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Conserved domains on  [gi|1805982337|gb|QHV94986|]
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LysR family transcriptional regulator [Spirosoma endbachense]

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];
3-279 2.60e-36

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 130.37  E-value: 2.60e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQ 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  83 QFQKSSKTDKATISIGmCFETFQFT-LEPHLATL----P-FNVIIKFGDYPDMQQDLDKGLLDLIITPQKGIQANLDYRP 156
Cdd:COG0583    81 ELRALRGGPRGTLRIG-APPSLARYlLPPLLARFrarhPgVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 157 FSKERIVLIGGAksntealsdllenkafgeaeawlkqqvwystaadmdnlkkfwhqnffKHPDFKPNYIVPNICSIVRCL 236
Cdd:COG0583   160 LGEERLVLVASP-----------------------------------------------DHPLARRAPLVNSLEALLAAV 192

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1805982337 237 SDGVGFSIIPDFLCRDEIEAGKVKLVWAGQNVIENTLYFGTRK 279
Cdd:COG0583   193 AAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRR 235
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-279 2.60e-36

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 130.37  E-value: 2.60e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQ 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  83 QFQKSSKTDKATISIGmCFETFQFT-LEPHLATL----P-FNVIIKFGDYPDMQQDLDKGLLDLIITPQKGIQANLDYRP 156
Cdd:COG0583    81 ELRALRGGPRGTLRIG-APPSLARYlLPPLLARFrarhPgVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 157 FSKERIVLIGGAksntealsdllenkafgeaeawlkqqvwystaadmdnlkkfwhqnffKHPDFKPNYIVPNICSIVRCL 236
Cdd:COG0583   160 LGEERLVLVASP-----------------------------------------------DHPLARRAPLVNSLEALLAAV 192

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1805982337 237 SDGVGFSIIPDFLCRDEIEAGKVKLVWAGQNVIENTLYFGTRK 279
Cdd:COG0583   193 AAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRR 235
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-262 3.98e-29

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: 112.71  E-value: 3.98e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQ 82
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  83 QFQKSSKTDKATISIGMCfetfqfTLePHLATLPfNVIIKFGD-YPD-----MQQDLDK-------GLLDLIITPQKGIQ 149
Cdd:NF040786   81 EFDRYGKESKGVLRIGAS------TI-PGQYLLP-ELLKKFKEkYPNvrfklMISDSIKviellleGEVDIGFTGTKLEK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 150 ANLDYRPFSKERIVLIggaksnTEALSDLLENKAFGEAEAWLKQQVWY------STAADMDNLKKFWHqnfFKHPDFKPN 223
Cdd:NF040786  153 KRLVYTPFYKDRLVLI------TPNGTEKYRMLKEEISISELQKEPFImreegsGTRKEAEKALKSLG---ISLEDLNVV 223

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1805982337 224 YIVPNICSIVRCLSDGVGFSIIPDFLCRDEIEAGKVKLV 262
Cdd:NF040786  224 ASLGSTEAIKQSVEAGLGISVISELAAEKEVERGRVLIF 262
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.28e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.20  E-value: 1.28e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   5 LEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGK 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-69 4.21e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.43  E-value: 4.21e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1805982337   5 LEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNY 69
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRY 71
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 118-279 9.09e-07

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: 48.37  E-value: 9.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 118 NVIIKFGDYPDMQQDLDKGLLDLIITPQKGIQANLDYRPFSKERIVLIGG-----AKSNTEALSDLLEnkafgeaEAWlk 192
Cdd:cd05466    30 ELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPpdhplAKRKSVTLADLAD-------EPL-- 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 193 qqVWYSTAADMDNLkkfwHQNFFKHPDFKPN--YIVPNICSIVRCLSDGVGFSIIPDFLCRdEIEAGKVKLVWAGQNVIE 270
Cdd:cd05466   101 --ILFERGSGLRRL----LDRAFAEAGFTPNiaLEVDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLPLEDPPLS 173


                  ....*....
gi 1805982337 271 NTLYFGTRK 279
Cdd:cd05466   174 RTIGLVWRK 182
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-279 2.60e-36

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 130.37  E-value: 2.60e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQ 82
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  83 QFQKSSKTDKATISIGmCFETFQFT-LEPHLATL----P-FNVIIKFGDYPDMQQDLDKGLLDLIITPQKGIQANLDYRP 156
Cdd:COG0583    81 ELRALRGGPRGTLRIG-APPSLARYlLPPLLARFrarhPgVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 157 FSKERIVLIGGAksntealsdllenkafgeaeawlkqqvwystaadmdnlkkfwhqnffKHPDFKPNYIVPNICSIVRCL 236
Cdd:COG0583   160 LGEERLVLVASP-----------------------------------------------DHPLARRAPLVNSLEALLAAV 192

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1805982337 237 SDGVGFSIIPDFLCRDEIEAGKVKLVWAGQNVIENTLYFGTRK 279
Cdd:COG0583   193 AAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRR 235
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-262 3.98e-29

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: 112.71  E-value: 3.98e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQ 82
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  83 QFQKSSKTDKATISIGMCfetfqfTLePHLATLPfNVIIKFGD-YPD-----MQQDLDK-------GLLDLIITPQKGIQ 149
Cdd:NF040786   81 EFDRYGKESKGVLRIGAS------TI-PGQYLLP-ELLKKFKEkYPNvrfklMISDSIKviellleGEVDIGFTGTKLEK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 150 ANLDYRPFSKERIVLIggaksnTEALSDLLENKAFGEAEAWLKQQVWY------STAADMDNLKKFWHqnfFKHPDFKPN 223
Cdd:NF040786  153 KRLVYTPFYKDRLVLI------TPNGTEKYRMLKEEISISELQKEPFImreegsGTRKEAEKALKSLG---ISLEDLNVV 223

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1805982337 224 YIVPNICSIVRCLSDGVGFSIIPDFLCRDEIEAGKVKLV 262
Cdd:NF040786  224 ASLGSTEAIKQSVEAGLGISVISELAAEKEVERGRVLIF 262
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-64 1.28e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 83.20  E-value: 1.28e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   5 LEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGK 64
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
rbcR CHL00180
LysR transcriptional regulator; Provisional
 5-69 4.21e-12

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 65.43  E-value: 4.21e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1805982337   5 LEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNY 69
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRY 71
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 3-67 6.29e-11

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 62.01  E-value: 6.29e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMY 67
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILY 65
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
2-164 4.57e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 59.65  E-value: 4.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   2 VINLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAE 81
Cdd:PRK15421    1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  82 QQFQKSSKTD-KATISIGMCFETFQFTLEPHLATLP-----FNVIIKFGDYPDMQQdldkGLLDLIITPQKGIQANLDYR 155
Cdd:PRK15421   81 QACNEPQQTRlRIAIECHSCIQWLTPALENFHKNWPqvemdFKSGVTFDPQPALQQ----GELDLVMTSDILPRSGLHYS 156

                         170
                  ....*....|.
gi 1805982337 156 P-FSKE-RIVL 164
Cdd:PRK15421  157 PmFDYEvRLVL 167
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-67 5.52e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 58.93  E-value: 5.52e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1805982337   1 MVINLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMY 67
Cdd:PRK10837    1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLY 67
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-63 1.65e-09

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 57.69  E-value: 1.65e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1805982337   1 MVINLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERG 63
Cdd:PRK11013    2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQG 64
PRK09986 PRK09986
LysR family transcriptional regulator;
3-66 5.19e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 56.27  E-value: 5.19e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVM 66
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKIL 70
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 9-69 7.15e-08

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 52.65  E-value: 7.15e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1805982337   9 RTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNY 69
Cdd:PRK11242    7 RYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRY 67
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 94-279 1.09e-07

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: 51.14  E-value: 1.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  94 TISIGmCFETF-QFTLEPHLATL----PF-NVIIKFGDYPDMQQDLDKGLLDLIITPQKGIQANLDYRPFSKERIVLIGG 167
Cdd:pfam03466   3 RLRIG-APPTLaSYLLPPLLARFreryPDvELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 168 -----AKSNTEALSDLLEnkafgeaEAWLKQQVWYSTAADMDnlkkfwhqNFFKHPDFKPN--YIVPNICSIVRCLSDGV 240
Cdd:pfam03466  82 pdhplARGEPVSLEDLAD-------EPLILLPPGSGLRDLLD--------RALRAAGLRPRvvLEVNSLEALLQLVAAGL 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1805982337 241 GFSIIPDFLCRDEIEAGKVK-LVWAGQnVIENTLYFGTRK 279
Cdd:pfam03466 147 GIALLPRSAVARELADGRLVaLPLPEP-PLPRELYLVWRK 185
PRK09791 PRK09791
LysR family transcriptional regulator;
3-99 4.16e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 50.53  E-value: 4.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQ 82
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                          90
                  ....*....|....*..
gi 1805982337  83 QFQKSSKTDKATISIGM 99
Cdd:PRK09791   85 DIRQRQGQLAGQINIGM 101
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 3-65 8.23e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 49.60  E-value: 8.23e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1805982337   3 INLEWFRTFKAIYETG-SLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVP-TERGKV 65
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKA 65
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 118-279 9.09e-07

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: 48.37  E-value: 9.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 118 NVIIKFGDYPDMQQDLDKGLLDLIITPQKGIQANLDYRPFSKERIVLIGG-----AKSNTEALSDLLEnkafgeaEAWlk 192
Cdd:cd05466    30 ELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPpdhplAKRKSVTLADLAD-------EPL-- 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 193 qqVWYSTAADMDNLkkfwHQNFFKHPDFKPN--YIVPNICSIVRCLSDGVGFSIIPDFLCRdEIEAGKVKLVWAGQNVIE 270
Cdd:cd05466   101 --ILFERGSGLRRL----LDRAFAEAGFTPNiaLEVDSLEAIKALVAAGLGIALLPESAVE-ELADGGLVVLPLEDPPLS 173


                  ....*....
gi 1805982337 271 NTLYFGTRK 279
Cdd:cd05466   174 RTIGLVWRK 182
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
3-269 1.68e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 48.51  E-value: 1.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQ 82
Cdd:PRK10082   11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  83 QFQKSSKTDKATISIGMCFETFQFTLEPHLATLP--FNVIIKFGDYPDMQQDLDKGLLDLIITPQkgiQANLDYRPFSKE 160
Cdd:PRK10082   91 ELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPplFTWAIEAIDVDEAVDKLREGQSDCIFSFH---DEDLLEAPFDHI 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337 161 RIVliggaksnTEALSDLLENKAFGEAEAWLKQQVW----YSTAADMDNLkkfWHQNFFKHPDFK-PNYIVPNICSIVRC 235
Cdd:PRK10082  168 RLF--------ESQLFPVCASDEHGEALFNLAQPHFpllnYSRNSYMGRL---INRTLTRHSELSfSTFFVSSMSELLKQ 236

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1805982337 236 LS-DGVGFSIIPDFLCRDEIEAGKVKLVWAGQNVI 269
Cdd:PRK10082  237 VAlDGCGIAWLPEYAIQQEIRSGQLVVLNRDELVI 271
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-67 6.89e-06

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 46.92  E-value: 6.89e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1805982337  10 TFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMY 67
Cdd:PRK10086   21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVF 78
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 20-82 9.14e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 46.57  E-value: 9.14e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1805982337  20 LTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVP-TERGKVMYNyIVEPI-----NKLEVAEQ 82
Cdd:PRK12683   19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGlTEPGKELLQ-IVERMlldaeNLRRLAEQ 86
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-63 2.21e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 45.18  E-value: 2.21e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1805982337   6 EWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERG 63
Cdd:PRK10094    5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAG 62
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
8-95 2.63e-05

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 45.04  E-value: 2.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   8 FRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQQFQKS 87
Cdd:PRK15243    9 LKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQEIGPT 88


                  ....*...
gi 1805982337  88 SKTDKATI 95
Cdd:PRK15243   89 GKTKQLEI 96
PRK10341 PRK10341
transcriptional regulator TdcA;
11-98 2.84e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 44.85  E-value: 2.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  11 FKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQQFQKSSKT 90
Cdd:PRK10341   15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSE 94


                  ....*...
gi 1805982337  91 DKATISIG 98
Cdd:PRK10341   95 AVVDVSFG 102
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
3-66 3.06e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 44.76  E-value: 3.06e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1805982337   3 INLEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRaARKMVPTERGKVM 66
Cdd:PRK03635    2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRL 64
nhaR PRK11062
transcriptional activator NhaR; Provisional
 11-69 3.14e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 44.61  E-value: 3.14e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1805982337  11 FKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNY 69
Cdd:PRK11062   12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRY 70
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
4-64 1.13e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 43.04  E-value: 1.13e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1805982337   4 NLEWFRTFKAIYETG-SLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVP-TERGK 64
Cdd:PRK12684    2 NLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGlTEPGR 64
cbl PRK12679
HTH-type transcriptional regulator Cbl;
8-66 3.07e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 41.72  E-value: 3.07e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1805982337   8 FRTFKAIYETG----SLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVP-TERGKVM 66
Cdd:PRK12679    3 FQQLKIIREAArqdyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGmTEPGKAL 66
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-67 5.12e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 40.90  E-value: 5.12e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1805982337  11 FKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMY 67
Cdd:PRK10632   10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYY 66
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 5-65 6.28e-04

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 40.52  E-value: 6.28e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1805982337   5 LEWFRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKV 65
Cdd:PRK09906    3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEV 63
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-98 1.05e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 39.95  E-value: 1.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   9 RTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRaARKMVPTERGKVMYNYiVEPINKLEVAEQQFQKSS 88
Cdd:PRK13348    8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRH-LRQVALLEADLLSTLPAE 85

                          90
                  ....*....|
gi 1805982337  89 KTDKATISIG 98
Cdd:PRK13348   86 RGSPPTLAIA 95
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 2-69 1.10e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 40.01  E-value: 1.10e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337   2 VINLEW--FRTFKAIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNY 69
Cdd:PRK15092    8 IINLDLdlLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGY 77
PRK09801 PRK09801
LysR family transcriptional regulator;
14-130 3.79e-03

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 38.48  E-value: 3.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  14 IYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQQFQKSSKTDKA 93
Cdd:PRK09801   17 IVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEG 96

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1805982337  94 TISIGMCFETFQFTLEPHLATLPFNviikfgdYPDMQ 130
Cdd:PRK09801   97 MIRIGCSFGFGRSHIAPAITELMRN-------YPELQ 126
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-97 4.13e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 38.00  E-value: 4.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  13 AIYETGSLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQQFQKSSKTDK 92
Cdd:PRK11074   12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWR 91


                  ....*
gi 1805982337  93 ATISI 97
Cdd:PRK11074   92 GQLSI 96
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-118 5.90e-03

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 37.52  E-value: 5.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1805982337  19 SLTAAAQVLYISQPGVSLHLNSLEAHTGYKLFDRAARKMVPTERGKVMYNYIVEPINKLEVAEQQFQKSSKTDKATISIG 98
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAKGALTVSLL 101

                          90       100
                  ....*....|....*....|
gi 1805982337  99 MCFeTFQFtLEPHLATlpFN 118
Cdd:PRK11139  102 PSF-AIQW-LVPRLSS--FN 117
 
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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