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Conserved domains on  [gi|1293417013|ref|WP_100675777|]
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MULTISPECIES: LuxR C-terminal-related transcriptional regulator [Klebsiella]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10006622)

helix-turn-helix (HTH) transcriptional regulator binds DNA and functions as a repressor or activator; similar to CsgD family transcriptional regulators which function in controlling the expression of structural components and assembly factors of curli fimbriae

Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  20466769

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
134-208 8.83e-13

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


:

Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 64.01  E-value: 8.83e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1293417013 134 RCLKCPRLTLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELarfsaIALALSSRAI 208
Cdd:COG2771   119 ARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAEL-----VALALRLGLI 188
 
Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
134-208 8.83e-13

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 64.01  E-value: 8.83e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1293417013 134 RCLKCPRLTLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELarfsaIALALSSRAI 208
Cdd:COG2771   119 ARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAEL-----VALALRLGLI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 142-196 5.87e-11

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 56.00  E-value: 5.87e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1293417013  142 TLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARF 196
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
142-196 1.13e-10

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 54.90  E-value: 1.13e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1293417013 142 TLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARF 196
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 143-196 3.12e-09

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 51.00  E-value: 3.12e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1293417013 143 LTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARF 196
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
PRK10360 PRK10360
transcriptional regulator UhpA;
115-195 7.56e-07

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 47.66  E-value: 7.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1293417013 115 NRLTALSKPVAGG-----PEKGSKrcLKCPRLT-LTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQID 188
Cdd:PRK10360  106 DELIAAVHTVATGgcyltPDIAIK--LASGRQDpLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVS 183


                  ....*..
gi 1293417013 189 TKQELAR 195
Cdd:PRK10360  184 NDVELAR 190
 
Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
134-208 8.83e-13

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 64.01  E-value: 8.83e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1293417013 134 RCLKCPRLTLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELarfsaIALALSSRAI 208
Cdd:COG2771   119 ARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAEL-----VALALRLGLI 188
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 140-196 4.69e-12

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 60.68  E-value: 4.69e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1293417013 140 RLTLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARF 196
Cdd:COG2197    67 RRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLL 123
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 142-196 5.87e-11

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 56.00  E-value: 5.87e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1293417013  142 TLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARF 196
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
142-196 1.13e-10

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 54.90  E-value: 1.13e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1293417013 142 TLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARF 196
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 143-196 3.12e-09

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 51.00  E-value: 3.12e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1293417013 143 LTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARF 196
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 143-208 7.31e-09

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 50.73  E-value: 7.31e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1293417013 143 LTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTkqelaRFSAIALALSSRAI 208
Cdd:COG5905    13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRN-----RVQAVVWALRLGLL 73
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 157-203 2.90e-08

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 51.64  E-value: 2.90e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1293417013 157 GMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARfsaIALAL 203
Cdd:COG4566   152 GLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVR---LALAL 195
PRK10360 PRK10360
transcriptional regulator UhpA;
115-195 7.56e-07

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 47.66  E-value: 7.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1293417013 115 NRLTALSKPVAGG-----PEKGSKrcLKCPRLT-LTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQID 188
Cdd:PRK10360  106 DELIAAVHTVATGgcyltPDIAIK--LASGRQDpLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVS 183


                  ....*..
gi 1293417013 189 TKQELAR 195
Cdd:PRK10360  184 NDVELAR 190
PRK15369 PRK15369
two component system response regulator;
139-197 8.83e-07

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 47.77  E-value: 8.83e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1293417013 139 PRLTLTKSQlyIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARFS 197
Cdd:PRK15369  148 PLLTPRERQ--ILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWA 204
fixJ PRK09390
response regulator FixJ; Provisional
 142-208 1.06e-06

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 47.30  E-value: 1.06e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1293417013 142 TLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARfsaiaLALSSRAI 208
Cdd:PRK09390  141 SLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVR-----MALRAGRG 202
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
154-203 1.28e-06

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 47.01  E-value: 1.28e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1293417013 154 IKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARFsAIALAL 203
Cdd:COG2909   134 LAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVAR-ARELGL 182
rcsA PRK15411
transcriptional regulator RcsA;
136-191 3.70e-06

transcriptional regulator RcsA;


Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 45.89  E-value: 3.70e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1293417013 136 LKCPRLTLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQ 191
Cdd:PRK15411  131 LNLPTLSLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQ 186
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 143-194 1.57e-04

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 41.17  E-value: 1.57e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1293417013 143 LTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELA 194
Cdd:PRK10651  156 LTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAA 207
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
142-197 5.29e-04

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 39.49  E-value: 5.29e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1293417013 142 TLTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARFS 197
Cdd:PRK09958  143 SLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFA 198
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
143-197 2.99e-03

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 37.55  E-value: 2.99e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1293417013 143 LTKSQLYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQIDTKQELARFS 197
Cdd:PRK09935  150 LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYA 204
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
148-186 3.80e-03

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 37.15  E-value: 3.80e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1293417013 148 LYIIDAIKTGMNNQQIAQELGISHKTVFSHKINIMKKFQ 186
Cdd:COG3677    66 LQAIRLLLNGISLRQIARVLGVSYKTVWRWLHRIREALD 104
 
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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