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Conserved domains on  [gi|478738947|gb|AGJ52127|]
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sXVE [Expression vector P16woS_XVE_GFPn]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
 198-435 5.00e-143

Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen); The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases.


:

Pssm-ID: 132747  Cd Length: 235  Bit Score: 409.51  E-value: 5.00e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 198 LTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMI 277
Cdd:cd06949    1 LSAEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLML 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 278 GLVWRSMEHPVKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFlssTLKSL 357
Cdd:cd06949   81 GLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTF---LLESL 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 478738947 358 EEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 435
Cdd:cd06949  158 ESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235
lexA super family cl36676
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 1-90 3.31e-44

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


The actual alignment was detected with superfamily member TIGR00498:

Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 154.10  E-value: 3.31e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947    1 MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVG 80
Cdd:TIGR00498   1 MKPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAIRILDDEPKGVPLIG 80

                          90
                  ....*....|
gi 478738947   81 RVAAGEPSSA 90
Cdd:TIGR00498  81 RVAAGEPILA 90
ESR1_C pfam12743
Oestrogen-type nuclear receptor final C-terminal; This is the very C-terminal region of a ...
 440-483 1.75e-22

Oestrogen-type nuclear receptor final C-terminal; This is the very C-terminal region of a subfamily of nuclear receptors that includes oestrogen receptors and other subfamily 3 group A members. The actual function of this region is not known, but the domain is absent from all the other types of nuclear receptors. Oestrogen receptors modulate AP-1-dependent transcription through two distinct mechanisms: via protein-protein interactions on DNA; and via non-genomic actions. The mechanism used depends on the cellular localization of the receptor. In addition to the more extensively studied cross-talk on DNA, additional non-genomic actions might be very important in target tissues in which membrane-associated ERs are found. These non-genomic actions probably contribute to the overall physiological responses mediated by ligand-bound ERs and might possibly be mediated via this C-terminal domain.


:

Pssm-ID: 432757  Cd Length: 44  Bit Score: 89.88  E-value: 1.75e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 478738947  440 PTSRGGASVEETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV 483
Cdd:pfam12743   1 PANRGGAPMEEDNQSQLATTGSTSSHSLQTYYITGEAESFPSTV 44
HSV_VP16_C pfam12149
Herpes simplex virus virion protein 16 C terminal; This domain is found in viruses, and is ...
 142-167 1.06e-11

Herpes simplex virus virion protein 16 C terminal; This domain is found in viruses, and is about 30 amino acids in length. It is found in association with pfam02232. This domain is the C terminal of the HSV virion protein 16. This protein is a transcription promoter. The C terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc.


:

Pssm-ID: 403392  Cd Length: 26  Bit Score: 59.18  E-value: 1.06e-11
                          10        20
                  ....*....|....*....|....*.
gi 478738947  142 YGALDMADFEFEQMFTDALGIDEYGG 167
Cdd:pfam12149   1 YGALDMADFEFEQMFTDALGIDDFGG 26
 
Name Accession Description Interval E-value
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
 198-435 5.00e-143

Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen); The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases.


Pssm-ID: 132747  Cd Length: 235  Bit Score: 409.51  E-value: 5.00e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 198 LTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMI 277
Cdd:cd06949    1 LSAEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLML 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 278 GLVWRSMEHPVKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFlssTLKSL 357
Cdd:cd06949   81 GLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTF---LLESL 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 478738947 358 EEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 435
Cdd:cd06949  158 ESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 1-90 3.31e-44

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 154.10  E-value: 3.31e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947    1 MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVG 80
Cdd:TIGR00498   1 MKPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAIRILDDEPKGVPLIG 80

                          90
                  ....*....|
gi 478738947   81 RVAAGEPSSA 90
Cdd:TIGR00498  81 RVAAGEPILA 90
LexA_DNA_bind pfam01726
LexA DNA binding domain; This is the DNA binding domain of the LexA SOS regulon repressor ...
 3-65 1.29e-30

LexA DNA binding domain; This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.


Pssm-ID: 396335 [Multi-domain]  Cd Length: 63  Bit Score: 112.86  E-value: 1.29e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 478738947    3 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRG 65
Cdd:pfam01726   1 PLTERQREVLDFIKASIEETGYPPSRREIARALGLRSPNAAEEHLKALERKGYIERDPGKPRA 63
HOLI smart00430
Ligand binding domain of hormone receptors;
238-405 2.27e-30

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 115.54  E-value: 2.27e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947   238 ADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLLDRN---QGKCVEGMVEIFD 314
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPdavLELRKLFSPFLDR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947   315 MLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEkdhihrVLDKITDTLIHLMAKAGltLQQQHQRLAQ 394
Cdd:smart00430  81 ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEK------LQEKYANALHDYYLKNY--PMNYPGRFAK 152

                          170
                   ....*....|.
gi 478738947   395 LLLILSHIRHM 405
Cdd:smart00430 153 LLLILPELRKI 163
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 1-90 1.12e-29

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 115.01  E-value: 1.12e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947   1 MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSpNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEE--GLPL 78
Cdd:COG1974    1 MKKLTKRQREILDFIKEYIRERGYPPSQREIAEALGLSS-SAVHRHLKALEKKGYLRRDPGKSRAIELLPASPEvvGLPL 79

                         90
                 ....*....|..
gi 478738947  79 VGRVAAGEPSSA 90
Cdd:COG1974   80 LGRVAAGFPIPA 91
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 224-406 1.72e-24

Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in binding the hormone in these receptors.


Pssm-ID: 459675 [Multi-domain]  Cd Length: 194  Bit Score: 100.50  E-value: 1.72e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947  224 PFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLLDRNQG 303
Cdd:pfam00104   6 KKLRKATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLMISDDD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947  304 --KCVEGMVEIFDM----------------LLATSSRFRMMNLQGEEFVCLKSIILLNSGvytflsstLKSLEEK--DHI 363
Cdd:pfam00104  86 amKFVEDDSSWCTNydleqllfflpffnsyFFELVKPLRELNPDDEELAYLLAQLLFDYA--------GDGLSGEilEIV 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 478738947  364 HRVLDKITDTLiHlmakaGLTLQQQHQRLAQLLLILSHIRHMS 406
Cdd:pfam00104 158 EKLQEKLANEL-H-----DYYVNKYSGRLAKLLKILPSLRKIS 194
ESR1_C pfam12743
Oestrogen-type nuclear receptor final C-terminal; This is the very C-terminal region of a ...
 440-483 1.75e-22

Oestrogen-type nuclear receptor final C-terminal; This is the very C-terminal region of a subfamily of nuclear receptors that includes oestrogen receptors and other subfamily 3 group A members. The actual function of this region is not known, but the domain is absent from all the other types of nuclear receptors. Oestrogen receptors modulate AP-1-dependent transcription through two distinct mechanisms: via protein-protein interactions on DNA; and via non-genomic actions. The mechanism used depends on the cellular localization of the receptor. In addition to the more extensively studied cross-talk on DNA, additional non-genomic actions might be very important in target tissues in which membrane-associated ERs are found. These non-genomic actions probably contribute to the overall physiological responses mediated by ligand-bound ERs and might possibly be mediated via this C-terminal domain.


Pssm-ID: 432757  Cd Length: 44  Bit Score: 89.88  E-value: 1.75e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 478738947  440 PTSRGGASVEETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV 483
Cdd:pfam12743   1 PANRGGAPMEEDNQSQLATTGSTSSHSLQTYYITGEAESFPSTV 44
HSV_VP16_C pfam12149
Herpes simplex virus virion protein 16 C terminal; This domain is found in viruses, and is ...
 142-167 1.06e-11

Herpes simplex virus virion protein 16 C terminal; This domain is found in viruses, and is about 30 amino acids in length. It is found in association with pfam02232. This domain is the C terminal of the HSV virion protein 16. This protein is a transcription promoter. The C terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc.


Pssm-ID: 403392  Cd Length: 26  Bit Score: 59.18  E-value: 1.06e-11
                          10        20
                  ....*....|....*....|....*.
gi 478738947  142 YGALDMADFEFEQMFTDALGIDEYGG 167
Cdd:pfam12149   1 YGALDMADFEFEQMFTDALGIDDFGG 26
 
Name Accession Description Interval E-value
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
 198-435 5.00e-143

Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen); The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases.


Pssm-ID: 132747  Cd Length: 235  Bit Score: 409.51  E-value: 5.00e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 198 LTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMI 277
Cdd:cd06949    1 LSAEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLML 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 278 GLVWRSMEHPVKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFlssTLKSL 357
Cdd:cd06949   81 GLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTF---LLESL 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 478738947 358 EEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 435
Cdd:cd06949  158 ESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235
NR_LBD_ER_like cd07068
The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ...
 203-434 1.70e-119

The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER and ERRs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132753  Cd Length: 221  Bit Score: 348.83  E-value: 1.70e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 203 MVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWR 282
Cdd:cd07068    1 LLSALLVAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 283 SMEHPVKLLFAPNLLLDRNQGKcVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTflsstlksLEEKDH 362
Cdd:cd07068   81 SLPHPGKLVFAPDLLLDREQAR-VEGLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRH--------LEDREA 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 478738947 363 IHRVLDKITDTLIHLMAKAGLTlqQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDA 434
Cdd:cd07068  152 VQQLRDAILDALVDVEAKRHGS--QQPRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLEA 221
NR_LBD_ERR cd06946
The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding ...
 203-434 7.78e-52

The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132744  Cd Length: 221  Bit Score: 174.86  E-value: 7.78e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 203 MVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWR 282
Cdd:cd06946    1 ILSHLLVAEPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 283 SMEHPVKLLFAPNLLLDRNQGKCVeGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVytflsstlKSLEEKDH 362
Cdd:cd06946   81 SLPFNGELVFAEDFILDEELAREA-GLLELYSACLQLVRRLQRLRLEKEEYVLLKALALANSDS--------VHIEDVEA 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 478738947 363 IHRVLDKITDTLIHLMakAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDA 434
Cdd:cd06946  152 VRQLRDALLEALSDYE--AGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLEA 221
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 1-90 3.31e-44

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 154.10  E-value: 3.31e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947    1 MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVG 80
Cdd:TIGR00498   1 MKPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAIRILDDEPKGVPLIG 80

                          90
                  ....*....|
gi 478738947   81 RVAAGEPSSA 90
Cdd:TIGR00498  81 RVAAGEPILA 90
NR_LBD_F2 cd06930
Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear ...
 231-405 1.50e-43

Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132728 [Multi-domain]  Cd Length: 165  Bit Score: 151.22  E-value: 1.50e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 231 MGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPV--KLLFAPNLLLDRNQGKCvEG 308
Cdd:cd06930    1 PESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELseLLLPSPLLVILTEREAL-LG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 309 MVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVytflsstlKSLEEKDHIHRVLDKITDTLIHLMAKAGltlQQQ 388
Cdd:cd06930   80 LAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDL--------PGLKNQQQVEELQEKAQQALQEYIRKRY---PQQ 148

                        170
                 ....*....|....*..
gi 478738947 389 HQRLAQLLLILSHIRHM 405
Cdd:cd06930  149 PARFAKLLLRLPELRSI 165
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 233-405 1.81e-37

The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132726  Cd Length: 168  Bit Score: 135.12  E-value: 1.81e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 233 LLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLL---DRNQGKCVEGM 309
Cdd:cd06157    2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHtddDKEDEMKLLLK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 310 VEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTflsstlkSLEEKDHIHRVLDKITDTLIHLMAKAGltLQQQH 389
Cdd:cd06157   82 GELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE-------SLEDRKIVEELQERLLEALQDYLRKNY--PEEAP 152

                        170
                 ....*....|....*.
gi 478738947 390 QRLAQLLLILSHIRHM 405
Cdd:cd06157  153 SRFAKLLLLLPSLRKL 168
LexA_DNA_bind pfam01726
LexA DNA binding domain; This is the DNA binding domain of the LexA SOS regulon repressor ...
 3-65 1.29e-30

LexA DNA binding domain; This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.


Pssm-ID: 396335 [Multi-domain]  Cd Length: 63  Bit Score: 112.86  E-value: 1.29e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 478738947    3 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRG 65
Cdd:pfam01726   1 PLTERQREVLDFIKASIEETGYPPSRREIARALGLRSPNAAEEHLKALERKGYIERDPGKPRA 63
HOLI smart00430
Ligand binding domain of hormone receptors;
238-405 2.27e-30

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 115.54  E-value: 2.27e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947   238 ADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLLDRN---QGKCVEGMVEIFD 314
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPdavLELRKLFSPFLDR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947   315 MLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEkdhihrVLDKITDTLIHLMAKAGltLQQQHQRLAQ 394
Cdd:smart00430  81 ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEK------LQEKYANALHDYYLKNY--PMNYPGRFAK 152

                          170
                   ....*....|.
gi 478738947   395 LLLILSHIRHM 405
Cdd:smart00430 153 LLLILPELRKI 163
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
 204-417 3.70e-30

The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily; The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear receptors. Ultraspiracle (USP) plays similar roles as DNA binding partner of other nuclear rec eptors in invertebrates. USP has no known high-affinity ligand and is thought to be a silent component in the heterodimeric complex with partner receptors. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR and USP have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132741  Cd Length: 207  Bit Score: 116.62  E-value: 3.70e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 204 VSALLDAEppILYSEYDPTRPFSEASMMGLLTNL---ADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLV 280
Cdd:cd06943    4 IERILEAE--LAVEPKSEAVAMVPPEYRDPVSNIcqaADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 281 WRSMEHPVKLLFAPNLLLDRNQGKCVeGMVEIFDMLLAT-SSRFRMMNLQGEEFVCLKSIILLNSGVytflsstlKSLEE 359
Cdd:cd06943   82 HRSIAVKDGILLATGLHLHRNSAHQA-GVGAIFDRILTElVVKMRDLKMDRTELGCLRAIILFNPDV--------KGLKS 152

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 478738947 360 KDHIHRVLDKITDTlihLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMK 417
Cdd:cd06943  153 RQEVESLREKVYAS---LEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 207
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 1-90 1.12e-29

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 115.01  E-value: 1.12e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947   1 MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSpNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEE--GLPL 78
Cdd:COG1974    1 MKKLTKRQREILDFIKEYIRERGYPPSQREIAEALGLSS-SAVHRHLKALEKKGYLRRDPGKSRAIELLPASPEvvGLPL 79

                         90
                 ....*....|..
gi 478738947  79 VGRVAAGEPSSA 90
Cdd:COG1974   80 LGRVAAGFPIPA 91
NR_LBD_PR cd07074
Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; ...
 202-416 5.95e-26

Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues like brain, liver, mammary gland and spermatozoa. There are two natural PR isoforms called PR-A and PR-B. PR-B has an additional stretc h of 164 amino acids at the N terminus. The extra domain in PR-B performs activation functions by recruiting coactivators that could not be recruited by PR-A. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD is not only involved in binding to progesterone, but also involved in coactivator binding and dimerization.


Pssm-ID: 132759  Cd Length: 248  Bit Score: 106.18  E-value: 5.95e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 202 QMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVW 281
Cdd:cd07074    1 PLINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 282 RSMEH--PVKLLFAPNLLLDRNQGKcvegMVEIFDMLLAT---SSRFRMMNLQGEEFVCLKSIILLNsgvyTFLSSTLKS 356
Cdd:cd07074   81 RSYKHvsGQMLYFAPDLILNEQRMK----ESSFYSLCLTMwqiPQEFVKLQVSQEEFLCMKALLLLN----TIPLEGLRS 152

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 478738947 357 LEEkdhihrvLDKITDTLIHLMAKAgLTLQQQ-----HQRLAQLLLILSHIRHMSNKgmEHLYSM 416
Cdd:cd07074  153 QTQ-------FDEMRSSYIRELIKA-IGLRQKgvvasSQRFYQLTKLMDNMHDLVKQ--LHLYCL 207
NR_LBD_GR_Like cd06947
Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid ...
 202-344 8.85e-25

Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor; The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator protein-1, to regulate gene expression patterns. Both pathways can up-regulate or down-regulate gene expression and require ligand activation of the receptor and recruitment of other cofactors such as chaperone proteins and coregulator proteins. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR, MR, PR, and AR share the same modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132745  Cd Length: 246  Bit Score: 102.82  E-value: 8.85e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 202 QMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVW 281
Cdd:cd06947    1 SLLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGW 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 478738947 282 RSMEH--PVKLLFAPNLLLDRNQGKcVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNS 344
Cdd:cd06947   81 RSYKHvnSQMLYFAPDLVFNEQRMH-QSAMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLST 144
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 224-406 1.72e-24

Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in binding the hormone in these receptors.


Pssm-ID: 459675 [Multi-domain]  Cd Length: 194  Bit Score: 100.50  E-value: 1.72e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947  224 PFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLLDRNQG 303
Cdd:pfam00104   6 KKLRKATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLMISDDD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947  304 --KCVEGMVEIFDM----------------LLATSSRFRMMNLQGEEFVCLKSIILLNSGvytflsstLKSLEEK--DHI 363
Cdd:pfam00104  86 amKFVEDDSSWCTNydleqllfflpffnsyFFELVKPLRELNPDDEELAYLLAQLLFDYA--------GDGLSGEilEIV 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 478738947  364 HRVLDKITDTLiHlmakaGLTLQQQHQRLAQLLLILSHIRHMS 406
Cdd:pfam00104 158 EKLQEKLANEL-H-----DYYVNKYSGRLAKLLKILPSLRKIS 194
NR_LBD_GR cd07076
Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor ...
 203-405 2.98e-24

Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily; The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription. GR can also function as a repressor of other gene transcription activators, such as NF-kappaB and AF-1 by directly binding to them, and bloc king the expression of their activated genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD also functions for dimerization and chaperone protein association.


Pssm-ID: 132761  Cd Length: 247  Bit Score: 101.16  E-value: 2.98e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 203 MVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWR 282
Cdd:cd07076    2 LVSLLEVIEPEVLYSGYDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 283 SMEHPVK--LLFAPNLLLDRNQGKcVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNsgvyTFLSSTLKSleek 360
Cdd:cd07076   82 SYRQSNGnlLCFAPDLIINEQRMT-LPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLS----TVPKDGLKS---- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 478738947 361 dhiHRVLDKITDTLIHLMAKAGLTLQ----QQHQRLAQLLLILSHIRHM 405
Cdd:cd07076  153 ---QELFDEIRMTYIKELGKAIVKREgnssQNWQRFYQLTKLLDSMHEV 198
ESR1_C pfam12743
Oestrogen-type nuclear receptor final C-terminal; This is the very C-terminal region of a ...
 440-483 1.75e-22

Oestrogen-type nuclear receptor final C-terminal; This is the very C-terminal region of a subfamily of nuclear receptors that includes oestrogen receptors and other subfamily 3 group A members. The actual function of this region is not known, but the domain is absent from all the other types of nuclear receptors. Oestrogen receptors modulate AP-1-dependent transcription through two distinct mechanisms: via protein-protein interactions on DNA; and via non-genomic actions. The mechanism used depends on the cellular localization of the receptor. In addition to the more extensively studied cross-talk on DNA, additional non-genomic actions might be very important in target tissues in which membrane-associated ERs are found. These non-genomic actions probably contribute to the overall physiological responses mediated by ligand-bound ERs and might possibly be mediated via this C-terminal domain.


Pssm-ID: 432757  Cd Length: 44  Bit Score: 89.88  E-value: 1.75e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 478738947  440 PTSRGGASVEETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV 483
Cdd:pfam12743   1 PANRGGAPMEEDNQSQLATTGSTSSHSLQTYYITGEAESFPSTV 44
NR_LBD_MR cd07075
Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor ...
 204-417 2.40e-21

Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily; The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD ). The LBD, in addition to binding ligand, contains a ligand-dependent activation function-2 (AF-2).


Pssm-ID: 132760  Cd Length: 248  Bit Score: 93.08  E-value: 2.40e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 204 VSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRS 283
Cdd:cd07075    3 VMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRS 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 284 MEHPVK--LLFAPNLLLDRNQGKcVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKD 361
Cdd:cd07075   83 YKHTNSqfLYFAPDLVFNEERMH-QSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRT 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 478738947 362 HIHRVLDKItdtlihlMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGME-HLYSMK 417
Cdd:cd07075  162 NYIKELRKM-------VTKAPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEfCFYTFR 211
NR_LBD_Ftz-F1_like cd06944
The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of ...
 216-434 1.95e-20

The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132742 [Multi-domain]  Cd Length: 237  Bit Score: 90.03  E-value: 1.95e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 216 YSEYDPTRPFseasmmGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVK---LLF 292
Cdd:cd06944   31 YNRGEELDTF------GLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEdsiLLV 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 293 APN----LLLDRNQGKCVEGMVEIFDMLLatsSRFRMMNLQGEEFVCLKSIILLNSGVytflsstlKSLEEKDHIHRVLD 368
Cdd:cd06944  105 TGQevdlSTLASQAGLGLSSLVDRAQELV---NKLRELQFDRQEFVCLKFLILFNPDV--------KGLENRQLVESVQE 173

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 478738947 369 KITDTL-IHLMAkaglTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDA 434
Cdd:cd06944  174 QVNAALlDYTLC----NYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHA 236
NR_LBD_Nurr1_like cd06945
The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear ...
 202-417 3.47e-20

The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily; The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of tr anscriptional initiation. Another group of receptor in this family is DHR38. DHR38 is the Drosophila homolog to the vertebrate NGFI-B-type orphan receptor. It interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. Nurr1_like proteins exhibit a modular structure that is characteristic for nuclear receptors; they have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132743 [Multi-domain]  Cd Length: 239  Bit Score: 89.38  E-value: 3.47e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 202 QMVSALLDAEPPIL---YSEY----DPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEI 274
Cdd:cd06945    7 ALVRAHVDSTPRKTdldYSKIqenvDPVPPKPDSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLEL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 275 LMIGLVWRSMEHPVKLLFAPNLLLDRNQgkCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLksIILLnsgvytFLSSTL 354
Cdd:cd06945   87 FVLRLAYRSNPVDGKLVFCNGLVLHRLQ--CVRGFGEWLDSILAFSSSLQSLLLDDISAFCC--LALL------LLITER 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 478738947 355 KSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHqRLAQLLLILSHIRHMSNKGMEHLYSMK 417
Cdd:cd06945  157 HGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPN-RLSKLLLKLPELRTLSKKGLQRIFFLK 218
NR_LBD_Lrh-1 cd07069
The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor ...
 229-436 5.35e-19

The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,; The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132754 [Multi-domain]  Cd Length: 241  Bit Score: 86.23  E-value: 5.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 229 SMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVK--LLFAPNLLLDRNQGKCV 306
Cdd:cd07069   40 STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEgsIFLVTGQQVDYSIIASQ 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 307 EGMVeiFDMLLATS----SRFRMMNLQGEEFVCLKSIILLnsgvytflSSTLKSLEEKDHIHRVLDKITDTLIHLMAkag 382
Cdd:cd07069  120 AGAT--LNNLMSHAqelvAKLRSLQFDQREFVCLKFLVLF--------SLDVKNLENFQLVEGVQEQVNAALLDYTM--- 186

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 478738947 383 LTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHR 436
Cdd:cd07069  187 CNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKR 240
NR_LBD_NGFI-B cd07348
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 203-423 1.91e-17

The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132762  Cd Length: 238  Bit Score: 81.41  E-value: 1.91e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 203 MVSALLDAEPPIL---YSEYDPTRPF----SEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEIL 275
Cdd:cd07348    8 LVRAHIDSNPSSAkldYSKFQESVSPlfekEDASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELF 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 276 MIGLVWRSMEHPVKLLFAPNLLLDRNQgkCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLnsgvytflsSTLK 355
Cdd:cd07348   88 ILRLAYRSNPEEGKLIFCNGVVLHRTQ--CVRGFGDWIDSILEFSQSLHRMNLDVSAFSCLAALVII---------TDRH 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 478738947 356 SLEEKDHIHRVLDKITDTLIHLMAKAGLTlQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVP 423
Cdd:cd07348  157 GLKEPKRVEELQNRLISCLKEHVSGSASE-PQRPNCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVP 223
NR_LBD_AR cd07073
Ligand binding domain of the nuclear receptor androgen receptor, ligand activated ...
 211-396 3.58e-17

Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator; The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD is not only involved in binding to androgen, but also involved in binding of coactivator proteins and dimerization. A ligand dependent nuclear export signal is also present at the ligand binding domain.


Pssm-ID: 132758  Cd Length: 246  Bit Score: 80.75  E-value: 3.58e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 211 EPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHpVK- 289
Cdd:cd07073   10 EPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTN-VNs 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 290 --LLFAPNLLLDRNQGKcVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNsgvyTFLSSTLKSLEEKDHIHRVL 367
Cdd:cd07073   89 rmLYFAPDLVFNEYRMH-KSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFS----IIPVDGLKNQKFFDELRMNY 163

                        170       180
                 ....*....|....*....|....*....
gi 478738947 368 DKITDTLIHLMAKAGLTLQQQHQRLAQLL 396
Cdd:cd07073  164 IKELDRIIACKRKNPTSCSRRFYQLTKLL 192
NR_LBD_HNF4_like cd06931
The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in ...
 204-431 2.24e-16

The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes; The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD domain is also responsible for recruiting co-activator proteins. More than 280 nuclear receptors are found in C. ele gans, most of which are originated from an explosive burst of duplications of HNF4.


Pssm-ID: 132729  Cd Length: 222  Bit Score: 78.19  E-value: 2.24e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 204 VSALLDAE-------PPILYSEYDpTRPFSEASMMGLLTNLADRELVhMINWAKRVPGFVDLTLHDQVHLLECAWLEILM 276
Cdd:cd06931    2 ISVLLQAEalsrqqsSPIPTCSGD-IRPKKIASINDVCESMKQQLLV-LVEWAKYIPAFCELPLDDQVALLRAHAGEHLL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 277 IGLVWRSMEHPVKLLFAPNLLLDRNQGKCVEGMV--EIFDMLLATssrFRMMNLQGEEFVCLKSIILLNSGVytflsstl 354
Cdd:cd06931   80 LGVARRSMPYKDILLLGNDLIIPRHCPEPEISRVanRILDELVLP---LRDLNIDDNEYACLKAIVFFDPDA-------- 148

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 478738947 355 KSLEEKDHIHRVLDKItdtLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEM 431
Cdd:cd06931  149 KGLSDPQKIKRLRFQV---QVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222
NR_LBD_SF-1 cd07070
The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear ...
 202-434 7.27e-16

The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily; The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132755  Cd Length: 237  Bit Score: 76.92  E-value: 7.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 202 QMVSALLDAEPP-------ILYSEYDPTRPFSEA-SMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLE 273
Cdd:cd07070    3 ELILQLLQLEPDedqvrarILGCLQEPQKSRPDQpAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 274 ILMIGLVWRSMEHPVK--LLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQ--GEEFVCLKSIILLNSGVyTF 349
Cdd:cd07070   83 LLVFDHIYRQVQHGKEgsILLVTGQEVELSTVAAQAGSLLHSLVLRAQELVLQLHALQldRQEFVCLKFLILFSLDV-KF 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 350 LS--STLKSLEEKDHiHRVLDKitdTLIHLmakagltlQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDL 427
Cdd:cd07070  162 LNnhSLVKDAQEKAN-AALLDY---TLCHY--------PHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNL 229


                 ....*..
gi 478738947 428 LLEMLDA 434
Cdd:cd07070  230 LIEMLQA 236
NR_LBD_Tlx_PNR_like cd06950
The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand ...
 246-417 1.24e-15

The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132748 [Multi-domain]  Cd Length: 206  Bit Score: 75.41  E-value: 1.24e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 246 INWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMehPVKL--LFAPNLLLDRNQGKCVEGMVEIfDMLLATSSRF 323
Cdd:cd06950   43 VKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSL--PLDScpLLAVPGLSPDNTEAERTFLSEV-RALQETLSRF 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 324 RMMNLQGEEFVCLKSIILLNSGvytflSSTLKSLEE----KDHIHRVLDKitdtliHLMAkaglTLQQQHQRLAQLLLIL 399
Cdd:cd06950  120 RQLRVDATEFACLKAIVLFKPE-----TRGLKDPAQvealQDQAQLMLNK------HIRT----RYPTQPARFGKLLLLL 184

                        170
                 ....*....|....*...
gi 478738947 400 SHIRHMSNKGMEHLYSMK 417
Cdd:cd06950  185 PSLRFISSSTIEELFFKK 202
NR_LBD_Nurr1 cd07071
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 203-423 1.71e-15

The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132756  Cd Length: 238  Bit Score: 75.84  E-value: 1.71e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 203 MVSALLDAEPPILYSEYDPTRPFSEASMMG-----------LLTnlADRELVHmiNWAKRVPGFVDLTLHDQVHLLECAW 271
Cdd:cd07071    8 LVRAHVDSNPAMTSLDYSRFQANPDYQMSGddtqhiqqfydLLT--GSMEIIR--GWAEKIPGFTDLPKADQDLLFESAF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 272 LEILMIGLVWRSMEHPVKLLFAPNLLLDRNQgkCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLnsgvytfls 351
Cdd:cd07071   84 LELFVLRLAYRSNPVEGKLIFCNGVVLHRLQ--CVRGFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV--------- 152

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 478738947 352 STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQrLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVP 423
Cdd:cd07071  153 TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNY-LSKLLGKLPELRTLCTQGLQRIFYLKLEDLVP 223
NR_LBD_DHR4_like cd06953
The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ...
 209-411 8.05e-15

The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132751  Cd Length: 213  Bit Score: 73.18  E-value: 8.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 209 DAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSM-EHP 287
Cdd:cd06953    7 DLEPLITPMLIEDGATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASlQNL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 288 VKLLFAPNLLLDRNQG--KCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLN-SGVYTFLSSTLKSLEEkdHIH 364
Cdd:cd06953   87 GLLQDCLSKYLPSEDEleRFGDEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNqDIDGLTNASQLESLQK--RYW 164

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 478738947 365 RVLDkitdtlIHLMAKAgltlQQQHQRLAQLLLILSHIRHMSNKGME 411
Cdd:cd06953  165 YVLQ------DFTELNY----PNQPNRFSDLLSCLPEIRAAAGKLLH 201
NR_LBD_RAR cd06937
The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear ...
 235-433 2.29e-14

The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily; The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to an inactive condensed chromatin structure, preventing transcription. Upon ligand binding, the corepressors are released, and coactivator complexes such as histone acetyltransferase or histone arginine methyltransferases are recruited to activate transcription. There are three RAR subtypes (alpha, beta, gamma), originating from three distinct genes. For each subtype, several isoforms exist that differ in their N-terminal region, allowing retinoids to exert their pleiotropic effects. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132735  Cd Length: 231  Bit Score: 72.54  E-value: 2.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 235 TNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLLDRNQGKcVEGMVEIFD 314
Cdd:cd06937   44 SELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMH-NAGFGPLTD 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 315 MLLATSSRFRMMNLQGEEFVCLKSIILlnsgvytfLSSTLKSLEEKDHIhrvlDKITDTLIH-LMAKAGLTLQQQHQRLA 393
Cdd:cd06937  123 LVFTFANQLLPLEMDDTEIGLLSAICL--------ICGDRQDLEEPDRV----EKLQEPLLEaLKIYARKRRPDKPHMFP 190

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 478738947 394 QLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLD 433
Cdd:cd06937  191 KMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEMLE 230
HSV_VP16_C pfam12149
Herpes simplex virus virion protein 16 C terminal; This domain is found in viruses, and is ...
 142-167 1.06e-11

Herpes simplex virus virion protein 16 C terminal; This domain is found in viruses, and is about 30 amino acids in length. It is found in association with pfam02232. This domain is the C terminal of the HSV virion protein 16. This protein is a transcription promoter. The C terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc.


Pssm-ID: 403392  Cd Length: 26  Bit Score: 59.18  E-value: 1.06e-11
                          10        20
                  ....*....|....*....|....*.
gi 478738947  142 YGALDMADFEFEQMFTDALGIDEYGG 167
Cdd:pfam12149   1 YGALDMADFEFEQMFTDALGIDDFGG 26
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
 204-432 1.80e-11

Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family; The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well cons erved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132746  Cd Length: 236  Bit Score: 64.01  E-value: 1.80e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 204 VSALLDAEPpilYSEYDPTRPFSEASMMGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVW 281
Cdd:cd06948    6 ISLLLRAEP---YPTSRYGSQCQPNNIMGIdnICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 282 RSME-HPVKLLFAPNLLLDRNQGK---CVEGMVEIFDMLLatsSRFRMMNLQGEEFVCLKSIILLNsgvytflsSTLKSL 357
Cdd:cd06948   83 CCMPlHVAPLLAAAGLHASPMSADrvvAFMDHIRIFQEQV---EKLKALHVDSAEFSCLKAIVLFT--------SDACGL 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 478738947 358 EEKDHIHRVLDKITDTLIHLMAKaglTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEML 432
Cdd:cd06948  152 SDPAHIESLQEKSQCALEEYVRT---QYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 223
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
 229-413 4.83e-09

Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132727  Cd Length: 174  Bit Score: 55.69  E-value: 4.83e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 229 SMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLLDRNQGKCVeG 308
Cdd:cd06929    2 EKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSRDVLLNG-G 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 309 MVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILlnsgvytfLSSTLKSLEEKDHIHRVLDKITDTLIHLmakAGLTLQQQ 388
Cdd:cd06929   81 FGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVL--------FSPDRPGLQDVDTVEKLQERLLEALQRY---LKVNHPDA 149

                        170       180
                 ....*....|....*....|....*
gi 478738947 389 HQRLAQLLLILSHIRHMSNKGMEHL 413
Cdd:cd06929  150 PQMFAKLLKKLTELRTLNELHAELL 174
NR_LBD_REV_ERB cd06940
The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; ...
 245-417 1.64e-08

The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132738  Cd Length: 189  Bit Score: 54.42  E-value: 1.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 245 MINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLV--WRSMEHPVKLLFAPNLLLDRNQGKcveGMVEIFDMLLATSSR 322
Cdd:cd06940   28 VVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFAslFDAKERSVTFLSGQKYSVDDLHSM---GAGDLLNSMFDFSEK 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 323 FRMMNLQGEEFVCLKSIILlnsgvytfLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKaglTLQQQHQRLAQLLLILSHI 402
Cdd:cd06940  105 LNSLQLSDEEMGLFTAVVL--------VSADRSGLENVNLVEALQETLIRALRTLIAK---NHPNEPSIFTKLLLKLPDL 173

                        170
                 ....*....|....*
gi 478738947 403 RHMSNKGMEHLYSMK 417
Cdd:cd06940  174 RTLNNLHSEKLLAFK 188
NR_LBD_VDR cd06933
The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; ...
 196-374 2.78e-08

The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132731  Cd Length: 238  Bit Score: 54.59  E-value: 2.78e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 196 LSLTADQMVSALLDAEPPIL---YSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 272
Cdd:cd06933    1 LSDEQQKIIDILLEAHHKTYdttYSDFNKFRPPVRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 273 EILMIglvwRS-----MEHPVKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILlnsgvy 347
Cdd:cd06933   81 EVIML----RSnqsfsLDDMSWTCGSPDFKYKVSDVTKAGHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICI------ 150

                        170       180
                 ....*....|....*....|....*..
gi 478738947 348 tfLSSTLKSLEEKDHIHRVLDKITDTL 374
Cdd:cd06933  151 --LSPDRPGVQDHALIEAIQDRLSDTL 175
NR_LBD_LXR cd06954
The ligand binding domain of Liver X receptors, a family of nuclear receptors of ...
 235-420 1.33e-07

The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors; The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, spleen, and adipose tissue, whereas LXRbeta is ubiquitously expressed at lower level. Both LXRalpha and LXRbeta function as heterodimers with the retinoid X receptor (RX R) which may be activated by either LXR ligands or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. LXR has typical NR modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and the ligand binding domain (LBD) at the C-terminal.


Pssm-ID: 132752  Cd Length: 236  Bit Score: 52.45  E-value: 1.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 235 TNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNLLLDRNQGKCVEGMVEIFD 314
Cdd:cd06954   49 TELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFARAGLQVEFIN 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 315 MLLATSSRFRMMNLQGEEFVCLKSIILlnsgvytfLSSTLKSLEEKDHIHRVLDKITDTlihLMAKAGLTLQQQHQRLAQ 394
Cdd:cd06954  129 PIFEFSKSMRELQLDDAEYALLIAINI--------FSADRPNVQDHHRVERLQETYVEA---LHSYIKIKRPSDRLMFPR 197

                        170       180
                 ....*....|....*....|....*.
gi 478738947 395 LLLILSHIRHMSNKGMEHLYSMKCKN 420
Cdd:cd06954  198 MLMKLVSLRTLSSVHSEQVFALRLQD 223
NR_LBD_EcR cd06938
The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors ...
 217-433 8.77e-06

The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family; The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcriptional activation of genes controlled by EcR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ec dysone receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132736 [Multi-domain]  Cd Length: 231  Bit Score: 47.05  E-value: 8.77e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 217 SEYDPTRPFSEASMMGLLTnladRELVHmiNWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAPNL 296
Cdd:cd06938   33 DEDQSDMRFRHITEMTILT----VQLIV--EFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQ 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 297 LLDRNQGKcVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLnsgvytflsSTLKSLEEKDHIHRVLDKITDTLih 376
Cdd:cd06938  107 PYTRDSYR-KAGMGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIF---------SDRPGLLQPKKVEKIQEIYLEAL-- 174

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 478738947 377 LMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKN-VVPlyDLLLEMLD 433
Cdd:cd06938  175 RAYVDNRRPPSQRVIFAKLLSILTELRTLGNQNSEMCFSLKLKNrKLP--PFLAEIWD 230
NR_LBD_TR2_like cd06952
The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding ...
 238-414 1.24e-05

The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, peroxisome proliferator-activated receptor. TR4/2 binds to HREs as a dimer. Like other members of the nuclea r receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132750  Cd Length: 222  Bit Score: 46.17  E-value: 1.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 238 ADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPVKLLFAP-------NLLLDRNQGKCVEGMV 310
Cdd:cd06952   30 ASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAiinhlqtSIQQDKLSADKVKQVM 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 311 EIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNsgvytflsSTLKSLEEKDHIHRVLDKITDTLIHLMAKaglTLQQQHQ 390
Cdd:cd06952  110 EHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFS--------PDHPGQELRQQIEKLQEKALMELRDYVGK---TYPEDEY 178

                        170       180
                 ....*....|....*....|....
gi 478738947 391 RLAQLLLILSHIRHMSNKGMEHLY 414
Cdd:cd06952  179 RLSKLLLRLPPLRSLSPAITEELF 202
NR_LBD_DmE78_like cd06941
The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear ...
 230-285 1.40e-04

The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily; The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132739  Cd Length: 195  Bit Score: 42.77  E-value: 1.40e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 478738947 230 MMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILmigLVWRSME 285
Cdd:cd06941    3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVW---LVRISRL 55
COG2345 COG2345
Predicted transcriptional regulator, ArsR family [Transcription];
4-57 6.08e-04

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441914 [Multi-domain]  Cd Length: 217  Bit Score: 41.06  E-value: 6.08e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 478738947   4 LTARQQEVFDLIRDHisqtgMPPTRAEIAQRLGFrSPNAAEEHLKALARKGVIE 57
Cdd:COG2345   11 ADPTRRRILELLKRA-----GPVTAAELAEALGL-TPNAVRRHLDALEEEGLVE 58
NR_LBD_SHP cd07349
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 237-432 1.19e-03

The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.


Pssm-ID: 132763  Cd Length: 222  Bit Score: 40.19  E-value: 1.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 237 LADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLV-----WRSMEHPVKLLFApNLLLDRNQGKCVEGMVE 311
Cdd:cd07349   27 EASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAqdrvtFEVAEAPVPSMLK-KILLEGQSSSGGSGQPD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 478738947 312 IFDMLLATSSR-------FRMMNLQGEEFVCLKSIILLNSGVytflsstlKSLEEKDHIHrvldkitdtliHLMAKAGLT 384
Cdd:cd07349  106 RPQPSLAAVQWlqcclnkFWSLDLSPKEYAYLKGTILFNPDV--------PGLTASSHVG-----------HLQQEAQWA 166

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 478738947 385 LQ--------QQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEML 432
Cdd:cd07349  167 LCevleplhpQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML 222
NR_LBD_ROR_like cd06939
The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor ...
 244-277 8.78e-03

The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily; The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been su ggested that cholesterol or a cholesterol derivative is the natural ligand of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132737 [Multi-domain]  Cd Length: 241  Bit Score: 37.73  E-value: 8.78e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 478738947 244 HMINWAKRVPGFVDLTLHDQVHLLECAWLEILMI 277
Cdd:cd06939   63 YVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLV 96
 
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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