Query psy1782
Match_columns 90
No_of_seqs 114 out of 1178
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 23:50:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1782.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1782hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 99.7 2.4E-18 5.2E-23 124.4 3.3 75 1-76 57-131 (432)
2 cd06961 NR_DBD_TR DNA-binding 99.6 1.3E-15 2.9E-20 91.0 2.1 46 1-46 37-82 (85)
3 cd06967 NR_DBD_TR2_like DNA-bi 99.5 4.7E-15 1E-19 89.0 2.3 44 1-44 41-84 (87)
4 cd07170 NR_DBD_ERR DNA-binding 99.5 8.1E-15 1.7E-19 89.6 2.9 47 1-47 42-88 (97)
5 cd07166 NR_DBD_REV_ERB DNA-bin 99.5 4.3E-15 9.4E-20 89.5 1.5 44 2-45 43-86 (89)
6 cd06964 NR_DBD_RAR DNA-binding 99.5 7.1E-15 1.5E-19 87.9 2.0 43 1-43 42-84 (85)
7 cd07164 NR_DBD_PNR_like_1 DNA- 99.5 8.2E-15 1.8E-19 86.3 2.3 41 2-42 37-77 (78)
8 cd07165 NR_DBD_DmE78_like DNA- 99.5 7.6E-15 1.7E-19 87.0 1.9 43 2-44 37-79 (81)
9 cd06957 NR_DBD_PNR_like_2 DNA- 99.5 8E-15 1.7E-19 87.1 1.7 44 2-45 37-81 (82)
10 cd07160 NR_DBD_LXR DNA-binding 99.5 1.1E-14 2.3E-19 89.6 2.2 44 1-44 56-99 (101)
11 cd06956 NR_DBD_RXR DNA-binding 99.5 1.1E-14 2.4E-19 85.5 2.1 40 1-40 38-77 (77)
12 cd07155 NR_DBD_ER_like DNA-bin 99.5 1.1E-14 2.3E-19 85.2 2.0 40 1-40 36-75 (75)
13 cd07168 NR_DBD_DHR4_like DNA-b 99.5 1.3E-14 2.9E-19 87.5 2.2 45 1-45 44-88 (90)
14 KOG4217|consensus 99.5 1.8E-14 4E-19 107.2 3.1 39 1-39 307-345 (605)
15 cd06960 NR_DBD_HNF4A DNA-bindi 99.5 1.5E-14 3.1E-19 84.8 1.9 40 2-41 37-76 (76)
16 cd07163 NR_DBD_TLX DNA-binding 99.5 2.7E-14 5.8E-19 86.5 2.5 43 2-44 45-89 (92)
17 cd06966 NR_DBD_CAR DNA-binding 99.5 6.3E-15 1.4E-19 89.6 -0.4 49 1-49 38-86 (94)
18 cd07167 NR_DBD_Lrh-1_like The 99.5 2.7E-14 5.9E-19 86.7 2.2 45 1-45 36-80 (93)
19 cd06970 NR_DBD_PNR DNA-binding 99.4 3.5E-14 7.6E-19 86.0 2.2 43 2-44 45-88 (92)
20 cd07171 NR_DBD_ER DNA-binding 99.4 3.2E-14 6.8E-19 84.6 1.9 40 2-41 42-81 (82)
21 cd07161 NR_DBD_EcR DNA-binding 99.4 2.6E-14 5.6E-19 86.4 1.3 45 1-45 39-83 (91)
22 cd07169 NR_DBD_GCNF_like DNA-b 99.4 3.8E-14 8.1E-19 85.6 1.7 43 2-44 45-87 (90)
23 cd06962 NR_DBD_FXR DNA-binding 99.4 4.6E-14 9.9E-19 84.2 1.9 42 1-42 39-80 (84)
24 cd06968 NR_DBD_ROR DNA-binding 99.4 3.4E-14 7.3E-19 86.5 1.2 44 2-45 44-87 (95)
25 KOG4216|consensus 99.4 4.8E-14 1E-18 103.0 1.6 43 2-44 85-127 (479)
26 cd07157 2DBD_NR_DBD1 The first 99.4 1.2E-13 2.6E-18 82.7 2.7 42 2-43 41-82 (86)
27 cd06965 NR_DBD_Ppar DNA-bindin 99.4 7.8E-14 1.7E-18 83.2 1.6 42 2-45 39-80 (84)
28 KOG4846|consensus 99.4 1.7E-13 3.7E-18 100.9 3.0 44 2-45 172-215 (538)
29 cd06969 NR_DBD_NGFI-B DNA-bind 99.4 1.6E-13 3.4E-18 80.3 2.3 38 1-38 38-75 (75)
30 cd06955 NR_DBD_VDR DNA-binding 99.4 1.2E-13 2.5E-18 85.8 1.7 39 1-39 44-82 (107)
31 cd07162 NR_DBD_PXR DNA-binding 99.4 1.5E-13 3.3E-18 82.4 1.8 40 2-41 38-77 (87)
32 cd06958 NR_DBD_COUP_TF DNA-bin 99.4 2.3E-13 4.9E-18 79.2 2.2 37 1-37 36-72 (73)
33 cd06916 NR_DBD_like DNA-bindin 99.4 2.5E-13 5.5E-18 78.8 2.2 37 1-37 36-72 (72)
34 cd07179 2DBD_NR_DBD2 The secon 99.4 2.8E-13 6E-18 79.0 2.4 38 1-38 36-73 (74)
35 cd07158 NR_DBD_Ppar_like The D 99.4 2.6E-13 5.7E-18 78.9 2.1 36 2-37 38-73 (73)
36 cd07156 NR_DBD_VDR_like The DN 99.3 4.5E-13 9.8E-18 77.8 2.2 36 2-37 37-72 (72)
37 cd07154 NR_DBD_PNR_like The DN 99.3 5.1E-13 1.1E-17 77.7 2.3 36 2-37 37-73 (73)
38 cd06959 NR_DBD_EcR_like The DN 99.3 5.8E-13 1.3E-17 77.5 2.5 37 1-37 37-73 (73)
39 cd06963 NR_DBD_GR_like The DNA 99.3 8.7E-13 1.9E-17 76.8 2.4 36 2-37 37-72 (73)
40 cd07172 NR_DBD_GR_PR DNA-bindi 99.3 2.7E-12 5.8E-17 75.6 2.8 36 2-37 41-76 (78)
41 cd07173 NR_DBD_AR DNA-binding 99.2 3.5E-12 7.6E-17 75.8 2.3 38 2-39 42-79 (82)
42 smart00399 ZnF_C4 c4 zinc fing 99.2 1.2E-11 2.5E-16 71.3 2.1 33 2-34 38-70 (70)
43 PF00105 zf-C4: Zinc finger, C 99.1 3E-11 6.4E-16 69.5 2.9 33 1-33 38-70 (70)
44 KOG4218|consensus 99.1 1.6E-11 3.5E-16 89.0 0.8 43 2-44 54-96 (475)
45 PF09289 FOLN: Follistatin/Ost 58.5 2 4.4E-05 19.2 -0.7 17 2-18 6-22 (22)
46 smart00274 FOLN Follistatin-N- 47.7 10 0.00022 17.5 0.8 18 1-18 6-23 (26)
47 KOG4004|consensus 40.6 11 0.00023 26.4 0.3 26 2-28 58-83 (259)
48 KOG3116|consensus 31.5 25 0.00053 23.4 0.9 10 22-31 29-38 (177)
49 PF12760 Zn_Tnp_IS1595: Transp 27.1 25 0.00055 17.9 0.3 15 10-24 32-46 (46)
50 PF10152 DUF2360: Predicted co 25.3 32 0.0007 22.2 0.7 22 17-38 113-134 (148)
51 PF05924 SAMP: SAMP Motif; In 21.6 63 0.0014 14.0 1.0 11 23-33 6-16 (20)
No 1
>KOG4215|consensus
Probab=99.72 E-value=2.4e-18 Score=124.44 Aligned_cols=75 Identities=55% Similarity=0.911 Sum_probs=62.8
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccccCCCCCcccccCCCCCccchhhHHHhhhhhhc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPSYEETTANNGLSVNSLLNAEMLSRQVGA 76 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 76 (90)
.|..+.+|.|||..||.||+|||+||+++||+++|||+|||+.+.+.+..+... .+..++..+..+|....++..
T Consensus 57 tCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg~Rr~~~~~~n-~~~~~id~L~~aE~~~~q~~~ 131 (432)
T KOG4215|consen 57 TCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIGSRRPSYEAGN-ENSPSIDALVQAEALVRQLRS 131 (432)
T ss_pred eeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccccccccCCCCCCCC-CCchhHHHHHhHHHHHhhhhc
Confidence 389999999999999999999999999999999999999999998777665443 345567788888876665544
No 2
>cd06961 NR_DBD_TR 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 he
Probab=99.56 E-value=1.3e-15 Score=91.01 Aligned_cols=46 Identities=41% Similarity=0.636 Sum_probs=42.7
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccccC
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCR 46 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~~ 46 (90)
.|..+++|.|+...|+.|++|||+||+++||++++||.+|++.+++
T Consensus 37 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~ 82 (85)
T cd06961 37 SCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKR 82 (85)
T ss_pred ccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCccccc
Confidence 3888999999999999999999999999999999999999987654
No 3
>cd06967 NR_DBD_TR2_like 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
Probab=99.52 E-value=4.7e-15 Score=88.98 Aligned_cols=44 Identities=41% Similarity=0.814 Sum_probs=41.0
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRIS 44 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~ 44 (90)
.|.++++|.|++..|..|++|||+|||++||++++||.+|++..
T Consensus 41 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~~ 84 (87)
T cd06967 41 SCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPID 84 (87)
T ss_pred ccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCCC
Confidence 38889999999999999999999999999999999999999754
No 4
>cd07170 NR_DBD_ERR 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
Probab=99.51 E-value=8.1e-15 Score=89.57 Aligned_cols=47 Identities=32% Similarity=0.576 Sum_probs=42.4
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccccCC
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRR 47 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~~~ 47 (90)
.|..+++|.|++..|..|++|||+|||++||++++||.+|+..+..+
T Consensus 42 ~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~~~~~ 88 (97)
T cd07170 42 SCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQK 88 (97)
T ss_pred eecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCCCCCC
Confidence 38889999999999999999999999999999999999988765544
No 5
>cd07166 NR_DBD_REV_ERB 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 porphyr
Probab=99.51 E-value=4.3e-15 Score=89.49 Aligned_cols=44 Identities=34% Similarity=0.607 Sum_probs=40.9
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISC 45 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~ 45 (90)
|..+++|.|+...|..|++|||+|||++||++++||.+|++.+.
T Consensus 43 C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~ 86 (89)
T cd07166 43 CTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKRE 86 (89)
T ss_pred hccCCcccccccccccccchhhhhcccccCCHHHhcCCCCCCcc
Confidence 88899999999999999999999999999999999999987543
No 6
>cd06964 NR_DBD_RAR 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 reg
Probab=99.50 E-value=7.1e-15 Score=87.89 Aligned_cols=43 Identities=42% Similarity=0.916 Sum_probs=40.1
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRI 43 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~ 43 (90)
.|..+++|.|++..|..|++|||+|||++||++++||.+|++.
T Consensus 42 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~~ 84 (85)
T cd06964 42 TCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK 84 (85)
T ss_pred ECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccCC
Confidence 3888999999999999999999999999999999999998863
No 7
>cd07164 NR_DBD_PNR_like_1 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-t
Probab=99.50 E-value=8.2e-15 Score=86.28 Aligned_cols=41 Identities=41% Similarity=0.765 Sum_probs=39.3
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDR 42 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~ 42 (90)
|..+++|.|+...|..|++|||+|||++||++++||.+|++
T Consensus 37 C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 77 (78)
T cd07164 37 CKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP 77 (78)
T ss_pred CCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence 88899999999999999999999999999999999999885
No 8
>cd07165 NR_DBD_DmE78_like 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,
Probab=99.50 E-value=7.6e-15 Score=87.00 Aligned_cols=43 Identities=37% Similarity=0.621 Sum_probs=40.4
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRIS 44 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~ 44 (90)
|..+++|.|++..|..|++|||+|||++||++++||.+|.+.+
T Consensus 37 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~ 79 (81)
T cd07165 37 CLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR 79 (81)
T ss_pred CCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence 8889999999999999999999999999999999999998744
No 9
>cd06957 NR_DBD_PNR_like_2 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
Probab=99.49 E-value=8e-15 Score=87.10 Aligned_cols=44 Identities=43% Similarity=0.744 Sum_probs=39.9
Q ss_pred CC-CCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccccc
Q psy1782 2 YS-KLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISC 45 (90)
Q Consensus 2 C~-~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~ 45 (90)
|. .+++|.|+...|+.|++|||+||+++||++++||.+|++..+
T Consensus 37 C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~~ 81 (82)
T cd06957 37 CIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRKL 81 (82)
T ss_pred ccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCCC
Confidence 67 468999999999999999999999999999999999887653
No 10
>cd07160 NR_DBD_LXR 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 seq
Probab=99.49 E-value=1.1e-14 Score=89.61 Aligned_cols=44 Identities=32% Similarity=0.520 Sum_probs=40.7
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRIS 44 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~ 44 (90)
.|.++++|.|+...|..|++|||+|||++||++++||.+|+...
T Consensus 56 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~~~ 99 (101)
T cd07160 56 VCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQIRL 99 (101)
T ss_pred ccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhhhh
Confidence 38889999999999999999999999999999999999988654
No 11
>cd06956 NR_DBD_RXR 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 rec
Probab=99.49 E-value=1.1e-14 Score=85.55 Aligned_cols=40 Identities=50% Similarity=0.943 Sum_probs=37.7
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNER 40 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r 40 (90)
.|+.+++|.|++..|+.|++|||+|||++||++++||.+|
T Consensus 38 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 38 TCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred ccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 3888999999999999999999999999999999999876
No 12
>cd07155 NR_DBD_ER_like 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. E
Probab=99.49 E-value=1.1e-14 Score=85.25 Aligned_cols=40 Identities=43% Similarity=0.760 Sum_probs=37.7
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNER 40 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r 40 (90)
.|+.+++|.|++..|..|++|||+||+++||++++||.+|
T Consensus 36 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 36 SCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred eCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 3888999999999999999999999999999999999876
No 13
>cd07168 NR_DBD_DHR4_like 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
Probab=99.48 E-value=1.3e-14 Score=87.55 Aligned_cols=45 Identities=31% Similarity=0.585 Sum_probs=41.6
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISC 45 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~ 45 (90)
.|..+++|.|+...|..|++|||+|||++||++++||.+|++.+.
T Consensus 44 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~~ 88 (90)
T cd07168 44 TCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGGR 88 (90)
T ss_pred cCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCCCC
Confidence 388899999999999999999999999999999999999988553
No 14
>KOG4217|consensus
Probab=99.48 E-value=1.8e-14 Score=107.19 Aligned_cols=39 Identities=41% Similarity=0.830 Sum_probs=36.8
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNE 39 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~ 39 (90)
+|-++++|+|||..||.||+|||+|||.|||-++-|+.+
T Consensus 307 vClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtd 345 (605)
T KOG4217|consen 307 VCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTD 345 (605)
T ss_pred EeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecc
Confidence 589999999999999999999999999999999988766
No 15
>cd06960 NR_DBD_HNF4A 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
Probab=99.48 E-value=1.5e-14 Score=84.80 Aligned_cols=40 Identities=63% Similarity=1.007 Sum_probs=38.1
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERD 41 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~ 41 (90)
|..+++|.|+...|..|++|||+|||++||++++||.+||
T Consensus 37 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 37 CRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred CCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 7889999999999999999999999999999999999875
No 16
>cd07163 NR_DBD_TLX 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).
Probab=99.46 E-value=2.7e-14 Score=86.52 Aligned_cols=43 Identities=53% Similarity=0.835 Sum_probs=38.9
Q ss_pred CCC--CCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccc
Q psy1782 2 YSK--LHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRIS 44 (90)
Q Consensus 2 C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~ 44 (90)
|.. +++|.|++..|..|++|||+||+++||++++||.+|++..
T Consensus 45 C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~~ 89 (92)
T cd07163 45 CKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPRN 89 (92)
T ss_pred CCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcCC
Confidence 666 4799999999999999999999999999999999998753
No 17
>cd06966 NR_DBD_CAR 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
Probab=99.46 E-value=6.3e-15 Score=89.60 Aligned_cols=49 Identities=33% Similarity=0.504 Sum_probs=44.1
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccccCCCC
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISCRRPS 49 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~~~~~ 49 (90)
.|..+++|.|+...|..|++|||+|||++||++++||.+|+...++..+
T Consensus 38 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~~r~~~ 86 (94)
T cd06966 38 KCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSEKRQKI 86 (94)
T ss_pred ccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhHHHHhh
Confidence 3888999999999999999999999999999999999999887765543
No 18
>cd07167 NR_DBD_Lrh-1_like 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 regu
Probab=99.46 E-value=2.7e-14 Score=86.66 Aligned_cols=45 Identities=38% Similarity=0.691 Sum_probs=41.0
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISC 45 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~ 45 (90)
.|+.+++|.|+...|+.|++|||+|||++||++++||.+|++...
T Consensus 36 ~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~ 80 (93)
T cd07167 36 TCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGR 80 (93)
T ss_pred ccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCc
Confidence 388899999999999999999999999999999999999876443
No 19
>cd06970 NR_DBD_PNR 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 hing
Probab=99.45 E-value=3.5e-14 Score=86.02 Aligned_cols=43 Identities=53% Similarity=0.788 Sum_probs=39.5
Q ss_pred CCCC-CCceecCCCCCCCchhhhhHHHHhcCCcccccccccccc
Q psy1782 2 YSKL-HKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRIS 44 (90)
Q Consensus 2 C~~~-~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~ 44 (90)
|..+ ++|.|+...|..|++|||+|||++||++++||.+|++..
T Consensus 45 C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~ 88 (92)
T cd06970 45 CQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPRN 88 (92)
T ss_pred eecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCccc
Confidence 6775 899999999999999999999999999999999998654
No 20
>cd07171 NR_DBD_ER 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-conserv
Probab=99.44 E-value=3.2e-14 Score=84.57 Aligned_cols=40 Identities=35% Similarity=0.824 Sum_probs=37.9
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERD 41 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~ 41 (90)
|..+++|.|+...|..|++|||+|||++||++++|+++|.
T Consensus 42 C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~ 81 (82)
T cd07171 42 CPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERR 81 (82)
T ss_pred CCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhhc
Confidence 8889999999999999999999999999999999998864
No 21
>cd07161 NR_DBD_EcR 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 h
Probab=99.44 E-value=2.6e-14 Score=86.44 Aligned_cols=45 Identities=31% Similarity=0.441 Sum_probs=40.7
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISC 45 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~ 45 (90)
.|..+++|.|+...|..|++|||+|||++||++++||.+++-..+
T Consensus 39 ~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~~~ 83 (91)
T cd07161 39 HCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCAIK 83 (91)
T ss_pred ecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhhHH
Confidence 388899999999999999999999999999999999999775543
No 22
>cd07169 NR_DBD_GCNF_like 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).
Probab=99.43 E-value=3.8e-14 Score=85.57 Aligned_cols=43 Identities=30% Similarity=0.710 Sum_probs=40.1
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRIS 44 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~ 44 (90)
|+.+++|.|+...|..|++|||+|||++||++++||.+|.+.+
T Consensus 45 C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~ 87 (90)
T cd07169 45 CSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGG 87 (90)
T ss_pred cCCCCcccccccccccccccchhhhccccCCHHHhccccCCCC
Confidence 8889999999999999999999999999999999999987654
No 23
>cd06962 NR_DBD_FXR 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
Probab=99.43 E-value=4.6e-14 Score=84.22 Aligned_cols=42 Identities=29% Similarity=0.431 Sum_probs=38.9
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDR 42 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~ 42 (90)
.|.++++|.|+...|+.|++|||+|||++||++++|+.+++.
T Consensus 39 ~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~ 80 (84)
T cd06962 39 KCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQC 80 (84)
T ss_pred ecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHH
Confidence 388899999999999999999999999999999999988664
No 24
>cd06968 NR_DBD_ROR 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. RORbe
Probab=99.43 E-value=3.4e-14 Score=86.53 Aligned_cols=44 Identities=34% Similarity=0.681 Sum_probs=40.5
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISC 45 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~ 45 (90)
|..+++|.|+...|..|++|||+||+++||++++||.+|.+...
T Consensus 44 C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~~~ 87 (95)
T cd06968 44 CPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQ 87 (95)
T ss_pred cCCCcccccccCCceeccccchhhcccccCChhhcccCcCChhh
Confidence 88899999999999999999999999999999999988776543
No 25
>KOG4216|consensus
Probab=99.42 E-value=4.8e-14 Score=103.02 Aligned_cols=43 Identities=35% Similarity=0.715 Sum_probs=40.6
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRIS 44 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~ 44 (90)
|+++.+|.||+..||.||+||++|||++||+++||.++|..++
T Consensus 85 CpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKK 127 (479)
T KOG4216|consen 85 CPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK 127 (479)
T ss_pred CCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHh
Confidence 9999999999999999999999999999999999999987544
No 26
>cd07157 2DBD_NR_DBD1 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.
Probab=99.41 E-value=1.2e-13 Score=82.74 Aligned_cols=42 Identities=29% Similarity=0.567 Sum_probs=39.1
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRI 43 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~ 43 (90)
|.++++|.|+...|+.|++|||+|||+|||++++++.+|+..
T Consensus 41 C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~~ 82 (86)
T cd07157 41 CPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRSD 82 (86)
T ss_pred CCCCCccccCccccccCccchhhHHhHcCCCccccccccccc
Confidence 888999999999999999999999999999999999888753
No 27
>cd06965 NR_DBD_Ppar 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 gene
Probab=99.40 E-value=7.8e-14 Score=83.21 Aligned_cols=42 Identities=31% Similarity=0.627 Sum_probs=37.7
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISC 45 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~ 45 (90)
|+. +|.|++..|+.|++|||+||+++||++++||.+|++...
T Consensus 39 C~~--~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~ 80 (84)
T cd06965 39 CDL--SCKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRVE 80 (84)
T ss_pred ccc--CCCcCccccccccchhhhhhhhccCCHHHcccCCCCchh
Confidence 654 399999999999999999999999999999999987554
No 28
>KOG4846|consensus
Probab=99.39 E-value=1.7e-13 Score=100.88 Aligned_cols=44 Identities=32% Similarity=0.696 Sum_probs=40.8
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRISC 45 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~~ 45 (90)
|-++.+|.|.++.||.||+|||+|||.|||++++|++++.+...
T Consensus 172 Clk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~rn 215 (538)
T KOG4846|consen 172 CLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKFRN 215 (538)
T ss_pred HhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhccccccc
Confidence 78899999999999999999999999999999999998776554
No 29
>cd06969 NR_DBD_NGFI-B 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 transcrip
Probab=99.39 E-value=1.6e-13 Score=80.26 Aligned_cols=38 Identities=42% Similarity=0.844 Sum_probs=35.4
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQN 38 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~ 38 (90)
.|..+++|.|++..|..|++|||+|||++||++++||.
T Consensus 38 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~ 75 (75)
T cd06969 38 VCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75 (75)
T ss_pred cCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence 38889999999999999999999999999999999973
No 30
>cd06955 NR_DBD_VDR 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 core
Probab=99.39 E-value=1.2e-13 Score=85.77 Aligned_cols=39 Identities=33% Similarity=0.619 Sum_probs=36.2
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNE 39 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~ 39 (90)
.|..+++|.|+...|+.|++|||+|||++||++++|+.+
T Consensus 44 ~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 82 (107)
T cd06955 44 TCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82 (107)
T ss_pred ccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence 388899999999999999999999999999999888776
No 31
>cd07162 NR_DBD_PXR 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
Probab=99.38 E-value=1.5e-13 Score=82.43 Aligned_cols=40 Identities=35% Similarity=0.703 Sum_probs=37.4
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERD 41 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~ 41 (90)
|..+++|.|+...|+.|++|||+|||++||++++|+.++.
T Consensus 38 C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~ 77 (87)
T cd07162 38 CPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA 77 (87)
T ss_pred cCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence 7889999999999999999999999999999999998844
No 32
>cd06958 NR_DBD_COUP_TF 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 recept
Probab=99.37 E-value=2.3e-13 Score=79.20 Aligned_cols=37 Identities=51% Similarity=0.949 Sum_probs=35.0
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQ 37 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq 37 (90)
.|..+++|.|++..|+.|++|||+|||++||++++||
T Consensus 36 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (73)
T cd06958 36 TCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred eCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 3888999999999999999999999999999999997
No 33
>cd06916 NR_DBD_like 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 hetero
Probab=99.37 E-value=2.5e-13 Score=78.79 Aligned_cols=37 Identities=46% Similarity=0.838 Sum_probs=34.8
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQ 37 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq 37 (90)
.|..+++|.|+...|..|++|||+|||++||++++||
T Consensus 36 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 36 TCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred cCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 3888999999999999999999999999999999886
No 34
>cd07179 2DBD_NR_DBD2 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.
Probab=99.37 E-value=2.8e-13 Score=79.04 Aligned_cols=38 Identities=24% Similarity=0.583 Sum_probs=35.6
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQN 38 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~ 38 (90)
.|+.+++|.|+...|..|++|||+|||++||++++|+.
T Consensus 36 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 73 (74)
T cd07179 36 VCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73 (74)
T ss_pred cCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence 38889999999999999999999999999999999985
No 35
>cd07158 NR_DBD_Ppar_like 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).
Probab=99.36 E-value=2.6e-13 Score=78.89 Aligned_cols=36 Identities=39% Similarity=0.870 Sum_probs=34.3
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQ 37 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq 37 (90)
|+++++|.|++..|..|++|||+|||++||++++|+
T Consensus 38 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 73 (73)
T cd07158 38 CLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred CCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence 888999999999999999999999999999999885
No 36
>cd07156 NR_DBD_VDR_like 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 chemi
Probab=99.34 E-value=4.5e-13 Score=77.76 Aligned_cols=36 Identities=42% Similarity=0.720 Sum_probs=33.9
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQ 37 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq 37 (90)
|..+++|.|++..|+.|++|||+|||++||++++|.
T Consensus 37 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd07156 37 CPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL 72 (72)
T ss_pred cCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence 788999999999999999999999999999999873
No 37
>cd07154 NR_DBD_PNR_like 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
Probab=99.34 E-value=5.1e-13 Score=77.71 Aligned_cols=36 Identities=50% Similarity=0.839 Sum_probs=33.5
Q ss_pred CC-CCCCceecCCCCCCCchhhhhHHHHhcCCccccc
Q psy1782 2 YS-KLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQ 37 (90)
Q Consensus 2 C~-~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq 37 (90)
|. .+++|.|+...|..|++|||+|||++||++++||
T Consensus 37 C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 37 CKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred cCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 66 6789999999999999999999999999999886
No 38
>cd06959 NR_DBD_EcR_like 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 domai
Probab=99.34 E-value=5.8e-13 Score=77.50 Aligned_cols=37 Identities=32% Similarity=0.547 Sum_probs=34.3
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCccccc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQ 37 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq 37 (90)
.|..+++|.|++..|..|++|||+|||++||+++.|+
T Consensus 37 ~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (73)
T cd06959 37 ACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73 (73)
T ss_pred cCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence 3888999999999999999999999999999998874
No 39
>cd06963 NR_DBD_GR_like 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 sha
Probab=99.32 E-value=8.7e-13 Score=76.79 Aligned_cols=36 Identities=36% Similarity=0.745 Sum_probs=33.9
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQ 37 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq 37 (90)
|+++++|.|++..|+.|++|||+||+++||+++++.
T Consensus 37 C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 37 CAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred CCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 888999999999999999999999999999998764
No 40
>cd07172 NR_DBD_GR_PR 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, p
Probab=99.27 E-value=2.7e-12 Score=75.61 Aligned_cols=36 Identities=36% Similarity=0.723 Sum_probs=33.9
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQ 37 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq 37 (90)
|.++++|.|+...|+.|++|||+|||++||+..++.
T Consensus 41 C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 41 CAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred CCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence 888999999999999999999999999999988775
No 41
>cd07173 NR_DBD_AR 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 modul
Probab=99.24 E-value=3.5e-12 Score=75.78 Aligned_cols=38 Identities=37% Similarity=0.676 Sum_probs=34.3
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNE 39 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~ 39 (90)
|..+++|.|++..|+.|++|||+||+++||++.....+
T Consensus 42 C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~ 79 (82)
T cd07173 42 CASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK 79 (82)
T ss_pred cCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence 88899999999999999999999999999998765533
No 42
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.17 E-value=1.2e-11 Score=71.35 Aligned_cols=33 Identities=39% Similarity=0.769 Sum_probs=31.1
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCcc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKE 34 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 34 (90)
|..+++|.|++..|+.|++|||+||+++||+++
T Consensus 38 C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 38 CDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred cCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 788999999999999999999999999999874
No 43
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=99.14 E-value=3e-11 Score=69.49 Aligned_cols=33 Identities=45% Similarity=0.864 Sum_probs=27.8
Q ss_pred CCCCCCCceecCCCCCCCchhhhhHHHHhcCCc
Q psy1782 1 MYSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKK 33 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~ 33 (90)
.|..+++|.|++..+..|++|||+|||++||++
T Consensus 38 ~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 38 KCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred cccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence 388999999999999999999999999999974
No 44
>KOG4218|consensus
Probab=99.11 E-value=1.6e-11 Score=89.02 Aligned_cols=43 Identities=40% Similarity=0.699 Sum_probs=39.8
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHHhcCCcccccccccccc
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFKAGMKKEAVQNERDRIS 44 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~~ 44 (90)
|....+|.||+..|..|.+|||+|||.|||+-++|+.+|.+.+
T Consensus 54 C~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMRGG 96 (475)
T KOG4218|consen 54 CSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMRGG 96 (475)
T ss_pred cccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhccc
Confidence 7888999999999999999999999999999999999987644
No 45
>PF09289 FOLN: Follistatin/Osteonectin-like EGF domain; InterPro: IPR015369 This domain is predominantly found in osteonectin and follistatin. They adopt an EGF-like structure [, ]. Follistatin is involved in diverse activities from embryonic development to cell secretion. ; GO: 0005515 protein binding; PDB: 1LR7_A 1LR8_A 1LR9_A 2ARP_F 3B4V_H 2KCX_A 3SEK_C 2P6A_D 3HH2_C 2B0U_D ....
Probab=58.49 E-value=2 Score=19.23 Aligned_cols=17 Identities=18% Similarity=0.313 Sum_probs=12.4
Q ss_pred CCCCCCceecCCCCCCC
Q psy1782 2 YSKLHKQLVDKDKRNQC 18 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C 18 (90)
|..+..|.+|+..+-.|
T Consensus 6 Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 6 CKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp -BTTEEEEEETTTCEEE
T ss_pred cCCCCEeeeCCCCCcCC
Confidence 78888899988776544
No 46
>smart00274 FOLN Follistatin-N-terminal domain-like. Follistatin-N-terminal domain-like, EGF-like. Region distinct from the kazal-like sequence
Probab=47.67 E-value=10 Score=17.45 Aligned_cols=18 Identities=22% Similarity=0.239 Sum_probs=13.7
Q ss_pred CCCCCCCceecCCCCCCC
Q psy1782 1 MYSKLHKQLVDKDKRNQC 18 (90)
Q Consensus 1 ~C~~~~~C~i~~~~r~~C 18 (90)
.|+.+..|.+|+..+-.|
T Consensus 6 ~C~~G~~C~~d~~g~p~C 23 (26)
T smart00274 6 QCPFGKVCVVDKGGNARC 23 (26)
T ss_pred ECCCCCEEEeCCCCCEEE
Confidence 388999999986666555
No 47
>KOG4004|consensus
Probab=40.62 E-value=11 Score=26.39 Aligned_cols=26 Identities=31% Similarity=0.561 Sum_probs=23.1
Q ss_pred CCCCCCceecCCCCCCCchhhhhHHHH
Q psy1782 2 YSKLHKQLVDKDKRNQCRYCRLKKCFK 28 (90)
Q Consensus 2 C~~~~~C~i~~~~r~~C~~CR~~KCl~ 28 (90)
|..+.+|.++....-.|-.|| .||.+
T Consensus 58 Cg~gk~C~vd~~~~P~Cvc~~-~kCP~ 83 (259)
T KOG4004|consen 58 CGPGKNCLVDLQTQPRCVCCR-YKCPR 83 (259)
T ss_pred CCCCceeeecCCCCceeEEec-CCCCc
Confidence 888999999999989999999 77876
No 48
>KOG3116|consensus
Probab=31.50 E-value=25 Score=23.36 Aligned_cols=10 Identities=50% Similarity=1.019 Sum_probs=8.8
Q ss_pred hhhHHHHhcC
Q psy1782 22 RLKKCFKAGM 31 (90)
Q Consensus 22 R~~KCl~vGM 31 (90)
|-+|||+.|-
T Consensus 29 rCQKClq~GH 38 (177)
T KOG3116|consen 29 RCQKCLQAGH 38 (177)
T ss_pred hHHHHHhhcc
Confidence 7799999995
No 49
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=27.10 E-value=25 Score=17.93 Aligned_cols=15 Identities=27% Similarity=0.742 Sum_probs=9.4
Q ss_pred ecCCCCCCCchhhhh
Q psy1782 10 VDKDKRNQCRYCRLK 24 (90)
Q Consensus 10 i~~~~r~~C~~CR~~ 24 (90)
+....+..|..||.+
T Consensus 32 ~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 32 LKTRGRYRCKACRKQ 46 (46)
T ss_pred eCCCCeEECCCCCCc
Confidence 344456778877753
No 50
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=25.33 E-value=32 Score=22.20 Aligned_cols=22 Identities=36% Similarity=0.590 Sum_probs=18.2
Q ss_pred CCchhhhhHHHHhcCCcccccc
Q psy1782 17 QCRYCRLKKCFKAGMKKEAVQN 38 (90)
Q Consensus 17 ~C~~CR~~KCl~vGM~~~~vq~ 38 (90)
-=+|-+|-|.+++||-..+|+.
T Consensus 113 dP~y~kYfKMl~~GvP~~aVk~ 134 (148)
T PF10152_consen 113 DPRYAKYFKMLKMGVPREAVKQ 134 (148)
T ss_pred CccHHHHHHHHHcCCCHHHHHH
Confidence 3467899999999999988874
No 51
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=21.62 E-value=63 Score=14.00 Aligned_cols=11 Identities=36% Similarity=0.806 Sum_probs=7.5
Q ss_pred hhHHHHhcCCc
Q psy1782 23 LKKCFKAGMKK 33 (90)
Q Consensus 23 ~~KCl~vGM~~ 33 (90)
+++|+...|-+
T Consensus 6 L~~CI~sAmPk 16 (20)
T PF05924_consen 6 LQECIGSAMPK 16 (20)
T ss_dssp HHHHHHCTS--
T ss_pred HHHHHHHhccc
Confidence 67899988864
Done!