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Conserved domains on  [gi|1429757502|emb|SSI23763|]
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Response regulator [Klebsiella pneumoniae]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 229396)

helix-turn-helix domain-containing protein may bind DNA and be involved in the regulation of gene expression

Gene Ontology:  GO:0003677|GO:0006355

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
FixJ super family cl34778
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 129-176 4.93e-14

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


The actual alignment was detected with superfamily member COG4566:

Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 67.05  E-value: 4.93e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1429757502 129 QLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:COG4566   137 SLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
8-176 2.55e-10

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


:

Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 57.07  E-value: 2.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502   8 LIGHSIYHYLIDSHENATRLSYADVIHEKHLPLAQTIIFNLINKDISAIRIVDLLNALRLSLLRCQQPVLMVKSDIVGLC 87
Cdd:COG2771     3 LLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502  88 RELINFDNAMIISEKSPLTLFSSIVQRAKGVSELPPRGLRKQ---LSPRECQILELLIANNNNKRIAALLGIAHKTVHSH 164
Cdd:COG2771    83 ALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARapgLTPREREVLRLLAEGLTLKEIARILGISERTVRTH 162

                         170
                  ....*....|..
gi 1429757502 165 RIHIMQKLGIDN 176
Cdd:COG2771   163 LKRIYRKLGVSS 174
 
Name Accession Description Interval E-value
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 129-176 4.93e-14

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: 67.05  E-value: 4.93e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1429757502 129 QLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:COG4566   137 SLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
GerE pfam00196
Bacterial regulatory proteins, luxR family;
130-179 5.03e-12

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 58.37  E-value: 5.03e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1429757502 130 LSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIdNSRT 179
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNV-HSRV 51
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 130-179 1.46e-11

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 57.15  E-value: 1.46e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1429757502  130 LSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIdNSRT 179
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGV-RSRT 52
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 130-176 5.28e-11

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: 55.62  E-value: 5.28e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1429757502 130 LSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKS 47
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
8-176 2.55e-10

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 57.07  E-value: 2.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502   8 LIGHSIYHYLIDSHENATRLSYADVIHEKHLPLAQTIIFNLINKDISAIRIVDLLNALRLSLLRCQQPVLMVKSDIVGLC 87
Cdd:COG2771     3 LLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502  88 RELINFDNAMIISEKSPLTLFSSIVQRAKGVSELPPRGLRKQ---LSPRECQILELLIANNNNKRIAALLGIAHKTVHSH 164
Cdd:COG2771    83 ALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARapgLTPREREVLRLLAEGLTLKEIARILGISERTVRTH 162

                         170
                  ....*....|..
gi 1429757502 165 RIHIMQKLGIDN 176
Cdd:COG2771   163 LKRIYRKLGVSS 174
PRK10360 PRK10360
transcriptional regulator UhpA;
103-184 6.04e-09

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 53.44  E-value: 6.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502 103 SPLTLFSSIVQRAKGVSELPPR-------GLRKQLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGID 175
Cdd:PRK10360  104 SPDELIAAVHTVATGGCYLTPDiaiklasGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVS 183


                  ....*....
gi 1429757502 176 NSRTMNQRI 184
Cdd:PRK10360  184 NDVELARRM 192
 
Name Accession Description Interval E-value
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 129-176 4.93e-14

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: 67.05  E-value: 4.93e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1429757502 129 QLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:COG4566   137 SLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 126-176 4.90e-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: 60.29  E-value: 4.90e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1429757502 126 LRKQLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:COG2197    66 LRRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRN 116
GerE pfam00196
Bacterial regulatory proteins, luxR family;
130-179 5.03e-12

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 58.37  E-value: 5.03e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1429757502 130 LSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIdNSRT 179
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNV-HSRV 51
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 130-179 1.46e-11

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 57.15  E-value: 1.46e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1429757502  130 LSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIdNSRT 179
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGV-RSRT 52
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 127-180 5.16e-11

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: 56.12  E-value: 5.16e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1429757502 127 RKQLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDNSRTM 180
Cdd:COG5905    10 PSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQA 63
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 130-176 5.28e-11

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: 55.62  E-value: 5.28e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1429757502 130 LSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKS 47
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
8-176 2.55e-10

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 57.07  E-value: 2.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502   8 LIGHSIYHYLIDSHENATRLSYADVIHEKHLPLAQTIIFNLINKDISAIRIVDLLNALRLSLLRCQQPVLMVKSDIVGLC 87
Cdd:COG2771     3 LLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502  88 RELINFDNAMIISEKSPLTLFSSIVQRAKGVSELPPRGLRKQ---LSPRECQILELLIANNNNKRIAALLGIAHKTVHSH 164
Cdd:COG2771    83 ALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARapgLTPREREVLRLLAEGLTLKEIARILGISERTVRTH 162

                         170
                  ....*....|..
gi 1429757502 165 RIHIMQKLGIDN 176
Cdd:COG2771   163 LKRIYRKLGVSS 174
PRK10360 PRK10360
transcriptional regulator UhpA;
103-184 6.04e-09

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 53.44  E-value: 6.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502 103 SPLTLFSSIVQRAKGVSELPPR-------GLRKQLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGID 175
Cdd:PRK10360  104 SPDELIAAVHTVATGGCYLTPDiaiklasGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVS 183


                  ....*....
gi 1429757502 176 NSRTMNQRI 184
Cdd:PRK10360  184 NDVELARRM 192
PRK15369 PRK15369
two component system response regulator;
109-176 4.55e-08

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 50.85  E-value: 4.55e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1429757502 109 SSIVQRAKGVSELPPRglrkqLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:PRK15369  134 EAILALLNADDTNPPL-----LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHK 196
fixJ PRK09390
response regulator FixJ; Provisional
 129-176 5.09e-07

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 48.07  E-value: 5.09e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1429757502 129 QLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:PRK09390  141 SLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGS 188
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 129-174 6.12e-06

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 45.02  E-value: 6.12e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1429757502 129 QLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGI 174
Cdd:PRK10651  155 QLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
139-188 1.73e-05

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 43.54  E-value: 1.73e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1429757502 139 ELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDNSRTMNQRIAALH 188
Cdd:COG2909   132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELG 181
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 88-175 1.02e-04

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 42.07  E-value: 1.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502  88 RELINF-DNAMIISEKSPLT---LFSSIVQRAKGVSELPPRGLRKQLSPRECQ-ILELLIANNNNKRIAA-LLGIAHKTV 161
Cdd:COG3829   359 RELENViERAVVLSEGDVITpehLPEYLLEEAEAASAAEEGSLKEALEEVEKElIEEALEKTGGNKSKAAkALGISRSTL 438

                          90
                  ....*....|....
gi 1429757502 162 HSHrihiMQKLGID 175
Cdd:COG3829   439 YRK----LKKYGIK 448
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
130-176 1.32e-03

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 38.77  E-value: 1.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1429757502 130 LSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:PRK04841  839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAH 885
rcsA PRK15411
transcriptional regulator RcsA;
97-176 5.10e-03

transcriptional regulator RcsA;


Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 36.26  E-value: 5.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1429757502  97 MIISEKS--PLTL---FSSIVQRAK---GVSELPPrgLRkqLSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHI 168
Cdd:PRK15411  101 LLISSKSikPESLddlLGDILKKETtitSFLNLPT--LS--LSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNI 176


                  ....*...
gi 1429757502 169 MQKLGIDN 176
Cdd:PRK15411  177 KRKIKTHN 184
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
130-176 6.08e-03

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 36.01  E-value: 6.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1429757502 130 LSPRECQILELLIANNNNKRIAALLGIAHKTVHSHRIHIMQKLGIDN 176
Cdd:PRK09935  150 LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196
 
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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