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Conserved domains on  [gi|636855161|ref|WP_024374534|]
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LuxR C-terminal-related transcriptional regulator [Vibrio fluvialis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10100 super family cl32463
transcriptional regulator CsgD;
73-214 6.56e-28

transcriptional regulator CsgD;


The actual alignment was detected with superfamily member PRK10100:

Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 104.95  E-value: 6.56e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161  73 LRLTSPHLETILFQVGKRLCTDDLLSFGNLKGLFYQPSEPEQIARGLAEIINGQNWLPRHVSSQLLHYYRHIFQNHHTKA 152
Cdd:PRK10100  75 LSRKNNNIKILLLNTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITHSGNYRYNSTESA 154

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 636855161 153 TieLTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQNL 214
Cdd:PRK10100 155 L--LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDNL 214
 
Name Accession Description Interval E-value
PRK10100 PRK10100
transcriptional regulator CsgD;
73-214 6.56e-28

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 104.95  E-value: 6.56e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161  73 LRLTSPHLETILFQVGKRLCTDDLLSFGNLKGLFYQPSEPEQIARGLAEIINGQNWLPRHVSSQLLHYYRHIFQNHHTKA 152
Cdd:PRK10100  75 LSRKNNNIKILLLNTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITHSGNYRYNSTESA 154

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 636855161 153 TieLTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQNL 214
Cdd:PRK10100 155 L--LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDNL 214
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 156-215 4.40e-20

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: 82.25  E-value: 4.40e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161 156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQNLL 215
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGL 129
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 156-210 2.03e-18

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 75.64  E-value: 2.03e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 636855161   156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWA 210
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 156-212 2.46e-16

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: 70.26  E-value: 2.46e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 636855161 156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQ 212
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
156-210 7.15e-16

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 68.77  E-value: 7.15e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 636855161  156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWA 210
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
 
Name Accession Description Interval E-value
PRK10100 PRK10100
transcriptional regulator CsgD;
73-214 6.56e-28

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 104.95  E-value: 6.56e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161  73 LRLTSPHLETILFQVGKRLCTDDLLSFGNLKGLFYQPSEPEQIARGLAEIINGQNWLPRHVSSQLLHYYRHIFQNHHTKA 152
Cdd:PRK10100  75 LSRKNNNIKILLLNTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITHSGNYRYNSTESA 154

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 636855161 153 TieLTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQNL 214
Cdd:PRK10100 155 L--LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDNL 214
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 156-215 4.40e-20

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: 82.25  E-value: 4.40e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161 156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQNLL 215
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGL 129
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 150-210 5.44e-19

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: 77.69  E-value: 5.44e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 636855161 150 TKATIELTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWA 210
Cdd:COG5905    7 TSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWA 67
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 156-210 2.03e-18

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 75.64  E-value: 2.03e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 636855161   156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWA 210
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 156-212 2.46e-16

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: 70.26  E-value: 2.46e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 636855161 156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQ 212
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
156-210 7.15e-16

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 68.77  E-value: 7.15e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 636855161  156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWA 210
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
142-215 2.07e-12

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 63.24  E-value: 2.07e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 636855161 142 RHIFQNHHTKATIELTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQNLL 215
Cdd:COG2771  114 LLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALRLGL 187
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 111-213 3.22e-12

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 63.12  E-value: 3.22e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161 111 EPEQIARGLAEIINGQNWLPRHVSSQLLHYYRHifQNHHTKATIE-LTTRELQILRSLKTGASNMQMAESLFISEFTVKS 189
Cdd:PRK10651 112 EPEDLLKALQQAAAGEMVLSEALTPVLAASLRA--NRATTERDVNqLTPRERDILKLIAQGLPNKMIARRLDITESTVKV 189

                         90       100
                 ....*....|....*....|....
gi 636855161 190 HLYQIFKKLSVKNRTQAIAWANQN 213
Cdd:PRK10651 190 HVKHMLKKMKLKSRVEAAVWVHQE 213
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
167-212 3.98e-11

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 59.72  E-value: 3.98e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 636855161 167 LKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQ 212
Cdd:COG2909  134 LAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARE 179
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
104-206 8.86e-11

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 59.10  E-value: 8.86e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161 104 GLFYQPSEPEQIARGLAEIINGQNWLPRHVSSQLLHyyRHIFQNHHTKATIeLTTRELQILRSLKTGASNMQMAESLFIS 183
Cdd:PRK10403 105 GYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLRE--REMFGAEEDPFSV-LTERELDVLHELAQGLSNKQIASVLNIS 181

                         90       100
                 ....*....|....*....|...
gi 636855161 184 EFTVKSHLYQIFKKLSVKNRTQA 206
Cdd:PRK10403 182 EQTVKVHIRNLLRKLNVRSRVAA 204
PRK15369 PRK15369
two component system response regulator;
156-210 2.10e-07

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 49.69  E-value: 2.10e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 636855161 156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWA 210
Cdd:PRK15369 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWA 204
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 156-210 5.83e-07

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: 48.17  E-value: 5.83e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 636855161 156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWA 210
Cdd:COG4566  138 LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLA 192
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
122-215 7.59e-07

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 47.95  E-value: 7.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161 122 IINGQNWLPrhvsSQLLHYYRHIFQNHHTKATIELTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVK 201
Cdd:PRK09935 120 ILSGYTFFP----SETLNYIKSNKCSTNSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLH 195

                         90
                 ....*....|....
gi 636855161 202 NRTQAIAWANQNLL 215
Cdd:PRK09935 196 SIVELIDYAKLHEL 209
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
111-215 9.49e-07

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 48.79  E-value: 9.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636855161 111 EPEQIARGLAEII--NGQNWLPRHVSSQLL----HYYRHIFQnHHTKATIE----------------LTTRELQILRSLK 168
Cdd:PRK04841 773 EGEAMAQQLRQLIqlNTLPELEQHRAQRILreinQHHRHKFA-HFDEAFVEkllnhpdvpelirtspLTQREWQVLGLIY 851

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 636855161 169 TGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWAnQNLL 215
Cdd:PRK04841 852 SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA-QDLL 897
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
156-213 2.06e-03

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 37.95  E-value: 2.06e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 636855161 156 LTTRELQILRSLKTGASNMQMAESLFISEFTVKSHLYQIFKKLSVKNRTQAIAWANQN 213
Cdd:PRK09958 144 LSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRN 201
 
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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