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Conserved domains on  [gi|171849140|pdb|3CLO|C]
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Chain C, Transcriptional regulator

Protein Classification

response regulator transcription factor( domain architecture ID 11450879)

response regulator transcription factor with a signal receiver (REC) domain and a LuxR family helix-turn-helix (HTH) domain that may be part of a two-component regulatory system; similar to Staphylococcus aureus response regulator VraR

CATH:  1.10.10.10
Gene Ontology:  GO:0000160|GO:0006355|GO:0003677
PubMed:  10966457
SCOP:  3001179

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 195-258 4.14e-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: 83.40  E-value: 4.14e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
3CLO_C      195 RNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL*KLL 258
Cdd:COG2197  67 RRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 195-258 4.14e-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: 83.40  E-value: 4.14e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
3CLO_C      195 RNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL*KLL 258
Cdd:COG2197  67 RRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 198-252 3.06e-18

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.03  E-value: 3.06e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
3CLO_C         198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAA 252
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 ...
 198-254 2.13e-17

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: 73.72  E-value: 2.13e-17
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
3CLO_C      198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL 254
Cdd:cd06170   1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
197-252 4.32e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 64.91  E-value: 4.32e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
3CLO_C        197 ILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAA 252
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
PRK10360 PRK10360
transcriptional regulator UhpA;
188-250 3.79e-09

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 54.98  E-value: 3.79e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
3CLO_C       188 LSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACR 250
Cdd:PRK10360 128 IKLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELAR 190
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 198-240 7.13e-05

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 42.16  E-value: 7.13e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
3CLO_C        198 LSEREKEILR-CIRKGLSSKEIAATLYISVNTVNRHRQNILEKL 240
Cdd:TIGR02985 114 LPEQCREIFIlSRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 195-258 4.14e-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: 83.40  E-value: 4.14e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
3CLO_C      195 RNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL*KLL 258
Cdd:COG2197  67 RRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 198-252 3.06e-18

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.03  E-value: 3.06e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
3CLO_C         198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAA 252
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 189-252 1.55e-17

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: 74.61  E-value: 1.55e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
3CLO_C      189 SLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAA 252
Cdd:COG5905   4 SSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWA 67
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 198-254 2.13e-17

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: 73.72  E-value: 2.13e-17
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
3CLO_C      198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL 254
Cdd:cd06170   1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
156-258 4.83e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 71.33  E-value: 4.83e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3CLO_C      156 LIFCLYSLSADQRPEQGIYATITQ*ERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQN 235
Cdd:COG2771  86 LLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKR 165

                        90       100
                ....*....|....*....|...
3CLO_C      236 ILEKLSVGNSIEACRAAEL*KLL 258
Cdd:COG2771 166 IYRKLGVSSRAELVALALRLGLI 188
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 198-253 2.50e-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: 69.36  E-value: 2.50e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
3CLO_C      198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAE 253
Cdd:COG4566 138 LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLAL 193
GerE pfam00196
Bacterial regulatory proteins, luxR family;
197-252 4.32e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 64.91  E-value: 4.32e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
3CLO_C        197 ILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAA 252
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
207-258 3.20e-11

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 60.49  E-value: 3.20e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
3CLO_C      207 RCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL*KLL 258
Cdd:COG2909 132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLL 183
PRK10360 PRK10360
transcriptional regulator UhpA;
188-250 3.79e-09

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 54.98  E-value: 3.79e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
3CLO_C       188 LSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACR 250
Cdd:PRK10360 128 IKLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELAR 190
PRK15369 PRK15369
two component system response regulator;
186-247 6.59e-09

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 54.31  E-value: 6.59e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
3CLO_C       186 ETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIE 247
Cdd:PRK15369 138 ALLNADDTNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAE 199
PRK10100 PRK10100
transcriptional regulator CsgD;
197-248 7.18e-09

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 54.49  E-value: 7.18e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
3CLO_C       197 ILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEA 248
Cdd:PRK10100 155 LLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQA 206
PRK10188 PRK10188
transcriptional regulator SdiA;
198-252 2.55e-08

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 53.25  E-value: 2.55e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
3CLO_C       198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIE-ACRAA 252
Cdd:PRK10188 180 FSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQiACYAA 235
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 166-248 3.38e-08

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 52.34  E-value: 3.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3CLO_C       166 DQRPEQgIYATITQ*ERGEV---ETL------SLSEEHR------NILSEREKEILRCIRKGLSSKEIAATLYISVNTVN 230
Cdd:PRK10651 110 DMEPED-LLKALQQAAAGEMvlsEALtpvlaaSLRANRAtterdvNQLTPRERDILKLIAQGLPNKMIARRLDITESTVK 188

                         90
                 ....*....|....*...
3CLO_C       231 RHRQNILEKLSVGNSIEA 248
Cdd:PRK10651 189 VHVKHMLKKMKLKSRVEA 206
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
197-248 3.58e-08

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 52.55  E-value: 3.58e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
3CLO_C       197 ILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEA 248
Cdd:PRK10403 153 VLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAA 204
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
198-258 2.07e-07

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 50.26  E-value: 2.07e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
3CLO_C       198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL*KLL 258
Cdd:PRK09935 150 LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLHELL 210
PRK09483 PRK09483
response regulator; Provisional
 198-258 2.06e-05

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 44.33  E-value: 2.06e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
3CLO_C       198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL*KLL 258
Cdd:PRK09483 149 LSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLL 209
fixJ PRK09390
response regulator FixJ; Provisional
 198-252 3.04e-05

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 43.84  E-value: 3.04e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
3CLO_C       198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAA 252
Cdd:PRK09390 142 LSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMA 196
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 198-240 7.13e-05

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 42.16  E-value: 7.13e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
3CLO_C        198 LSEREKEILR-CIRKGLSSKEIAATLYISVNTVNRHRQNILEKL 240
Cdd:TIGR02985 114 LPEQCREIFIlSRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 174-240 9.11e-05

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: 41.56  E-value: 9.11e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
3CLO_C        174 YATITQ*ERGEVETLSLSEEHRNI------LSEREKEILRCIR-KGLSSKEIAATLYISVNTVNRHRQNILEKL 240
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALrealekLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 198-240 6.56e-04

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 39.81  E-value: 6.56e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
3CLO_C      198 LSEREKEILRCIR-KGLSSKEIAATLYISVNTVNRHRQNILEKL 240
Cdd:COG1191 187 LPERERLVLSLYYfEELTLKEIAEVLGVSESRVSRLHKKALARL 230
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 198-240 6.76e-04

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 36.67  E-value: 6.76e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
3CLO_C        198 LSEREKEILRCIR-KGLSSKEIAATLYISVNTVNRHRQNILEKL 240
Cdd:pfam08281  11 LPPRQREVFLLRYlEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
198-257 9.59e-04

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 40.31  E-value: 9.59e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
3CLO_C       198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAE-L*KL 257
Cdd:PRK04841 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQdLLKM 899
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 179-240 1.95e-03

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 38.52  E-value: 1.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
3CLO_C       179 Q*ERG--EVETLSLSEEHRNILSEREKEILRCI-RKGLSSKEIAATLYISVNTVNRHRQNILEKL 240
Cdd:PRK08583 185 QQEDGyeLTEQRMILEKILPVLSDREKSIIQCTfIENLSQKETGERLGISQMHVSRLQRQAIKKL 249
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 194-254 2.14e-03

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 38.19  E-value: 2.14e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
3CLO_C       194 HRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAEL 254
Cdd:PRK11475 131 QSRMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLDAADI 191
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 198-240 2.76e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 37.67  E-value: 2.76e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
3CLO_C      198 LSEREKEILRCIR-KGLSSKEIAATLYISVNTVNRHRQNILEKL 240
Cdd:COG1595 128 LPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
200-232 4.88e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 34.33  E-value: 4.88e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
3CLO_C        200 EREKEILRCIRK--GLSSKEIAATLYISVNTVNRH 232
Cdd:pfam13412   1 ETDRKILNLLQEnpRISQRELAERLGLSPSTVNRR 35
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 198-246 5.57e-03

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 37.12  E-value: 5.57e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
3CLO_C       198 LSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSI 246
Cdd:PRK10840 151 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDI 199
 
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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