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Conserved domains on  [gi|71987181|ref|NP_001024547.1|]
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DAF-12, isoform a [Caenorhabditis elegans]

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List of domain hits

Name Accession Description Interval E-value
NR_DBD_CAR cd06966
DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc ...
116-209 2.19e-61

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: 201.91  E-value: 2.19e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 116 KTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLR 195
Cdd:cd06966   1 KICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS 80
                        90
                ....*....|....
gi 71987181 196 RRKNSRLNNTGTCN 209
Cdd:cd06966  81 EKRQKIEENRAKKR 94
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
548-733 1.91e-43

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


:

Pssm-ID: 132727  Cd Length: 174  Bit Score: 155.07  E-value: 1.91e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 548 NKTPADIMNIMDVTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNSFKTPTIKGqnvsvnvDDM 627
Cdd:cd06929   1 QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKG-------NSR 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 628 FAKLNANAQAQKAKCLEFFGFFD-EEIKKNELAvyLVMLAVLFSvrSDPPmNENDVRIVTERHNHFMSLLNRYLESLFGe 706
Cdd:cd06929  74 DVLLNGGFGEFIEPLFEFAEKMNkLQLDDNEYA--LLTAIVLFS--PDRP-GLQDVDTVEKLQERLLEALQRYLKVNHP- 147
                       170       180
                ....*....|....*....|....*..
gi 71987181 707 QARRIFERIPKALGLLNEIARNAGMLF 733
Cdd:cd06929 148 DAPQMFAKLLKKLTELRTLNELHAELL 174
YppG super family cl16686
YppG-like protein; The YppG-like protein family includes the B. subtilis YppG protein, which ...
209-286 7.62e-03

YppG-like protein; The YppG-like protein family includes the B. subtilis YppG protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 181 amino acids in length. There are two completely conserved residues (F and G) that may be functionally important.


The actual alignment was detected with superfamily member pfam14179:

Pssm-ID: 258379  Cd Length: 110  Bit Score: 35.49  E-value: 7.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 71987181   209 NKRSQPGNQQSPQGPNQQPHLSPHHPGVAIYPPQPqrpltinPMDNQMMHHMqanrpnampqlisPPGAQPYPLTSPV 286
Cdd:pfam14179   1 NMYQQNHNPYLPYNQQQQPYQQQPYHQQMPPPPYS-------PPQQQQAHFM-------------PPQPQPYPKPSPQ 58
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
213-410 1.25e-06

Protein of unknown function (DUF1421); This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.


:

Pssm-ID: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 49.94  E-value: 1.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   213 QPGNQQSPQGPNQQPhLSPHHPGVAIYPPQPQRPLTINPmDNQMMHHMQANRPNAMP-QLISPPGAQPYPLTSPVGSSAS 291
Cdd:pfam07223 131 PPAQQPQAQQPQPPP-QVPQQQQYQSPPQQPQYQQNPPP-QAQSAPQVSGLYPEESPyQPQSYPPNEPLPSSMAMQPPYS 208
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   292 DSPPnrSLTMMHNGEKSPDGYDPNIM-------AHRAPPPSFNNRPKMDSGqvvlSTEEYKQLLSRIPGAqvpglmneee 364
Cdd:pfam07223 209 GAPP--SQQFYGPPQPSPYMYGGPGGrpnsgfpSGQQPPPSQGQEGYGYSG----PPPSKGNHGSVASYA---------- 272
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 71987181   365 PINKRAAYNCNGHPMPAETTPPYSAPMSDMSLSRHNSTSSGTEKNH 410
Cdd:pfam07223 273 PQGSSQSYSTAYPSLPAATVLPQALPMSSAPMSGGGSGSPQSGNRV 318
 
Name Accession Description Interval E-value
NR_DBD_CAR cd06966
DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc ...
116-209 2.19e-61

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: 201.91  E-value: 2.19e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 116 KTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLR 195
Cdd:cd06966   1 KICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS 80
                        90
                ....*....|....
gi 71987181 196 RRKNSRLNNTGTCN 209
Cdd:cd06966  81 EKRQKIEENRAKKR 94
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
548-733 1.91e-43

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


Pssm-ID: 132727  Cd Length: 174  Bit Score: 155.07  E-value: 1.91e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 548 NKTPADIMNIMDVTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNSFKTPTIKGqnvsvnvDDM 627
Cdd:cd06929   1 QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKG-------NSR 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 628 FAKLNANAQAQKAKCLEFFGFFD-EEIKKNELAvyLVMLAVLFSvrSDPPmNENDVRIVTERHNHFMSLLNRYLESLFGe 706
Cdd:cd06929  74 DVLLNGGFGEFIEPLFEFAEKMNkLQLDDNEYA--LLTAIVLFS--PDRP-GLQDVDTVEKLQERLLEALQRYLKVNHP- 147
                       170       180
                ....*....|....*....|....*..
gi 71987181 707 QARRIFERIPKALGLLNEIARNAGMLF 733
Cdd:cd06929 148 DAPQMFAKLLKKLTELRTLNELHAELL 174
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
117-186 2.34e-32

c4 zinc finger in nuclear hormone receptors;


Pssm-ID: 197701  Cd Length: 70  Bit Score: 120.71  E-value: 2.34e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181    117 TCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:smart00399   1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
116-185 2.93e-30

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: 249591  Cd Length: 70  Bit Score: 114.61  E-value: 2.93e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   116 KTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKK 185
Cdd:pfam00105   1 ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRLKKCLEVGMSK 70
HOLI smart00430
Ligand binding domain of hormone receptors;
558-725 1.66e-09

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 56.60  E-value: 1.66e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181    558 MDVTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNSfktpTIKGQNVSVNVDDMFAKLNANAQA 637
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKE----LLLAPDGTYIRPDAVLELRKLFSP 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181    638 QKAKCLEFFGFFDEEIKKNELAvYLVMLA-VLFSVrSDPPMNENDVRIVTERHNHFMSLLNRYLESLFGEQARrifERIP 716
Cdd:smart00430  77 FLDRILSELVKPLRELKLDDEE-YALLKAiVLFNP-AVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPMNYP---GRFA 151

                   ....*....
gi 71987181    717 KALGLLNEI 725
Cdd:smart00430 152 KLLLILPEL 160
YppG pfam14179
YppG-like protein; The YppG-like protein family includes the B. subtilis YppG protein, which ...
209-286 7.62e-03

YppG-like protein; The YppG-like protein family includes the B. subtilis YppG protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 181 amino acids in length. There are two completely conserved residues (F and G) that may be functionally important.


Pssm-ID: 258379  Cd Length: 110  Bit Score: 35.49  E-value: 7.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 71987181   209 NKRSQPGNQQSPQGPNQQPHLSPHHPGVAIYPPQPqrpltinPMDNQMMHHMqanrpnampqlisPPGAQPYPLTSPV 286
Cdd:pfam14179   1 NMYQQNHNPYLPYNQQQQPYQQQPYHQQMPPPPYS-------PPQQQQAHFM-------------PPQPQPYPKPSPQ 58
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
213-410 1.25e-06

Protein of unknown function (DUF1421); This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.


Pssm-ID: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 49.94  E-value: 1.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   213 QPGNQQSPQGPNQQPhLSPHHPGVAIYPPQPQRPLTINPmDNQMMHHMQANRPNAMP-QLISPPGAQPYPLTSPVGSSAS 291
Cdd:pfam07223 131 PPAQQPQAQQPQPPP-QVPQQQQYQSPPQQPQYQQNPPP-QAQSAPQVSGLYPEESPyQPQSYPPNEPLPSSMAMQPPYS 208
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   292 DSPPnrSLTMMHNGEKSPDGYDPNIM-------AHRAPPPSFNNRPKMDSGqvvlSTEEYKQLLSRIPGAqvpglmneee 364
Cdd:pfam07223 209 GAPP--SQQFYGPPQPSPYMYGGPGGrpnsgfpSGQQPPPSQGQEGYGYSG----PPPSKGNHGSVASYA---------- 272
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 71987181   365 PINKRAAYNCNGHPMPAETTPPYSAPMSDMSLSRHNSTSSGTEKNH 410
Cdd:pfam07223 273 PQGSSQSYSTAYPSLPAATVLPQALPMSSAPMSGGGSGSPQSGNRV 318
PLN02983 PLN02983
biotin carboxyl carrier protein of acetyl-CoA carboxylase
241-364 1.60e-03

biotin carboxyl carrier protein of acetyl-CoA carboxylase


Pssm-ID: 215533 [Multi-domain]  Cd Length: 274  Bit Score: 39.82  E-value: 1.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181  241 PQPQRPLTInpmdnqmmHHMQANRPNAMPQLiSPPGAQPYPLT---SPVGSSASDSPPnRSLTMMHNGEKSPdgydpniM 317
Cdd:PLN02983 142 PQPPPPAPV--------VMMQPPPPHAMPPA-SPPAAQPAPSApasSPPPTPASPPPA-KAPKSSHPPLKSP-------M 204
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 71987181  318 A---HRAP----PPSFNNRPKMDSGQVVLSTEEYKqllsripgaqvpgLMNEEE 364
Cdd:PLN02983 205 AgtfYRSPapgePPFVKVGDKVQKGQVVCIIEAMK-------------LMNEIE 245
Polyadenylate-binding_protein_3 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
213-348 3.32e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 39.40  E-value: 3.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   213 QPGNQQSPQG-PNQ----QPHLSPHHPGvAIYPPQPQRpltiNPMDNQMMHHMQANRPNAmPQLISPPGAQpypltspvg 287
Cdd:TIGR01628 379 QPRMRQLPMGsPMGgamgQPPYYGQGPQ-QQFNGQPLG----WPRMSMMPTPMGPGGPLR-PNGLAPMNAV--------- 443
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   288 ssasDSPPNRSLTMMHNGEKSPDGYDPNIMAHRAPPP---------SFNNRPKMDSGQVVLSTEEYKQLL 348
Cdd:TIGR01628 444 ----RAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDlpqpqstasQGGQNKKLAQVLASATPQMQKQVL 509
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
214-302 6.66e-03

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 36.69  E-value: 6.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181    214 PGNQQSPQGPNQQPH-----LSPHHPGVaiyppqPQRPLTINPMDNQMM--HHMQANRPNAM-----PQLISPPGAQPYP 281
Cdd:smart00818  41 PVSQQHPPTHTLQPHhhipvLPAQQPVV------PQQPLMPVPGQHSMTptQHHQPNLPQPAqqpfqPQPLQPPQPQQPM 114
                           90       100
                   ....*....|....*....|.
gi 71987181    282 LTSPVGSSASDSPPNRSLTMM 302
Cdd:smart00818 115 QPQPPVHPIPPLPPQPPLPPM 135
 
Name Accession Description Interval E-value
NR_DBD_CAR cd06966
DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc ...
116-209 2.19e-61

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: 201.91  E-value: 2.19e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 116 KTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLR 195
Cdd:cd06966   1 KICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS 80
                        90
                ....*....|....
gi 71987181 196 RRKNSRLNNTGTCN 209
Cdd:cd06966  81 EKRQKIEENRAKKR 94
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
548-733 1.91e-43

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


Pssm-ID: 132727  Cd Length: 174  Bit Score: 155.07  E-value: 1.91e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 548 NKTPADIMNIMDVTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNSFKTPTIKGqnvsvnvDDM 627
Cdd:cd06929   1 QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKG-------NSR 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 628 FAKLNANAQAQKAKCLEFFGFFD-EEIKKNELAvyLVMLAVLFSvrSDPPmNENDVRIVTERHNHFMSLLNRYLESLFGe 706
Cdd:cd06929  74 DVLLNGGFGEFIEPLFEFAEKMNkLQLDDNEYA--LLTAIVLFS--PDRP-GLQDVDTVEKLQERLLEALQRYLKVNHP- 147
                       170       180
                ....*....|....*....|....*..
gi 71987181 707 QARRIFERIPKALGLLNEIARNAGMLF 733
Cdd:cd06929 148 DAPQMFAKLLKKLTELRTLNELHAELL 174
NR_DBD_VDR_like cd07156
The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed ...
118-189 1.65e-43

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: 151.77  E-value: 1.65e-43
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWIL 189
Cdd:cd07156   1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL 72
NR_DBD_like cd06916
DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding ...
118-188 9.57e-38

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: 135.77  E-value: 9.57e-38
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWI 188
Cdd:cd06916   1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAV 71
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
117-186 2.34e-32

c4 zinc finger in nuclear hormone receptors;


Pssm-ID: 197701  Cd Length: 70  Bit Score: 120.71  E-value: 2.34e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181    117 TCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:smart00399   1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70
NR_DBD_PXR cd07162
DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers; ...
118-198 1.38e-30

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: 116.18  E-value: 1.38e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLRRR 197
Cdd:cd07162   2 CRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEAVEKR 81

                .
gi 71987181 198 K 198
Cdd:cd07162  82 R 82
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
116-185 2.93e-30

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: 249591  Cd Length: 70  Bit Score: 114.61  E-value: 2.93e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   116 KTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKK 185
Cdd:pfam00105   1 ELCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRLKKCLEVGMSK 70
NR_DBD_TR cd06961
DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers; ...
118-198 7.08e-30

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: 114.05  E-value: 7.08e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQ-LRR 196
Cdd:cd06961   2 CVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKrGAK 81

                ..
gi 71987181 197 RK 198
Cdd:cd06961  82 RK 83
NR_DBD_VDR cd06955
DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers; ...
110-198 2.16e-29

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: 113.50  E-value: 2.16e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 110 ESRRRQKTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWIL 189
Cdd:cd06955   1 FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFIL 80

                ....*....
gi 71987181 190 NEEQLRRRK 198
Cdd:cd06955  81 TDEEVQRKR 89
NR_DBD_LXR cd07160
DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers; ...
118-198 2.31e-26

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: 104.58  E-value: 2.31e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLRRR 197
Cdd:cd07160  21 CSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQIRLK 100

                .
gi 71987181 198 K 198
Cdd:cd07160 101 K 101
NR_DBD_HNF4A cd06960
DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc ...
118-192 4.65e-25

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: 99.96  E-value: 4.65e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEE 192
Cdd:cd06960   1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNER 75
NR_DBD_EcR cd07161
DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers; ...
115-193 9.76e-25

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: 99.57  E-value: 9.76e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987181 115 QKTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQ 193
Cdd:cd07161   1 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQ 79
NR_DBD_RAR cd06964
DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers; ...
113-196 6.64e-24

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: 97.29  E-value: 6.64e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 113 RRQKTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEE 192
Cdd:cd06964   2 RIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDR 81

                ....
gi 71987181 193 QLRR 196
Cdd:cd06964  82 NKKK 85
NR_DBD_ER cd07171
DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers; ...
116-185 9.47e-24

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: 96.49  E-value: 9.47e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 116 KTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKK 185
Cdd:cd07171   4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 73
NR_DBD_FXR cd06962
DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc ...
118-198 3.43e-23

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: 95.03  E-value: 3.43e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLRRR 197
Cdd:cd06962   4 CVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCKSK 83

                .
gi 71987181 198 K 198
Cdd:cd06962  84 R 84
NR_DBD_EcR_like cd06959
The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of ...
118-189 4.34e-23

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: 94.44  E-value: 4.34e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWIL 189
Cdd:cd06959   2 CVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73
2DBD_NR_DBD2 cd07179
The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type ...
118-186 6.19e-23

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: 94.11  E-value: 6.19e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd07179   1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKT 69
NR_DBD_ERR cd07170
DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers; ...
115-186 1.97e-22

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: 93.39  E-value: 1.97e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71987181 115 QKTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd07170   4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKE 75
NR_DBD_Lrh-1_like cd07167
The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type ...
118-188 4.95e-22

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: 92.13  E-value: 4.95e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWI 188
Cdd:cd07167   1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAV 71
NR_DBD_ROR cd06968
DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc ...
118-188 7.40e-22

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: 91.44  E-value: 7.40e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWI 188
Cdd:cd06968   8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAV 78
NR_DBD_DmE78_like cd07165
DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two ...
118-186 8.90e-22

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: 91.08  E-value: 8.90e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd07165   1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKD 69
NR_DBD_ER_like cd07155
DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed ...
118-186 1.79e-21

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: 89.84  E-value: 1.79e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd07155   1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKE 69
NR_DBD_GCNF_like cd07169
DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc ...
112-188 3.90e-20

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: 86.47  E-value: 3.90e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 71987181 112 RRRQKTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWI 188
Cdd:cd07169   3 RAEQRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAI 79
NR_DBD_AR cd07173
DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers; ...
115-183 1.18e-19

DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers; DNA-binding domain of androgen receptor (AR) 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. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modulates their expression. Another mode of action of androgen receptor is independent of their interactions with DNA. The receptor interacts directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143547  Cd Length: 82  Bit Score: 84.97  E-value: 1.18e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987181 115 QKTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGM 183
Cdd:cd07173   3 QKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGM 71
2DBD_NR_DBD1 cd07157
The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type ...
116-185 8.82e-19

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: 82.53  E-value: 8.82e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71987181 116 KTCRVCGDHATGYNFNVITCESCKAFFRR--NALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKK 185
Cdd:cd07157   1 QTCQVCGEPAAGFHHGAYVCEACKKFFMRssNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSL 72
NR_DBD_Ppar_like cd07158
The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear ...
118-188 9.61e-19

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: 82.23  E-value: 9.61e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFK-CPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWI 188
Cdd:cd07158   1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRrCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAV 72
NR_DBD_TR2_like cd06967
DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two ...
118-186 1.42e-18

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: 82.12  E-value: 1.42e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd06967   6 CVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSD 74
NR_DBD_DHR4_like cd07168
DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type ...
110-183 1.58e-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: 81.84  E-value: 1.58e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 71987181 110 ESRRRQKTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGM 183
Cdd:cd07168   1 DEDESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGM 74
NR_DBD_PNR_like_1 cd07164
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is ...
118-195 1.65e-18

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: 81.36  E-value: 1.65e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLR 195
Cdd:cd07164   1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAPR 78
NR_DBD_NGFI-B cd06969
DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B; DNA-binding ...
116-186 2.30e-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: 80.95  E-value: 2.30e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 71987181 116 KTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd06969   1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKE 71
NR_DBD_REV_ERB cd07166
DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers; ...
118-186 2.37e-18

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: 81.44  E-value: 2.37e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFK-CPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd07166   6 CKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRkCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRD 75
NR_DBD_COUP_TF cd06958
DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is ...
118-186 5.75e-18

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: 79.89  E-value: 5.75e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd06958   1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRRE 69
NR_DBD_RXR cd06956
DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers; ...
118-191 1.26e-17

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: 79.13  E-value: 1.26e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNE 191
Cdd:cd06956   3 CAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEE 76
NR_DBD_Ppar cd06965
DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two ...
118-183 3.70e-17

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: 77.90  E-value: 3.70e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFK-CPYSedCEINSVSRRFCQKCRLRKCFTVGM 183
Cdd:cd06965   2 CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKpCDLS--CKIHKKSRNKCQYCRFQKCLNVGM 66
NR_DBD_TLX cd07163
DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers; DNA-binding ...
118-202 1.03e-16

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: 76.77  E-value: 1.03e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKC--PYSEDCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEeqlR 195
Cdd:cd07163   9 CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCksKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHE---R 85

                ....*..
gi 71987181 196 RRKNSRL 202
Cdd:cd07163  86 GPRNSTL 92
NR_DBD_GR_PR cd07172
DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers; ...
115-184 1.38e-16

DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers; DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR and PR 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: 143546  Cd Length: 78  Bit Score: 76.02  E-value: 1.38e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 115 QKTCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGMK 184
Cdd:cd07172   2 QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMN 71
NR_DBD_GR_like cd06963
The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers; ...
118-183 2.93e-16

The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers; The DNA binding domain of GR_like 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 specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and share similar functional mechanisms. The dominant mechanism of function is by direct DNA binding and transcriptional regulation of target genes . The GR, MR, PR, and AR exhibit same modular structure. 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: 143521  Cd Length: 73  Bit Score: 74.98  E-value: 2.93e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSEDCEINSVSRRFCQKCRLRKCFTVGM 183
Cdd:cd06963   1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGM 66
NR_DBD_PNR cd06970
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of ...
117-195 1.10e-15

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: 73.82  E-value: 1.10e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 117 TCRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSED-CEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLR 195
Cdd:cd06970   8 LCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGmCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR 87
NR_DBD_PNR_like cd07154
The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear ...
118-186 9.79e-15

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: 70.68  E-value: 9.79e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSE-DCEINSVSRRFCQKCRLRKCFTVGMKKE 186
Cdd:cd07154   1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNgSCVVDKARRNQCQACRLKKCLEVSMNKD 70
NR_DBD_PNR_like_2 cd06957
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed ...
118-198 2.80e-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: 66.72  E-value: 2.80e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 118 CRVCGDHATGYNFNVITCESCKAFFRRNALRPKEFKCPYSE-DCEINSVSRRFCQKCRLRKCFTVGMKKEWILNEEQLRR 196
Cdd:cd06957   1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNgNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK 80

                ..
gi 71987181 197 RK 198
Cdd:cd06957  81 LR 82
HOLI smart00430
Ligand binding domain of hormone receptors;
558-725 1.66e-09

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 56.60  E-value: 1.66e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181    558 MDVTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNSfktpTIKGQNVSVNVDDMFAKLNANAQA 637
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKE----LLLAPDGTYIRPDAVLELRKLFSP 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181    638 QKAKCLEFFGFFDEEIKKNELAvYLVMLA-VLFSVrSDPPMNENDVRIVTERHNHFMSLLNRYLESLFGEQARrifERIP 716
Cdd:smart00430  77 FLDRILSELVKPLRELKLDDEE-YALLKAiVLFNP-AVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPMNYP---GRFA 151

                   ....*....
gi 71987181    717 KALGLLNEI 725
Cdd:smart00430 152 KLLLILPEL 160
NR_LBD_REV_ERB cd06940
The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; ...
533-633 2.22e-08

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


Pssm-ID: 132738  Cd Length: 189  Bit Score: 53.26  E-value: 2.22e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 533 DPMEQGRQMQSFLKANKTPAdimnimdvtMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNS--- 609
Cdd:cd06940   5 DPPKSGHEIWEEFSMSFTPA---------VREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSvtf 75
                        90       100       110
                ....*....|....*....|....*....|..
gi 71987181 610 -----FKTPTIKGQNVSVNVDDMF---AKLNA 633
Cdd:cd06940  76 lsgqkYSVDDLHSMGAGDLLNSMFdfsEKLNS 107
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
553-725 1.72e-06

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: 47.30  E-value: 1.72e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 553 DIMNIMDVTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNSFKTPTIKGQNVSVNVDDMFAKLN 632
Cdd:cd06157   2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 633 AnaqAQKAKCLEFFGFFDE-EIKKNELAvYLVMLaVLFSvrSDPPMNENDVRIVTERHNHFMSLLNRYLESLFGEQARri 711
Cdd:cd06157  82 G---ELIRLLFEFVNPLRAlKLDDEEYA-LLKAI-VLFS--PDRKESLEDRKIVEELQERLLEALQDYLRKNYPEEAP-- 152
                       170
                ....*....|....
gi 71987181 712 fERIPKALGLLNEI 725
Cdd:cd06157 153 -SRFAKLLLLLPSL 165
NR_LBD_EcR cd06938
The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors ...
554-609 9.03e-05

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


Pssm-ID: 132736 [Multi-domain]  Cd Length: 231  Bit Score: 43.19  E-value: 9.03e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 71987181 554 IMNIMDVTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNS 609
Cdd:cd06938  44 ITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDS 99
NR_LBD_LXR cd06954
The ligand binding domain of Liver X receptors, a family of nuclear receptors of ...
560-609 1.59e-03

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


Pssm-ID: 132752  Cd Length: 236  Bit Score: 39.35  E-value: 1.59e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 71987181 560 VTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNS 609
Cdd:cd06954  54 LSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEA 103
NR_LBD_PXR_like cd06934
The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive ...
552-725 1.93e-03

The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor; The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor 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. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR 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, 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: 132732  Cd Length: 226  Bit Score: 39.33  E-value: 1.93e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 552 ADIMNIMdvtMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNSFKTptikGQnVSVNVDDMFAkl 631
Cdd:cd06934  41 ADLTTYM---IKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWEC----GP-LTYCIEDAAR-- 110
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181 632 nANAQAQkakCLEFFGFFDEEIKKNEL--AVYLVMLAV-LFSvrSDPPmNENDVRIVTERHNHFMSLLNRYLESLFGEQA 708
Cdd:cd06934 111 -AGFQQL---LLEPLLRFHYTLRKLQLqeEEYVLMQAMsLFS--PDRP-GVTQHDVIDQLQEKMALTLKSYIDSKRPGPE 183
                       170
                ....*....|....*..
gi 71987181 709 RRIFerIPKALGLLNEI 725
Cdd:cd06934 184 KRFL--YPKILACLTEL 198
NR_LBD_ROR_like cd06939
The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor ...
566-609 3.30e-03

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


Pssm-ID: 132737  Cd Length: 241  Bit Score: 38.50  E-value: 3.30e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 71987181 566 VKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTNS 609
Cdd:cd06939  65 VEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNT 108
YppG pfam14179
YppG-like protein; The YppG-like protein family includes the B. subtilis YppG protein, which ...
209-286 7.62e-03

YppG-like protein; The YppG-like protein family includes the B. subtilis YppG protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 181 amino acids in length. There are two completely conserved residues (F and G) that may be functionally important.


Pssm-ID: 258379  Cd Length: 110  Bit Score: 35.49  E-value: 7.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 71987181   209 NKRSQPGNQQSPQGPNQQPHLSPHHPGVAIYPPQPqrpltinPMDNQMMHHMqanrpnampqlisPPGAQPYPLTSPV 286
Cdd:pfam14179   1 NMYQQNHNPYLPYNQQQQPYQQQPYHQQMPPPPYS-------PPQQQQAHFM-------------PPQPQPYPKPSPQ 58
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
213-410 1.25e-06

Protein of unknown function (DUF1421); This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.


Pssm-ID: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 49.94  E-value: 1.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   213 QPGNQQSPQGPNQQPhLSPHHPGVAIYPPQPQRPLTINPmDNQMMHHMQANRPNAMP-QLISPPGAQPYPLTSPVGSSAS 291
Cdd:pfam07223 131 PPAQQPQAQQPQPPP-QVPQQQQYQSPPQQPQYQQNPPP-QAQSAPQVSGLYPEESPyQPQSYPPNEPLPSSMAMQPPYS 208
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   292 DSPPnrSLTMMHNGEKSPDGYDPNIM-------AHRAPPPSFNNRPKMDSGqvvlSTEEYKQLLSRIPGAqvpglmneee 364
Cdd:pfam07223 209 GAPP--SQQFYGPPQPSPYMYGGPGGrpnsgfpSGQQPPPSQGQEGYGYSG----PPPSKGNHGSVASYA---------- 272
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 71987181   365 PINKRAAYNCNGHPMPAETTPPYSAPMSDMSLSRHNSTSSGTEKNH 410
Cdd:pfam07223 273 PQGSSQSYSTAYPSLPAATVLPQALPMSSAPMSGGGSGSPQSGNRV 318
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
212-356 1.64e-04

Protein of unknown function (DUF1421); This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.


Pssm-ID: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 43.01  E-value: 1.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   212 SQPGNQQSPQGPNQQ----------PHLSPHHPGVAIYPPQPQRPLTINPmDNQMMHHmqanrpnamPQLISPPGAQPYP 281
Cdd:pfam07223 149 QQQQYQSPPQQPQYQqnpppqaqsaPQVSGLYPEESPYQPQSYPPNEPLP-SSMAMQP---------PYSGAPPSQQFYG 218
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71987181   282 LTSPVgSSASDSPPNRSLTMMHNGEKSPDGYDPNIMAHRAPPPSFNNRPKMDSGQVVLSTEEYKQLLSRIPGAQV 356
Cdd:pfam07223 219 PPQPS-PYMYGGPGGRPNSGFPSGQQPPPSQGQEGYGYSGPPPSKGNHGSVASYAPQGSSQSYSTAYPSLPAATV 292
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
213-373 1.82e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 255543 [Multi-domain]  Cd Length: 806  Bit Score: 43.61  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   213 QPGNQQSPQGPNQQPHLSPH--------HPGVAIYPPQPQRPLTINPMDNQMM--HHMQANRPNAMPQL----------- 271
Cdd:pfam09770 175 PPQQVLPQGMPPRQAAFPQQgppeqppgYPQPPQGHPEQVQPQQFLPAPSQAPaqPPLPPQLPQQPPPLqqpqfpglsqq 254
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   272 ISPPGAQPYPLTSPVGSSASDSPPNRSLTMMHNGEKSPdgydpniMAHRAPPPSFNNRPKMDSGQVVLSTEEYK-QLLSR 350
Cdd:pfam09770 255 MPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQ-------NAPLPPPQQPQLLPLVQQPQGQQRGPQFReQLVQL 327
                         170       180
                  ....*....|....*....|...
gi 71987181   351 IPGAQVPGLMNEEEPINKRAAYN 373
Cdd:pfam09770 328 SQQQREALSQEEAKRAKRRHKIV 350
Amelogenin pfam02948
Amelogenin; Amelogenins play a role in biomineralisation. They seem to regulate the formation ...
219-295 1.11e-03

Amelogenin; Amelogenins play a role in biomineralisation. They seem to regulate the formation of crystallites during the secretory stage of tooth enamel development. thought to play a major role in the structural organisation and mineralisation of developing enamel. They are found in the extracellular matrix. Mutations in X-chromosomal amelogenin can cause Amelogenesis imperfecta.


Pssm-ID: 251635 [Multi-domain]  Cd Length: 174  Bit Score: 39.13  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   219 SPQGPNQQPH----LSPHHPgvaIYPPQPQRPLTINPMDNQMMhHMQANRPNAMPQLISPpgAQPYPLTSPVGSSASDSP 294
Cdd:pfam02948  54 SPQMPQQQQSahpkLTPHHQ---LLILPPQQPMMPVPGHHPMV-PMTGQQPHLQPPAQHP--LQPTYGQNPQPQQPTHTQ 127

                  .
gi 71987181   295 P 295
Cdd:pfam02948 128 P 128
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
211-285 1.37e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 255543 [Multi-domain]  Cd Length: 806  Bit Score: 40.53  E-value: 1.37e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71987181   211 RSQPGNQQSPQGPNQQPHLSPHHPGVaiyPPQPQRPLTINPMDNQMMHHMQA-NRPNAMPQLISPPGAQPYPLTSP 285
Cdd:pfam09770 230 PPLPPQLPQQPPPLQQPQFPGLSQQM---PPPPPQPPQQQQQPPQPQAQPPPqNQPTPHPGLPQGQNAPLPPPQQP 302
PLN02983 PLN02983
biotin carboxyl carrier protein of acetyl-CoA carboxylase
241-364 1.60e-03

biotin carboxyl carrier protein of acetyl-CoA carboxylase


Pssm-ID: 215533 [Multi-domain]  Cd Length: 274  Bit Score: 39.82  E-value: 1.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181  241 PQPQRPLTInpmdnqmmHHMQANRPNAMPQLiSPPGAQPYPLT---SPVGSSASDSPPnRSLTMMHNGEKSPdgydpniM 317
Cdd:PLN02983 142 PQPPPPAPV--------VMMQPPPPHAMPPA-SPPAAQPAPSApasSPPPTPASPPPA-KAPKSSHPPLKSP-------M 204
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 71987181  318 A---HRAP----PPSFNNRPKMDSGQVVLSTEEYKqllsripgaqvpgLMNEEE 364
Cdd:PLN02983 205 AgtfYRSPapgePPFVKVGDKVQKGQVVCIIEAMK-------------LMNEIE 245
Polyadenylate-binding_protein_3 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
213-348 3.32e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 39.40  E-value: 3.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   213 QPGNQQSPQG-PNQ----QPHLSPHHPGvAIYPPQPQRpltiNPMDNQMMHHMQANRPNAmPQLISPPGAQpypltspvg 287
Cdd:TIGR01628 379 QPRMRQLPMGsPMGgamgQPPYYGQGPQ-QQFNGQPLG----WPRMSMMPTPMGPGGPLR-PNGLAPMNAV--------- 443
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   288 ssasDSPPNRSLTMMHNGEKSPDGYDPNIMAHRAPPP---------SFNNRPKMDSGQVVLSTEEYKQLL 348
Cdd:TIGR01628 444 ----RAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDlpqpqstasQGGQNKKLAQVLASATPQMQKQVL 509
TFIIA pfam03153
Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a ...
218-367 4.77e-03

Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.


Pssm-ID: 251762 [Multi-domain]  Cd Length: 302  Bit Score: 38.19  E-value: 4.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181   218 QSPQGPNQQPHLSPHHPGvaiyPPQPQRPLTINPMDNQMMHHMQANRPNAMP--QLISPPG--AQPYPLTSPVGSSASDS 293
Cdd:pfam03153  51 PSPPAPPPPLQLPQPLPP----PPQAPPALQALPAGDAQQHNTPTSSPAAAPpaAFATPAGmgAGPTIQTPPGQLYQVNV 126
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71987181   294 PPNRSLTMMHNGEKSPDGYDPNIMAH-RAPPPSFNNRPkmdsgqVVLSTEEYKQLLSRIPGAQVPGLMNEEEPIN 367
Cdd:pfam03153 127 PVMVNQNSANSQLAQPAQERAAQQLTqRYGAPASGQAS------VLQQQPAPVQSNDESQLQQQPNGLIPPQQTD 195
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
214-302 6.66e-03

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 36.69  E-value: 6.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987181    214 PGNQQSPQGPNQQPH-----LSPHHPGVaiyppqPQRPLTINPMDNQMM--HHMQANRPNAM-----PQLISPPGAQPYP 281
Cdd:smart00818  41 PVSQQHPPTHTLQPHhhipvLPAQQPVV------PQQPLMPVPGQHSMTptQHHQPNLPQPAqqpfqPQPLQPPQPQQPM 114
                           90       100
                   ....*....|....*....|.
gi 71987181    282 LTSPVGSSASDSPPNRSLTMM 302
Cdd:smart00818 115 QPQPPVHPIPPLPPQPPLPPM 135
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.13
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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