Query psy9232
Match_columns 119
No_of_seqs 121 out of 1178
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 22:16:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9232hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 99.9 3.8E-25 8.2E-30 168.3 2.8 65 2-67 35-99 (432)
2 cd06957 NR_DBD_PNR_like_2 DNA- 99.9 7.1E-24 1.5E-28 132.9 2.3 66 2-68 14-80 (82)
3 cd06964 NR_DBD_RAR DNA-binding 99.9 1.2E-23 2.6E-28 132.7 2.8 64 2-66 20-83 (85)
4 cd07155 NR_DBD_ER_like DNA-bin 99.9 5E-24 1.1E-28 131.6 1.1 62 2-64 14-75 (75)
5 cd06961 NR_DBD_TR DNA-binding 99.9 6E-24 1.3E-28 134.1 1.4 65 2-67 15-79 (85)
6 cd06956 NR_DBD_RXR DNA-binding 99.9 4.2E-24 9.1E-29 132.5 0.7 62 2-64 16-77 (77)
7 cd06967 NR_DBD_TR2_like DNA-bi 99.9 1.4E-23 3.1E-28 132.8 2.9 65 2-67 19-83 (87)
8 cd07164 NR_DBD_PNR_like_1 DNA- 99.9 1.2E-23 2.5E-28 130.8 2.3 64 2-66 14-77 (78)
9 cd06970 NR_DBD_PNR DNA-binding 99.9 2E-23 4.3E-28 133.4 3.3 66 2-68 22-88 (92)
10 cd06960 NR_DBD_HNF4A DNA-bindi 99.9 1.3E-23 2.9E-28 130.0 2.4 63 2-65 14-76 (76)
11 cd07163 NR_DBD_TLX DNA-binding 99.9 2.1E-23 4.5E-28 133.4 2.7 66 2-68 22-89 (92)
12 cd07165 NR_DBD_DmE78_like DNA- 99.9 1.1E-23 2.5E-28 131.8 0.9 66 2-68 14-79 (81)
13 cd07170 NR_DBD_ERR DNA-binding 99.9 1.6E-23 3.5E-28 134.9 1.4 64 2-66 20-83 (97)
14 cd07160 NR_DBD_LXR DNA-binding 99.9 2.3E-23 4.9E-28 135.1 2.1 64 2-66 34-97 (101)
15 cd07166 NR_DBD_REV_ERB DNA-bin 99.9 2E-23 4.3E-28 132.7 1.7 66 2-68 19-85 (89)
16 cd07168 NR_DBD_DHR4_like DNA-b 99.9 1.7E-23 3.6E-28 133.3 1.3 66 2-68 22-87 (90)
17 cd06962 NR_DBD_FXR DNA-binding 99.9 2.8E-23 6E-28 130.7 2.1 63 2-65 17-79 (84)
18 cd06969 NR_DBD_NGFI-B DNA-bind 99.9 5.1E-23 1.1E-27 127.1 3.1 60 2-62 16-75 (75)
19 cd07171 NR_DBD_ER DNA-binding 99.9 2E-23 4.3E-28 130.8 1.2 63 2-65 19-81 (82)
20 cd07167 NR_DBD_Lrh-1_like The 99.9 1.4E-23 3.1E-28 134.2 0.4 65 2-67 14-78 (93)
21 cd07169 NR_DBD_GCNF_like DNA-b 99.9 1.9E-23 4.2E-28 133.0 0.8 66 2-68 22-87 (90)
22 cd06916 NR_DBD_like DNA-bindin 99.9 5.5E-23 1.2E-27 126.0 2.6 59 2-61 14-72 (72)
23 cd06968 NR_DBD_ROR DNA-binding 99.9 3.3E-23 7.2E-28 133.1 1.3 67 2-69 21-87 (95)
24 cd07154 NR_DBD_PNR_like The DN 99.9 7.3E-23 1.6E-27 125.8 2.7 59 2-61 14-73 (73)
25 cd07161 NR_DBD_EcR DNA-binding 99.9 2.7E-23 5.8E-28 132.6 0.7 65 2-67 17-81 (91)
26 cd06958 NR_DBD_COUP_TF DNA-bin 99.9 6.4E-23 1.4E-27 126.0 2.1 59 2-61 14-72 (73)
27 cd07156 NR_DBD_VDR_like The DN 99.9 7.7E-23 1.7E-27 125.4 2.2 59 2-61 14-72 (72)
28 cd07179 2DBD_NR_DBD2 The secon 99.9 5.1E-23 1.1E-27 126.8 1.2 60 2-62 14-73 (74)
29 cd07157 2DBD_NR_DBD1 The first 99.9 1.5E-22 3.2E-27 128.0 3.0 63 2-65 16-80 (86)
30 cd06963 NR_DBD_GR_like The DNA 99.9 8.7E-23 1.9E-27 125.4 1.9 59 2-61 14-72 (73)
31 cd06966 NR_DBD_CAR DNA-binding 99.9 5.6E-23 1.2E-27 131.8 0.2 65 2-67 16-80 (94)
32 cd06959 NR_DBD_EcR_like The DN 99.9 1E-22 2.3E-27 125.1 1.2 59 2-61 15-73 (73)
33 cd07158 NR_DBD_Ppar_like The D 99.9 9.9E-23 2.2E-27 125.2 1.1 59 2-61 14-73 (73)
34 cd06965 NR_DBD_Ppar DNA-bindin 99.9 2E-22 4.2E-27 126.9 2.4 65 2-69 15-80 (84)
35 cd07172 NR_DBD_GR_PR DNA-bindi 99.8 2.9E-22 6.2E-27 124.5 2.3 59 2-61 18-76 (78)
36 cd06955 NR_DBD_VDR DNA-binding 99.8 3.4E-22 7.3E-27 130.8 2.3 61 2-63 22-82 (107)
37 cd07162 NR_DBD_PXR DNA-binding 99.8 2.1E-22 4.5E-27 127.6 1.2 63 2-65 15-77 (87)
38 KOG4217|consensus 99.8 1.7E-21 3.6E-26 152.3 4.8 63 2-65 285-347 (605)
39 cd07173 NR_DBD_AR DNA-binding 99.8 3.5E-22 7.7E-27 125.1 0.8 62 2-64 19-80 (82)
40 KOG4216|consensus 99.8 1.2E-21 2.6E-26 150.3 0.4 68 2-70 62-129 (479)
41 smart00399 ZnF_C4 c4 zinc fing 99.8 4.6E-21 1E-25 116.9 2.1 56 2-58 15-70 (70)
42 KOG4846|consensus 99.8 1.7E-21 3.7E-26 150.4 0.1 67 2-69 148-215 (538)
43 KOG4218|consensus 99.8 2.8E-20 6.1E-25 141.2 1.3 65 2-67 31-95 (475)
44 PF00105 zf-C4: Zinc finger, C 99.7 8.2E-20 1.8E-24 111.2 -1.0 55 1-56 15-69 (70)
45 PF09289 FOLN: Follistatin/Ost 36.6 9.3 0.0002 17.8 -0.3 19 24-42 4-22 (22)
46 PF03002 Somatostatin: Somatos 35.6 14 0.00031 16.2 0.2 10 8-18 6-15 (18)
47 PF13790 DUF4182: Domain of un 32.0 14 0.0003 19.7 -0.2 12 1-12 1-12 (38)
48 PF05924 SAMP: SAMP Motif; In 21.0 60 0.0013 14.7 0.9 11 47-57 6-16 (20)
49 PF00357 Integrin_alpha: Integ 20.5 20 0.00043 15.1 -0.7 6 11-17 3-8 (15)
50 smart00401 ZnF_GATA zinc finge 20.4 22 0.00048 19.9 -0.8 14 3-17 25-38 (52)
No 1
>KOG4215|consensus
Probab=99.90 E-value=3.8e-25 Score=168.28 Aligned_cols=65 Identities=29% Similarity=0.635 Sum_probs=63.1
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYP 67 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~ 67 (119)
||.+|+|||+| |||+|+++..|.|+.+.+|.|++..|+.||+|||+||+.+||.++|||.+|+..
T Consensus 35 GA~SCdGCKGF-FRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrI 99 (432)
T KOG4215|consen 35 GAISCDGCKGF-FRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRI 99 (432)
T ss_pred ceeecCcchHH-HHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccccc
Confidence 89999999999 999999999999999999999999999999999999999999999999998844
No 2
>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=99.88 E-value=7.1e-24 Score=132.94 Aligned_cols=66 Identities=30% Similarity=0.608 Sum_probs=61.7
Q ss_pred CCCCChhccCccceeeeecCCeeeeC-CCCcccccccccccCcchhHHHHHHhcccccceecCCCCCc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCK-ERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPS 68 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~-~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~ 68 (119)
||++|+||++| |||+|..+..|.|. .+++|.++...+..|++|||+|||++||++++|+.+|++..
T Consensus 14 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~ 80 (82)
T cd06957 14 GVYCCDGCSCF-FKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK 80 (82)
T ss_pred CcceEeeeeeE-EEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCC
Confidence 89999999999 99999999999999 46899999999999999999999999999999999887554
No 3
>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=99.88 E-value=1.2e-23 Score=132.72 Aligned_cols=64 Identities=28% Similarity=0.638 Sum_probs=61.3
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWY 66 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~ 66 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++||.+|..
T Consensus 20 Gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~ 83 (85)
T cd06964 20 GVSACEGCKGF-FRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK 83 (85)
T ss_pred CcceeeeeeeE-EeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence 89999999999 99999999999999999999999999999999999999999999999998874
No 4
>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=99.88 E-value=5e-24 Score=131.61 Aligned_cols=62 Identities=37% Similarity=0.725 Sum_probs=59.7
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGF 64 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r 64 (119)
||++|+||++| |||++..+..|.|+.+++|.++...+..|++|||+|||++||++++||.+|
T Consensus 14 gv~sC~aCk~F-FRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 14 GVASCEACKAF-FKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred ChhhhhhhHHH-HHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 89999999999 999999999999999999999999999999999999999999999999875
No 5
>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=99.88 E-value=6e-24 Score=134.09 Aligned_cols=65 Identities=34% Similarity=0.683 Sum_probs=62.3
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYP 67 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~ 67 (119)
||++|+||++| |||+|..+..|.|..+++|.++...+..|++|||+|||++||++++||.+|++.
T Consensus 15 gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~ 79 (85)
T cd06961 15 RCITCEGCKGF-FRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRG 79 (85)
T ss_pred ChhhhhhhhHh-hHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCcc
Confidence 89999999999 999999999999999999999999999999999999999999999999998754
No 6
>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=99.88 E-value=4.2e-24 Score=132.53 Aligned_cols=62 Identities=29% Similarity=0.750 Sum_probs=59.7
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGF 64 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r 64 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++||.+|
T Consensus 16 gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 16 GVYSCEGCKGF-FKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred CceeehhHHHH-HHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 89999999999 999999999999999999999999999999999999999999999999875
No 7
>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=99.88 E-value=1.4e-23 Score=132.85 Aligned_cols=65 Identities=29% Similarity=0.622 Sum_probs=62.1
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYP 67 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~ 67 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++||.+|++.
T Consensus 19 Gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~ 83 (87)
T cd06967 19 GAVSCEGCKGF-FKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPI 83 (87)
T ss_pred CcceEeeeeeE-eeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCC
Confidence 89999999999 999999999999999999999999999999999999999999999999998854
No 8
>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=99.88 E-value=1.2e-23 Score=130.83 Aligned_cols=64 Identities=53% Similarity=0.915 Sum_probs=61.6
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWY 66 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~ 66 (119)
||++|++|++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++||.+|++
T Consensus 14 G~~~C~~C~~F-FRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 77 (78)
T cd07164 14 GVPSCDGCRGF-FKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP 77 (78)
T ss_pred Ccchhhhhhhh-hhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence 89999999999 99999999999999999999999999999999999999999999999999874
No 9
>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=99.88 E-value=2e-23 Score=133.35 Aligned_cols=66 Identities=38% Similarity=0.660 Sum_probs=62.1
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCC-CcccccccccccCcchhHHHHHHhcccccceecCCCCCc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKER-GHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPS 68 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~-~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~ 68 (119)
||++|+||++| |||+|..+..|.|..+ ++|.++...+..|++|||+|||++||++++||.+|++..
T Consensus 22 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~ 88 (92)
T cd06970 22 GIYACNGCSGF-FKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPRN 88 (92)
T ss_pred CccEEeeeeeE-eeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCccc
Confidence 89999999999 9999999999999985 899999999999999999999999999999999988554
No 10
>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=99.88 E-value=1.3e-23 Score=130.00 Aligned_cols=63 Identities=33% Similarity=0.705 Sum_probs=60.4
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFW 65 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~ 65 (119)
||++|+||++| |||++..++.|.|..+++|.++...+..|++|||+|||++||++++|+.+|+
T Consensus 14 gv~~C~aC~~F-FrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 14 GVLSCNGCKGF-FRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred Ccceeeeehhe-eCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 89999999999 9999999999999999999999999999999999999999999999998764
No 11
>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=99.87 E-value=2.1e-23 Score=133.39 Aligned_cols=66 Identities=39% Similarity=0.724 Sum_probs=61.5
Q ss_pred CCCCChhccCccceeeeecCCeeeeCC--CCcccccccccccCcchhHHHHHHhcccccceecCCCCCc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKE--RGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPS 68 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~--~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~ 68 (119)
||++|+||++| |||++..+..|.|.. +++|.++...+..|++|||+|||++||++++||.+|++.+
T Consensus 22 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~~ 89 (92)
T cd07163 22 GIYACDGCSGF-FKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPRN 89 (92)
T ss_pred CceeeeeeeeE-EeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcCC
Confidence 89999999999 999999999999998 4799999999999999999999999999999999887543
No 12
>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=99.87 E-value=1.1e-23 Score=131.76 Aligned_cols=66 Identities=32% Similarity=0.647 Sum_probs=62.9
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCCc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPS 68 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~ 68 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++||.+|.++.
T Consensus 14 G~~sC~aC~~F-FRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~ 79 (81)
T cd07165 14 GVTSCEGCKGF-FRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR 79 (81)
T ss_pred CchhhhhHHHH-HHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence 89999999999 9999999999999999999999999999999999999999999999999988653
No 13
>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=99.87 E-value=1.6e-23 Score=134.92 Aligned_cols=64 Identities=34% Similarity=0.686 Sum_probs=61.2
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWY 66 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~ 66 (119)
||++|+||++| |||+|..+..|.|..+++|.++...+..|++|||+|||++||++++||.+|..
T Consensus 20 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~ 83 (97)
T cd07170 20 GVASCEACKAF-FKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVR 83 (97)
T ss_pred CceeehhhhHH-HHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCC
Confidence 89999999999 99999999999999999999999999999999999999999999999998763
No 14
>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=99.87 E-value=2.3e-23 Score=135.10 Aligned_cols=64 Identities=28% Similarity=0.616 Sum_probs=61.2
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWY 66 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~ 66 (119)
||++|+||++| |||++..+..|.|..+++|.|+...+..|++|||+|||++||++++||.+|.+
T Consensus 34 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~ 97 (101)
T cd07160 34 NVLSCEGCKGF-FRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI 97 (101)
T ss_pred Ccceehhhhhh-hhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence 89999999999 99999999999999999999999999999999999999999999999988763
No 15
>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=99.87 E-value=2e-23 Score=132.74 Aligned_cols=66 Identities=32% Similarity=0.658 Sum_probs=62.2
Q ss_pred CCCCChhccCccceeeeecCCee-eeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCCc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEY-VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPS 68 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~-~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~ 68 (119)
||++|+||++| |||+|..+..| .|..+++|.++...+..|++|||+|||++||++++||.+|.++.
T Consensus 19 Gv~sC~aCk~F-FRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~ 85 (89)
T cd07166 19 GVHACEGCKGF-FRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKR 85 (89)
T ss_pred ChhhhhhHhhE-ecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCCCCc
Confidence 89999999999 99999999999 69999999999999999999999999999999999999987643
No 16
>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=99.87 E-value=1.7e-23 Score=133.34 Aligned_cols=66 Identities=26% Similarity=0.527 Sum_probs=62.8
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCCc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPS 68 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~ 68 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+|+++.
T Consensus 22 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~ 87 (90)
T cd07168 22 GIITCEGCKGF-FKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGG 87 (90)
T ss_pred CceehhhhhHh-hhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCCC
Confidence 89999999999 9999999999999999999999999999999999999999999999999988653
No 17
>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=99.87 E-value=2.8e-23 Score=130.74 Aligned_cols=63 Identities=30% Similarity=0.617 Sum_probs=60.0
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFW 65 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~ 65 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.++.
T Consensus 17 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~ 79 (84)
T cd06962 17 NALTCEGCKGF-FRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQ 79 (84)
T ss_pred Ccceeecceee-eeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHH
Confidence 89999999999 9999999999999999999999999999999999999999999999997654
No 18
>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=99.87 E-value=5.1e-23 Score=127.08 Aligned_cols=60 Identities=42% Similarity=0.797 Sum_probs=57.5
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceec
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRL 62 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~ 62 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++||.
T Consensus 16 Gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~ 75 (75)
T cd06969 16 GVRTCEGCKGF-FKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75 (75)
T ss_pred Ccceeeeeeee-eeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence 89999999999 9999999999999999999999999999999999999999999999873
No 19
>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=99.87 E-value=2e-23 Score=130.83 Aligned_cols=63 Identities=29% Similarity=0.637 Sum_probs=60.1
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFW 65 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~ 65 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+|.
T Consensus 19 Gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~ 81 (82)
T cd07171 19 GVWSCEGCKAF-FKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERR 81 (82)
T ss_pred CceeehhhHHh-HHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhhc
Confidence 89999999999 9999999999999999999999999999999999999999999999998763
No 20
>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=99.87 E-value=1.4e-23 Score=134.20 Aligned_cols=65 Identities=31% Similarity=0.620 Sum_probs=62.0
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYP 67 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~ 67 (119)
||++|+||++| |||+|..+..|.|..+++|.++...+..|++|||+|||++||++++||.+|..+
T Consensus 14 Gv~sC~aCk~F-FRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~ 78 (93)
T cd07167 14 GLLTCESCKGF-FKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRG 78 (93)
T ss_pred CchhhhhHHHH-HHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCC
Confidence 89999999999 999999999999999999999999999999999999999999999999988644
No 21
>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=99.87 E-value=1.9e-23 Score=133.00 Aligned_cols=66 Identities=29% Similarity=0.576 Sum_probs=62.6
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCCc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPS 68 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~ 68 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+|+++.
T Consensus 22 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~ 87 (90)
T cd07169 22 GIISCEGCKGF-FKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGG 87 (90)
T ss_pred CcceehhhHHH-HHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccCCCC
Confidence 89999999999 9999999999999999999999999999999999999999999999999987553
No 22
>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=99.87 E-value=5.5e-23 Score=126.03 Aligned_cols=59 Identities=42% Similarity=0.906 Sum_probs=56.8
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhccccccee
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~ 61 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++||
T Consensus 14 gv~sC~aC~~F-FRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 14 GVLTCEGCKGF-FRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred Ccceeeeeeee-EeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 89999999999 999999999999999999999999999999999999999999998886
No 23
>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=99.86 E-value=3.3e-23 Score=133.10 Aligned_cols=67 Identities=31% Similarity=0.700 Sum_probs=63.2
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCCcc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPSF 69 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~~ 69 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+|..+.+
T Consensus 21 Gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~~~ 87 (95)
T cd06968 21 GVITCEGCKGF-FRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQ 87 (95)
T ss_pred CceeehhhHHh-hHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCChhh
Confidence 89999999999 99999999999999999999999999999999999999999999999999875544
No 24
>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=99.86 E-value=7.3e-23 Score=125.78 Aligned_cols=59 Identities=47% Similarity=0.942 Sum_probs=56.2
Q ss_pred CCCCChhccCccceeeeecCCeeeeC-CCCcccccccccccCcchhHHHHHHhccccccee
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCK-ERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~-~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~ 61 (119)
||++|+||++| |||++..+..|.|. .+++|.++...+..|++|||+|||++||++++||
T Consensus 14 Gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 14 GVYACDGCSGF-FKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred CcceeeeeeeE-eeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 89999999999 99999999999999 6789999999999999999999999999999886
No 25
>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=99.86 E-value=2.7e-23 Score=132.57 Aligned_cols=65 Identities=29% Similarity=0.541 Sum_probs=61.6
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYP 67 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~ 67 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.++..+
T Consensus 17 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~ 81 (91)
T cd07161 17 NALTCEGCKGF-FRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCA 81 (91)
T ss_pred CceeehhhHHH-HHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhh
Confidence 89999999999 999999999999999999999999999999999999999999999999887643
No 26
>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=99.86 E-value=6.4e-23 Score=126.02 Aligned_cols=59 Identities=37% Similarity=0.817 Sum_probs=57.1
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhccccccee
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~ 61 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++||
T Consensus 14 gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (73)
T cd06958 14 GQFTCEGCKSF-FKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred Chhhhhhhhhh-hhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 89999999999 999999999999999999999999999999999999999999999987
No 27
>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=99.86 E-value=7.7e-23 Score=125.37 Aligned_cols=59 Identities=29% Similarity=0.713 Sum_probs=56.4
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhccccccee
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~ 61 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|.
T Consensus 14 gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd07156 14 NAMTCEGCKGF-FRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL 72 (72)
T ss_pred Ccceehhhhhh-hchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence 89999999999 999999999999999999999999999999999999999999998873
No 28
>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=99.86 E-value=5.1e-23 Score=126.78 Aligned_cols=60 Identities=32% Similarity=0.726 Sum_probs=57.9
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceec
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRL 62 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~ 62 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.
T Consensus 14 gv~sC~aC~~F-FRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 73 (74)
T cd07179 14 GALTCEGCKGF-FRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73 (74)
T ss_pred CceeehhHHHH-HHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence 89999999999 9999999999999999999999999999999999999999999999985
No 29
>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=99.86 E-value=1.5e-22 Score=127.99 Aligned_cols=63 Identities=33% Similarity=0.577 Sum_probs=58.9
Q ss_pred CCCCChhccCccceeeeecCC--eeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNL--EYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFW 65 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~--~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~ 65 (119)
||++|+||++| |||++..++ .|.|..+++|.++...+..|++|||+|||++||++++++.+|.
T Consensus 16 Gv~sC~aCk~F-FRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~ 80 (86)
T cd07157 16 GAYVCEACKKF-FMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRR 80 (86)
T ss_pred CcceeeEeeeE-EecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCccccccccc
Confidence 89999999999 999998764 8899999999999999999999999999999999999998765
No 30
>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=99.86 E-value=8.7e-23 Score=125.42 Aligned_cols=59 Identities=34% Similarity=0.744 Sum_probs=56.6
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhccccccee
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~ 61 (119)
||++|+||++| |||++..+..|.|..+++|.|+...+..|++|||+|||++||+++++.
T Consensus 14 gv~sC~aCk~F-FRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 14 GVLTCGSCKVF-FKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred CceeehhhhHh-HHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 89999999999 999999999999999999999999999999999999999999998875
No 31
>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=99.85 E-value=5.6e-23 Score=131.82 Aligned_cols=65 Identities=25% Similarity=0.524 Sum_probs=61.5
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYP 67 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~ 67 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+|+..
T Consensus 16 Gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~ 80 (94)
T cd06966 16 NAITCESCKAF-FRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS 80 (94)
T ss_pred Ccceeeeehhe-ehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhh
Confidence 89999999999 999999999999999999999999999999999999999999999999987643
No 32
>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=99.85 E-value=1e-22 Score=125.09 Aligned_cols=59 Identities=29% Similarity=0.604 Sum_probs=56.3
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhccccccee
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~ 61 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||+++.|+
T Consensus 15 gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (73)
T cd06959 15 GVLSCEGCKGF-FRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73 (73)
T ss_pred CceeehhhHHH-HHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence 89999999999 999999999999999999999999999999999999999999998764
No 33
>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=99.85 E-value=9.9e-23 Score=125.19 Aligned_cols=59 Identities=37% Similarity=0.822 Sum_probs=56.7
Q ss_pred CCCCChhccCccceeeeecCCee-eeCCCCcccccccccccCcchhHHHHHHhccccccee
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEY-VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~-~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~ 61 (119)
||++|++|++| |||++..+..| .|..+++|.++...+..|++|||+|||++||++++|+
T Consensus 14 Gv~~C~aC~~F-FRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 73 (73)
T cd07158 14 GVHSCEGCKGF-FRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred CcchhhHHHHH-HhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence 89999999999 99999999999 8999999999999999999999999999999999875
No 34
>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=99.85 E-value=2e-22 Score=126.92 Aligned_cols=65 Identities=31% Similarity=0.589 Sum_probs=59.5
Q ss_pred CCCCChhccCccceeeeecCCee-eeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCCcc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEY-VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPSF 69 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~-~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~~ 69 (119)
||++|+||++| |||++..+..| .|... |.++...+..|++|||+|||++||++++|+.+|+++..
T Consensus 15 Gv~sC~aCk~F-FRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~ 80 (84)
T cd06965 15 GVHACEGCKGF-FRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRVE 80 (84)
T ss_pred Chhhhhhhhhh-eeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCchh
Confidence 89999999999 99999999989 49754 99999999999999999999999999999999886543
No 35
>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=99.85 E-value=2.9e-22 Score=124.54 Aligned_cols=59 Identities=37% Similarity=0.799 Sum_probs=56.5
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhccccccee
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTR 61 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~ 61 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||+..++.
T Consensus 18 Gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 18 GVLTCGSCKVF-FKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred CceeehhhHHh-HHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence 89999999999 999999999999999999999999999999999999999999988775
No 36
>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=99.85 E-value=3.4e-22 Score=130.78 Aligned_cols=61 Identities=25% Similarity=0.628 Sum_probs=58.5
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLG 63 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~ 63 (119)
||++|+||++| |||+|..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+
T Consensus 22 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 82 (107)
T cd06955 22 NAMTCEGCKGF-FRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82 (107)
T ss_pred Ccceeeeecce-ecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence 89999999999 99999999999999999999999999999999999999999999988875
No 37
>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=99.85 E-value=2.1e-22 Score=127.56 Aligned_cols=63 Identities=29% Similarity=0.614 Sum_probs=59.7
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFW 65 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~ 65 (119)
||++|+||++| |||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.++.
T Consensus 15 gv~sC~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~ 77 (87)
T cd07162 15 NAMTCEGCKGF-FRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA 77 (87)
T ss_pred CcceehhhHHH-HHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence 89999999999 9999999999999999999999999999999999999999999999997743
No 38
>KOG4217|consensus
Probab=99.84 E-value=1.7e-21 Score=152.33 Aligned_cols=63 Identities=38% Similarity=0.726 Sum_probs=60.5
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFW 65 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~ 65 (119)
||-+|+|||+| |||+|+++.+|.|-++.+|.||+..|+.|++|||||||.|||-++.|+.+-+
T Consensus 285 GvRTCEGCKGF-FKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSL 347 (605)
T KOG4217|consen 285 GVRTCEGCKGF-FKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSL 347 (605)
T ss_pred CccccccchHH-HHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecccc
Confidence 89999999999 9999999999999999999999999999999999999999999999998644
No 39
>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=99.84 E-value=3.5e-22 Score=125.15 Aligned_cols=62 Identities=31% Similarity=0.693 Sum_probs=57.6
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGF 64 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r 64 (119)
||++|+||++| |||+|..+..|.|..+++|.++...+..|++|||+|||++||++.....++
T Consensus 19 Gv~sC~aCk~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~~ 80 (82)
T cd07173 19 GALTCGSCKVF-FKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKK 80 (82)
T ss_pred CcchhhhHHHH-HHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhhc
Confidence 89999999999 999999999999999999999999999999999999999999987666544
No 40
>KOG4216|consensus
Probab=99.82 E-value=1.2e-21 Score=150.26 Aligned_cols=68 Identities=31% Similarity=0.665 Sum_probs=64.4
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCCccc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPSFL 70 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~~~ 70 (119)
||++|+|||+| |||+=+.+..|.|+++.+|.||...|+.|++|||+|||++||+.+||..+|+.+++.
T Consensus 62 GVITCEGCKGF-FRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKKQR 129 (479)
T KOG4216|consen 62 GVITCEGCKGF-FRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQR 129 (479)
T ss_pred eeEeeccchHh-hhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHhhH
Confidence 89999999999 999988889999999999999999999999999999999999999999999876554
No 41
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.81 E-value=4.6e-21 Score=116.85 Aligned_cols=56 Identities=27% Similarity=0.687 Sum_probs=53.5
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhccccc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRD 58 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~ 58 (119)
||++|+||++| |||+|..+..|.|..+++|.++...+..|++|||+|||++||+++
T Consensus 15 gv~~C~aC~~F-FRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 15 GVCSCRACKAF-FRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CCcEechhhhh-hhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 89999999999 999999999999999999999999999999999999999999863
No 42
>KOG4846|consensus
Probab=99.81 E-value=1.7e-21 Score=150.39 Aligned_cols=67 Identities=31% Similarity=0.643 Sum_probs=63.3
Q ss_pred CCCCChhccCccceeeeecCCee-eeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCCcc
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEY-VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYPSF 69 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~-~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~~~ 69 (119)
||.+|+|||+| |||+|+.+..| .|-++.+|.|....|+.|+.|||+|||.|||..++|+.+++....
T Consensus 148 GV~aCEGCKGF-FRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~rn 215 (538)
T KOG4846|consen 148 GVTACEGCKGF-FRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKFRN 215 (538)
T ss_pred ceeecccchHH-HHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhccccccc
Confidence 89999999999 99999999999 999999999999999999999999999999999999998764433
No 43
>KOG4218|consensus
Probab=99.78 E-value=2.8e-20 Score=141.19 Aligned_cols=65 Identities=32% Similarity=0.668 Sum_probs=62.3
Q ss_pred CCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhcccccceecCCCCC
Q psy9232 2 AALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDVTRLGFWYP 67 (119)
Q Consensus 2 g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~v~~~r~~~ 67 (119)
|-++|++||+| |+|+|+.++.|.|....+|.||+..|..|++|||||||.+||..+||+.+|+..
T Consensus 31 GLLTCESCKGF-FKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMRG 95 (475)
T KOG4218|consen 31 GLLTCESCKGF-FKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMRG 95 (475)
T ss_pred eeeehhhhhhH-HHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhcc
Confidence 77899999999 999999999999999999999999999999999999999999999999998744
No 44
>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=99.75 E-value=8.2e-20 Score=111.24 Aligned_cols=55 Identities=35% Similarity=0.853 Sum_probs=48.6
Q ss_pred CCCCCChhccCccceeeeecCCeeeeCCCCcccccccccccCcchhHHHHHHhccc
Q psy9232 1 MAALDCPDCGVVSCQFVFVRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMN 56 (119)
Q Consensus 1 ~g~~sC~~C~~F~frR~i~~~~~~~C~~~~~C~~~~~~r~~C~~CR~~kCl~~GM~ 56 (119)
.||++|++|++| |||++..+..+.|..+++|.++...+..|++|||+|||++||+
T Consensus 15 ygv~sC~~C~~F-FrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~ 69 (70)
T PF00105_consen 15 YGVLSCNACKMF-FRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMK 69 (70)
T ss_dssp TTEEEEHHHHHH-HHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBS
T ss_pred ccccccccceee-eeecccccccccccccccccccccCCCEeCcchHHHHHHHCCc
Confidence 389999999999 9999999888999999999999999999999999999999997
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=36.57 E-value=9.3 Score=17.83 Aligned_cols=19 Identities=32% Similarity=0.758 Sum_probs=11.7
Q ss_pred eeeCCCCcccccccccccC
Q psy9232 24 YVCKERGHCIVDVTRRNQC 42 (119)
Q Consensus 24 ~~C~~~~~C~~~~~~r~~C 42 (119)
+.|+.+..|.++...+..|
T Consensus 4 ~~Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 4 FHCKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp ---BTTEEEEEETTTCEEE
T ss_pred cccCCCCEeeeCCCCCcCC
Confidence 6788888898877665443
No 46
>PF03002 Somatostatin: Somatostatin/Cortistatin family; InterPro: IPR018142 Somatostatin inhibits the release of the pituitary growth hormone, somatotropin and inhibits the release of glucagon and insulin from the pancreas of fasted animals. Cortistatin is a cortical neuropeptide with neuronal depressant and sleep-modulating properties [].; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=35.63 E-value=14 Score=16.24 Aligned_cols=10 Identities=20% Similarity=0.288 Sum_probs=7.5
Q ss_pred hccCccceeee
Q psy9232 8 DCGVVSCQFVF 18 (119)
Q Consensus 8 ~C~~F~frR~i 18 (119)
+|+-| |..++
T Consensus 6 ~Cknf-fWK~~ 15 (18)
T PF03002_consen 6 GCKNF-FWKTF 15 (18)
T ss_pred cccce-eeccc
Confidence 68888 87664
No 47
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=31.97 E-value=14 Score=19.66 Aligned_cols=12 Identities=25% Similarity=0.750 Sum_probs=10.7
Q ss_pred CCCCCChhccCc
Q psy9232 1 MAALDCPDCGVV 12 (119)
Q Consensus 1 ~g~~sC~~C~~F 12 (119)
||.+.|..|..-
T Consensus 1 MGtIvCq~C~~~ 12 (38)
T PF13790_consen 1 MGTIVCQHCNET 12 (38)
T ss_pred CCEEEeccccce
Confidence 899999999884
No 48
>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=21.05 E-value=60 Score=14.72 Aligned_cols=11 Identities=18% Similarity=0.649 Sum_probs=7.5
Q ss_pred HHHHHHhcccc
Q psy9232 47 FSKCLQVKMNR 57 (119)
Q Consensus 47 ~~kCl~~GM~~ 57 (119)
|++|+...|-.
T Consensus 6 L~~CI~sAmPk 16 (20)
T PF05924_consen 6 LQECIGSAMPK 16 (20)
T ss_dssp HHHHHHCTS--
T ss_pred HHHHHHHhccc
Confidence 67899888763
No 49
>PF00357 Integrin_alpha: Integrin alpha cytoplasmic region; InterPro: IPR018184 Some alpha subunits are cleaved post- translationally to produce a heavy and a light chain linked by a disulphide bond [, ]. Integrin alpha chains share a conserved sequence which is found at the beginning of the cytoplasmic domain, just after the end of the transmembrane region. Within the N-terminal domain of alpha subunits, seven sequence repeats, each of approximately 60 amino acids, have been found []. It has been predicted that these repeats assume the beta-propeller fold. The domains contain seven four-stranded beta-sheets arranged in a torus around a pseudosymmetry axis []. Integrin ligands and a putative Mg2+ ion are predicted to bind to the upper face of the propeller, in a manner analogous to the way in which the trimeric G-protein beta subunit (G beta) (which also has a beta-propeller fold) binds the G protein alpha subunit []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences []. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first ten residues of the alpha-subunit cytoplasmic domain appear to form an alpha helix that is terminated by a proline residue. The remainder of the domain is highly acidic in nature and this loops back to contact the membrane-proximal lysine anchor residue. This entry represents the conserved site of the C-terminal integrin alpha chain. ; PDB: 2LKJ_A 2LKE_A 2K8O_A 1DPK_A 2K9J_A 1DPQ_A 1S4W_A 1M8O_A 2K1A_A 2KNC_A ....
Probab=20.47 E-value=20 Score=15.13 Aligned_cols=6 Identities=0% Similarity=-0.396 Sum_probs=3.5
Q ss_pred Cccceee
Q psy9232 11 VVSCQFV 17 (119)
Q Consensus 11 ~F~frR~ 17 (119)
+| |+|.
T Consensus 3 GF-FKR~ 8 (15)
T PF00357_consen 3 GF-FKRQ 8 (15)
T ss_dssp CH-HHHH
T ss_pred cc-cccc
Confidence 46 6664
No 50
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=20.43 E-value=22 Score=19.87 Aligned_cols=14 Identities=21% Similarity=0.456 Sum_probs=10.9
Q ss_pred CCCChhccCccceee
Q psy9232 3 ALDCPDCGVVSCQFV 17 (119)
Q Consensus 3 ~~sC~~C~~F~frR~ 17 (119)
...|++|+.+ ++..
T Consensus 25 ~~LCnaCgl~-~~k~ 38 (52)
T smart00401 25 KTLCNACGLY-YKKH 38 (52)
T ss_pred CcEeecccHH-HHHc
Confidence 3789999998 7754
Done!