NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|212646489|ref|NP_506036|]
View 

Nuclear hormone receptor family member nhr-209 [Caenorhabditis elegans]

Protein Classification

nuclear hormone receptor family protein( domain architecture ID 10161315)

nuclear hormone receptor family protein is a ligand-regulated transcriptional modulator that may play a role in many developmental processes

Gene Ontology:  GO:0004879|GO:0008270|GO:0003677
PubMed:  15242336|10892345|15242339
SCOP:  4003622

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
219-384 1.97e-28

Ligand binding domain of hormone receptors;


:

Pssm-ID: 214658  Cd Length: 163  Bit Score: 109.38  E-value: 1.97e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489   219 MHSALLAAVEASKTFEFFSKISHEARMILIRHVSLIGSNMMSASFSMHHRKSdELLLPDGTVFGSIGGCLASEVLGEIKY 298
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKE-LLLAPDGTYIRPDAVLELRKLFSPFLD 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489   299 KnQLQQILHAFLRINVDRVEYMILKAILMRNPSVPGLTLDDQLIIENERNQYAKALLEYTILHHGvLSGPARFGSLIAIN 378
Cdd:smart00430  80 R-ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYP-MNYPGRFAKLLLIL 157


                   ....*.
gi 212646489   379 PIIETQ 384
Cdd:smart00430 158 PELRKI 163
NR_DBD_HNF4A cd06960
DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc ...
 46-120 3.69e-28

DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers; DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. 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).


:

Pssm-ID: 143518  Cd Length: 76  Bit Score: 105.73  E-value: 3.69e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQRL-CKGCRFARCIEVGMDSTAIR 120
Cdd:cd06960    1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNC----VVDKDKRNaCRYCRFKKCLEVGMDPEAVQ 72
 
Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
219-384 1.97e-28

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 109.38  E-value: 1.97e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489   219 MHSALLAAVEASKTFEFFSKISHEARMILIRHVSLIGSNMMSASFSMHHRKSdELLLPDGTVFGSIGGCLASEVLGEIKY 298
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKE-LLLAPDGTYIRPDAVLELRKLFSPFLD 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489   299 KnQLQQILHAFLRINVDRVEYMILKAILMRNPSVPGLTLDDQLIIENERNQYAKALLEYTILHHGvLSGPARFGSLIAIN 378
Cdd:smart00430  80 R-ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYP-MNYPGRFAKLLLIL 157


                   ....*.
gi 212646489   379 PIIETQ 384
Cdd:smart00430 158 PELRKI 163
NR_DBD_HNF4A cd06960
DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc ...
 46-120 3.69e-28

DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers; DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. 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).


Pssm-ID: 143518  Cd Length: 76  Bit Score: 105.73  E-value: 3.69e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQRL-CKGCRFARCIEVGMDSTAIR 120
Cdd:cd06960    1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNC----VVDKDKRNaCRYCRFKKCLEVGMDPEAVQ 72
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
45-115 2.80e-26

c4 zinc finger in nuclear hormone receptors;


Pssm-ID: 197701  Cd Length: 70  Bit Score: 100.68  E-value: 2.80e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 212646489    45 KCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLDeieSDESQRLCKGCRFARCIEVGMD 115
Cdd:smart00399   1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSI---NKRYRCRCRACRLKKCLGVGMD 68
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
 46-115 2.95e-20

Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.


Pssm-ID: 395055  Cd Length: 68  Bit Score: 83.80  E-value: 2.95e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 212646489   46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQR-LCKGCRFARCIEVGMD 115
Cdd:pfam00105   2 CKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCKFNKDC----VIDKRNRnRCQYCRLKKCLEVGMS 68
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 204-385 7.47e-16

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: 75.46  E-value: 7.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  204 TPVSNKAPKLICMTYMHSALLAAVEASKTFEFFSKISHEARMILIRHVSLIGSNMMSASFSMHHRKSDeLLLPDGTVFGS 283
Cdd:pfam00104   5 LKKLRKATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKK-ILGEDVLMISD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  284 IGGCLASEVLGEIKYKNQLQQIL--------------HAFLRINVDRVEYMILKAILMRNPSVPGLTLDDQLIIENERNQ 349
Cdd:pfam00104  84 DDAMKFVEDDSSWCTNYDLEQLLfflpffnsyffelvKPLRELNPDDEELAYLLAQLLFDYAGDGLSGEILEIVEKLQEK 163

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 212646489  350 YAKALLEYTILHHgvlsgPARFGSLIAINPIIETQS 385
Cdd:pfam00104 164 LANELHDYYVNKY-----SGRLAKLLKILPSLRKIS 194
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 223-384 2.27e-15

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: 73.49  E-value: 2.27e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 223 LLAAVEASKTFEFFSKISHEARMILIRHVSLigSNMM--SASFSMHHRKSDELLLPDGTVFGSIGGCLASEVLGEIKYKn 300
Cdd:cd06157   11 LLLIVEWAKSIPGFRELPLEDQIVLLKSFWL--ELLVldLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELIRL- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 301 qLQQILHAFLRINVDRVEYMILKAILMRNPSVPGlTLDDQLIIENERNQYAKALLEYTILHHGVlSGPARFGSLIAINPI 380
Cdd:cd06157   88 -LFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE-SLEDRKIVEELQERLLEALQDYLRKNYPE-EAPSRFAKLLLLLPS 164


                 ....
gi 212646489 381 IETQ 384
Cdd:cd06157  165 LRKL 168
 
Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
219-384 1.97e-28

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 109.38  E-value: 1.97e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489   219 MHSALLAAVEASKTFEFFSKISHEARMILIRHVSLIGSNMMSASFSMHHRKSdELLLPDGTVFGSIGGCLASEVLGEIKY 298
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKE-LLLAPDGTYIRPDAVLELRKLFSPFLD 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489   299 KnQLQQILHAFLRINVDRVEYMILKAILMRNPSVPGLTLDDQLIIENERNQYAKALLEYTILHHGvLSGPARFGSLIAIN 378
Cdd:smart00430  80 R-ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYP-MNYPGRFAKLLLIL 157


                   ....*.
gi 212646489   379 PIIETQ 384
Cdd:smart00430 158 PELRKI 163
NR_DBD_HNF4A cd06960
DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc ...
 46-120 3.69e-28

DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers; DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. 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).


Pssm-ID: 143518  Cd Length: 76  Bit Score: 105.73  E-value: 3.69e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQRL-CKGCRFARCIEVGMDSTAIR 120
Cdd:cd06960    1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNC----VVDKDKRNaCRYCRFKKCLEVGMDPEAVQ 72
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
45-115 2.80e-26

c4 zinc finger in nuclear hormone receptors;


Pssm-ID: 197701  Cd Length: 70  Bit Score: 100.68  E-value: 2.80e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 212646489    45 KCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLDeieSDESQRLCKGCRFARCIEVGMD 115
Cdd:smart00399   1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSI---NKRYRCRCRACRLKKCLGVGMD 68
NR_DBD_like cd06916
DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding ...
 46-120 6.75e-24

DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. 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). Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers.


Pssm-ID: 143512  Cd Length: 72  Bit Score: 94.17  E-value: 6.75e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldEIESdESQRLCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06916    1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNC--VIDK-RNRNRCQACRLKKCLAVGMRKEAVR 72
NR_DBD_Lrh-1_like cd07167
The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type ...
 46-121 2.37e-20

The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers; The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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 is required at several stages of development. Particularly, FTZ-F1 regulated 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 monomers. 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: 143541  Cd Length: 93  Bit Score: 85.20  E-value: 2.37e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQR-LCKGCRFARCIEVGMDSTAIRA 121
Cdd:cd07167    1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNC----QIDKTQRkRCPYCRFQKCLSVGMKLEAVRA 73
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
 46-115 2.95e-20

Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.


Pssm-ID: 395055  Cd Length: 68  Bit Score: 83.80  E-value: 2.95e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 212646489   46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQR-LCKGCRFARCIEVGMD 115
Cdd:pfam00105   2 CKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCKFNKDC----VIDKRNRnRCQYCRLKKCLEVGMS 68
NR_DBD_VDR_like cd07156
The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed ...
 46-114 1.53e-19

The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers; The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. Like other nuclear receptors, xenobiotic 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: 143531  Cd Length: 72  Bit Score: 82.04  E-value: 1.53e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldEIESDeSQRLCKGCRFARCIEVGM 114
Cdd:cd07156    1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDC--EITKD-NRRHCQACRLKKCLDIGM 66
2DBD_NR_DBD2 cd07179
The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type ...
 46-120 1.59e-19

The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers; The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.


Pssm-ID: 143548  Cd Length: 74  Bit Score: 82.17  E-value: 1.59e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeIESDESQRLCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07179    1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNC---AITPATRNACKSCRFRRCLAVGMSKTGSR 72
NR_DBD_DHR4_like cd07168
DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type ...
 43-120 1.76e-18

DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers; DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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: 143542  Cd Length: 90  Bit Score: 79.91  E-value: 1.76e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 212646489  43 PEKCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07168    6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRC----EITKAQRnRCQYCRFRKCIRKGMMLAAVR 80
NR_DBD_NGFI-B cd06969
DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B; DNA-binding ...
 46-120 1.97e-18

DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B; DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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 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. NGFI-B binds to the NGFI-B response element (NBRE) 5'-(A/T)AAAGGTCA as a monomer. 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: 143527  Cd Length: 75  Bit Score: 79.03  E-value: 1.97e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06969    3 CAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNC----PVDKRRRnRCQYCRFQKCLQVGMVKEVVR 74
NR_DBD_LXR cd07160
DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers; ...
 26-114 3.41e-17

DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells 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. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist 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. The ideal LXRE sequence is a direct repeat-4 (DR-4) DNA fragment consisting of two AGGTCA hexameric half-sites separated by a 4-nucleotide spacer. 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: 143534  Cd Length: 101  Bit Score: 76.46  E-value: 3.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  26 PEKDLKKPYQLLSKNqfpEKCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDE-SQRLCKGC 104
Cdd:cd07160    4 PRKRKKGPAPKMLGN---EVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKC----QMDMyMRRKCQEC 76

                         90
                 ....*....|
gi 212646489 105 RFARCIEVGM 114
Cdd:cd07160   77 RLRKCREAGM 86
NR_DBD_GCNF_like cd07169
DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc ...
 46-121 3.46e-17

DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF 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: 143543  Cd Length: 90  Bit Score: 76.07  E-value: 3.46e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeIESDESQRLCKGCRFARCIEVGMDSTAIRA 121
Cdd:cd07169    9 CLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNC---VMSRKQRNRCQYCRLLKCLQMGMNRKAIRE 81
NR_DBD_ER cd07171
DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers; ...
 45-120 5.27e-17

DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers; DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. 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 non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143545  Cd Length: 82  Bit Score: 75.30  E-value: 5.27e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 212646489  45 KCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07171    5 FCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQC----TIDKNRRkSCQACRLRKCYEVGMMKGGIR 77
NR_DBD_CAR cd06966
DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc ...
 46-146 8.54e-17

DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers; DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian relative of PXR and is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, CAR has a central well conserved DNA binding domain, a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain.


Pssm-ID: 143524  Cd Length: 94  Bit Score: 75.17  E-value: 8.54e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldEIESdESQRLCKGCRFARCIEVGMDSTAIRASvkt 125
Cdd:cd06966    3 CGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESC--EINV-VTRRFCQKCRLDKCFAIGMKKEWIMSE--- 76

                         90       100
                 ....*....|....*....|.
gi 212646489 126 vegKYLLEEVLRKQKNRKIQM 146
Cdd:cd06966   77 ---EDKSEKRQKIEENRAKKR 94
NR_DBD_TR cd06961
DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers; ...
 46-120 1.01e-16

DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR 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: 143519  Cd Length: 85  Bit Score: 74.76  E-value: 1.01e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06961    2 CVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKC----EIDKVTRnQCQECRFKKCIAVGMAKDLVL 73
NR_DBD_RAR cd06964
DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers; ...
 46-120 1.59e-16

DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural 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. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter regions of retinoid target genes. 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: 143522  Cd Length: 85  Bit Score: 74.18  E-value: 1.59e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldEIESDESQRlCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06964    7 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNC--IINKVTRNR-CQYCRLQKCFEVGMSKESVR 78
NR_DBD_DmE78_like cd07165
DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two ...
 46-120 3.20e-16

DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers; DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. 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. The 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: 143539  Cd Length: 81  Bit Score: 73.36  E-value: 3.20e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLdeiESDESQRLCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07165    1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCE---IIRLNRNRCQYCRFKKCLAAGMSKDSVR 72
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 204-385 7.47e-16

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: 75.46  E-value: 7.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  204 TPVSNKAPKLICMTYMHSALLAAVEASKTFEFFSKISHEARMILIRHVSLIGSNMMSASFSMHHRKSDeLLLPDGTVFGS 283
Cdd:pfam00104   5 LKKLRKATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKK-ILGEDVLMISD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  284 IGGCLASEVLGEIKYKNQLQQIL--------------HAFLRINVDRVEYMILKAILMRNPSVPGLTLDDQLIIENERNQ 349
Cdd:pfam00104  84 DDAMKFVEDDSSWCTNYDLEQLLfflpffnsyffelvKPLRELNPDDEELAYLLAQLLFDYAGDGLSGEILEIVEKLQEK 163

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 212646489  350 YAKALLEYTILHHgvlsgPARFGSLIAINPIIETQS 385
Cdd:pfam00104 164 LANELHDYYVNKY-----SGRLAKLLKILPSLRKIS 194
NR_DBD_ER_like cd07155
DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed ...
 46-120 1.08e-15

DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers; DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. ERRs and ERs exhibit the common modular structure with other nuclear receptors. They have a central highly conserved DNA binding domain (DBD), a non-conserved N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143530  Cd Length: 75  Bit Score: 71.35  E-value: 1.08e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLDEIESDESqrlCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07155    1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKS---CQACRLQKCLKVGMLKEGVR 72
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 223-384 2.27e-15

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: 73.49  E-value: 2.27e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 223 LLAAVEASKTFEFFSKISHEARMILIRHVSLigSNMM--SASFSMHHRKSDELLLPDGTVFGSIGGCLASEVLGEIKYKn 300
Cdd:cd06157   11 LLLIVEWAKSIPGFRELPLEDQIVLLKSFWL--ELLVldLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELIRL- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 301 qLQQILHAFLRINVDRVEYMILKAILMRNPSVPGlTLDDQLIIENERNQYAKALLEYTILHHGVlSGPARFGSLIAINPI 380
Cdd:cd06157   88 -LFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE-SLEDRKIVEELQERLLEALQDYLRKNYPE-EAPSRFAKLLLLLPS 164


                 ....
gi 212646489 381 IETQ 384
Cdd:cd06157  165 LRKL 168
NR_DBD_VDR cd06955
DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers; ...
 43-150 3.76e-15

DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. 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 a 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: 143513  Cd Length: 107  Bit Score: 71.13  E-value: 3.76e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  43 PEKCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldEIESDeSQRLCKGCRFARCIEVGMDSTAIRAS 122
Cdd:cd06955    6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDC--RITKD-NRRHCQACRLKRCVDIGMMKEFILTD 82

                         90       100
                 ....*....|....*....|....*...
gi 212646489 123 vktvegkyllEEVLRKqknRKIQMQQKD 150
Cdd:cd06955   83 ----------EEVQRK---REMILKRKE 97
NR_DBD_ERR cd07170
DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers; ...
 46-121 3.81e-15

DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers; DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. 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 non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143544  Cd Length: 97  Bit Score: 70.66  E-value: 3.81e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldEIeSDESQRLCKGCRFARCIEVGMDSTAIRA 121
Cdd:cd07170    7 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNEC--EI-TKRRRKSCQACRFMKCLKVGMLKEGVRL 79
NR_DBD_PNR_like_1 cd07164
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is ...
 46-120 6.03e-15

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers; DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. 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. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR 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: 143538  Cd Length: 78  Bit Score: 69.42  E-value: 6.03e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLdeieSDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07164    1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCV----VDVARRnQCQACRFKKCLQVNMNRDAVQ 72
NR_DBD_FXR cd06962
DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc ...
 44-114 9.24e-15

DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR 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: 143520  Cd Length: 84  Bit Score: 69.22  E-value: 9.24e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 212646489  44 EKCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLDEIesdESQRLCKGCRFARCIEVGM 114
Cdd:cd06962    2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDM---YMRRKCQECRLRKCKEMGM 69
NR_DBD_Ppar cd06965
DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two ...
 45-120 9.53e-15

DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers; DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive genes, and interacts with co-activators. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143523  Cd Length: 84  Bit Score: 69.04  E-value: 9.53e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  45 KCAVCKNAAIGYHYNVPSCNGCKTFFRRTI---LNGKR--FICMNHKncldeiesdESQRLCKGCRFARCIEVGMDSTAI 119
Cdd:cd06965    1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIrlkLVYKPcdLSCKIHK---------KSRNKCQYCRFQKCLNVGMSHNAI 71


                 .
gi 212646489 120 R 120
Cdd:cd06965   72 R 72
NR_DBD_EcR_like cd06959
The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of ...
 46-114 1.53e-14

The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers; The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-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: 143517  Cd Length: 73  Bit Score: 68.24  E-value: 1.53e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESD-ESQRLCKGCRFARCIEVGM 114
Cdd:cd06959    2 CVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKC----EMDmYMRRKCQECRLRKCKAAGM 67
NR_DBD_Ppar_like cd07158
The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear ...
 46-120 2.05e-14

The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family; The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-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: 143533  Cd Length: 73  Bit Score: 67.97  E-value: 2.05e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTI-LNGKRFICMNHKNCLDEiesDESQRLCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07158    1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIqHNLTYRRCLNGGKCVIQ---RKNRNRCQYCRFKKCLSVGMSRNAVR 73
NR_DBD_RXR cd06956
DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers; ...
 46-120 2.72e-14

DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR 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. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR 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: 143514  Cd Length: 77  Bit Score: 67.57  E-value: 2.72e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLdeieSDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06956    3 CAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCL----IDKRQRnRCQYCRYQKCLAMGMKREAVQ 74
NR_DBD_EcR cd07161
DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers; ...
 44-121 2.78e-14

DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers; DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR 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 EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs 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: 143535  Cd Length: 91  Bit Score: 67.98  E-value: 2.78e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 212646489  44 EKCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldEIESdESQRLCKGCRFARCIEVGMDSTAIRA 121
Cdd:cd07161    2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRAC--EMDM-YMRRKCQECRLKKCLSVGMRPECVVP 76
NR_DBD_TR2_like cd06967
DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two ...
 44-127 1.71e-13

DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers; DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. 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. It has been 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, and peroxisome proliferator-activated receptor. TR4/2 binds to HREs as dimers. Like other members of the nuclear 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: 143525  Cd Length: 87  Bit Score: 65.55  E-value: 1.71e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489  44 EKCAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldEIESDESQRlCKGCRFARCIEVGMDSTAIRASV 123
Cdd:cd06967    4 ELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDC--VINKHHRNR-CQYCRLQKCLAMGMKSDSVQCER 80


                 ....
gi 212646489 124 KTVE 127
Cdd:cd06967   81 KPID 84
NR_DBD_PXR cd07162
DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers; ...
 46-114 2.35e-13

DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers; DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding domain, a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain.


Pssm-ID: 143536  Cd Length: 87  Bit Score: 65.33  E-value: 2.35e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeIESDESQRLCKGCRFARCIEVGM 114
Cdd:cd07162    2 CRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGC---VITKSNRRQCQACRLRKCLSIGM 67
NR_DBD_TLX cd07163
DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers; DNA-binding ...
 46-120 2.69e-13

DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers; DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX 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: 143537  Cd Length: 92  Bit Score: 65.21  E-value: 2.69e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLDEIesDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07163    9 CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPV--DKTHRnQCRACRLKKCFEVGMNKDAVQ 82
NR_DBD_REV_ERB cd07166
DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers; ...
 46-120 3.27e-13

DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers; DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors 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. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB receptor. 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: 143540  Cd Length: 89  Bit Score: 64.88  E-value: 3.27e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRF-ICMNHKNCLdeIESDESQRlCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07166    6 CKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYrKCTKNETCS--IMRINRNR-CQYCRFKKCLAVGMSRDAVR 78
NR_DBD_PNR_like_2 cd06957
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed ...
 46-120 3.29e-13

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers; The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells 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, PNR-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: 143515  Cd Length: 82  Bit Score: 64.79  E-value: 3.29e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHK-NCLdeieSDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06957    1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNgNCV----VDKARRnWCPFCRLQKCFAVGMNRAAVQ 73
NR_DBD_ROR cd06968
DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc ...
 46-120 3.55e-13

DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which 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 suggested that cholesterol or a cholesterol derivative are the natural ligands 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: 143526  Cd Length: 95  Bit Score: 64.86  E-value: 3.55e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLdeIESDESQRlCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06968    8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCL--IDRTNRNR-CQHCRLQKCLALGMSRDAVK 79
NR_DBD_PNR_like cd07154
The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear ...
 46-120 9.06e-13

The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family; The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells 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, PNR-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: 143529  Cd Length: 73  Bit Score: 63.36  E-value: 9.06e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMN-HKNCLdeieSDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd07154    1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAgNGSCV----VDKARRnQCQACRLKKCLEVSMNKDAVQ 73
NR_DBD_COUP_TF cd06958
DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is ...
 46-120 4.99e-12

DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers; DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. 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. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. 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 conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143516  Cd Length: 73  Bit Score: 61.01  E-value: 4.99e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCldeiESDESQR-LCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06958    1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNC----PIDQHHRnQCQYCRLKKCLKVGMRREAVQ 72
2DBD_NR_DBD1 cd07157
The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type ...
 44-114 1.81e-10

The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers; The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.


Pssm-ID: 143532  Cd Length: 86  Bit Score: 57.11  E-value: 1.81e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212646489  44 EKCAVCKNAAIGYHYNVPSCNGCKTFFRRTILN--GKRFICMNHKNCldEIESDeSQRLCKGCRFARCIEVGM 114
Cdd:cd07157    1 QTCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAisFTISECPNGGKC--IIDKK-NRTKCQACRYRKCLNVGM 70
NR_DBD_PNR cd06970
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of ...
 46-120 4.56e-10

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers; DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. 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. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR 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: 143528  Cd Length: 92  Bit Score: 56.10  E-value: 4.56e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489  46 CAVCKNAAIGYHYNVPSCNGCKTFFRRTILNGKRFICMNHKNCLDEIESDESQrlCKGCRFARCIEVGMDSTAIR 120
Cdd:cd06970    9 CRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQ--CQACRLKKCLQAGMNKDAVQ 81
NR_LBD_Ftz-F1_like cd06944
The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of ...
 265-404 7.63e-10

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: 58.83  E-value: 7.63e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 265 MHHRKSDELLLPDGTVF--GSIGGCLASEVLGEIKYKNQLQQILHAflrINVDRVEYMILKAILMRNPSVPGltLDDQLI 342
Cdd:cd06944   93 VHHGKEDSILLVTGQEVdlSTLASQAGLGLSSLVDRAQELVNKLRE---LQFDRQEFVCLKFLILFNPDVKG--LENRQL 167

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 212646489 343 IENERNQYAKALLEYTILHHGVLSGpaRFGSLIAINPIIETQSKKQKDvYVFMKTLSAQREC 404
Cdd:cd06944  168 VESVQEQVNAALLDYTLCNYPQQTD--KFGQLLLRLPEIRAISMQAEE-YLYYKHLNGEVPC 226
NR_LBD_F2 cd06930
Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear ...
 223-374 2.43e-09

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: 56.08  E-value: 2.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 223 LLAAVEASKTFEFFSKISHEARMILIRHV--SLIgsnMMSASF-SMHHRKSDELLLPDGTVFGSIGGclASEVLGEikYK 299
Cdd:cd06930   12 LFKTVDWAKNLPAFRNLPLDDQLTLLQNSwaELL---LLGLAQrSVHFELSELLLPSPLLVILTERE--ALLGLAE--LV 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489 300 NQLQQILHAFLRINVDRVEYMILKAILMRNPSVPGLTldDQLIIENERNQYAKALLEYTILHHGvlSGPARFGSL 374
Cdd:cd06930   85 QRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLK--NQQQVEELQEKAQQALQEYIRKRYP--QQPARFAKL 155
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
 203-375 1.66e-07

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: 51.52  E-value: 1.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 203 LTPVSNKAPKLICMTYMHSALLAAVEASKTFEFFSKISHEARMILIRHvsliGSN-MMSASFSmhHRK---SDELLLPDG 278
Cdd:cd06943   23 MVPPEYRDPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRA----GWNeLLIAAFA--HRSiavKDGILLATG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 279 TVFG-----SIG-GCLASEVLGEIKYKnqlqqilhaFLRINVDRVEYMILKAILMRNPSVPGLTldDQLIIENERNQYAK 352
Cdd:cd06943   97 LHLHrnsahQAGvGAIFDRILTELVVK---------MRDLKMDRTELGCLRAIILFNPDVKGLK--SRQEVESLREKVYA 165

                        170       180
                 ....*....|....*....|...
gi 212646489 353 ALLEYTILHHGvlSGPARFGSLI 375
Cdd:cd06943  166 SLEEYCRQKHP--EQPGRFAKLL 186
NR_LBD_DHR4_like cd06953
The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ...
 302-387 2.39e-06

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: 48.14  E-value: 2.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 302 LQQILHAFLRINVDRVEYMILKAILMRNPSVPGLTLDDQLIIENERnqYAKALLEYTILHHGvlSGPARFGSLIAINPII 381
Cdd:cd06953  117 LTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKR--YWYVLQDFTELNYP--NQPNRFSDLLSCLPEI 192


                 ....*.
gi 212646489 382 ETQSKK 387
Cdd:cd06953  193 RAAAGK 198
NR_LBD_Tlx_PNR_like cd06950
The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand ...
 301-397 8.95e-06

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: 46.13  E-value: 8.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 301 QLQQILHAFLRINVDRVEYMILKAILMRNPSVPGLTldDQLIIENERNQYAKALLEYTILHHGvlSGPARFGSLIAINPI 380
Cdd:cd06950  111 ALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLK--DPAQVEALQDQAQLMLNKHIRTRYP--TQPARFGKLLLLLPS 186

                         90
                 ....*....|....*..
gi 212646489 381 IETQSKKQKDVYVFMKT 397
Cdd:cd06950  187 LRFISSSTIEELFFKKT 203
NR_LBD_HNF4_like cd06931
The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in ...
 302-379 2.30e-04

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: 42.36  E-value: 2.30e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 212646489 302 LQQILHAFLRINVDRVEYMILKAILMRNPSVPGLTldDQLIIENERNQYAKALLEYTILHHGVLSGpaRFGSLIAINP 379
Cdd:cd06931  118 LDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLS--DPQKIKRLRFQVQVSLEDYINDRQYDSRG--RFGELLLLLP 191
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
 223-375 5.59e-03

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: 38.21  E-value: 5.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212646489 223 LLAAVEASKTFEFFSKISHEARMILIRhvsLIGSNMMSASFSMHHR--KSDELLLPDGTVFGSIGgclASEVLGEIKYKN 300
Cdd:cd06948   43 LFSAVEWARNIPFFPDLQVTDQVALLR---LSWSELFVLNAAQCCMplHVAPLLAAAGLHASPMS---ADRVVAFMDHIR 116

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212646489 301 QLQQILHAFLRINVDRVEYMILKAILMRNPSVPGLTldDQLIIENERNQYAKALLEYtiLHHGVLSGPARFGSLI 375
Cdd:cd06948  117 IFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLS--DPAHIESLQEKSQCALEEY--VRTQYPNQPTRFGKLL 187
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH