NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1493166354|gb|RLO54277|]
View 

LuxR family transcriptional regulator [Serratia marcescens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
120-176 1.08e-09

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


:

Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 55.15  E-value: 1.08e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLNRHREFMYWLIS 176
Cdd:COG2771   128 LTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALR 184
PRK15201 super family cl28472
fimbriae biosynthesis transcriptional regulator FimW;
4-174 1.15e-09

fimbriae biosynthesis transcriptional regulator FimW;


The actual alignment was detected with superfamily member PRK15201:

Pssm-ID: 185123  Cd Length: 198  Bit Score: 55.05  E-value: 1.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354   4 INIVIDDDNAYFVAGLRFSITEYAEKNHKTVSFLSPDDGVQADMVIAAsmwRAQRWRKMNpCEAVSaIMTIKEKRVGRVN 83
Cdd:PRK15201    2 LSIAIKEQNSHFEHGLKIIMTRLANQWQQKIDFLPPEEIDNADIAFLA---LDDDWFSAG-CYQIP-MHTQHQLRVIICN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354  84 ESESV-------------LYRTDN----RSRLFELLAKSLVKNSAEKQLLGYVLTSR----EKQVIGFLKRGFDQSQTAK 142
Cdd:PRK15201   77 KCDKEklmfrpclymlphIYREDDveeiTRKMILILHKRALRHSVPSGICHYCTTRHfsvtERHLLKLIASGYHLSETAA 156

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1493166354 143 LLGINVKTVHSHKRSVMKKLMLNRHREFMYWL 174
Cdd:PRK15201  157 LLSLSEEQTKSLRRSIMRKLHVKTEQQFLKYI 188
 
Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
120-176 1.08e-09

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 55.15  E-value: 1.08e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLNRHREFMYWLIS 176
Cdd:COG2771   128 LTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALR 184
PRK15201 PRK15201
fimbriae biosynthesis transcriptional regulator FimW;
4-174 1.15e-09

fimbriae biosynthesis transcriptional regulator FimW;


Pssm-ID: 185123  Cd Length: 198  Bit Score: 55.05  E-value: 1.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354   4 INIVIDDDNAYFVAGLRFSITEYAEKNHKTVSFLSPDDGVQADMVIAAsmwRAQRWRKMNpCEAVSaIMTIKEKRVGRVN 83
Cdd:PRK15201    2 LSIAIKEQNSHFEHGLKIIMTRLANQWQQKIDFLPPEEIDNADIAFLA---LDDDWFSAG-CYQIP-MHTQHQLRVIICN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354  84 ESESV-------------LYRTDN----RSRLFELLAKSLVKNSAEKQLLGYVLTSR----EKQVIGFLKRGFDQSQTAK 142
Cdd:PRK15201   77 KCDKEklmfrpclymlphIYREDDveeiTRKMILILHKRALRHSVPSGICHYCTTRHfsvtERHLLKLIASGYHLSETAA 156

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1493166354 143 LLGINVKTVHSHKRSVMKKLMLNRHREFMYWL 174
Cdd:PRK15201  157 LLSLSEEQTKSLRRSIMRKLHVKTEQQFLKYI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 120-162 4.90e-09

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 50.22  E-value: 4.90e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1493166354  120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKL 162
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 120-162 1.14e-07

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: 46.37  E-value: 1.14e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKL 162
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
GerE pfam00196
Bacterial regulatory proteins, luxR family;
119-162 3.78e-06

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 42.57  E-value: 3.78e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1493166354 119 VLTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKL 162
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKL 45
PRK15369 PRK15369
two component system response regulator;
119-173 7.18e-06

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 44.68  E-value: 7.18e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1493166354 119 VLTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLNRHREFMYW 173
Cdd:PRK15369  149 LLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNW 203
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 76-162 4.33e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.17  E-value: 4.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354  76 EKRVGRVNESESVLYRTDNRSRLFELLAKslvknsaekqllgyvLTSREKQVIgFLKR--GFDQSQTAKLLGINVKTVHS 153
Cdd:TIGR02937  82 EELLDSDPSPEEELEQEEEREALREALEK---------------LPEREREVL-VLRYleGLSYKEIAEILGISVGTVKR 145


                  ....*....
gi 1493166354 154 HKRSVMKKL 162
Cdd:TIGR02937 146 RLKRARKKL 154
 
Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
120-176 1.08e-09

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 55.15  E-value: 1.08e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLNRHREFMYWLIS 176
Cdd:COG2771   128 LTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALR 184
PRK15201 PRK15201
fimbriae biosynthesis transcriptional regulator FimW;
4-174 1.15e-09

fimbriae biosynthesis transcriptional regulator FimW;


Pssm-ID: 185123  Cd Length: 198  Bit Score: 55.05  E-value: 1.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354   4 INIVIDDDNAYFVAGLRFSITEYAEKNHKTVSFLSPDDGVQADMVIAAsmwRAQRWRKMNpCEAVSaIMTIKEKRVGRVN 83
Cdd:PRK15201    2 LSIAIKEQNSHFEHGLKIIMTRLANQWQQKIDFLPPEEIDNADIAFLA---LDDDWFSAG-CYQIP-MHTQHQLRVIICN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354  84 ESESV-------------LYRTDN----RSRLFELLAKSLVKNSAEKQLLGYVLTSR----EKQVIGFLKRGFDQSQTAK 142
Cdd:PRK15201   77 KCDKEklmfrpclymlphIYREDDveeiTRKMILILHKRALRHSVPSGICHYCTTRHfsvtERHLLKLIASGYHLSETAA 156

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1493166354 143 LLGINVKTVHSHKRSVMKKLMLNRHREFMYWL 174
Cdd:PRK15201  157 LLSLSEEQTKSLRRSIMRKLHVKTEQQFLKYI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 120-162 4.90e-09

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 50.22  E-value: 4.90e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1493166354  120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKL 162
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 115-162 5.04e-08

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: 49.12  E-value: 5.04e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1493166354 115 LLGYVLTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKL 162
Cdd:COG2197    65 ALRRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKL 112
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 120-162 1.14e-07

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: 46.37  E-value: 1.14e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKL 162
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
GerE pfam00196
Bacterial regulatory proteins, luxR family;
119-162 3.78e-06

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 42.57  E-value: 3.78e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1493166354 119 VLTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKL 162
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKL 45
PRK15369 PRK15369
two component system response regulator;
119-173 7.18e-06

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 44.68  E-value: 7.18e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1493166354 119 VLTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLNRHREFMYW 173
Cdd:PRK15369  149 LLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNW 203
PRK10360 PRK10360
transcriptional regulator UhpA;
120-173 1.24e-05

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 43.81  E-value: 1.24e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLNR-----HREFMYW 173
Cdd:PRK10360  138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNdvelaRRMFDGW 196
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 120-175 2.17e-04

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: 38.02  E-value: 2.17e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLNRHREFMYWLI 175
Cdd:COG5905    13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWAL 68
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 120-162 3.03e-04

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: 39.70  E-value: 3.03e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKL 162
Cdd:COG4566   138 LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKL 180
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 97-178 8.18e-04

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 38.47  E-value: 8.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354  97 RLFELLAKSLVKNSAEKQLLGYVLTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLNRHREFMYWLIS 176
Cdd:PRK10651  133 ALTPVLAASLRANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQ 212


                  ..
gi 1493166354 177 QD 178
Cdd:PRK10651  213 ER 214
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 120-165 1.87e-03

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 37.42  E-value: 1.87e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1493166354 120 LTSREKQVIGFLKRGFDQSQTAKLLGINVKTVHSHKRSVMKKLMLN 165
Cdd:PRK11475  135 LSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVS 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 76-162 4.33e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.17  E-value: 4.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493166354  76 EKRVGRVNESESVLYRTDNRSRLFELLAKslvknsaekqllgyvLTSREKQVIgFLKR--GFDQSQTAKLLGINVKTVHS 153
Cdd:TIGR02937  82 EELLDSDPSPEEELEQEEEREALREALEK---------------LPEREREVL-VLRYleGLSYKEIAEILGISVGTVKR 145


                  ....*....
gi 1493166354 154 HKRSVMKKL 162
Cdd:TIGR02937 146 RLKRARKKL 154
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH