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Conserved domains on  [gi|2053272652|gb|QWR16512|]
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LysR family transcriptional regulator [Clostridioides difficile]

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];
3-291 1.66e-52

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 172.36  E-value: 1.66e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   3 IKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGED 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  83 RINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVEC 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 163 IEIHDIFVCANDYieykgrkisleelntlPLIMLENKANsrlyvneyflskgiklnpdielgSHELLLEFAYINLGVSCV 242
Cdd:COG0583   161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2053272652 243 IEEFSIDYLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:COG0583   202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-291 1.66e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 172.36  E-value: 1.66e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   3 IKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGED 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  83 RINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVEC 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 163 IEIHDIFVCANDYieykgrkisleelntlPLIMLENKANsrlyvneyflskgiklnpdielgSHELLLEFAYINLGVSCV 242
Cdd:COG0583   161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2053272652 243 IEEFSIDYLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:COG0583   202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-294 3.21e-46

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: 157.39  E-value: 3.21e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIKLelYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSG 80
Cdd:NF040786    1 MNLKQ--LEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  81 EDRINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDtlNIV 160
Cdd:NF040786   79 EEEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKK--RLV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 161 ECIEIHDIFV----CANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGI---KLNPDIELGSHELLLEFA 233
Cdd:NF040786  157 YTPFYKDRLVlitpNGTEKYRMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGIsleDLNVVASLGSTEAIKQSV 236

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2053272652 234 YINLGVScVIEEFSI-DYLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMISNN 294
Cdd:NF040786  237 EAGLGIS-VISELAAeKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKER 297
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-291 1.68e-40

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: 139.66  E-value: 1.68e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDIFVCAN 173
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 174 DYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVScVIEEFSIDYLEN 253
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIA-LLPESAVEELAD 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2053272652 254 EKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd05466   160 GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 9-242 4.86e-33

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 122.54  E-value: 4.86e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   9 KVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRINKFK 88
Cdd:TIGR03339   3 KAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRESG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  89 KLEYGSLKIGVgdTAArFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDI 168
Cdd:TIGR03339  83 ALREGSLRIAA--TAP-YYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLV 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2053272652 169 FVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVSCV 242
Cdd:TIGR03339 160 AVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVV 233
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-291 1.17e-32

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 119.32  E-value: 1.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  93 GSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDIFVCA 172
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 173 NDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVSCVIEEFSIDYLE 252
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2053272652 253 NEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-293 4.18e-29

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 112.42  E-value: 4.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   5 LELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRI 84
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  85 NKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAII--NMPIE-DDTLNIVE 161
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTElKKILEITP 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 162 CIEIHDIFVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGI---KLNPDIELGSHELLLEFAYINLG 238
Cdd:CHL00180  167 YVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIdskRFKIEMELNSIEAIKNAVQSGLG 246

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2053272652 239 VSCVieefSIDYLENEklFKLDIKEPIPKRNIgychlkdislslATKEFLSMISN 293
Cdd:CHL00180  247 AAFV----SVSAIEKE--LELGLLHWIKIENI------------TIKRMLSIITN 283
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 14-218 1.52e-06

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: 48.58  E-value: 1.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  14 VVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRINKFKKLEYg 93
Cdd:NF041036   12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKGRQR- 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 sLKIGVGDTAARFFLLKYLEIFHKKYPHIH-VSTINRTSRELISLLKDGNIDIAII------------NMPIEDDTLniv 160
Cdd:NF041036   91 -LSICCTPTFGMAHLPGVLNRFMLRNADVVdLKFLFHSPAQALEGIQNKEFDLAIIehcadldlgrfhTYPLPQDEL--- 166

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2053272652 161 ecieihdIFVCANDYiEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLN 218
Cdd:NF041036  167 -------VFVSAPSL-GLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLD 216
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 24-64 8.23e-03

Helix-turn-helix diphteria tox regulatory element; iron dependent repressor


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 34.89  E-value: 8.23e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2053272652   24 AKELFMSQPAVSQSIKQLEEqlDTLLFYRNNKGVKLTPEGK 64
Cdd:smart00529   5 AERLNVSPPTVTEMLKKLEK--MGLVEYEPYRGITLTEKGR 43
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-291 1.66e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 172.36  E-value: 1.66e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   3 IKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGED 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  83 RINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVEC 162
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 163 IEIHDIFVCANDYieykgrkisleelntlPLIMLENKANsrlyvneyflskgiklnpdielgSHELLLEFAYINLGVSCV 242
Cdd:COG0583   161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 2053272652 243 IEEFSIDYLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:COG0583   202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-294 3.21e-46

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: 157.39  E-value: 3.21e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIKLelYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSG 80
Cdd:NF040786    1 MNLKQ--LEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  81 EDRINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDtlNIV 160
Cdd:NF040786   79 EEEFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKK--RLV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 161 ECIEIHDIFV----CANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGI---KLNPDIELGSHELLLEFA 233
Cdd:NF040786  157 YTPFYKDRLVlitpNGTEKYRMLKEEISISELQKEPFIMREEGSGTRKEAEKALKSLGIsleDLNVVASLGSTEAIKQSV 236

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2053272652 234 YINLGVScVIEEFSI-DYLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMISNN 294
Cdd:NF040786  237 EAGLGIS-VISELAAeKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKER 297
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-291 1.68e-40

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: 139.66  E-value: 1.68e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDIFVCAN 173
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 174 DYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVScVIEEFSIDYLEN 253
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIA-LLPESAVEELAD 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2053272652 254 EKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd05466   160 GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 9-242 4.86e-33

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 122.54  E-value: 4.86e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   9 KVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRINKFK 88
Cdd:TIGR03339   3 KAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRESG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  89 KLEYGSLKIGVgdTAArFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDI 168
Cdd:TIGR03339  83 ALREGSLRIAA--TAP-YYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLV 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2053272652 169 FVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVSCV 242
Cdd:TIGR03339 160 AVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVV 233
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-291 1.17e-32

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


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 119.32  E-value: 1.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  93 GSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDIFVCA 172
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 173 NDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVSCVIEEFSIDYLE 252
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2053272652 253 NEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:pfam03466 162 DGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-293 4.18e-29

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 112.42  E-value: 4.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   5 LELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRI 84
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  85 NKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAII--NMPIE-DDTLNIVE 161
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTElKKILEITP 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 162 CIEIHDIFVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGI---KLNPDIELGSHELLLEFAYINLG 238
Cdd:CHL00180  167 YVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIdskRFKIEMELNSIEAIKNAVQSGLG 246

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2053272652 239 VSCVieefSIDYLENEklFKLDIKEPIPKRNIgychlkdislslATKEFLSMISN 293
Cdd:CHL00180  247 AAFV----SVSAIEKE--LELGLLHWIKIENI------------TIKRMLSIITN 283
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-232 3.20e-27

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 107.35  E-value: 3.20e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  11 FNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRINKFKKL 90
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  91 EYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVStINRTSRELI-SLLKDGNIDIAIINMP-----IE-----DDTLNI 159
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLT-IREMSQERIeALLADDELDVGIAFAPvhspeIEaqplfTETLAL 167

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2053272652 160 VecieihdifVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEF 232
Cdd:PRK11242  168 V---------VGRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEI 231
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 94-291 1.12e-24

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: 98.33  E-value: 1.12e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDIFVCAN 173
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 174 DYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGI---KLNPDIELGSHELLLEFAYINLGVSCViEEFSI-D 249
Cdd:cd08420    81 DHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLdglDLNIVMELGSTEAIKEAVEAGLGISIL-SRLAVrK 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2053272652 250 YLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd08420   160 ELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 9.72e-23

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 88.60  E-value: 9.72e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   5 LELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGK 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-223 1.68e-22

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 94.67  E-value: 1.68e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIKlELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVK-LTPEGKILSEHVTTALKLISS 79
Cdd:PRK12682    1 MNLQ-QLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  80 GEDRINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDT-LN 158
Cdd:PRK12682   80 IKRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPdLA 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2053272652 159 IVECIEIHDIFVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGikLNPDIEL 223
Cdd:PRK12682  160 TLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAG--LQPDIVL 222
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-223 6.73e-21

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 90.42  E-value: 6.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIKlELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVK-LTPEGKILSEHVTTALKLISS 79
Cdd:PRK12684    1 MNLH-QLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVEN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  80 ----GEDrinkFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIED- 154
Cdd:PRK12684   80 lkrvGKE----FAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADy 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2053272652 155 DTLNIVECIEIHDIFVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGikLNPDIEL 223
Cdd:PRK12684  156 KELVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRG--LKPDIVL 222
PRK09986 PRK09986
LysR family transcriptional regulator;
3-196 1.90e-20

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 89.01  E-value: 1.90e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   3 IKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGED 82
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  83 RINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVeC 162
Cdd:PRK09986   87 RVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFT-S 165

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2053272652 163 IEIHD---IFVCANDYIEYKGRKISLEELNTLPLIML 196
Cdd:PRK09986  166 RRLHEsafAVAVPEEHPLASRSSVPLKALRNEYFITL 202
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-289 1.54e-19

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 86.28  E-value: 1.54e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILsehVTTALKLISSG 80
Cdd:PRK10837    1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLL---YPRALALLEQA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  81 EDrINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIA----------IINM 150
Cdd:PRK10837   78 VE-IEQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGliegpchspeLISE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 151 PIEDDTLnIVECIEIHDIFvcandyieykGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLL 230
Cdd:PRK10837  157 PWLEDEL-VVFAAPDSPLA----------RGPVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIK 225

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2053272652 231 EFAYINLGVSCVIEEFSIDYLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLS 289
Cdd:PRK10837  226 HAVRHGLGISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLS 284
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 9-147 8.68e-19

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 84.12  E-value: 8.68e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   9 KVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRINkfK 88
Cdd:PRK11139   12 RAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLR--A 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2053272652  89 KLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHV--STINRtsreLISLLKDGnIDIAI 147
Cdd:PRK11139   90 RSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVrlKAVDR----LEDFLRDD-VDVAI 145
PRK09791 PRK09791
LysR family transcriptional regulator;
2-147 3.59e-18

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 82.50  E-value: 3.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   2 NIKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGE 81
Cdd:PRK09791    4 QVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQ 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2053272652  82 DRINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAI 147
Cdd:PRK09791   84 EDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTI 149
cbl PRK12679
HTH-type transcriptional regulator Cbl;
24-262 9.98e-16

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 76.00  E-value: 9.98e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  24 AKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGV-KLTPEGKILsehVTTALKLIssgeDRINKFKKL-------EYGSL 95
Cdd:PRK12679   23 ANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLlGMTEPGKAL---LVIAERIL----NEASNVRRLadlftndTSGVL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  96 KIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDD-TLNIVECIEIHDIFVCAND 174
Cdd:PRK12679   96 TIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDpQLVAFPWFRWHHSLLVPHD 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 175 YIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKlnPDIELGSHELLLEFAYINLGVSC-VIEEFSIDYLEN 253
Cdd:PRK12679  176 HPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLL--ADIVLSAQDSDVIKTYVALGLGIgLVAEQSSGEQEE 253


                  ....*....
gi 2053272652 254 EKLFKLDIK 262
Cdd:PRK12679  254 SNLIRLDTR 262
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-147 2.17e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 75.04  E-value: 2.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  10 VFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSgedRINKFKK 89
Cdd:PRK10086   21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ---EILDIKN 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2053272652  90 LEY-GSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVsTInRTSRELISLLKDGnIDIAI 147
Cdd:PRK10086   98 QELsGTLTVYSRPSIAQCWLVPRLADFTRRYPSISL-TI-LTGNENVNFQRAG-IDLAI 153
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-291 3.57e-15

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: 72.17  E-value: 3.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 115 FHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLniveciEIHDIF------VCANDYIEYKGRKISLEEL 188
Cdd:cd08440    22 FRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDL------EFEPLLrdpfvlVCPKDHPLARRRSVTWAEL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 189 NTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVSCViEEFSIDYLENEKLFKLDIKEPIPKR 268
Cdd:cd08440    96 AGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVL-PALALPLADHPGLVARPLTEPVVTR 174

                         170       180
                  ....*....|....*....|...
gi 2053272652 269 NIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd08440   175 TVGLIRRRGRSLSPAAQAFLDLL 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 11-243 3.99e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 74.04  E-value: 3.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  11 FNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRINKFKKl 90
Cdd:PRK09906    9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQ- 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  91 EYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDIFV 170
Cdd:PRK09906   88 EDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDEPLVVV 167

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2053272652 171 CANDYIEYKGRKISLEELNTLPLIMLENKANSRLY--VNEYFLSKGIKLNpdIELGSHELLLEFAYINLGVSCVI 243
Cdd:PRK09906  168 LPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLApiIKAWFAQHNSQPN--IVQVATNILVTMNLVGMGLGCTI 240
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-223 8.72e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 73.15  E-value: 8.72e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIKlELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVK-LTPEGKILSEHVTTAL----K 75
Cdd:PRK12683    1 MNFQ-QLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLldaeN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  76 LISSGEDrinkFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIeDD 155
Cdd:PRK12683   80 LRRLAEQ----FADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAL-DR 154

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 156 TLNIV--ECIEIHDIFVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGikLNPDIEL 223
Cdd:PRK12683  155 EPDLVsfPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAG--LVPDIVL 222
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 94-288 4.75e-13

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: 66.38  E-value: 4.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGdTAARFFLLKYLEIFHKKYPHIHVSTI--NRtsRELISLLKDGNIDIAIINMPIEDdtLNiVECIEIHD---I 168
Cdd:cd08419     1 RLRLAVV-STAKYFAPRLLGAFCRRHPGVEVSLRvgNR--EQVLERLADNEDDLAIMGRPPED--LD-LVAEPFLDnplV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 169 FVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVSCVieefSI 248
Cdd:cd08419    75 VIAPPDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVL----SL 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2053272652 249 DYLENE----KLFKLDIKE-PIPKRnigYC--HLKDISLSLATKEFL 288
Cdd:cd08419   151 HTLALElatgRLAVLDVEGfPIRRQ---WYvvHRKGKRLSPAAQAFL 194
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-197 9.15e-12

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 64.28  E-value: 9.15e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEG--------KILSEHVTT 72
Cdd:PRK15092    9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGiqllgyarKILRFNDEA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  73 ALKLISSGEDrinkfkkleyGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPI 152
Cdd:PRK15092   89 CSSLMYSNLQ----------GVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRP 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2053272652 153 EDDTLNIVECIEIHdiFVCANDYIEYKGRkisleelnTLPLIMLE 197
Cdd:PRK15092  159 SSFPALNLRTSPTL--WYCAAEYVLQKGE--------PIPLVLLD 193
PRK10341 PRK10341
transcriptional regulator TdcA;
10-147 1.31e-11

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 64.11  E-value: 1.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  10 VFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKIL---SEHVTTALK----LISSGED 82
Cdd:PRK10341   14 VFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLlsrSESITREMKnmvnEINGMSS 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2053272652  83 RINKFKKLEYGSLkigVGDTaarfFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAI 147
Cdd:PRK10341   94 EAVVDVSFGFPSL---IGFT----FMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAI 151
PRK12680 PRK12680
LysR family transcriptional regulator;
21-244 1.95e-11

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 63.49  E-value: 1.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  21 SLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVK-LTPEGKILSEHVTTALKLISSGEDRINKFKKLEYGSLKIGV 99
Cdd:PRK12680   20 TLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTLTT 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 100 GDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNI-VECIEIHDIFVCANDY-IE 177
Cdd:PRK12680  100 THTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIaVPLYRWRRLVVVPRGHaLD 179

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2053272652 178 YKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGikLNPDIELGS--HELLLEFAYINLGVSCVIE 244
Cdd:PRK12680  180 TPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLG--LEPSIALTAldADLIKTYVRAGLGVGLLAE 246
cysB PRK12681
HTH-type transcriptional regulator CysB;
14-194 3.48e-11

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 62.61  E-value: 3.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  14 VVN-NKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVK-LTPEGK--------ILSEhvTTALKLISsgedr 83
Cdd:PRK12681   12 VVNhNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEeiiriareILSK--VESIKSVA----- 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  84 iNKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYP----HIHVSTINRTSrELISllkDGNIDIAIINMPIE--DDtL 157
Cdd:PRK12681   85 -GEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPrvslHMHQGSPTQIA-EAAA---KGNADFAIATEALHlyDD-L 158

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2053272652 158 NIVECIEIHDIFVCANDYIEYKGRKISLEELNTLPLI 194
Cdd:PRK12681  159 IMLPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLV 195
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-215 7.56e-11

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 61.62  E-value: 7.56e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNikLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSG 80
Cdd:PRK11233    1 MN--FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  81 EDRINKFKKLEYGSLKIGVG-DTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAII--NMPIedDTL 157
Cdd:PRK11233   79 QLAVHNVGQALSGQVSIGLApGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIyeHSPV--AGL 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2053272652 158 NIVECIEIHDIFVCANDyieYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGI 215
Cdd:PRK11233  157 SSQPLLKEDLFLVGTQD---CPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRL 211
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 97-288 3.45e-10

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: 58.38  E-value: 3.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  97 IGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNiVECIEIHDIF-VCANDY 175
Cdd:cd08433     4 VGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLS-TEPLLEEDLFlVGPADA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 176 IEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGV-----SCVIEEfsidy 250
Cdd:cd08433    83 PLPRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYtilpaSAVAAE----- 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2053272652 251 LENEKLFKLDIKEPIPKRNIGYCHLKDISLS---LATKEFL 288
Cdd:cd08433   158 VAAGRLVAAPIVDPALTRTLSLATPRDRPLSpaaLAVRDLL 198
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-71 5.43e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.83  E-value: 5.43e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2053272652   9 KVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRnNKGVKLTPEGKILSEHVT 71
Cdd:PRK13348    8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLR 69
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-246 5.65e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 59.26  E-value: 5.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   3 IKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGED 82
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  83 RINKFKKLEygsLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVEC 162
Cdd:PRK15421   82 ACNEPQQTR---LRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPM 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 163 IEIHDIFVCANDYIEYKGRKISLEELNTLPLIMLENKaNSRLYVNEYFLSKGiKLNPDIELGSHELLL-EFAYINLGVSC 241
Cdd:PRK15421  159 FDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQ-RSRLDVWRHFLQPA-GVSPSLKSVDNTLLLiQMVAARMGIAA 236


                  ....*....
gi 2053272652 242 ----VIEEF 246
Cdd:PRK15421  237 lphwVVESF 245
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 95-291 9.82e-10

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: 57.18  E-value: 9.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  95 LKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEiHDIFVCAND 174
Cdd:cd08438     2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCN-EPLVAVLPR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 175 YIEYKGRK-ISLEELNTLPLIMLenkaNSRLYVNEYFLSKGIKL--NPDI--ELGSHELLLEFAYINLGVSCVIEefSI- 248
Cdd:cd08438    81 GHPLAGRKtVSLADLADEPFILF----NEDFALHDRIIDACQQAgfTPNIaaRSSQWDFIAELVAAGLGVALLPR--SIa 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2053272652 249 DYLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd08438   155 QRLDNAGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
11-70 1.34e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 57.86  E-value: 1.34e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  11 FNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRnNKGVKLTPEGKILSEHV 70
Cdd:PRK03635   10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHA 68
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-271 1.90e-09

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 57.35  E-value: 1.90e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIK-LElYKVfnAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISS 79
Cdd:PRK11151    1 MNIRdLE-YLV--ALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  80 GEDRINKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLni 159
Cdd:PRK11151   78 LKEMASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAF-- 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 160 vecIEIhDIF------VCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFA 233
Cdd:PRK11151  156 ---IEV-PLFdepmllAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMV 231

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 2053272652 234 YINLGVScVIEEFSIdylENEK----LFKLDIKEPIPKRNIG 271
Cdd:PRK11151  232 AAGSGIT-LLPALAV---PNERkrdgVCYLPCIKPEPRRTIG 269
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 94-205 2.11e-09

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: 55.98  E-value: 2.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNiVECIEIHDIFVC-- 171
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLA-SRPLLREPLVVAlp 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2053272652 172 -----AndyieyKGRKISLEELNTLPLIMLENKANSRLY 205
Cdd:cd08414    80 adhplA------ARESVSLADLADEPFVLFPREPGPGLY 112
PRK09801 PRK09801
LysR family transcriptional regulator;
9-259 2.33e-09

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 57.35  E-value: 2.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   9 KVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHvttALKLISSGE---DRIN 85
Cdd:PRK09801   12 QVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEH---ALEILTQYQrlvDDVT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  86 KFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYP--HIHVSTINRTsrelISLLKDgNIDIAI-INMPIEDdtLNIVEC 162
Cdd:PRK09801   89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPelQVHFELFDRQ----IDLVQD-NIDLDIrINDEIPD--YYIAHL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 163 IEIHDIFVCAN-DYIEYKGRKISLEELNTLP-LIMLENKANSRLY-VNEYFLSKGIKLNPDIELGSHELLLEFAYINLGV 239
Cdd:PRK09801  162 LTKNKRILCAApEYLQKYPQPQSLQELSRHDcLVTKERDMTHGIWeLGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGI 241

                         250       260
                  ....*....|....*....|
gi 2053272652 240 SCVIEEFSIDYLENEKLFKL 259
Cdd:PRK09801  242 MLRSEWDVLPFLESGKLVQV 261
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
4-157 2.94e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 57.08  E-value: 2.94e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   4 KLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDR 83
Cdd:PRK10632    3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQ 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2053272652  84 INKFKKLEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTInrTSRELISLLKDGnIDIAIINMPIEDDTL 157
Cdd:PRK10632   83 LYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLV--TGIPAPDLIADG-LDVVIRVGALQDSSL 153
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-79 9.50e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.58  E-value: 9.50e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2053272652   6 ELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISS 79
Cdd:PRK10094    5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLES 78
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-227 9.61e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 55.21  E-value: 9.61e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  28 FMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKilsehvttalKLISSGEDRINKFKKLE----------YGSLKI 97
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGE----------ELRPFAQQTLLQWQQLRhtldqqgpslSGELSL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  98 GVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPiedDTL-NIVECIEIHDI-------- 168
Cdd:PRK11716   72 FCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKP---ETLpASVAFSPIDEIplvliapa 148

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2053272652 169 FVCANDyieykgRKISLEELN--TLPLIMLEnKANSRLYVNEYFLSKGIKlnPDI--ELGSHE 227
Cdd:PRK11716  149 LPCPVR------QQLSQEKPDwsRIPFILPE-HGPARRRIDLWFRRHKIK--PNIyaTVSGHE 202
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 93-271 1.19e-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: 1.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  93 GSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLniveciEIHDIF--- 169
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGL------EEEPLFdep 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 170 ---VCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVScVIEEF 246
Cdd:cd08411    75 fllAVPKDHPLAKRKSVTPEDLAGERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAGLGIT-LLPEL 153

                         170       180
                  ....*....|....*....|....*..
gi 2053272652 247 SIDYLENE--KLFKLDIKEPIPKRNIG 271
Cdd:cd08411   154 AVPSEELRgdRLVVRPFAEPAPSRTIG 180
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-65 1.62e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 54.56  E-value: 1.62e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2053272652  10 VFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKI 65
Cdd:PRK11074    9 VVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEW 64
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
6-66 2.09e-08

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 54.25  E-value: 2.09e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2053272652   6 ELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKIL 66
Cdd:PRK03601    4 ELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERL 64
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 115-287 4.17e-08

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: 52.15  E-value: 4.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 115 FHKKYPHIHVSTINRTSRELISLLKDGNIDIAII-NMPIEDDtlniVECIEIHD---IFVCANDYIEYKGRKISLEELNT 190
Cdd:cd08434    22 FRKEYPNVTFELHQGSTDELLDDLKNGELDLALCsPVPDEPD----IEWIPLFTeelVLVVPKDHPLAGRDSVDLAELAD 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 191 LPLIMLENKANSRLYVNEYFLSKGIKlnPDIELGSHEL--LLEFAYINLGVScVIEEFSIDYLENEKlfKLDIKEPIPKR 268
Cdd:cd08434    98 EPFVLLSPGFGLRPIVDELCAAAGFT--PKIAFEGEEDstIAGLVAAGLGVA-ILPEMTLLNPPGVK--KIPIKDPDAER 172

                         170
                  ....*....|....*....
gi 2053272652 269 NIGYCHLKDISLSLATKEF 287
Cdd:cd08434   173 TIGLAWLKDRYLSPAARRF 191
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 93-232 4.71e-08

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: 52.33  E-value: 4.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  93 GSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVStINRTSRELI-SLLKDGNIDIAIINMPIEDDTLnivECIEIHD---- 167
Cdd:cd08425     1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALS-LREMPQERIeAALADDRLDLGIAFAPVRSPDI---DAQPLFDerla 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2053272652 168 IFVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEF 232
Cdd:cd08425    77 LVVGATHPLAQRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEV 141
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-242 4.72e-08

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 52.22  E-value: 4.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDdtLNIVECIEIHD---IFV 170
Cdd:cd08436     1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERR--PPGLASRELAReplVAV 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2053272652 171 CANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVSCV 242
Cdd:cd08436    79 VAPDHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALL 150
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 94-266 1.77e-07

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


Pssm-ID: 176134  Cd Length: 198  Bit Score: 50.64  E-value: 1.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIED-DTLNIVECIEIHDIFVCA 172
Cdd:cd08443     1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDyDDLITLPCYHWNRCVVVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 173 NDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGikLNPDIELGSHELLLEFAYINLGVSC-VIEEFSIDYL 251
Cdd:cd08443    81 RDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAG--LTPNIVLTATDADVIKTYVRLGLGVgVIASMAYDPV 158

                         170
                  ....*....|....*
gi 2053272652 252 ENEKLFKLDIKEPIP 266
Cdd:cd08443   159 DDPDLVIRDARDLFP 173
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 11-199 3.76e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 50.37  E-value: 3.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  11 FNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRINKFKKL 90
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  91 EYGSLKIGVGDTAARFFLLKYLEIFHKKYPHI--HVSTINRTsrelISLLKDGnIDIAI--INMPIEDDTLNIVECIEIH 166
Cdd:PRK14997   90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVslQLEATNRR----VDVVGEG-VDVAIrvRPRPFEDSDLVMRVLADRG 164

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2053272652 167 DIFVCANDYIEYKGRKISLEELNTLP-LIMLENK 199
Cdd:PRK14997  165 HRLFASPDLIARMGIPSAPAELSHWPgLSLASGK 198
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 94-223 6.65e-07

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: 48.77  E-value: 6.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIED-DTLNIVECIEIHDIFVCA 172
Cdd:cd08413     1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDhPDLVTLPCYRWNHCVIVP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2053272652 173 NDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGikLNPDIEL 223
Cdd:cd08413    81 PGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAG--LEPNIVL 129
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 95-290 7.16e-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: 48.69  E-value: 7.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  95 LKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAI---INMPIEddtlniVECIEIHD---- 167
Cdd:cd08412     2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALtydLDLPED------IAFEPLARlppy 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 168 IFVCANDYIEYKgRKISLEELNTLPLIMLENKaNSRLYVNEYFLSKGIKlnPDIELGSH--ELLLEFAYINLGVSCVIEE 245
Cdd:cd08412    76 VWLPADHPLAGK-DEVSLADLAAEPLILLDLP-HSREYFLSLFAAAGLT--PRIAYRTSsfEAVRSLVANGLGYSLLNDR 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2053272652 246 FSIDY-LENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSM 290
Cdd:cd08412   152 PYRPWsYDGKRLVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDF 197
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 94-291 8.99e-07

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: 48.42  E-value: 8.99e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPiEDDTLNIVECIEIHD---IFV 170
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLA-DDEQPPDLASEELADeplVVV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 171 CANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPD-IELGSHELLLEFAYINLGVSCVIEEFSID 249
Cdd:cd08435    80 ARPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNvVETASISALLALLARSDMLAVLPRSVAED 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2053272652 250 YLENEKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd08435   160 ELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 94-261 1.01e-06

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 48.27  E-value: 1.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIvECIEIHDIFVCAN 173
Cdd:cd08452     1 LLVIGFVGAAIYEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHI-ETVQSSPCVLALP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 174 DYIEYKGR-KISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDI--ELGSHELLLEFAYINLGVSCVIEEFsidy 250
Cdd:cd08452    80 KQHPLASKeEITIEDLRDEPIITVAREAWPTLYDEIIQLCEQAGFRPKIvqEATEYQTVIGLVSAGIGVTFVPSSA---- 155

                         170
                  ....*....|.
gi 2053272652 251 lenEKLFKLDI 261
Cdd:cd08452   156 ---KKLFNLEV 163
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 14-218 1.52e-06

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: 48.58  E-value: 1.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  14 VVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGEDRINKFKKLEYg 93
Cdd:NF041036   12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKGRQR- 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 sLKIGVGDTAARFFLLKYLEIFHKKYPHIH-VSTINRTSRELISLLKDGNIDIAII------------NMPIEDDTLniv 160
Cdd:NF041036   91 -LSICCTPTFGMAHLPGVLNRFMLRNADVVdLKFLFHSPAQALEGIQNKEFDLAIIehcadldlgrfhTYPLPQDEL--- 166

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2053272652 161 ecieihdIFVCANDYiEYKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLN 218
Cdd:NF041036  167 -------VFVSAPSL-GLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQGRDLD 216
leuO PRK09508
leucine transcriptional activator; Reviewed
 2-77 2.87e-06

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 48.10  E-value: 2.87e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2053272652   2 NIKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLI 77
Cdd:PRK09508   21 MVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLV 96
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 95-247 6.71e-06

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: 45.94  E-value: 6.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  95 LKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHD-IFVCAN 173
Cdd:cd08457     2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAvVAVPMG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2053272652 174 DYIEYKGRkISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVScVIEEFS 247
Cdd:cd08457    82 HPLAQLDV-VSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIA-IIDPAT 153
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 94-288 8.49e-06

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 45.63  E-value: 8.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHdiFVCA- 172
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGR--AVCVl 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 173 --NDYIEYKGRkISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVScVIEEFSIDY 250
Cdd:cd08415    79 ppGHPLARKDV-VTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVA-IVDPLTAAG 156

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2053272652 251 LENEKLFKLDIKEPIPKRnIGYCHLKDISLSLATKEFL 288
Cdd:cd08415   157 YAGAGLVVRPFRPAIPFE-FALVRPAGRPLSRLAQAFI 193
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-131 9.47e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 46.14  E-value: 9.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   1 MNIKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTA---LKLI 77
Cdd:PRK11013    2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRI 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2053272652  78 SSGEDRINKFkklEYGSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTS 131
Cdd:PRK11013   82 VSAAESLREF---RQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQES 132
PBP_like_2 pfam12849
PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
 98-176 2.31e-05

PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.


Pssm-ID: 432831 [Multi-domain]  Cd Length: 267  Bit Score: 44.84  E-value: 2.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  98 GVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTL---NIVECIEIHDIFVCAND 174
Cdd:pfam12849  14 IAGSSTQAPGLLDLAEAFEKKYPGAKVKVTSVGSGEGIKALLNGDVDVALVSRPLTEEEFeafGANGAGGLVEVPVAYDG 93


                  ..
gi 2053272652 175 YI 176
Cdd:pfam12849  94 IA 95
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 106-291 1.04e-04

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


Pssm-ID: 176128  Cd Length: 198  Bit Score: 42.32  E-value: 1.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 106 FFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIIN--MPIEDDTLNIVECIEIHDIFVCANDYIEYKGRKI 183
Cdd:cd08437    13 YYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGslTPLENSALHSKIIKTQHFMIIVSKDHPLAKAKKV 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 184 SLEELNTLPLIMLENkaNSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYI--NLGVSCVIeEFSIDYLENekLFKLDI 261
Cdd:cd08437    93 NFADLKKENFILLNE--HFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVreNVGIGFLT-DIAVKPDDH--LVAIPL 167

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2053272652 262 KE-PIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd08437   168 LDnEQPTFYISLAHRKDQLLTPAQKKLLDLL 198
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-291 1.07e-04

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 42.30  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 115 FHKKYPHIHVSTINRTSRELISLLKDGNIDIAI-INMPIEDDtlniVECIEIHDIFVCA---NDYIEYKGRKISLEELNT 190
Cdd:cd08426    22 FRQRYPGVFFTVDVASTADVLEAVLSGEADIGLaFSPPPEPG----IRVHSRQPAPIGAvvpPGHPLARQPSVTLAQLAG 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 191 LPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVScVIEEFSI-DYLENEKLFKLDIKEPIPK-R 268
Cdd:cd08426    98 YPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGIS-LLTELAVrREIRRGQLVAVPLADPHMNhR 176

                         170       180
                  ....*....|....*....|...
gi 2053272652 269 NIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd08426   177 QLELQTRAGRQLPAAASAFLQLL 199
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 102-291 2.06e-04

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176121  Cd Length: 199  Bit Score: 41.41  E-value: 2.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 102 TAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPiedDTL-NIVECIEIHD---IFVCANDYIE 177
Cdd:cd08430     9 TASYSFLPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARP---DKLpARLAFLPLATsplVFIAPNIACA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 178 YKgRKISLEEL--NTLPLIMLENKAnSRLYVNEYFLSKGIKlnPDI--ELGSHELLLEFAYINLGVSCVIEEFsidyLEN 253
Cdd:cd08430    86 VT-QQLSQGEIdwSRLPFILPERGL-ARERLDQWFRRRGIK--PNIyaQVAGHEAIVSMVALGCGVGIVPELV----LDN 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2053272652 254 ----EKLFKLDIKEPIPKRNIGYCHLKDISLSLATKEFLSMI 291
Cdd:cd08430   158 splkDKVRILEVQPELEPFEVGLCCLKKRLNEPLIKAFWQVA 199
PRK11482 PRK11482
DNA-binding transcriptional regulator;
2-82 3.34e-04

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 41.63  E-value: 3.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652   2 NIKLELYKVFNAVVNNKSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISSGE 81
Cdd:PRK11482   28 NIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGAL 107


                  .
gi 2053272652  82 D 82
Cdd:PRK11482  108 D 108
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 94-158 5.54e-04

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: 40.28  E-value: 5.54e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2053272652  94 SLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLN 158
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLE 65
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 108-242 6.44e-04

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: 40.05  E-value: 6.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 108 LLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDIFVCANDYIEYKGRKISLEE 187
Cdd:cd08450    15 LPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREKIPPQD 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2053272652 188 LNTLPLIMLENKANS-RLYVNEYFLSKGIKLNPDIELGSHELLLEFAYINLGVSCV 242
Cdd:cd08450    95 LAGENFISPAPTAPVlQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALL 150
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
18-79 6.83e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 40.42  E-value: 6.83e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2053272652  18 KSFSLAAKELFMSQPAVSQSIKQLEEQLDTLLFYRNNKGVKLTPEGKILSEHVTTALKLISS 79
Cdd:PRK10082   26 RNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLES 87
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-195 9.51e-04

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


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 39.57  E-value: 9.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  93 GSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINM-PIEDDTlnIVECIEIHDIFVC 171
Cdd:cd08446     1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFyPVEPDI--AVENVAQERLYLA 78

                          90       100
                  ....*....|....*....|....*
gi 2053272652 172 AN-DYIEYKGRKISLEELNTLPLIM 195
Cdd:cd08446    79 VPkSHPLAARPAVSLADLRNEPLIL 103
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-256 1.48e-03

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 5. 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: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 38.98  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  93 GSLKIGVGDTAARFFLLKYLEIFHKKYPHIHVstinrtsrELISllKDGNIDIA-----------------IINMPIEDD 155
Cdd:cd08474     3 GTLRINAPRVAARLLLAPLLARFLARYPDIRL--------ELVV--DDGLVDIVaegfdagirlgesvekdMVAVPLGPP 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652 156 TLNIVecieihdifVCANDYIEYKGRKISLEELNTLPLIMLENKANSRLYVNEyFLSKGIKLNPDIE----LGSHELLLE 231
Cdd:cd08474    73 LRMAV---------VASPAYLARHGTPEHPRDLLNHRCIRYRFPTSGALYRWE-FERGGRELEVDVEgpliLNDSDLMLD 142

                         170       180
                  ....*....|....*....|....*
gi 2053272652 232 FAYINLGVSCVIEEFSIDYLENEKL 256
Cdd:cd08474   143 AALDGLGIAYLFEDLVAEHLASGRL 167
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 93-196 1.61e-03

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: 38.96  E-value: 1.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  93 GSLKIGVGDTAARFFLLKYLEIFHKKYPHIHV--STINRtsreLISLLKDGnIDIAIINMPIEDDTLnIVECI-EIHDIF 169
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLelVLSDR----LVDLVEEG-FDLAIRIGELPDSSL-VARRLgPVRRVL 74

                          90       100
                  ....*....|....*....|....*..
gi 2053272652 170 VCANDYIEYKGRKISLEELNTLPLIML 196
Cdd:cd08422    75 VASPAYLARHGTPQTPEDLARHRCLGY 101
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 97-233 1.80e-03

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 38.73  E-value: 1.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2053272652  97 IGVGDTAARFFLLKYLEIFHKKYPHIHVSTINRTSRELISLLKDGNIDIAIINMPIEDDTLNIVECIEIHDIFVCANDYI 176
Cdd:cd08417     4 IAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHP 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2053272652 177 EyKGRKISLEELNTLPLIMLENKANSRLYVNEYFLSKGIKLNPDIELGSHELLLEFA 233
Cdd:cd08417    84 L-AGGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALV 139
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
24-70 2.23e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 37.49  E-value: 2.23e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2053272652  24 AKELFMSQPAVSQSIKQLEEqlDTLLFYRNNKGVKLTPEGKILSEHV 70
Cdd:COG1321    31 AERLGVSPPSVTEMLKKLEE--KGLVEYEPYGGITLTEEGRELALRI 75
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 24-64 8.23e-03

Helix-turn-helix diphteria tox regulatory element; iron dependent repressor


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 34.89  E-value: 8.23e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2053272652   24 AKELFMSQPAVSQSIKQLEEqlDTLLFYRNNKGVKLTPEGK 64
Cdd:smart00529   5 AERLNVSPPTVTEMLKKLEK--MGLVEYEPYRGITLTEKGR 43
 
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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