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Conserved domains on  [gi|488140447|ref|WP_002211655|]
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MULTISPECIES: LuxR family transcriptional regulator [Yersinia pseudotuberculosis complex]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10507063)

helix-turn-helix (HTH) transcriptional regulator containing an N-terminal an autoinducer binding domain and a LuxR family HTH DNA-binding domain; may act as an activator or repressor in response to an inducer

Gene Ontology:  GO:0006355|GO:0003677|GO:0003700
PubMed:  15808743|19076237|10473770|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 12-158 8.07e-36

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


:

Pssm-ID: 427319  Cd Length: 148  Bit Score: 124.40  E-value: 8.07e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447   12 IETLRDYIDRKLTIYDSPKYTYMVI--NKKNPGDIFIVTSYPNEWAELYTNNNYQNIDPVVLIAFRRFSPFSWDENITVL 89
Cdd:pfam03472   2 EEELFDALARLAAALGFDHFAYGARapLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAE 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488140447   90 SELKLSKIFTLSKKYNIVNGFTFVLHDTMNNLAMLSLIMDDSALNGVESRVlnDRDRLQMLLIETHEKM 158
Cdd:pfam03472  82 ARGAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIE--AAARLQLLAIYAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
127-242 1.26e-18

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


:

Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 80.96  E-value: 1.26e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447 127 IMDDSALNGVESRVLNDRDRLQMLLIETHEKMLTLSQRNMNIQERQGKGMPGKAILSPRENEVLYWASMGKTYQEIAIIT 206
Cdd:COG2771   73 ALLLLLLLLLALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARIL 152

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488140447 207 NITPRTVKYHIGNVVKKLGVINAKQAIGLGVELEII 242
Cdd:COG2771  153 GISERTVRTHLKRIYRKLGVSSRAELVALALRLGLI 188
 
Name Accession Description Interval E-value
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 12-158 8.07e-36

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 427319  Cd Length: 148  Bit Score: 124.40  E-value: 8.07e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447   12 IETLRDYIDRKLTIYDSPKYTYMVI--NKKNPGDIFIVTSYPNEWAELYTNNNYQNIDPVVLIAFRRFSPFSWDENITVL 89
Cdd:pfam03472   2 EEELFDALARLAAALGFDHFAYGARapLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAE 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488140447   90 SELKLSKIFTLSKKYNIVNGFTFVLHDTMNNLAMLSLIMDDSALNGVESRVlnDRDRLQMLLIETHEKM 158
Cdd:pfam03472  82 ARGAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIE--AAARLQLLAIYAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
127-242 1.26e-18

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 80.96  E-value: 1.26e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447 127 IMDDSALNGVESRVLNDRDRLQMLLIETHEKMLTLSQRNMNIQERQGKGMPGKAILSPRENEVLYWASMGKTYQEIAIIT 206
Cdd:COG2771   73 ALLLLLLLLLALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARIL 152

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488140447 207 NITPRTVKYHIGNVVKKLGVINAKQAIGLGVELEII 242
Cdd:COG2771  153 GISERTVRTHLKRIYRKLGVSSRAELVALALRLGLI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 179-233 1.60e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 74.10  E-value: 1.60e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 488140447   179 KAILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAI 233
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAV 55
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 182-233 2.76e-15

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: 67.94  E-value: 2.76e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488140447 182 LSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAI 233
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLV 52
PRK10188 PRK10188
transcriptional regulator SdiA;
48-235 6.06e-14

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 69.04  E-value: 6.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447  48 TSYPNEWAELYTNNNYQNIDPVVLIAFRRFSPFSWDENITVLSElklsKIFTLSKKYNIVNGFTFVLHDTMNNLAMLSLi 127
Cdd:PRK10188  61 TTYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFSEAQ----ALWDAARAHGLRRGVTQCLMLPNRALGFLSF- 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447 128 mddSALNGVESRVLNDRD--RLQMLlieTHEKMLTLSQRNMNIQerqgkgMPGKAILSPRENEVLYWASMGKTYQEIAII 205
Cdd:PRK10188 136 ---SRCSAREIPILSDELelRLQLL---VRESLMALMRLEDEMV------MTPEMNFSKREKEILKWTAEGKTSAEIAMI 203

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 488140447 206 TNITPRTVKYHIGNVVKKLGVINAKQ------AIGL 235
Cdd:PRK10188 204 LSISENTVNFHQKNMQKKFNAPNKTQiacyaaATGL 239
GerE pfam00196
Bacterial regulatory proteins, luxR family;
180-233 1.75e-12

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 60.68  E-value: 1.75e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 488140447  180 AILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAI 233
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 182-224 1.10e-04

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: 1.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 488140447  182 LSPRENEVLYWA-SMGKTYQEIAIITNITPRTVKYHIGNVVKKL 224
Cdd:TIGR02937 111 LPEREREVLVLRyLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
180-226 1.93e-04

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 41.38  E-value: 1.93e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 488140447 180 AILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGV 226
Cdd:PRK10403 152 SVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198
 
Name Accession Description Interval E-value
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 12-158 8.07e-36

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 427319  Cd Length: 148  Bit Score: 124.40  E-value: 8.07e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447   12 IETLRDYIDRKLTIYDSPKYTYMVI--NKKNPGDIFIVTSYPNEWAELYTNNNYQNIDPVVLIAFRRFSPFSWDENITVL 89
Cdd:pfam03472   2 EEELFDALARLAAALGFDHFAYGARapLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAE 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488140447   90 SELKLSKIFTLSKKYNIVNGFTFVLHDTMNNLAMLSLIMDDSALNGVESRVlnDRDRLQMLLIETHEKM 158
Cdd:pfam03472  82 ARGAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIE--AAARLQLLAIYAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
127-242 1.26e-18

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 80.96  E-value: 1.26e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447 127 IMDDSALNGVESRVLNDRDRLQMLLIETHEKMLTLSQRNMNIQERQGKGMPGKAILSPRENEVLYWASMGKTYQEIAIIT 206
Cdd:COG2771   73 ALLLLLLLLLALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARIL 152

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488140447 207 NITPRTVKYHIGNVVKKLGVINAKQAIGLGVELEII 242
Cdd:COG2771  153 GISERTVRTHLKRIYRKLGVSSRAELVALALRLGLI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 179-233 1.60e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 74.10  E-value: 1.60e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 488140447   179 KAILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAI 233
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAV 55
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 176-242 1.40e-16

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: 73.77  E-value: 1.40e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488140447 176 MPG-------KAILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAIGLGVELEII 242
Cdd:COG2197   57 MPGmdglealRRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 182-233 2.76e-15

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: 67.94  E-value: 2.76e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488140447 182 LSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAI 233
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLV 52
PRK10188 PRK10188
transcriptional regulator SdiA;
48-235 6.06e-14

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 69.04  E-value: 6.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447  48 TSYPNEWAELYTNNNYQNIDPVVLIAFRRFSPFSWDENITVLSElklsKIFTLSKKYNIVNGFTFVLHDTMNNLAMLSLi 127
Cdd:PRK10188  61 TTYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFSEAQ----ALWDAARAHGLRRGVTQCLMLPNRALGFLSF- 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447 128 mddSALNGVESRVLNDRD--RLQMLlieTHEKMLTLSQRNMNIQerqgkgMPGKAILSPRENEVLYWASMGKTYQEIAII 205
Cdd:PRK10188 136 ---SRCSAREIPILSDELelRLQLL---VRESLMALMRLEDEMV------MTPEMNFSKREKEILKWTAEGKTSAEIAMI 203

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 488140447 206 TNITPRTVKYHIGNVVKKLGVINAKQ------AIGL 235
Cdd:PRK10188 204 LSISENTVNFHQKNMQKKFNAPNKTQiacyaaATGL 239
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 179-244 7.37e-14

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: 64.60  E-value: 7.37e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488140447 179 KAILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAIGLGVELEIIKP 244
Cdd:COG5905   10 PSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLLSL 75
GerE pfam00196
Bacterial regulatory proteins, luxR family;
180-233 1.75e-12

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 60.68  E-value: 1.75e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 488140447  180 AILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAI 233
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
138-242 1.60e-09

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 55.48  E-value: 1.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447 138 SRVLNDRDRLQMLLiethEKMLTLSQRNMN------IQERQGKGMPGKAILSPRenevlyWASMGKTYQEIAIITNITPR 211
Cdd:COG2909   83 ARLALDPEEALALL----ERLLALAEAAGRlllralALRALGDREEALAALRRR------LLAEGLSNKEIAERLFISVN 152

                         90       100       110
                 ....*....|....*....|....*....|.
gi 488140447 212 TVKYHIGNVVKKLGVINAKQAIGLGVELEII 242
Cdd:COG2909  153 TVKTHLRNIYRKLGVRSRTEAVARARELGLL 183
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 31-242 5.92e-09

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 54.61  E-value: 5.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447  31 YTYMVINKKNpgdIFIVTSYPNEWAELYTNNNYQNIDPVVLIAFRRFSPFSW--DENITVLSELKLSkIFTLSKKYNIVN 108
Cdd:PRK13870  37 YAYLHIQHRH---ITAVTNYHREWQSVYFDKKFDALDPVVKRARSRKHIFTWsgEQERPRLSKDERA-FYAHAADFGIRS 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488140447 109 GFTFVLHDTMNNLAMLSLIMDDSALngvesrvlnDRDRlqmlLIETHEKMLTLSQRNMNIQ-ERQGKGMPGKAILSPREN 187
Cdd:PRK13870 113 GITIPIKTANGSMSMFTLASEKPVI---------DLDR----EIDAVAAAATIGQIHARISfLRTTPTAEDAAWLDPKEA 179

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488140447 188 EVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAIGLGVELEII 242
Cdd:PRK13870 180 TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 182-240 6.34e-09

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: 53.95  E-value: 6.34e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488140447 182 LSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAIGLGVELE 240
Cdd:COG4566  138 LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLALALG 196
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 182-224 2.12e-05

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: 40.90  E-value: 2.12e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 488140447  182 LSPRENEVLYWASM-GKTYQEIAIITNITPRTVKYHIGNVVKKL 224
Cdd:pfam08281  11 LPPRQREVFLLRYLeGLSYAEIAELLGISEGTVKSRLSRARKKL 54
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 182-224 1.10e-04

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: 1.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 488140447  182 LSPRENEVLYWA-SMGKTYQEIAIITNITPRTVKYHIGNVVKKL 224
Cdd:TIGR02937 111 LPEREREVLVLRyLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
180-226 1.93e-04

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 41.38  E-value: 1.93e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 488140447 180 AILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGV 226
Cdd:PRK10403 152 SVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 196-224 4.47e-04

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: 39.47  E-value: 4.47e-04
                          10        20
                  ....*....|....*....|....*....
gi 488140447  196 GKTYQEIAIITNITPRTVKYHIGNVVKKL 224
Cdd:TIGR02985 129 GLSNKEIAEELGISVKTVEYHITKALKFL 157
PRK10100 PRK10100
transcriptional regulator CsgD;
180-233 7.79e-04

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 39.47  E-value: 7.79e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488140447 180 AILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAI 233
Cdd:PRK10100 154 ALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAV 207
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 182-224 9.23e-04

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: 38.82  E-value: 9.23e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 488140447 182 LSPRENEVLYWASM-GKTYQEIAIITNITPRTVKYHIGNVVKKL 224
Cdd:COG1595  128 LPPRQREVLVLRYLeGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 148-225 2.37e-03

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 38.09  E-value: 2.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488140447 148 QMLLIETHEKMLTLSQRnmniQERQgKGMPGKAILSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLG 225
Cdd:PRK10651 127 EMVLSEALTPVLAASLR----ANRA-TTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
182-239 5.18e-03

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 38.00  E-value: 5.18e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488140447 182 LSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGVINAKQAIGLGVEL 239
Cdd:PRK04841 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQDL 896
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 182-226 7.67e-03

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 36.65  E-value: 7.67e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 488140447 182 LSPRENEVLYWASMGKTYQEIAIITNITPRTVKYHIGNVVKKLGV 226
Cdd:PRK11475 135 LSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 182-214 8.73e-03

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 33.62  E-value: 8.73e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 488140447 182 LSPRENEVLYWAS-MGKTYQEIAIITNITPRTVK 214
Cdd:cd06171   11 LPEREREVILLRFgEGLSYEEIAEILGISRSTVR 44
 
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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