--IKQCVAANLGI 234
Cdd:PRK12682  182 ERITLED-------LAEYPLITYHPGFTGRSRIDRAfaaaGLQPDIVLEAIDSdvIKTYVRLGLGV 240
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-285 3.20e-14

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: 69.86  E-value: 3.20e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  92 LRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVASPl 171
Cdd:cd08440     2 VRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 172 lqDADFTQPDQ-------HIPcsFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVER 244
Cdd:cd08440    81 --DHPLARRRSvtwaelaGYP--LIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPL 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1167872373 245 eLSTGQLKELPFGAPSLS--IMALcaHHAGKAVSPAMQIFMQC 285
Cdd:cd08440   157 -ADHPGLVARPLTEPVVTrtVGLI--RRRGRSLSPAAQAFLDL 196
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 92-284 7.84e-14

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: 68.79  E-value: 7.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  92 LRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDlGVF-YRVGNDDALTMQQLGEQSLALVAS- 169
Cdd:cd08442     2 LRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLD-GAFvAGPVEHPRLEQEPVFQEELVLVSPk 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 170 ---PLLQDADFTQPdqhipcSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVEREL 246
Cdd:cd08442    81 ghpPVSRAEDLAGS------TLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQ 154

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1167872373 247 STGQLKELPFGAPSLSIMALCAHHAGkAVSPAMQIFMQ 284
Cdd:cd08442   155 GRGSVSIHPLPEPFADVTTWLVWRKD-SFTAALQAFLD 191
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-172 1.30e-13

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 69.63  E-value: 1.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 A-ARQDAEPGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNcyvIRDALLNDEVDLGVFYRVG--NDDALTMQ 157
Cdd:PRK14997   82 AiAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATN---RRVDVVGEGVDVAIRVRPRpfEDSDLVMR 158

                         170
                  ....*....|....*
gi 1167872373 158 QLGEQSLALVASPLL 172
Cdd:PRK14997  159 VLADRGHRLFASPDL 173
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-285 1.80e-13

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: 67.68  E-value: 1.80e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  92 LRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDL--GVFYRVGNDDALTMQQLGEQSLALVAS 169
Cdd:cd08435     2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLaiGRLADDEQPPDLASEELADEPLVVVAR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 170 ---PLLQDADFTQPDQhIPCSFIINEPQCVFRQLFESTLRQRRITL-ENTIELWSIESIKQCVAANLGISFLPRFTVERE 245
Cdd:cd08435    82 pghPLARRARLTLADL-ADYPWVLPPPGTPLRQRLEQLFAAAGLPLpRNVVETASISALLALLARSDMLAVLPRSVAEDE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1167872373 246 LSTGQLKELPFGAPSL--SIMALCahHAGKAVSPAMQIFMQC 285
Cdd:cd08435   161 LRAGVLRELPLPLPTSrrPIGITT--RRGGPLSPAARALLDA 200
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 90-283 1.82e-13

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 67.47  E-value: 1.82e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  90 GELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVirDaLLNDEVDLGVfyRVGN--DDALTMQQLGEQSLALV 167
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLV--D-LVEEGFDLAI--RIGElpDSSLVARRLGPVRRVLV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 168 ASP--LLQDADFTQPD---QHiPCsFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTV 242
Cdd:cd08422    76 ASPayLARHGTPQTPEdlaRH-RC-LGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLV 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1167872373 243 ERELSTGQLKE-LP-FGAPSLSIMALCAHHagKAVSPAMQIFM 283
Cdd:cd08422   154 AEDLASGRLVRvLPdWRPPPLPIYAVYPSR--RHLPAKVRAFI 194
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
3-284 7.79e-13

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 67.52  E-value: 7.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   3 LRRFITlktVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIREAA 82
Cdd:PRK10094    7 LRTFIA---VAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSEL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  83 RQdAEPGGELRVATGETLLAYKmPQVLQR----FKLRAPNVKLSLqSLNCYV-IRDALLNDEVDL--GVfyrVGND---D 152
Cdd:PRK10094   84 QQ-VNDGVERQVNIVINNLLYN-PQAVAQllawLNERYPFTQFHI-SRQIYMgVWDSLLYEGFSLaiGV---TGTEalaN 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 153 ALTMQQLGEQSLALVASPLLQDADFTQPdqhipcsfiinepqcvfrqLFESTLRQ----------RRITL--------EN 214
Cdd:PRK10094  158 TFSLDPLGSVQWRFVMAADHPLANVEEP-------------------LTEAQLRRfpavniedsaRTLTKrvawrlpgQK 218

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1167872373 215 TIELWSIESIKQCVAANLGISFLPRFTVERELSTGQL--KELPFG-APSLSIMALCAHHAGKAVSPAMQIFMQ 284
Cdd:PRK10094  219 EIIVPDMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLvsRVIPTMrPPSPLSLAWRKFGSGKAVEDIVTLFTQ 291
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 91-286 1.18e-11

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: 62.58  E-value: 1.18e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEqSLALVASP 170
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLAS-GRAVCVLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 171 L---LQDADFTQPDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVeRELS 247
Cdd:cd08415    80 PghpLARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTA-AGYA 158

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1167872373 248 TGQLKELPFgAPSLSIMALCAHHAGKAVSPAMQIFMQCM 286
Cdd:cd08415   159 GAGLVVRPF-RPAIPFEFALVRPAGRPLSRLAQAFIDLL 196
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-238 1.84e-11

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 63.25  E-value: 1.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQDAEPGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGvFYR--VGNDdaltmqq 158
Cdd:PRK09906   81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVG-FMRhpVYSD------- 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 159 lGEQSLALVASPLLqdadFTQPDQH-------IPCS------FIINEPQ--CVFRQLFESTLRQRRITLeNTIELW-SIE 222
Cdd:PRK09906  153 -EIDYLELLDEPLV----VVLPVDHplahekeITAAqldgvnFISTDPAysGSLAPIIKAWFAQHNSQP-NIVQVAtNIL 226

                         250
                  ....*....|....*.
gi 1167872373 223 SIKQCVAANLGISFLP 238
Cdd:PRK09906  227 VTMNLVGMGLGCTIIP 242
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
17-170 2.70e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 63.10  E-value: 2.70e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  17 SFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMphiHELTRVMESIREA--ARQDAEPGGELRV 94
Cdd:PRK10086   30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF---WALKSSLDTLNQEilDIKNQELSGTLTV 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  95 atgetllaYKMPQVLQ--------RFKLRAPNVKLSLQSLNCYVirdALLNDEVDLGVFYRVGNDDALTMQQLGEQSLAL 166
Cdd:PRK10086  107 --------YSRPSIAQcwlvprlaDFTRRYPSISLTILTGNENV---NFQRAGIDLAIYFDDAPSAQLTHHFLMDEEILP 175


                  ....
gi 1167872373 167 VASP 170
Cdd:PRK10086  176 VCSP 179
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 106-280 2.80e-11

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: 61.46  E-value: 2.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 106 PQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVASPllqdADFTQPDQHIP 185
Cdd:cd08433    16 VPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA----DAPLPRGAPVP 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 186 CSFIINEPQCV------FRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVERELSTGQLKELPFGAP 259
Cdd:cd08433    92 LAELARLPLILpsrghgLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAAGRLVAAPIVDP 171

                         170       180
                  ....*....|....*....|.
gi 1167872373 260 SLSIMALCAHHAGKAVSPAMQ 280
Cdd:cd08433   172 ALTRTLSLATPRDRPLSPAAL 192
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-286 1.31e-10

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: 59.44  E-value: 1.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALV--- 167
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVAlpa 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 168 ASPLLQD-----ADFTQpdqhipCSFII--NEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRF 240
Cdd:cd08414    81 DHPLAAResvslADLAD------EPFVLfpREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPAS 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1167872373 241 TveRELSTGQLKELPFGAPSLSIMALCAHHAGKAvSPAMQIFMQCM 286
Cdd:cd08414   155 V--ARLQRPGVVYRPLADPPPRSELALAWRRDNA-SPALRAFLELA 197
PRK09986 PRK09986
LysR family transcriptional regulator;
1-167 1.41e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 60.89  E-value: 1.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMphiHELTRVMESIRE 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILM---EESRRLLDNAEQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQDAEPG----GELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGvFYRVGNDD---A 153
Cdd:PRK09986   84 SLARVEQIGrgeaGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAG-IWRMADLEpnpG 162

                         170
                  ....*....|....
gi 1167872373 154 LTMQQLGEQSLALV 167
Cdd:PRK09986  163 FTSRRLHESAFAVA 176
cbl PRK12679
HTH-type transcriptional regulator Cbl;
25-154 1.23e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 58.28  E-value: 1.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  25 LCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHE--LTRVMESIREAARQDAEPGGELRVATGETLLA 102
Cdd:PRK12679   26 LFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVIAEriLNEASNVRRLADLFTNDTSGVLTIATTHTQAR 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1167872373 103 YKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFY-RVGNDDAL 154
Cdd:PRK12679  106 YSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASeRLSNDPQL 158
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-142 1.96e-09

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 57.60  E-value: 1.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  21 ASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMC-LTTEGKKLMPHIHELTRVMESIREAARQDAEPG-GELRVATGE 98
Cdd:PRK12681   22 TAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDkGSLYIATTH 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1167872373  99 TLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDL 142
Cdd:PRK12681  102 TQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADF 145
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 99-282 3.52e-09

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: 55.62  E-value: 3.52e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  99 TLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVAS---PL---- 171
Cdd:cd08434     9 SLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPkdhPLagrd 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 172 ---LQDAdftqpdqhIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVereLST 248
Cdd:cd08434    89 svdLAEL--------ADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEMTL---LNP 157

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1167872373 249 GQLKELPFGAP----SLSImalcAHHAGKAVSPAMQIF 282
Cdd:cd08434   158 PGVKKIPIKDPdaerTIGL----AWLKDRYLSPAARRF 191
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-285 3.85e-09

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 55.27  E-value: 3.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYR--VGNDDALTMQQLGEQSLALVA 168
Cdd:cd08427     1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEppFPLPKDLVWTPLVREPLVLIA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 169 SPLLQDADF-----TQPdqhipcsFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVE 243
Cdd:cd08427    81 PAELAGDDPrellaTQP-------FIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVP 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1167872373 244 RElSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQC 285
Cdd:cd08427   154 LP-AGPRVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEA 194
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 90-260 1.08e-08

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: 54.07  E-value: 1.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  90 GELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVAS 169
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 170 ---PLLQDADFTQPDQHIPCSFIINEPQCvFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVEREL 246
Cdd:cd08411    81 kdhPLAKRKSVTPEDLAGERLLLLEEGHC-LRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGITLLPELAVPSEE 159

                         170
                  ....*....|....*
gi 1167872373 247 STGQ-LKELPFGAPS 260
Cdd:cd08411   160 LRGDrLVVRPFAEPA 174
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 3-234 1.32e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 55.03  E-value: 1.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   3 LRRFITlktVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMEsirEAA 82
Cdd:PRK15092   16 LRTFVA---VADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFND---EAC 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  83 ----RQDAEpgGELRVA----TGETLLaykmPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVfyrvgnddaL 154
Cdd:PRK15092   90 sslmYSNLQ--GVLTIGasddTADTIL----PFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAV---------T 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 155 TMQQLGEQSLALVASPLLQ--DADFT-QPDQHIPCsFIINEPQcVFRQLFESTLRQRRITLENTIELWSIESIKQCVAAN 231
Cdd:PRK15092  155 THRPSSFPALNLRTSPTLWycAAEYVlQKGEPIPL-VLLDEPS-PFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAG 232


                  ...
gi 1167872373 232 LGI 234
Cdd:PRK15092  233 LGV 235
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 88-251 1.33e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 53.71  E-value: 1.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  88 PGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVirDaLLNDEVDLGVfyRV----GNDDALTMQQLGEQS 163
Cdd:cd08473     1 PRGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRV--D-LIEEGIDVAL--RVrfppLEDSSLVMRVLGQSR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 164 LALVASPLL--QDADFTQPDQ--HIP-CSFIINEPQCVFRqLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLP 238
Cdd:cd08473    76 QRLVASPALlaRLGRPRSPEDlaGLPtLSLGDVDGRHSWR-LEGPDGESITVRHRPRLVTDDLLTLRQAALAGVGIALLP 154

                         170
                  ....*....|...
gi 1167872373 239 RFTVERELSTGQL 251
Cdd:cd08473   155 DHLCREALRAGRL 167
PRK09791 PRK09791
LysR family transcriptional regulator;
3-202 3.99e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.61  E-value: 3.99e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   3 LRRFITlktVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPH----IHELTRVMESI 78
Cdd:PRK09791   10 IRAFVE---VARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHasliLEELRAAQEDI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  79 REaaRQdAEPGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV--FYRVGNDDALTM 156
Cdd:PRK09791   87 RQ--RQ-GQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIntYYQGPYDHEFTF 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1167872373 157 QQLGEQSLALVASPLLQDADFTQPDQHIPCSFIINEPQ-CVFRQLFE 202
Cdd:PRK09791  164 EKLLEKQFAVFCRPGHPAIGARSLKQLLDYSWTMPTPHgSYYKQLSE 210
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 105-286 8.60e-08

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: 51.40  E-value: 8.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 105 MPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALV---ASPLLQDADFTQPD 181
Cdd:cd08438    15 FAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVlprGHPLAGRKTVSLAD 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 182 qhipcsfIINEPQCVFRQlfESTL--------RQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVEReLSTGQLKE 253
Cdd:cd08438    95 -------LADEPFILFNE--DFALhdriidacQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQR-LDNAGVKV 164

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1167872373 254 LPFGAPSLSI-MALcAHHAGKAVSPAMQIFMQCM 286
Cdd:cd08438   165 IPLTDPDLRWqLAL-IWRKGRYLSHAARAWLALL 197
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 91-286 1.39e-07

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 51.01  E-value: 1.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGE-QSLALVAS 169
Cdd:cd08412     1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARlPPYVWLPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 170 --PLLQDADFTQPDqhipcsfIINEPQCVF-----RQLFESTLRQR----RITLENTielwSIESIKQCVAANLGISFLP 238
Cdd:cd08412    81 dhPLAGKDEVSLAD-------LAAEPLILLdlphsREYFLSLFAAAgltpRIAYRTS----SFEAVRSLVANGLGYSLLN 149

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1167872373 239 -RFTVERELSTGQLKELPFGAPSLSIMALCAHHAGKAVSPAMQIFMQCM 286
Cdd:cd08412   150 dRPYRPWSYDGKRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDFA 198
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 92-242 2.09e-07

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: 50.18  E-value: 2.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  92 LRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGeQSLALVASPL 171
Cdd:cd08457     2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETR-SLPAVVAVPM 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1167872373 172 ---LQDADFTQPDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTV 242
Cdd:cd08457    81 ghpLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATA 154
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
8-124 2.42e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 50.93  E-value: 2.42e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   8 TLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLErefslqlfEKIGR------RMCLTTE-GKKLMPHIHElTRVMEsiRE 80
Cdd:PRK03635    9 ALAAVVREGSFERAAQKLHITQSAVSQRIKALE--------ERVGQvllvrtQPCRPTEaGQRLLRHARQ-VRLLE--AE 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1167872373  81 AARQDAEPGGE---LRVATGETLLAYKMPQVLQRFkLRAPNVKLSLQ 124
Cdd:PRK03635   78 LLGELPALDGTpltLSIAVNADSLATWFLPALAPV-LARSGVLLDLV 123
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 90-224 5.59e-07

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: 49.25  E-value: 5.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  90 GELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV-FYRVGNDDaLTMQQLGEQSLALVA 168
Cdd:cd08425     1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIaFAPVRSPD-IDAQPLFDERLALVV 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1167872373 169 S---PLLQDADFTQPDQHIPCSFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESI 224
Cdd:cd08425    80 GathPLAQRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAV 138
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 1-95 8.97e-07

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 49.53  E-value: 8.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLErefslqlfEKIGRRMCL-------TTEGKKLMPHIhELTR 73
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALE--------ERLGQPLLVrtqpcraTEAGQRLLRHA-RQVR 71

                          90       100
                  ....*....|....*....|..
gi 1167872373  74 VMESIREAARQDAEPGGELRVA 95
Cdd:TIGR03298  72 LLEAELLAELPGLAPGAPTRLT 93
PRK12680 PRK12680
LysR family transcriptional regulator;
21-259 1.57e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 48.85  E-value: 1.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  21 ASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRM-CLTTEGKKLMPHIHELTRVMESIRE-AARQDAEPGGELRVATGE 98
Cdd:PRK12680   22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTyAANQRRESQGQLTLTTTH 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  99 TLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGND--DALTMQQLGEQSLALVASPLLQDAD 176
Cdd:PRK12680  102 TQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEpsAGIAVPLYRWRRLVVVPRGHALDTP 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 177 FTQPDQHIpcsfIINEPQCVfrqlFESTLR-----QR---RITLENTIELWSIES--IKQCVAANLGISFLPRFTVERel 246
Cdd:PRK12680  182 RRAPDMAA----LAEHPLIS----YESSTRpgsslQRafaQLGLEPSIALTALDAdlIKTYVRAGLGVGLLAEMAVNA-- 251

                         250
                  ....*....|...
gi 1167872373 247 STGQLKELPFGAP 259
Cdd:PRK12680  252 NDEDLRAWPAPAP 264
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 91-266 1.70e-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: 47.59  E-value: 1.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVAS- 169
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARk 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 170 --PLLQD----ADFTQPDqHIPCSFiINEPQCVFRQLFESTLRQRRITLentiELWSIESIKQCVAA-NLgISFLPRFTV 242
Cdd:cd08417    81 dhPLAGGpltlEDYLAAP-HVLVSP-RGRGHGLVDDALAELGLSRRVAL----TVPHFLAAPALVAGtDL-IATVPRRLA 153

                         170       180
                  ....*....|....*....|....*.
gi 1167872373 243 ERELSTGQLK--ELPFGAPSLSIMAL 266
Cdd:cd08417   154 EALAERLGLRvlPLPFELPPFTVSLY 179
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-211 2.61e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 47.89  E-value: 2.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  30 STVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIREAARQDAEP-GGELRVATGETlLAYK-MPQ 107
Cdd:PRK11716    6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSlSGELSLFCSVT-AAYShLPP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 108 VLQRFKLRAPNVKLSL------QSLncyvirDALLNDEVDLGVFYRVGN-DDALTMQQLGEQSLALVA----SPLLQDAD 176
Cdd:PRK11716   85 ILDRFRAEHPLVEIKLttgdaaDAV------EKVQSGEADLAIAAKPETlPASVAFSPIDEIPLVLIApalpCPVRQQLS 158

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1167872373 177 FTQPD-QHIPcsFIINEpQCVFRQLFESTLRQRRIT 211
Cdd:PRK11716  159 QEKPDwSRIP--FILPE-HGPARRRIDLWFRRHKIK 191
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-280 4.09e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 47.24  E-value: 4.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  11 TVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIREAARQDAEpG- 89
Cdd:PRK11074   12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVAN-Gw 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  90 -GELRVATGETLLAYKMPQVLQRFKLRAPNVKLslqslncyVIR--------DALLNDEVDLGV----FYRVGNDdaLTM 156
Cdd:PRK11074   91 rGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVEL--------IIRqevfngvwDALADGRVDIAIgatrAIPVGGR--FAF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 157 QQLGEQSLALVASPllqDADFTQPDQHIPCSFIINEPQCVfrqlFESTLR------------QRRITLENtielWsiESI 224
Cdd:PRK11074  161 RDMGMLSWACVVSS---DHPLASMDGPLSDDELRPYPSLC----LEDTSRtlpkritwlldnQRRLVVPD----W--ESA 227

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 225 KQCVAANLGISFLPRFTVERELSTGQLKEL----PFgAPSlsimALCAHHAGKAVSPAMQ 280
Cdd:PRK11074  228 INCLSAGLCVGMVPTHFAKPLINSGKLVELtlenPF-PDS----PCCLTWQQNDMSPALA 282
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 91-144 1.15e-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: 45.31  E-value: 1.15e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV 144
Cdd:cd08413     1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAI 54
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-243 2.01e-05

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 45.39  E-value: 2.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMphiHELTRVMESIRE 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILL---QLANQVLPQISQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQDAEP-GGELRVATG-ETLLAYKMPqVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQ 158
Cdd:PRK15421   79 ALQACNEPqQTRLRIAIEcHSCIQWLTP-ALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 159 LGEQSLALVASPLLQDADFTQ--PDQHIPCSFIINEPQC----VFRQLFE-STLRQRRITLENTIELWsiesikQCVAAN 231
Cdd:PRK15421  158 MFDYEVRLVLAPDHPLAAKTRitPEDLASETLLIYPVQRsrldVWRHFLQpAGVSPSLKSVDNTLLLI------QMVAAR 231

                         250
                  ....*....|..
gi 1167872373 232 LGISFLPRFTVE 243
Cdd:PRK15421  232 MGIAALPHWVVE 243
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 105-238 2.22e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 44.29  E-value: 2.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 105 MPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALV--ASPLLQDADFTQPDQ 182
Cdd:cd08450    15 LPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVlpADHRLAGREKIPPQD 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1167872373 183 HIPCSFIINEPQC-VFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLP 238
Cdd:cd08450    95 LAGENFISPAPTApVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLP 151
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 91-261 2.29e-05

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: 44.33  E-value: 2.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLA----- 165
Cdd:cd08456     1 ELRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVcvlpp 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 166 ---LVASPLLQDADFTQPDqhipcsFIINEPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTV 242
Cdd:cd08456    81 ghrLAVKKVLTPSDLEGEP------FISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTA 154

                         170
                  ....*....|....*....
gi 1167872373 243 ERELSTGqLKELPFgAPSL 261
Cdd:cd08456   155 LDYAAAG-LVVRRF-SPAV 171
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-238 3.33e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 44.67  E-value: 3.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 AARQdaePGGELR------VATGETLLAYKMPqVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDAL 154
Cdd:PRK11233   81 AVHN---VGQALSgqvsigLAPGTAASSLTMP-LLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 155 TMQQLGEQSLALVASpllQDAdftqPDQHIPCSFIIN------EPQCVFRQLFESTLRQRRITLENTIELWSIESIKQCV 228
Cdd:PRK11233  157 SSQPLLKEDLFLVGT---QDC----PGQSVDLAAVAQmnlflpRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAI 229

                         250
                  ....*....|
gi 1167872373 229 AANLGISFLP 238
Cdd:PRK11233  230 ASGMGVTVLP 239
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
8-77 4.16e-05

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 44.19  E-value: 4.16e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   8 TLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKiGRRMCLTTEGKKLMPHIHELtRVMES 77
Cdd:PRK13348    9 ALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV-ALLEA 76
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 91-239 5.30e-05

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: 43.32  E-value: 5.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVA-TGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLgVFYR--VGNDDALTMQQLGEQSLALV 167
Cdd:cd08451     1 RLRVGfTSSAAFHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDA-AFVRppVARSDGLVLELLLEEPMLVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 168 ---ASPLLQDADftqpdqhIPCSFIINEPQCVFRQ-----LFESTL---RQRRITLENTIELWSIESIKQCVAANLGISF 236
Cdd:cd08451    80 lpaGHPLARERS-------IPLAALADEPFILFPRpvgpgLYDAIIaacRRAGFTPRIGQEAPQMASAINLVAAGLGVSI 152


                  ...
gi 1167872373 237 LPR 239
Cdd:cd08451   153 VPA 155
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 91-284 6.45e-05

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: 43.03  E-value: 6.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGvFYRVG---NDDALTMQQLGEQSLALV 167
Cdd:cd08449     1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLG-FVRFAdtlNDPPLASELLWREPMVVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 168 AS---PL----------LQDADFT--QPDQHIPCSFIINepqCVFRQLFESTLRQRritlenTIELWSIESIkqcVAANL 232
Cdd:cd08449    80 LPeehPLagrksltladLRDEPFVflRLANSRFADFLIN---CCLQAGFTPQITQE------VVEPQTLMAL---VAAGF 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1167872373 233 GISFLPRFTveRELSTGQLKELPFgAPSLSiMALCAHHAGKAVSPAMQIFMQ 284
Cdd:cd08449   148 GVALVPESY--ARLPWPGVRFIPL-KQAIS-ADLYAVYHPDSATPVIQAFLA 195
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-259 7.71e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 43.48  E-value: 7.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   1 MDLRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVMESIRE 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  81 -AARQDAEPGGELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQS--------------LNCYV----------IRDAL 135
Cdd:PRK11151   81 mASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEaqthqllaqldsgkLDCAIlalvkeseafIEVPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 136 LNDEVDLGVF--YRVGNDDALTMQQL-GEQSLALVASPLLQDA--DF-----TQPDQHipcsfiinepqcvfrqlFESTl 205
Cdd:PRK11151  161 FDEPMLLAVYedHPWANRDRVPMSDLaGEKLLMLEDGHCLRDQamGFcfeagADEDTH-----------------FRAT- 222

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1167872373 206 rqrritlentielwSIESIKQCVAANLGISFLPRFTVERELSTGQLKELPFGAP 259
Cdd:PRK11151  223 --------------SLETLRNMVAAGSGITLLPALAVPNERKRDGVCYLPCIKP 262
PRK09801 PRK09801
LysR family transcriptional regulator;
9-170 1.67e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 42.71  E-value: 1.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   9 LKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHE-LTRVMESIREAARQDAE 87
Cdd:PRK09801   14 LVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEiLTQYQRLVDDVTQIKTR 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  88 PGGELRVAT----GETLLAYKMPQVLQRFklraPNVKLSLQSLNCYVirdALLNDEVDLGVfyRVGND--DALTMQQLGE 161
Cdd:PRK09801   94 PEGMIRIGCsfgfGRSHIAPAITELMRNY----PELQVHFELFDRQI---DLVQDNIDLDI--RINDEipDYYIAHLLTK 164


                  ....*....
gi 1167872373 162 QSLALVASP 170
Cdd:PRK09801  165 NKRILCAAP 173
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-67 2.00e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 42.31  E-value: 2.00e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1167872373   9 LKTVVEEGS---FLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPH 67
Cdd:PRK03601    6 LKTFLEVSRtrhFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPY 67
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 91-144 2.16e-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: 41.34  E-value: 2.16e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV 144
Cdd:cd08444     1 ELTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGI 54
PRK10341 PRK10341
transcriptional regulator TdcA;
12-123 3.45e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 41.39  E-value: 3.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  12 VVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHELTRVME-SIREAARQDAEpgG 90
Cdd:PRK10341   18 VIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKnMVNEINGMSSE--A 95

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1167872373  91 ELRVATG-ETLLAYK-MPQVLQRFKLRAPNVKLSL 123
Cdd:PRK10341   96 VVDVSFGfPSLIGFTfMSDMINKFKEVFPKAQVSM 130
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-144 8.87e-04

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 39.52  E-value: 8.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1167872373 105 MPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGV 144
Cdd:cd08464    15 APPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAI 54
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 105-282 1.14e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 39.20  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 105 MPQvLQRFKLRAPNVKLSLqslncyVIRD---ALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVASP-LLQDADFTQP 180
Cdd:cd08481    16 IPR-LPDFLARHPDITVNL------VTRDepfDFSQGSFDAAIHFGDPVWPGAESEYLMDEEVVPVCSPaLLAGRALAAP 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 181 DQ--HIPCSFIINEPQcVFRQLFESTLRQRRITLENT-IELWSIesIKQCVAANLGISFLPRFTVERELSTGQLKeLPFG 257
Cdd:cd08481    89 ADlaHLPLLQQTTRPE-AWRDWFEEVGLEVPTAYRGMrFEQFSM--LAQAAVAGLGVALLPRFLIEEELARGRLV-VPFN 164

                         170       180
                  ....*....|....*....|....*...
gi 1167872373 258 APSLSIMA---LCAHHagKAVSPAMQIF 282
Cdd:cd08481   165 LPLTSDKAyylVYPED--KAESPPVQAF 190
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 93-256 1.27e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 39.16  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  93 RVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVAS--- 169
Cdd:cd08466     3 NIAANETLDLLLLPRLLARLKQLAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARkdh 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 170 PLLQDadftqpdqhiPCSF--IINEPQCVFR---------QLF-ESTLRQRRITLENTielwSIESIKQCVAANLGISFL 237
Cdd:cd08466    83 PRIQG----------SLSLeqYLAEKHVVLSlrrgnlsalDLLtEEVLPQRNIAYEVS----SLLSMLAVVSQTDLIAIA 148

                         170       180
                  ....*....|....*....|.
gi 1167872373 238 PRFTVERELSTGQLK--ELPF 256
Cdd:cd08466   149 PRWLADQYAEQLNLQilPLPF 169
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-143 1.74e-03

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 38.79  E-value: 1.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1167872373  91 ELRVATGETLLAYKMPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLG 143
Cdd:cd08448     1 RLRIGFVGSMLYRGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLG 53
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
3-100 2.12e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 38.97  E-value: 2.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373   3 LRRFITLKTVVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKlmpHIHELTRVMESIREAA 82
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRI---YYQGCRRMLHEVQDVH 80

                          90       100
                  ....*....|....*....|..
gi 1167872373  83 RQ----DAEPGGELRVATGETL 100
Cdd:PRK10632   81 EQlyafNNTPIGTLRIGCSSTM 102
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 105-255 2.92e-03

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: 38.10  E-value: 2.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 105 MPQVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDL--GVFYRVGNDDALTMQQLGEQSLALVASPL----------- 171
Cdd:cd08418    15 MPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFaiGTLPDEMYLKELISEPLFESDFVVVARKDhplqgarslee 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 172 LQDADFTQPDQHipcsfiiNEPqcvFRQLFEsTLRQRRITLENTIELWSIESIKQCVAANLGISFLPRFTVERELSTGQL 251
Cdd:cd08418    95 LLDASWVLPGTR-------MGY---YNNLLE-ALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSRDMGRGPLDSFRL 163


                  ....
gi 1167872373 252 KELP 255
Cdd:cd08418   164 ITIP 167
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 12-122 3.25e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 38.43  E-value: 3.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373  12 VVEEGSFLRASQKLCCTQSTVTFHIQQLEREFSLQLFEKIGRRMCLTTEGKKLMPHIHE----LTRVM---ESIREAArq 84
Cdd:PRK11013   15 VMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRsyygLDRIVsaaESLREFR-- 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1167872373  85 daepGGELRVAT----GETLLaykmPQVLQRFKLRAPNVKLS 122
Cdd:PRK11013   93 ----QGQLSIAClpvfSQSLL----PGLCQPFLARYPDVSLN 126
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 105-284 8.12e-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: 36.78  E-value: 8.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 105 MPqVLQRFKLRAPNVKLSLQSLNCYVIRDALLNDEVDLGVFYRVGNDDALTMQQLGEQSLALVASP--LLQDADFTQPdQ 182
Cdd:cd08441    16 MP-VLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPdhPLAAKEFITP-E 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167872373 183 HIPCSFIINEPQC-----VFRQLFE----STLRQRriTLENTIelwsieSIKQCVAANLGISFLPRFTVERELSTGQLKE 253
Cdd:cd08441    94 DLADETLITYPVErerldVFRHFLQpagiEPKRRR--TVELTL------MILQLVASGRGVAALPNWAVREYLDQGLVVA 165

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1167872373 254 LPFGAPSLSIMALCAHHAGKAVSPAMQIFMQ 284
Cdd:cd08441   166 RPLGEEGLWRTLYAAVRTEDADQPYLQDFLE 196
 
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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