Query psy13208
Match_columns 120
No_of_seqs 141 out of 1286
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 22:54:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13208.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13208hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06957 NR_DBD_PNR_like_2 DNA- 99.9 1.5E-23 3.3E-28 129.9 2.5 72 2-77 9-80 (82)
2 cd07164 NR_DBD_PNR_like_1 DNA- 99.9 6.5E-23 1.4E-27 126.0 2.3 69 2-75 9-77 (78)
3 cd07163 NR_DBD_TLX DNA-binding 99.9 9.9E-23 2.2E-27 128.7 2.4 72 2-77 17-89 (92)
4 cd06964 NR_DBD_RAR DNA-binding 99.9 1E-22 2.3E-27 126.9 2.5 70 2-76 15-84 (85)
5 cd06970 NR_DBD_PNR DNA-binding 99.9 8.6E-23 1.9E-27 128.9 1.8 71 2-76 17-87 (92)
6 cd06961 NR_DBD_TR DNA-binding 99.9 9.1E-23 2E-27 127.2 1.7 70 2-76 10-79 (85)
7 cd06956 NR_DBD_RXR DNA-binding 99.9 7.7E-23 1.7E-27 125.4 1.2 67 2-73 11-77 (77)
8 cd07165 NR_DBD_DmE78_like DNA- 99.9 1.1E-22 2.5E-27 125.7 1.6 71 2-77 9-79 (81)
9 cd06967 NR_DBD_TR2_like DNA-bi 99.9 1.5E-22 3.2E-27 126.7 2.1 70 2-76 14-83 (87)
10 cd07155 NR_DBD_ER_like DNA-bin 99.9 1.3E-22 2.8E-27 123.9 1.5 67 2-73 9-75 (75)
11 cd07166 NR_DBD_REV_ERB DNA-bin 99.8 2.4E-22 5.3E-27 126.2 1.9 71 2-77 14-85 (89)
12 cd06960 NR_DBD_HNF4A DNA-bindi 99.8 3.1E-22 6.7E-27 122.5 2.3 68 2-74 9-76 (76)
13 cd07168 NR_DBD_DHR4_like DNA-b 99.8 3E-22 6.5E-27 126.1 2.1 70 2-76 17-86 (90)
14 cd07160 NR_DBD_LXR DNA-binding 99.8 3.2E-22 6.9E-27 128.2 2.0 70 2-76 29-98 (101)
15 cd07170 NR_DBD_ERR DNA-binding 99.8 3.7E-22 8.1E-27 127.1 2.1 69 2-75 15-83 (97)
16 cd07154 NR_DBD_PNR_like The DN 99.8 4.1E-22 8.8E-27 121.1 2.0 65 2-70 9-73 (73)
17 cd06962 NR_DBD_FXR DNA-binding 99.8 6.2E-22 1.3E-26 123.1 2.4 68 2-74 12-79 (84)
18 cd07171 NR_DBD_ER DNA-binding 99.8 6E-22 1.3E-26 122.7 2.3 68 2-74 14-81 (82)
19 cd07169 NR_DBD_GCNF_like DNA-b 99.8 5.2E-22 1.1E-26 124.9 1.8 69 2-75 17-85 (90)
20 cd07167 NR_DBD_Lrh-1_like The 99.8 5.2E-22 1.1E-26 125.5 1.8 69 2-75 9-77 (93)
21 cd07161 NR_DBD_EcR DNA-binding 99.8 6.2E-22 1.4E-26 124.8 1.9 68 2-74 12-79 (91)
22 cd06968 NR_DBD_ROR DNA-binding 99.8 7.6E-22 1.6E-26 125.3 1.7 72 2-78 16-87 (95)
23 cd06969 NR_DBD_NGFI-B DNA-bind 99.8 1E-21 2.2E-26 119.9 1.8 65 2-71 11-75 (75)
24 cd06966 NR_DBD_CAR DNA-binding 99.8 1.1E-21 2.3E-26 124.4 2.0 69 2-75 11-79 (94)
25 cd06916 NR_DBD_like DNA-bindin 99.8 1.1E-21 2.5E-26 118.8 2.0 64 2-70 9-72 (72)
26 cd06958 NR_DBD_COUP_TF DNA-bin 99.8 1.3E-21 2.7E-26 118.9 2.2 64 2-70 9-72 (73)
27 KOG4215|consensus 99.8 3.7E-22 8.1E-27 150.2 -0.2 71 2-77 30-100 (432)
28 cd07156 NR_DBD_VDR_like The DN 99.8 1.6E-21 3.4E-26 118.2 2.1 63 2-69 9-71 (72)
29 cd07179 2DBD_NR_DBD2 The secon 99.8 1.1E-21 2.3E-26 119.5 1.0 65 2-71 9-73 (74)
30 cd07157 2DBD_NR_DBD1 The first 99.8 1.9E-21 4.2E-26 121.4 2.0 70 2-76 11-82 (86)
31 cd06963 NR_DBD_GR_like The DNA 99.8 2.1E-21 4.6E-26 117.9 1.8 64 2-70 9-72 (73)
32 cd07158 NR_DBD_Ppar_like The D 99.8 2.5E-21 5.5E-26 117.6 2.0 64 2-70 9-73 (73)
33 cd06965 NR_DBD_Ppar DNA-bindin 99.8 2.5E-21 5.5E-26 120.5 2.0 70 2-78 10-80 (84)
34 cd07162 NR_DBD_PXR DNA-binding 99.8 2.3E-21 5E-26 121.4 1.9 68 2-74 10-77 (87)
35 cd06959 NR_DBD_EcR_like The DN 99.8 2.1E-21 4.5E-26 117.9 1.5 63 2-69 10-72 (73)
36 cd07172 NR_DBD_GR_PR DNA-bindi 99.8 5.3E-21 1.2E-25 117.4 1.7 64 2-70 13-76 (78)
37 cd07173 NR_DBD_AR DNA-binding 99.8 7.7E-21 1.7E-25 117.7 2.1 66 2-72 14-79 (82)
38 KOG4216|consensus 99.8 2.9E-21 6.3E-26 146.3 0.1 70 3-77 58-127 (479)
39 cd06955 NR_DBD_VDR DNA-binding 99.8 7.7E-21 1.7E-25 122.9 2.0 66 2-72 17-82 (107)
40 KOG4217|consensus 99.8 1.2E-20 2.5E-25 145.9 -0.4 64 4-72 282-345 (605)
41 smart00399 ZnF_C4 c4 zinc fing 99.8 5.9E-20 1.3E-24 110.7 2.4 61 2-67 10-70 (70)
42 KOG4846|consensus 99.8 2.1E-20 4.5E-25 142.7 -1.8 69 3-76 144-213 (538)
43 PF00105 zf-C4: Zinc finger, C 99.7 2.2E-19 4.7E-24 108.2 -0.3 60 2-66 11-70 (70)
44 KOG4218|consensus 99.7 3.6E-18 7.8E-23 128.2 0.4 67 3-74 27-93 (475)
45 cd07156 NR_DBD_VDR_like The DN 99.2 1E-11 2.2E-16 75.1 1.5 59 46-118 13-71 (72)
46 cd06963 NR_DBD_GR_like The DNA 99.1 1.4E-11 3E-16 74.7 1.5 60 46-119 13-72 (73)
47 KOG4216|consensus 99.1 1.3E-11 2.8E-16 94.3 1.5 59 46-118 61-119 (479)
48 cd07154 NR_DBD_PNR_like The DN 99.1 1.5E-11 3.3E-16 74.5 1.3 60 46-118 13-72 (73)
49 cd06969 NR_DBD_NGFI-B DNA-bind 99.1 1.5E-11 3.3E-16 74.9 1.1 59 46-118 15-73 (75)
50 cd07179 2DBD_NR_DBD2 The secon 99.1 1.5E-11 3.3E-16 74.7 0.7 59 46-118 13-71 (74)
51 cd07158 NR_DBD_Ppar_like The D 99.1 1.5E-11 3.2E-16 74.6 0.6 59 46-118 13-72 (73)
52 cd06958 NR_DBD_COUP_TF DNA-bin 99.1 2E-11 4.4E-16 74.0 1.1 59 46-118 13-71 (73)
53 cd06959 NR_DBD_EcR_like The DN 99.1 2.4E-11 5.2E-16 73.7 1.2 59 46-118 14-72 (73)
54 cd06916 NR_DBD_like DNA-bindin 99.1 2.4E-11 5.1E-16 73.5 1.0 59 46-118 13-71 (72)
55 cd06956 NR_DBD_RXR DNA-binding 99.1 2E-11 4.3E-16 74.7 0.1 59 46-118 15-73 (77)
56 cd07171 NR_DBD_ER DNA-binding 99.1 2.4E-11 5.2E-16 75.2 0.1 59 46-118 18-76 (82)
57 cd07170 NR_DBD_ERR DNA-binding 99.1 4E-11 8.7E-16 76.4 1.1 60 45-118 18-77 (97)
58 cd06962 NR_DBD_FXR DNA-binding 99.1 4.3E-11 9.4E-16 74.4 1.2 59 46-118 16-74 (84)
59 KOG4215|consensus 99.1 4E-11 8.6E-16 91.0 1.1 59 46-118 34-92 (432)
60 cd07163 NR_DBD_TLX DNA-binding 99.1 3.4E-11 7.3E-16 76.1 0.6 61 46-118 21-81 (92)
61 cd06960 NR_DBD_HNF4A DNA-bindi 99.1 3.6E-11 7.7E-16 73.4 0.6 59 46-118 13-71 (76)
62 cd07172 NR_DBD_GR_PR DNA-bindi 99.1 5.8E-11 1.3E-15 72.8 1.6 61 46-120 17-77 (78)
63 cd07155 NR_DBD_ER_like DNA-bin 99.1 2.7E-11 5.8E-16 73.8 0.0 59 46-118 13-71 (75)
64 cd06961 NR_DBD_TR DNA-binding 99.1 3.1E-11 6.8E-16 75.2 0.2 59 46-118 14-72 (85)
65 cd07164 NR_DBD_PNR_like_1 DNA- 99.0 4.4E-11 9.5E-16 73.4 0.7 59 46-118 13-71 (78)
66 cd07160 NR_DBD_LXR DNA-binding 99.0 6.6E-11 1.4E-15 75.9 1.3 59 46-118 33-91 (101)
67 cd07161 NR_DBD_EcR DNA-binding 99.0 5.7E-11 1.2E-15 74.9 0.8 59 46-118 16-74 (91)
68 cd06964 NR_DBD_RAR DNA-binding 99.0 5.3E-11 1.1E-15 74.1 0.5 59 46-118 19-77 (85)
69 KOG4846|consensus 99.0 6.3E-11 1.4E-15 91.2 1.0 60 46-119 147-207 (538)
70 cd07162 NR_DBD_PXR DNA-binding 99.0 6E-11 1.3E-15 74.2 0.6 59 46-118 14-72 (87)
71 cd06967 NR_DBD_TR2_like DNA-bi 99.0 6.3E-11 1.4E-15 74.1 0.5 59 46-118 18-76 (87)
72 cd06955 NR_DBD_VDR DNA-binding 99.0 1.4E-10 2.9E-15 75.1 1.9 60 45-118 20-79 (107)
73 cd06970 NR_DBD_PNR DNA-binding 99.0 9.2E-11 2E-15 74.0 0.6 61 45-118 20-80 (92)
74 cd06957 NR_DBD_PNR_like_2 DNA- 99.0 6.1E-11 1.3E-15 73.4 -0.4 60 46-118 13-72 (82)
75 cd07173 NR_DBD_AR DNA-binding 99.0 1.1E-10 2.5E-15 72.1 0.5 59 46-118 18-76 (82)
76 cd07165 NR_DBD_DmE78_like DNA- 99.0 7E-11 1.5E-15 73.0 -0.4 60 46-119 13-72 (81)
77 KOG4217|consensus 99.0 1.4E-10 3E-15 90.5 1.0 71 29-116 270-340 (605)
78 cd07168 NR_DBD_DHR4_like DNA-b 99.0 1.1E-10 2.3E-15 73.5 0.3 59 46-118 21-79 (90)
79 cd07157 2DBD_NR_DBD1 The first 99.0 2.5E-10 5.4E-15 71.2 1.8 61 46-118 15-75 (86)
80 cd07169 NR_DBD_GCNF_like DNA-b 99.0 8.6E-11 1.9E-15 73.9 -0.4 59 46-118 21-79 (90)
81 cd06968 NR_DBD_ROR DNA-binding 99.0 1E-10 2.2E-15 74.2 -0.2 60 46-119 20-79 (95)
82 cd07167 NR_DBD_Lrh-1_like The 99.0 6.2E-11 1.4E-15 74.9 -1.2 59 46-118 13-71 (93)
83 cd06966 NR_DBD_CAR DNA-binding 98.9 1.1E-10 2.5E-15 73.9 -0.1 59 46-118 15-73 (94)
84 KOG4218|consensus 98.9 1.5E-10 3.3E-15 87.4 0.1 57 48-118 32-88 (475)
85 smart00399 ZnF_C4 c4 zinc fing 98.9 3.4E-10 7.4E-15 68.0 1.5 57 46-116 14-70 (70)
86 cd07166 NR_DBD_REV_ERB DNA-bin 98.9 1.2E-10 2.7E-15 73.1 -0.6 59 46-118 18-77 (89)
87 cd06965 NR_DBD_Ppar DNA-bindin 98.9 3.6E-10 7.8E-15 70.2 0.2 57 46-118 14-71 (84)
88 PF00105 zf-C4: Zinc finger, C 98.8 2E-09 4.4E-14 64.5 1.0 55 46-114 15-69 (70)
89 PF07699 GCC2_GCC3: GCC2 and G 30.5 44 0.00094 17.8 1.7 31 3-36 3-33 (48)
90 PF05924 SAMP: SAMP Motif; In 22.8 64 0.0014 14.4 1.2 11 105-115 6-16 (20)
91 PF01286 XPA_N: XPA protein N- 22.2 43 0.00093 17.0 0.6 13 3-15 19-31 (34)
No 1
>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=1.5e-23 Score=129.91 Aligned_cols=72 Identities=33% Similarity=0.624 Sum_probs=65.5
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL 77 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~ 77 (120)
+-+||||.+|+||++ ||+|++..+..|.|..++++|.|+...+..|++|||+||+++||++++|+.+|+|+.
T Consensus 9 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~ 80 (82)
T cd06957 9 YGKHYGVYCCDGCSC----FFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK 80 (82)
T ss_pred cceEECcceEeeeee----EEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCC
Confidence 458999999999987 888999888999998546899999999999999999999999999999999998754
No 2
>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=99.86 E-value=6.5e-23 Score=126.03 Aligned_cols=69 Identities=41% Similarity=0.791 Sum_probs=63.6
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS 75 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~ 75 (120)
+.+||||.+|+||++ ||+|++..+..+.|.. +++|.|+...+..|++|||+|||++||++++||.+|+|
T Consensus 9 ~g~hyG~~~C~~C~~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 77 (78)
T cd07164 9 SGKHYGVPSCDGCRG----FFKRSIRRNLAYVCKE-NGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP 77 (78)
T ss_pred cceEECcchhhhhhh----hhhhhccCCCCccCCC-CCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence 458999999999987 7888888888899996 69999999999999999999999999999999999986
No 3
>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=99.86 E-value=9.9e-23 Score=128.73 Aligned_cols=72 Identities=42% Similarity=0.757 Sum_probs=64.6
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCC-CCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAG-TGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL 77 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g-~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~ 77 (120)
+-+||||.+|+||++ ||+|++..+..|.|..+ +++|.++...+..|++|||+||+++||++++||.+|+|+.
T Consensus 17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~~ 89 (92)
T cd07163 17 SGKHYGIYACDGCSG----FFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPRN 89 (92)
T ss_pred cccEECceeeeeeee----EEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcCC
Confidence 458999999999987 78899988888999863 3699999999999999999999999999999999999754
No 4
>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=99.86 E-value=1e-22 Score=126.90 Aligned_cols=70 Identities=30% Similarity=0.667 Sum_probs=63.9
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~ 76 (120)
+.+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|+++
T Consensus 15 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~~ 84 (85)
T cd06964 15 SGYHYGVSACEGCKG----FFRRSIQKNMVYTCHR-DKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK 84 (85)
T ss_pred cccEECcceeeeeee----EEeeeecCCCCeECCC-CCccccCCcccccCccchhhhhhhhCCCHHHhhccccCC
Confidence 468999999999987 7888988888899986 689999999999999999999999999999999999853
No 5
>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=99.86 E-value=8.6e-23 Score=128.88 Aligned_cols=71 Identities=49% Similarity=0.806 Sum_probs=64.4
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~ 76 (120)
+-+||||.+|+||++ ||+|++..+..|.|..++++|.++...+..|++|||+|||++||++++|+.+|++.
T Consensus 17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~ 87 (92)
T cd06970 17 SGKHYGIYACNGCSG----FFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR 87 (92)
T ss_pred cccEECccEEeeeee----EeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCcc
Confidence 358999999999987 78899988889999864489999999999999999999999999999999999864
No 6
>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=99.86 E-value=9.1e-23 Score=127.21 Aligned_cols=70 Identities=31% Similarity=0.590 Sum_probs=64.3
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~ 76 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++||.++++.
T Consensus 10 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~ 79 (85)
T cd06961 10 TGYHYRCITCEGCKG----FFRRTVQKKLSYSCKG-EGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRG 79 (85)
T ss_pred cceEEChhhhhhhhH----hhHhhhccCCccccCC-CCccccCccccccCccchhhhhhhccCCHHHcccccCcc
Confidence 468999999999988 7888998888999996 699999999999999999999999999999999999864
No 7
>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=99.86 E-value=7.7e-23 Score=125.41 Aligned_cols=67 Identities=30% Similarity=0.698 Sum_probs=61.5
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLK 73 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r 73 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++||.+|
T Consensus 11 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 11 SGKHYGVYSCEGCKG----FFKRTVRKDLTYTCRD-NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred cceEECceeehhHHH----HHHHHhhCCCccccCC-CCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 458999999999988 7888998888999996 799999999999999999999999999999999875
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=99.85 E-value=1.1e-22 Score=125.74 Aligned_cols=71 Identities=30% Similarity=0.540 Sum_probs=64.6
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL 77 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~ 77 (120)
+.+||||.+|+||++ ||+|++.....+.|.. +++|.|+...+..|++|||+|||++||++++||.+|+|+.
T Consensus 9 ~g~hyG~~sC~aC~~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~ 79 (81)
T cd07165 9 SGYHYGVTSCEGCKG----FFRRSIQKQIEYRCLR-DGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR 79 (81)
T ss_pred cceEECchhhhhHHH----HHHhHhccCCceeCCC-CCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence 468999999999988 6778888888899996 6899999999999999999999999999999999998753
No 9
>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=99.85 E-value=1.5e-22 Score=126.71 Aligned_cols=70 Identities=34% Similarity=0.725 Sum_probs=64.5
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~ 76 (120)
+-+||||.+|+||++ ||+|++..+..+.|.. +++|.|+...+..|++|||+|||++||++++||.+|++.
T Consensus 14 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~ 83 (87)
T cd06967 14 SGRHYGAVSCEGCKG----FFKRSIRKNLGYSCRG-SKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPI 83 (87)
T ss_pred CcCEeCcceEeeeee----EeeeeeeCCCCcccCC-CCccccCccccccCccchhhhhhHcCCCHHHhccccCCC
Confidence 458999999999987 7889998888999995 799999999999999999999999999999999999973
No 10
>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=99.85 E-value=1.3e-22 Score=123.87 Aligned_cols=67 Identities=36% Similarity=0.657 Sum_probs=61.3
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLK 73 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r 73 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|
T Consensus 9 ~g~hygv~sC~aCk~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 9 SGYHYGVASCEACKA----FFKRTIQGNLGYSCPS-TSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred cceEEChhhhhhhHH----HHHHHhhCCCceeCCc-CCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 458999999999988 7888988888899996 799999999999999999999999999999999875
No 11
>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=99.85 E-value=2.4e-22 Score=126.22 Aligned_cols=71 Identities=25% Similarity=0.506 Sum_probs=63.9
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcce-eccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQ-ACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL 77 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~-~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~ 77 (120)
+-+||||.+|+||++ ||+|++..+..| .|.. +++|.|+...+..|++|||+|||++||++++||.+|+|+.
T Consensus 14 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~ 85 (89)
T cd07166 14 SGFHYGVHACEGCKG----FFRRSIQQKIQYRKCTK-NETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKR 85 (89)
T ss_pred cceEEChhhhhhHhh----EecceeEcCCcchhhcc-CCcccccccccccccchhhhhcccccCCHHHhcCCCCCCc
Confidence 458999999999988 788888877888 5985 7999999999999999999999999999999999998754
No 12
>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=99.85 E-value=3.1e-22 Score=122.48 Aligned_cols=68 Identities=34% Similarity=0.742 Sum_probs=62.0
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~ 74 (120)
+-+||||.+|+||++ ||+|++..+..+.|.. +++|.|+...+..|++|||+|||++||++++|+.+|+
T Consensus 9 ~~~hygv~~C~aC~~----FFrR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 9 TGKHYGVLSCNGCKG----FFRRSVRKNRTYTCRF-GGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred cccEECcceeeeehh----eeCccccCCCceeCCC-CCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 358999999999987 7888988888899996 6899999999999999999999999999999998874
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=99.85 E-value=3e-22 Score=126.05 Aligned_cols=70 Identities=29% Similarity=0.566 Sum_probs=64.0
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~ 76 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+.+|+|.
T Consensus 17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~ 86 (90)
T cd07168 17 TGLHYGIITCEGCKG----FFKRTVQNKRVYTCVG-DGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPG 86 (90)
T ss_pred cceEECceehhhhhH----hhhhhhcCCCCccCCC-CCCccccccccccccccchhhhhhcCCCHHHhhcccCCC
Confidence 458999999999988 7788888888899995 799999999999999999999999999999999999874
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=99.84 E-value=3.2e-22 Score=128.17 Aligned_cols=70 Identities=23% Similarity=0.451 Sum_probs=63.9
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~ 76 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||+++++.
T Consensus 29 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~~ 98 (101)
T cd07160 29 SGFHYNVLSCEGCKG----FFRRSVIKGAQYVCKN-GGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQIR 98 (101)
T ss_pred cceEECcceehhhhh----hhhhcccccCccccCC-CCccccCCcccccCccchhHHHHHhCCCHHHhcChhhhh
Confidence 458999999999987 7888888888999996 699999999999999999999999999999999998853
No 15
>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=99.84 E-value=3.7e-22 Score=127.05 Aligned_cols=69 Identities=32% Similarity=0.577 Sum_probs=63.1
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS 75 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~ 75 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+++.
T Consensus 15 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~ 83 (97)
T cd07170 15 SGYHYGVASCEACKA----FFKRTIQGNIEYSCPA-TNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVR 83 (97)
T ss_pred cceEECceeehhhhH----HHHHHhccCCceeecC-CCccccCcccCccCCccccchhhhcCCCHHHcccccCC
Confidence 458999999999988 7788888888899995 79999999999999999999999999999999998874
No 16
>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=99.84 E-value=4.1e-22 Score=121.06 Aligned_cols=65 Identities=49% Similarity=0.865 Sum_probs=59.1
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~ 70 (120)
+.+||||.+|+||++ ||+|++..+..|.|..++++|.|+...+..|++|||+|||++||++++||
T Consensus 9 ~~~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 9 SGKHYGVYACDGCSG----FFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred cceEECcceeeeeee----EeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 458999999999987 88899988889999855789999999999999999999999999998875
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=99.84 E-value=6.2e-22 Score=123.12 Aligned_cols=68 Identities=26% Similarity=0.479 Sum_probs=62.5
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~ 74 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||+.++|+++.+
T Consensus 12 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~ 79 (84)
T cd06962 12 SGYHYNALTCEGCKG----FFRRSITKNAVYKCKN-GGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQ 79 (84)
T ss_pred cceEECcceeeccee----eeeeeeccCCceecCC-CCcCccCccccccCccchhhHHHHhCCChHHccCHHH
Confidence 458999999999987 7889998888999996 6999999999999999999999999999999998876
No 18
>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=99.84 E-value=6e-22 Score=122.69 Aligned_cols=68 Identities=32% Similarity=0.616 Sum_probs=61.6
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~ 74 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+.++.
T Consensus 14 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~ 81 (82)
T cd07171 14 SGYHYGVWSCEGCKA----FFKRSIQGHNDYICPA-TNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERR 81 (82)
T ss_pred cceEECceeehhhHH----hHHHHeeCCCceeCCC-CCccccCCcccccCccchhHHHhHhcCCHHHHHHhhc
Confidence 458999999999988 6778888788899985 7999999999999999999999999999999998763
No 19
>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=99.84 E-value=5.2e-22 Score=124.93 Aligned_cols=69 Identities=29% Similarity=0.583 Sum_probs=63.2
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS 75 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~ 75 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+.++++
T Consensus 17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 85 (90)
T cd07169 17 TGLHYGIISCEGCKG----FFKRSICNKRVYRCSR-DKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP 85 (90)
T ss_pred cceEECcceehhhHH----HHHHHhcCCCceecCC-CCcccccccccccccccchhhhccccCCHHHhccccCC
Confidence 458999999999988 7788888888899996 68999999999999999999999999999999999875
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=99.84 E-value=5.2e-22 Score=125.50 Aligned_cols=69 Identities=23% Similarity=0.560 Sum_probs=63.3
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS 75 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~ 75 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++||.+|+.
T Consensus 9 ~g~hyGv~sC~aCk~----FFRRsv~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~ 77 (93)
T cd07167 9 SGYHYGLLTCESCKG----FFKRTVQNKKRYTCIE-NQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMR 77 (93)
T ss_pred cceEECchhhhhHHH----HHHHHeeCCCccccCC-CCccccCccccCcCCCcccchhhhccCCHHHhhhcccC
Confidence 358999999999988 7788988888999996 69999999999999999999999999999999999874
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=99.84 E-value=6.2e-22 Score=124.77 Aligned_cols=68 Identities=25% Similarity=0.465 Sum_probs=62.6
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~ 74 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++++|+++++
T Consensus 12 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~ 79 (91)
T cd07161 12 SGYHYNALTCEGCKG----FFRRSVTKSAVYHCKY-GRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQ 79 (91)
T ss_pred cceEECceeehhhHH----HHHHHhccCCceecCC-CCccccCccccccCccchhhHHhHcCCCHHHcCchhh
Confidence 458999999999988 7788988888999996 6899999999999999999999999999999999976
No 22
>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=99.83 E-value=7.6e-22 Score=125.29 Aligned_cols=72 Identities=29% Similarity=0.612 Sum_probs=65.2
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccch
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLY 78 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~ 78 (120)
+.+||||.+|+||++ ||+|++..+..+.|.. +++|.++...+..|++|||+||+++||++++|+.++.++..
T Consensus 16 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~~~ 87 (95)
T cd06968 16 SGIHYGVITCEGCKG----FFRRSQQNNVSYSCPR-QKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQ 87 (95)
T ss_pred cceEECceeehhhHH----hhHHheeCCCceecCC-CcccccccCCceeccccchhhcccccCChhhcccCcCChhh
Confidence 468999999999988 7788888888899996 68999999999999999999999999999999999887544
No 23
>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=99.83 E-value=1e-21 Score=119.89 Aligned_cols=65 Identities=34% Similarity=0.680 Sum_probs=59.2
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~ 71 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++||.
T Consensus 11 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~ 75 (75)
T cd06969 11 ACQHYGVRTCEGCKG----FFKRTVQKNAKYVCLA-NKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75 (75)
T ss_pred cceEECcceeeeeee----eeeeeeecCCcccCCc-CCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence 458999999999987 7888988888899996 7999999999999999999999999999999873
No 24
>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=99.83 E-value=1.1e-21 Score=124.45 Aligned_cols=69 Identities=25% Similarity=0.443 Sum_probs=63.4
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNS 75 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~ 75 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++|+++++.
T Consensus 11 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~ 79 (94)
T cd06966 11 LGYNFNAITCESCKA----FFRRNALKNKEFKCPF-NESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDK 79 (94)
T ss_pred cceEECcceeeeehh----eehhcccCCCccccCC-CCccccCccccccCccchhhhCcccCCCHHHccchhhh
Confidence 468999999999987 7888998888899996 69999999999999999999999999999999999874
No 25
>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=99.83 E-value=1.1e-21 Score=118.81 Aligned_cols=64 Identities=41% Similarity=0.785 Sum_probs=58.6
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~ 70 (120)
+.+||||.+|+||++ ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++||
T Consensus 9 ~~~hygv~sC~aC~~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 9 SGYHYGVLTCEGCKG----FFRRSVRRNLEYTCPA-GGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred cccEECcceeeeeee----eEeEeecCCCCccCCC-CCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 458999999999987 8889998888899996 699999999999999999999999999998875
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=99.83 E-value=1.3e-21 Score=118.90 Aligned_cols=64 Identities=38% Similarity=0.753 Sum_probs=58.5
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~ 70 (120)
+-+||||.+|+||++ ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++||
T Consensus 9 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (73)
T cd06958 9 SGKHYGQFTCEGCKS----FFKRSVRRNLTYTCRG-NRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred cceEEChhhhhhhhh----hhhhhhcCCCceeCCC-CCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 458999999999988 7788888888899995 799999999999999999999999999999887
No 27
>KOG4215|consensus
Probab=99.83 E-value=3.7e-22 Score=150.16 Aligned_cols=71 Identities=28% Similarity=0.628 Sum_probs=66.6
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL 77 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~ 77 (120)
|-+|||+.+|+||| +||||||.++..|.|+. +.+|.||+..|+.|++|||+||+.+||.+++||++|++..
T Consensus 30 TGKHYGA~SCdGCK----GFFRRSVrk~~~YtCRF-~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg 100 (432)
T KOG4215|consen 30 TGKHYGAISCDGCK----GFFRRSVRKNHQYTCRF-NKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIG 100 (432)
T ss_pred cccccceeecCcch----HHHHHHHHhcceeeeec-cccccccchhhhhhhHhhHHHHHHhcccHHhhhccccccc
Confidence 67899999999995 69999999999999997 7999999999999999999999999999999999998643
No 28
>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=99.83 E-value=1.6e-21 Score=118.19 Aligned_cols=63 Identities=35% Similarity=0.640 Sum_probs=57.6
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDA 69 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v 69 (120)
+-+||||.+|+||++ ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++|
T Consensus 9 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (72)
T cd07156 9 TGYHFNAMTCEGCKG----FFRRSMKRKARFTCPF-NGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71 (72)
T ss_pred cccEECcceehhhhh----hhchhccCcCccccCC-CCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence 458999999999988 7788888888899996 69999999999999999999999999999876
No 29
>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=99.83 E-value=1.1e-21 Score=119.49 Aligned_cols=65 Identities=25% Similarity=0.562 Sum_probs=59.2
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQH 71 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~ 71 (120)
+-+||||.+|+||++ ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||++++|+.
T Consensus 9 ~g~hygv~sC~aC~~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 73 (74)
T cd07179 9 SGFHFGALTCEGCKG----FFRRTELSSNSYVCPG-GQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73 (74)
T ss_pred cceEECceeehhHHH----HHHHHhhCCCcccCCC-CCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence 458999999999988 7788888888999996 6889999999999999999999999999999875
No 30
>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=99.82 E-value=1.9e-21 Score=121.43 Aligned_cols=70 Identities=31% Similarity=0.619 Sum_probs=62.0
Q ss_pred CCccCCccCChhhhhcccceeeeccccCc--ceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQ--CQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~--~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~ 76 (120)
+-+||||.+|+||++ ||+|++.... .|.|.. +++|.++...+..|++|||+|||++||+.++++.+|+..
T Consensus 11 ~g~hyGv~sC~aCk~----FFRR~~~~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~~ 82 (86)
T cd07157 11 AGFHHGAYVCEACKK----FFMRSSNAISFTISECPN-GGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRSD 82 (86)
T ss_pred cccEECcceeeEeee----EEecceecCCCccccCCC-CCccccCccccccCccchhhHHhHcCCCccccccccccc
Confidence 458999999999987 7888887654 789996 699999999999999999999999999999999888743
No 31
>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=99.82 E-value=2.1e-21 Score=117.86 Aligned_cols=64 Identities=30% Similarity=0.616 Sum_probs=58.1
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~ 70 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||+++++.
T Consensus 9 ~~~hygv~sC~aCk~----FFRR~~~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 9 SGCHYGVLTCGSCKV----FFKRAAEGQHNYLCAG-RNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred cceEECceeehhhhH----hHHHhhcCCCceeCCC-CCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 468999999999987 7888998888899985 799999999999999999999999999998764
No 32
>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=99.82 E-value=2.5e-21 Score=117.59 Aligned_cols=64 Identities=30% Similarity=0.709 Sum_probs=57.9
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcce-eccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQ-ACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~-~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~ 70 (120)
+-+||||.+|+||++ ||+|++..+..+ .|.. +++|.++...+..|++|||+|||++||++++|+
T Consensus 9 ~g~hyGv~~C~aC~~----FFRR~v~~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 73 (73)
T cd07158 9 SGFHYGVHSCEGCKG----FFRRTIQHNLTYRRCLN-GGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred cceEECcchhhHHHH----HHhhhhcCCCCcccCCC-CCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence 458999999999988 778888888888 8985 699999999999999999999999999998875
No 33
>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=99.82 E-value=2.5e-21 Score=120.45 Aligned_cols=70 Identities=26% Similarity=0.514 Sum_probs=61.5
Q ss_pred CCccCCccCChhhhhcccceeeeccccCccee-ccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccch
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQA-CQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLY 78 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~-C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~ 78 (120)
+-+||||.+|+||++ ||+|++..+..|. |.. +|.|+...+..|++|||+||+++||++++|+.+|+|+..
T Consensus 10 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~~C~~---~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~ 80 (84)
T cd06965 10 SGFHYGVHACEGCKG----FFRRTIRLKLVYKPCDL---SCKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRVE 80 (84)
T ss_pred cceEEChhhhhhhhh----heeeeeecCCCcccccc---CCCcCccccccccchhhhhhhhccCCHHHcccCCCCchh
Confidence 458999999999987 7888888777884 973 399999999999999999999999999999999997543
No 34
>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=99.82 E-value=2.3e-21 Score=121.38 Aligned_cols=68 Identities=32% Similarity=0.574 Sum_probs=61.3
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~ 74 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++|++++.
T Consensus 10 ~g~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~ 77 (87)
T cd07162 10 TGYHFNAMTCEGCKG----FFRRAMKRNARLCCPF-QKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA 77 (87)
T ss_pred cceEECcceehhhHH----HHHhhhccCceeEcCC-CCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence 468999999999988 6778888888899996 6899999999999999999999999999999888754
No 35
>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=99.82 E-value=2.1e-21 Score=117.94 Aligned_cols=63 Identities=29% Similarity=0.555 Sum_probs=57.5
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDA 69 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v 69 (120)
+-+||||.+|+||++ ||||++..+..|.|.. +++|.++...+..|++|||+|||++||+++.|
T Consensus 10 ~~~hygv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (73)
T cd06959 10 SGFHYGVLSCEGCKG----FFRRSVTKGAVYACKF-GNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL 72 (73)
T ss_pred cceEECceeehhhHH----HHHHhhcCCCCccCCC-CCcCCcCCcccccCccchhHHHHHhCCChhhc
Confidence 468999999999988 7788888888999996 69999999999999999999999999999876
No 36
>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=99.81 E-value=5.3e-21 Score=117.43 Aligned_cols=64 Identities=31% Similarity=0.642 Sum_probs=57.9
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQ 70 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~ 70 (120)
+-+||||.+|+||++ ||||++..+..|.|.. +++|.|+...+..|++|||+|||++||+..++.
T Consensus 13 ~g~hyGv~sC~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 13 SGCHYGVLTCGSCKV----FFKRAVEGQHNYLCAG-RNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred cceEECceeehhhHH----hHHHHeeCCCceeCCC-CCccccCCcccccCccchhHHHHHhCCCccccc
Confidence 458999999999988 7788888888899985 799999999999999999999999999987765
No 37
>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=99.81 E-value=7.7e-21 Score=117.69 Aligned_cols=66 Identities=27% Similarity=0.546 Sum_probs=58.9
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHL 72 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~ 72 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.|+...+..|++|||+|||++||++.....+
T Consensus 14 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~ 79 (82)
T cd07173 14 SGCHYGALTCGSCKV----FFKRAAEGKQKYLCAS-RNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK 79 (82)
T ss_pred cceEECcchhhhHHH----HHHHHhcCCCceecCC-CCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence 358999999999988 7788888888899996 79999999999999999999999999998776654
No 38
>KOG4216|consensus
Probab=99.81 E-value=2.9e-21 Score=146.31 Aligned_cols=70 Identities=30% Similarity=0.618 Sum_probs=65.3
Q ss_pred CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccc
Q psy13208 3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLL 77 (120)
Q Consensus 3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~ 77 (120)
-.||||.+||||| +|||||-+.+..|.|++ ..+|.||...|+.|+.|||+|||++||++++|..+|++++
T Consensus 58 GiHYGVITCEGCK----GFFRRSQ~s~a~YsCpR-qknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKK 127 (479)
T KOG4216|consen 58 GIHYGVITCEGCK----GFFRRSQQSNANYSCPR-QKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK 127 (479)
T ss_pred cceeeeEeeccch----HhhhhhhhccccccCCc-ccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHh
Confidence 3799999999995 68999999999999996 8999999999999999999999999999999999998764
No 39
>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=99.81 E-value=7.7e-21 Score=122.88 Aligned_cols=66 Identities=30% Similarity=0.543 Sum_probs=59.5
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhh
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHL 72 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~ 72 (120)
+-+||||.+|+||++ ||+|++..+..|.|.. +++|.++...+..|++|||+|||++||++++|+++
T Consensus 17 ~g~hyGv~sC~aCk~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 82 (107)
T cd06955 17 TGFHFNAMTCEGCKG----FFRRSMKRKALFTCPF-NGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82 (107)
T ss_pred cccEECcceeeeecc----eecceeccCCccccCC-CCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence 458999999999987 7888998888899986 79999999999999999999999999998777765
No 40
>KOG4217|consensus
Probab=99.78 E-value=1.2e-20 Score=145.85 Aligned_cols=64 Identities=34% Similarity=0.658 Sum_probs=59.4
Q ss_pred ccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhh
Q psy13208 4 RHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHL 72 (120)
Q Consensus 4 ~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~ 72 (120)
-||||.+||||| +||+|+++++..|+|.+ +.+|+||+..|+.|++|||+|||+|||-.+.|+.+
T Consensus 282 qHYGvRTCEGCK----GFFKRTVQKnaKYvCla-nKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtd 345 (605)
T KOG4217|consen 282 QHYGVRTCEGCK----GFFKRTVQKNAKYVCLA-NKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTD 345 (605)
T ss_pred hhcCccccccch----HHHHHHHhcCCeeEeec-CCCCCcchhhhhhchhhhHhHHHHhhhhhhheecc
Confidence 399999999995 69999999999999995 89999999999999999999999999998888754
No 41
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.78 E-value=5.9e-20 Score=110.70 Aligned_cols=61 Identities=31% Similarity=0.625 Sum_probs=55.0
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCch
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKD 67 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~ 67 (120)
+.+||||.+|+||++ ||+|++..+..+.|.. +++|.++...+..|++|||+|||++||+++
T Consensus 10 ~~~hygv~~C~aC~~----FFRR~v~~~~~~~C~~-~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 10 SGFHFGVCSCRACKA----FFRRTVNLRYKYRCDR-KNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred cccEeCCcEechhhh----hhhhheeCCCCeecCC-CcccccCCCccccCccCcChhHhhccCcCC
Confidence 468999999999987 7888988888899996 688999999999999999999999999863
No 42
>KOG4846|consensus
Probab=99.77 E-value=2.1e-20 Score=142.69 Aligned_cols=69 Identities=28% Similarity=0.547 Sum_probs=63.4
Q ss_pred CccCCccCChhhhhcccceeeeccccCcce-eccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhcc
Q psy13208 3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQ-ACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSL 76 (120)
Q Consensus 3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~-~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~ 76 (120)
-|||||.+||||| +||||+|+.+..| .|- ++.+|.|....|+.|+.|||+|||.+||++++|+.++++.
T Consensus 144 GfHYGV~aCEGCK----GFFRRSIQqkI~YrrCl-k~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~ 213 (538)
T KOG4846|consen 144 GFHYGVTACEGCK----GFFRRSIQQKIDYRRCL-KQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKF 213 (538)
T ss_pred cceeceeecccch----HHHHHHHHHhhhHHHHh-hhhceehhhhccchhhhhhHHHHHhcccchhhhhhccccc
Confidence 4899999999995 6999999999988 798 4899999999999999999999999999999999887754
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=99.74 E-value=2.2e-19 Score=108.19 Aligned_cols=60 Identities=30% Similarity=0.733 Sum_probs=50.4
Q ss_pred CCccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCc
Q psy13208 2 TFRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNK 66 (120)
Q Consensus 2 ~~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~ 66 (120)
+.+||||.+|++|++ ||+|++.....+.|.. +++|.++...+..|++|||+|||++||..
T Consensus 11 ~~~~ygv~sC~~C~~----FFrR~~~~~~~~~C~~-~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 11 SGYHYGVLSCNACKM----FFRRSVKKKKPYKCKK-NGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp SEEETTEEEEHHHHH----HHHHHHHTTCG-STSS-SST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred Cccccccccccccee----eeeecccccccccccc-cccccccccCCCEeCcchHHHHHHHCCcC
Confidence 458999999999987 7788888888899995 79999999999999999999999999973
No 44
>KOG4218|consensus
Probab=99.69 E-value=3.6e-18 Score=128.18 Aligned_cols=67 Identities=25% Similarity=0.597 Sum_probs=63.3
Q ss_pred CccCCccCChhhhhcccceeeeccccCcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhh
Q psy13208 3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKN 74 (120)
Q Consensus 3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~ 74 (120)
-||||-++||.|| +||+|+++.++.|.|.. +.+|.||+..|..|++|||+|||.+||..++|+-+|+
T Consensus 27 GYHYGLLTCESCK----GFFKRTVQNnK~YtC~e-~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRM 93 (475)
T KOG4218|consen 27 GYHYGLLTCESCK----GFFKRTVQNNKQYTCSE-EQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRM 93 (475)
T ss_pred cceeeeeehhhhh----hHHHHHhhcCcceeccc-ccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhh
Confidence 5899999999995 68999999999999995 8999999999999999999999999999999998886
No 45
>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=99.16 E-value=1e-11 Score=75.10 Aligned_cols=59 Identities=36% Similarity=0.797 Sum_probs=50.0
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++.+..+.. |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 13 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (72)
T cd07156 13 FNAMTCEGCK-------GFFRRSMKRKAR-----FTCPF--NGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71 (72)
T ss_pred ECcceehhhh-------hhhchhccCcCc-----cccCC--CCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence 3456899999 898888875543 77874 57899999999999999999999999999876
No 46
>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=99.14 E-value=1.4e-11 Score=74.70 Aligned_cols=60 Identities=33% Similarity=0.725 Sum_probs=50.6
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS 119 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~ 119 (120)
.+...|.+|. +++++.++.+.. |.|.. +++|.|+...++.|++|||+|||++||+++++-
T Consensus 13 ygv~sC~aCk-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 13 YGVLTCGSCK-------VFFKRAAEGQHN-----YLCAG--RNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred ECceeehhhh-------HhHHHhhcCCCc-----eeCCC--CCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 3456899999 888888876644 77864 578999999999999999999999999998873
No 47
>KOG4216|consensus
Probab=99.14 E-value=1.3e-11 Score=94.28 Aligned_cols=59 Identities=36% Similarity=0.898 Sum_probs=52.8
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+..-|..|+ |+++++-++.-. |.|+. ..+|+||+.+||.|++|||+|||++||+.+||
T Consensus 61 YGVITCEGCK-------GFFRRSQ~s~a~-----YsCpR--qknC~iDRtnRNRCQ~CRLqKClaLGMSRDAV 119 (479)
T KOG4216|consen 61 YGVITCEGCK-------GFFRRSQQSNAN-----YSCPR--QKNCLIDRTNRNRCQHCRLQKCLALGMSRDAV 119 (479)
T ss_pred eeeEeeccch-------Hhhhhhhhcccc-----ccCCc--ccCCcccccccchhhHHHHHHHHHhccchhhH
Confidence 4457899999 999887777766 99985 69999999999999999999999999999998
No 48
>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=99.13 E-value=1.5e-11 Score=74.48 Aligned_cols=60 Identities=45% Similarity=0.806 Sum_probs=50.3
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+-..|.+|. +++++.++.+.. |.|.. ..++|.|+...+..|++|||+|||++||++++|
T Consensus 13 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~-~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (73)
T cd07154 13 YGVYACDGCS-------GFFKRSIRRNLL-----YTCKA-GNGSCVVDKARRNQCQACRLKKCLEVSMNKDAV 72 (73)
T ss_pred ECcceeeeee-------eEeeeeecCCCC-----cccCC-CCCCCccCCcccccCccchhhHhhHhCCChHHC
Confidence 4457899999 999888876644 77863 246899999999999999999999999999876
No 49
>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=99.12 E-value=1.5e-11 Score=74.89 Aligned_cols=59 Identities=37% Similarity=0.780 Sum_probs=50.1
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++++++.+.. |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 15 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 73 (75)
T cd06969 15 YGVRTCEGCK-------GFFKRTVQKNAK-----YVCLA--NKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVV 73 (75)
T ss_pred ECcceeeeee-------eeeeeeeecCCc-----ccCCc--CCccccCCcccccCcccHhHHHHHhCCCHHHc
Confidence 4457899999 999888875543 77874 57899999999999999999999999999876
No 50
>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=99.11 E-value=1.5e-11 Score=74.71 Aligned_cols=59 Identities=29% Similarity=0.795 Sum_probs=49.7
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++++++.... |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 13 ygv~sC~aC~-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (74)
T cd07179 13 FGALTCEGCK-------GFFRRTELSSNS-----YVCPG--GQNCAITPATRNACKSCRFRRCLAVGMSKTGS 71 (74)
T ss_pred ECceeehhHH-------HHHHHHhhCCCc-----ccCCC--CCccccCCcccccCccchhHHHHHhCCCHhHe
Confidence 3456899998 888888876544 77875 46799999999999999999999999999887
No 51
>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=99.11 E-value=1.5e-11 Score=74.56 Aligned_cols=59 Identities=34% Similarity=0.862 Sum_probs=49.5
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++.++.+.. | .|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 13 yGv~~C~aC~-------~FFRR~v~~~~~-----~~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 72 (73)
T cd07158 13 YGVHSCEGCK-------GFFRRTIQHNLT-----YRRCLN--GGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAV 72 (73)
T ss_pred ECcchhhHHH-------HHHhhhhcCCCC-----cccCCC--CCCcCCCccccccCccchhhhhhHccCChHHc
Confidence 3456899999 888888876644 6 6764 47899999999999999999999999999876
No 52
>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=99.11 E-value=2e-11 Score=73.97 Aligned_cols=59 Identities=36% Similarity=0.822 Sum_probs=49.7
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++++..+.. |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 13 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (73)
T cd06958 13 YGQFTCEGCK-------SFFKRSVRRNLT-----YTCRG--NRNCPIDQHHRNQCQYCRLKKCLKVGMRREAV 71 (73)
T ss_pred EChhhhhhhh-------hhhhhhhcCCCc-----eeCCC--CCcCccCCcccccCccchhhHhhHhCCCHHHc
Confidence 3456899999 888888876543 77864 57899999999999999999999999999876
No 53
>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=99.10 E-value=2.4e-11 Score=73.65 Aligned_cols=59 Identities=31% Similarity=0.637 Sum_probs=49.2
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++++++.+.. |.|.. +++|.|+...+..|++|||+|||++||+++.|
T Consensus 14 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (73)
T cd06959 14 YGVLSCEGCK-------GFFRRSVTKGAV-----YACKF--GNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL 72 (73)
T ss_pred ECceeehhhH-------HHHHHhhcCCCC-----ccCCC--CCcCCcCCcccccCccchhHHHHHhCCChhhc
Confidence 3456899999 888888875533 77874 47899999999999999999999999998765
No 54
>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=99.10 E-value=2.4e-11 Score=73.47 Aligned_cols=59 Identities=37% Similarity=0.844 Sum_probs=50.1
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+-..|.+|. +++++++..+.. |.|.. ++.|.|+...+..|++|||+|||++||++++|
T Consensus 13 ygv~sC~aC~-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (72)
T cd06916 13 YGVLTCEGCK-------GFFRRSVRRNLE-----YTCPA--GGNCVIDKRNRNRCQACRLKKCLAVGMRKEAV 71 (72)
T ss_pred ECcceeeeee-------eeEeEeecCCCC-----ccCCC--CCccccCCcccccCccchhhHhhHhCCChHHc
Confidence 3456899999 999888886644 77874 47899999999999999999999999998875
No 55
>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=99.07 E-value=2e-11 Score=74.71 Aligned_cols=59 Identities=34% Similarity=0.834 Sum_probs=49.6
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++.++.+.. |.|.. +++|.|+...++.|++|||+|||++||++++|
T Consensus 15 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 73 (77)
T cd06956 15 YGVYSCEGCK-------GFFKRTVRKDLT-----YTCRD--NKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV 73 (77)
T ss_pred ECceeehhHH-------HHHHHHhhCCCc-----cccCC--CCccccCCCccccCccchhHHHhHhCCCHHHh
Confidence 3456899998 888888875543 78874 57899999999999999999999999998876
No 56
>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=99.06 E-value=2.4e-11 Score=75.21 Aligned_cols=59 Identities=36% Similarity=0.782 Sum_probs=49.7
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+-..|.+|. +++++++.... +|.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 18 yGv~sC~aC~-------~FFRR~v~~~~-----~~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 76 (82)
T cd07171 18 YGVWSCEGCK-------AFFKRSIQGHN-----DYICPA--TNQCTIDKNRRKSCQACRLRKCYEVGMMKGGI 76 (82)
T ss_pred ECceeehhhH-------HhHHHHeeCCC-----ceeCCC--CCccccCCcccccCccchhHHHhHhcCCHHHH
Confidence 3456899999 88888887654 377874 58899999999999999999999999999876
No 57
>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=99.06 E-value=4e-11 Score=76.36 Aligned_cols=60 Identities=35% Similarity=0.732 Sum_probs=50.6
Q ss_pred CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
..+...|.+|. ++++++++.... |.|.. .+.|.|+...+..|++|||+|||++||++++|
T Consensus 18 hyGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 77 (97)
T cd07170 18 HYGVASCEACK-------AFFKRTIQGNIE-----YSCPA--TNECEITKRRRKSCQACRFMKCLKVGMLKEGV 77 (97)
T ss_pred EECceeehhhh-------HHHHHHhccCCc-----eeecC--CCccccCcccCccCCccccchhhhcCCCHHHc
Confidence 34557899999 999888876543 77874 57899999999999999999999999998776
No 58
>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=99.06 E-value=4.3e-11 Score=74.37 Aligned_cols=59 Identities=31% Similarity=0.669 Sum_probs=49.9
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++++..... |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 16 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 74 (84)
T cd06962 16 YNALTCEGCK-------GFFRRSITKNAV-----YKCKN--GGNCEMDMYMRRKCQECRLRKCKEMGMLAECL 74 (84)
T ss_pred ECcceeecce-------eeeeeeeccCCc-----eecCC--CCcCccCccccccCccchhhHHHHhCCChHHc
Confidence 4457899999 999888875433 78874 47899999999999999999999999998876
No 59
>KOG4215|consensus
Probab=99.06 E-value=4e-11 Score=91.03 Aligned_cols=59 Identities=29% Similarity=0.789 Sum_probs=53.7
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
++-.+|..|+ |++++.|+.+.+ |+|.- ..+|+||+..||.|++|||+||+.+||.++||
T Consensus 34 YGA~SCdGCK-------GFFRRSVrk~~~-----YtCRF--~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAi 92 (432)
T KOG4215|consen 34 YGAISCDGCK-------GFFRRSVRKNHQ-----YTCRF--NKQCVVDKDKRNACRYCRFQKCVRAGMKREAI 92 (432)
T ss_pred cceeecCcch-------HHHHHHHHhcce-----eeeec--cccccccchhhhhhhHhhHHHHHHhcccHHhh
Confidence 4457999999 999999998888 99974 68999999999999999999999999999876
No 60
>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=99.06 E-value=3.4e-11 Score=76.07 Aligned_cols=61 Identities=43% Similarity=0.835 Sum_probs=50.6
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+-..|.+|. +++++++..+.. |.|.....+.|.|+...+..|++|||+|||++||++++|
T Consensus 21 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 81 (92)
T cd07163 21 YGIYACDGCS-------GFFKRSIRRNRQ-----YVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAV 81 (92)
T ss_pred ECceeeeeee-------eEEeeeecCCCC-----cCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHh
Confidence 4457899999 999888876654 778652246899999999999999999999999998776
No 61
>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=99.06 E-value=3.6e-11 Score=73.41 Aligned_cols=59 Identities=32% Similarity=0.790 Sum_probs=49.9
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++.+..+.. |.|.. ++.|.|+..++..|++|||+|||++||++++|
T Consensus 13 ygv~~C~aC~-------~FFrR~~~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (76)
T cd06960 13 YGVLSCNGCK-------GFFRRSVRKNRT-----YTCRF--GGNCVVDKDKRNACRYCRFKKCLEVGMDPEAV 71 (76)
T ss_pred ECcceeeeeh-------heeCccccCCCc-----eeCCC--CCcccccCcccccCccchhhhhhhcCCCHHHc
Confidence 4457899999 898888876654 77874 47899999999999999999999999998776
No 62
>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=99.06 E-value=5.8e-11 Score=72.83 Aligned_cols=61 Identities=34% Similarity=0.737 Sum_probs=51.1
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCccC
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKSM 120 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~~ 120 (120)
.+-..|.+|. +++++.++.+.. |.|.. +++|.|+..+++.|++|||+|||++||+..++-|
T Consensus 17 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~ 77 (78)
T cd07172 17 YGVLTCGSCK-------VFFKRAVEGQHN-----YLCAG--RNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKT 77 (78)
T ss_pred ECceeehhhH-------HhHHHHeeCCCc-----eeCCC--CCccccCCcccccCccchhHHHHHhCCCcccccC
Confidence 3456899999 888888876554 77874 5889999999999999999999999999987643
No 63
>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=99.05 E-value=2.7e-11 Score=73.78 Aligned_cols=59 Identities=41% Similarity=0.807 Sum_probs=49.6
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++++++.+.. |.|.. ++.|.|+...+..|++|||+|||++||++++|
T Consensus 13 ygv~sC~aCk-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 71 (75)
T cd07155 13 YGVASCEACK-------AFFKRTIQGNLG-----YSCPS--TSECEVDKKRRKSCQACRLQKCLKVGMLKEGV 71 (75)
T ss_pred EChhhhhhhH-------HHHHHHhhCCCc-----eeCCc--CCCcccCCcccccCccchhhhhhHhCCCHHHc
Confidence 3456899998 888888876644 77874 57899999999999999999999999998876
No 64
>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=99.05 E-value=3.1e-11 Score=75.17 Aligned_cols=59 Identities=39% Similarity=0.828 Sum_probs=49.9
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++++..+.. |.|.. +++|.|+...++.|++|||+|||++||++++|
T Consensus 14 ygv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (85)
T cd06961 14 YRCITCEGCK-------GFFRRTVQKKLS-----YSCKG--EGKCEIDKVTRNQCQECRFKKCIAVGMAKDLV 72 (85)
T ss_pred EChhhhhhhh-------HhhHhhhccCCc-----cccCC--CCccccCccccccCccchhhhhhhccCCHHHc
Confidence 3456899999 898888876543 88875 47899999999999999999999999998776
No 65
>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=99.05 E-value=4.4e-11 Score=73.37 Aligned_cols=59 Identities=42% Similarity=0.848 Sum_probs=49.7
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++++++.... |.|.. +++|.|+...++.|++|||+|||++||++++|
T Consensus 13 yG~~~C~~C~-------~FFRR~~~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 71 (78)
T cd07164 13 YGVPSCDGCR-------GFFKRSIRRNLA-----YVCKE--NGSCVVDVARRNQCQACRFKKCLQVNMNRDAV 71 (78)
T ss_pred ECcchhhhhh-------hhhhhhccCCCC-----ccCCC--CCcccccCcccccCccchhhhhhHhcCCHHHh
Confidence 4456899999 888888876543 77875 57899999999999999999999999998776
No 66
>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=99.04 E-value=6.6e-11 Score=75.86 Aligned_cols=59 Identities=29% Similarity=0.677 Sum_probs=50.4
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+-..|.+|. ++++++++.... |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 33 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 91 (101)
T cd07160 33 YNVLSCEGCK-------GFFRRSVIKGAQ-----YVCKN--GGKCQMDMYMRRKCQECRLRKCREAGMREQCV 91 (101)
T ss_pred ECcceehhhh-------hhhhhcccccCc-----cccCC--CCccccCCcccccCccchhHHHHHhCCCHHHh
Confidence 4457899999 999888876543 88875 47899999999999999999999999999876
No 67
>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=99.03 E-value=5.7e-11 Score=74.87 Aligned_cols=59 Identities=31% Similarity=0.697 Sum_probs=49.8
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++++++.... |.|.. .++|.|+...+..|++|||+|||++||++++|
T Consensus 16 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 74 (91)
T cd07161 16 YNALTCEGCK-------GFFRRSVTKSAV-----YHCKY--GRACEMDMYMRRKCQECRLKKCLSVGMRPECV 74 (91)
T ss_pred ECceeehhhH-------HHHHHHhccCCc-----eecCC--CCccccCccccccCccchhhHHhHcCCCHHHc
Confidence 3456899999 888888875544 78875 47899999999999999999999999998876
No 68
>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=99.03 E-value=5.3e-11 Score=74.14 Aligned_cols=59 Identities=34% Similarity=0.836 Sum_probs=49.8
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++.+..... |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 19 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 77 (85)
T cd06964 19 YGVSACEGCK-------GFFRRSIQKNMV-----YTCHR--DKNCIINKVTRNRCQYCRLQKCFEVGMSKESV 77 (85)
T ss_pred ECcceeeeee-------eEEeeeecCCCC-----eECCC--CCccccCCcccccCccchhhhhhhhCCCHHHh
Confidence 4557899999 898888875433 77874 47899999999999999999999999998776
No 69
>KOG4846|consensus
Probab=99.02 E-value=6.3e-11 Score=91.20 Aligned_cols=60 Identities=32% Similarity=0.787 Sum_probs=53.5
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS 119 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~ 119 (120)
++...|..|+ |++++.+|.+-+ | .|. +..+|.|-+.+||.|++||++|||++||+.|+|-
T Consensus 147 YGV~aCEGCK-------GFFRRSIQqkI~-----YrrCl--k~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVR 207 (538)
T KOG4846|consen 147 YGVTACEGCK-------GFFRRSIQQKID-----YRRCL--KQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVR 207 (538)
T ss_pred eceeecccch-------HHHHHHHHHhhh-----HHHHh--hhhceehhhhccchhhhhhHHHHHhcccchhhhh
Confidence 4567999999 999999998877 6 676 4689999999999999999999999999999983
No 70
>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=99.02 E-value=6e-11 Score=74.19 Aligned_cols=59 Identities=34% Similarity=0.807 Sum_probs=49.2
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++.+..+. .|.|.. .++|.|+...++.|++|||+|||++||++++|
T Consensus 14 ygv~sC~aC~-------~FFRR~v~~~~-----~~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 72 (87)
T cd07162 14 FNAMTCEGCK-------GFFRRAMKRNA-----RLCCPF--QKGCVITKSNRRQCQACRLRKCLSIGMKKELI 72 (87)
T ss_pred ECcceehhhH-------HHHHhhhccCc-----eeEcCC--CCceecCCcccccCccchhhHHhHhCCCHHHc
Confidence 3457899999 88888887553 377875 47899999999999999999999999999765
No 71
>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=99.01 E-value=6.3e-11 Score=74.09 Aligned_cols=59 Identities=37% Similarity=0.861 Sum_probs=49.8
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+-..|.+|. ++++++++.+.. +.|.. ++.|.|+...+..|++|||+|||++||++++|
T Consensus 18 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 76 (87)
T cd06967 18 YGAVSCEGCK-------GFFKRSIRKNLG-----YSCRG--SKDCVINKHHRNRCQYCRLQKCLAMGMKSDSV 76 (87)
T ss_pred eCcceEeeee-------eEeeeeeeCCCC-----cccCC--CCccccCccccccCccchhhhhhHcCCCHHHh
Confidence 4557899999 999888875543 77864 57899999999999999999999999998776
No 72
>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=99.01 E-value=1.4e-10 Score=75.11 Aligned_cols=60 Identities=32% Similarity=0.729 Sum_probs=50.7
Q ss_pred CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
..+...|.+|. +++++.+..... |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 20 hyGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 79 (107)
T cd06955 20 HFNAMTCEGCK-------GFFRRSMKRKAL-----FTCPF--NGDCRITKDNRRHCQACRLKRCVDIGMMKEFI 79 (107)
T ss_pred EECcceeeeec-------ceecceeccCCc-----cccCC--CCccccccCCccccccchhHHHHHcCCCchhc
Confidence 34457899999 999988876644 77864 58899999999999999999999999998765
No 73
>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=98.99 E-value=9.2e-11 Score=74.04 Aligned_cols=61 Identities=48% Similarity=0.796 Sum_probs=50.4
Q ss_pred CcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 45 KAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 45 ~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
..+-..|.+|. +++++.++.+.. |.|... .++|.|+...+..|++|||+|||++||++++|
T Consensus 20 hyGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 80 (92)
T cd06970 20 HYGIYACNGCS-------GFFKRSVRRKLI-----YRCQAG-TGMCPVDKAHRNQCQACRLKKCLQAGMNKDAV 80 (92)
T ss_pred EECccEEeeee-------eEeeeeeecCCC-----ceeecC-CCcCccCCCccccCccchhhHhhHhCCCHHHc
Confidence 34457899999 999888886544 788642 36899999999999999999999999998765
No 74
>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=98.98 E-value=6.1e-11 Score=73.39 Aligned_cols=60 Identities=33% Similarity=0.643 Sum_probs=50.0
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++++++.+.. |.|... .+.|.|+...+..|++|||+|||++||++++|
T Consensus 13 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~~-~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (82)
T cd06957 13 YGVYCCDGCS-------CFFKRSVRKGII-----YTCIAG-NGNCVVDKARRNWCPFCRLQKCFAVGMNRAAV 72 (82)
T ss_pred ECcceEeeee-------eEEEEeecCCCc-----eEccCc-cCCCccCCCccCcccCcchhhcccccCCHHHh
Confidence 3457899999 999888876544 888732 46899999999999999999999999998776
No 75
>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=98.97 E-value=1.1e-10 Score=72.15 Aligned_cols=59 Identities=29% Similarity=0.704 Sum_probs=49.5
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++++..+.. |.|.. +++|.|+...++.|++|||+|||++||++.+.
T Consensus 18 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~ 76 (82)
T cd07173 18 YGALTCGSCK-------VFFKRAAEGKQK-----YLCAS--RNDCTIDKFRRKNCPSCRLRKCFEAGMTLGAR 76 (82)
T ss_pred ECcchhhhHH-------HHHHHHhcCCCc-----eecCC--CCccccCCCccCcCcchhhhhhhhcCCCcChH
Confidence 4457899999 888888876544 78874 58899999999999999999999999998764
No 76
>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=98.97 E-value=7e-11 Score=72.96 Aligned_cols=60 Identities=35% Similarity=0.775 Sum_probs=49.6
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS 119 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~ 119 (120)
.+...|.+|. ++++..+.... .|.|.. +++|.|+...+..|++|||+|||++||++++|-
T Consensus 13 yG~~sC~aC~-------~FFRR~~~~~~-----~~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~ 72 (81)
T cd07165 13 YGVTSCEGCK-------GFFRRSIQKQI-----EYRCLR--DGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVR 72 (81)
T ss_pred ECchhhhhHH-------HHHHhHhccCC-----ceeCCC--CCCccccccccccccchhhhhcccccCCHHHcc
Confidence 4456899999 88888776543 377875 478999999999999999999999999998763
No 77
>KOG4217|consensus
Probab=98.97 E-value=1.4e-10 Score=90.55 Aligned_cols=71 Identities=35% Similarity=0.812 Sum_probs=59.5
Q ss_pred CcceeccCCCCCccccCcccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHH
Q psy13208 29 NQCQACQAGTGRCIVDKAHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKC 108 (120)
Q Consensus 29 ~~~~~C~~g~~~C~i~~~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kc 108 (120)
++.-+|.+ +.-|. ..+..-|..|+ |++.+.||.+-. |.|.. .++|.||+..||.|++||++||
T Consensus 270 ~~CAVCgD-nAaCq--HYGvRTCEGCK-------GFFKRTVQKnaK-----YvCla--nKnCPVDKRrRnRCQyCRfQKC 332 (605)
T KOG4217|consen 270 GLCAVCGD-NAACQ--HYGVRTCEGCK-------GFFKRTVQKNAK-----YVCLA--NKNCPVDKRRRNRCQYCRFQKC 332 (605)
T ss_pred ceeeecCC-hHHhh--hcCccccccch-------HHHHHHHhcCCe-----eEeec--CCCCCcchhhhhhchhhhHhHH
Confidence 34557763 55665 56678999999 999999998877 99974 6899999999999999999999
Q ss_pred HHhcCCcC
Q psy13208 109 LNMGMNKD 116 (120)
Q Consensus 109 l~~gm~~~ 116 (120)
|+|||-.+
T Consensus 333 L~VGMVKE 340 (605)
T KOG4217|consen 333 LAVGMVKE 340 (605)
T ss_pred HHhhhhhh
Confidence 99999753
No 78
>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=98.97 E-value=1.1e-10 Score=73.49 Aligned_cols=59 Identities=34% Similarity=0.753 Sum_probs=49.8
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++.++.... |.|.. +++|.|+..++..|++|||+|||++||++++|
T Consensus 21 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 79 (90)
T cd07168 21 YGIITCEGCK-------GFFKRTVQNKRV-----YTCVG--DGRCEITKAQRNRCQYCRFRKCIRKGMMLAAV 79 (90)
T ss_pred ECceehhhhh-------HhhhhhhcCCCC-----ccCCC--CCCccccccccccccccchhhhhhcCCCHHHh
Confidence 4457899999 888888876544 77873 57899999999999999999999999998765
No 79
>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=98.96 E-value=2.5e-10 Score=71.24 Aligned_cols=61 Identities=36% Similarity=0.743 Sum_probs=49.2
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+-..|.+|. ++++++++.... ..|.|.. +++|.|+...+..|++|||+|||++||+++++
T Consensus 15 yGv~sC~aCk-------~FFRR~~~~~~~---~~~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~ 75 (86)
T cd07157 15 HGAYVCEACK-------KFFMRSSNAISF---TISECPN--GGKCIIDKKNRTKCQACRYRKCLNVGMSLGGP 75 (86)
T ss_pred ECcceeeEee-------eEEecceecCCC---ccccCCC--CCccccCccccccCccchhhHHhHcCCCcccc
Confidence 4456899999 888887765431 1377874 47899999999999999999999999998765
No 80
>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=98.96 E-value=8.6e-11 Score=73.91 Aligned_cols=59 Identities=34% Similarity=0.809 Sum_probs=49.9
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++++..... |.|.. ++.|.|+...+..|++|||+|||++||++++|
T Consensus 21 yGv~sC~aCk-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 79 (90)
T cd07169 21 YGIISCEGCK-------GFFKRSICNKRV-----YRCSR--DKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAI 79 (90)
T ss_pred ECcceehhhH-------HHHHHHhcCCCc-----eecCC--CCcccccccccccccccchhhhccccCCHHHh
Confidence 4557899999 888888876544 77874 47899999999999999999999999998776
No 81
>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=98.96 E-value=1e-10 Score=74.25 Aligned_cols=60 Identities=33% Similarity=0.868 Sum_probs=50.1
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCcc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGKS 119 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~~ 119 (120)
.+...|.+|. +++++++..... |.|.. +++|.|+...+..|++|||+|||++||++++|-
T Consensus 20 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~ 79 (95)
T cd06968 20 YGVITCEGCK-------GFFRRSQQNNVS-----YSCPR--QKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVK 79 (95)
T ss_pred ECceeehhhH-------HhhHHheeCCCc-----eecCC--CcccccccCCceeccccchhhcccccCChhhcc
Confidence 4457899999 888888875533 77875 478999999999999999999999999988763
No 82
>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=98.95 E-value=6.2e-11 Score=74.93 Aligned_cols=59 Identities=32% Similarity=0.795 Sum_probs=49.6
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++++..+.. |.|.. +++|.|+...++.|++|||+|||++||++++|
T Consensus 13 yGv~sC~aCk-------~FFRRsv~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V 71 (93)
T cd07167 13 YGLLTCESCK-------GFFKRTVQNKKR-----YTCIE--NQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAV 71 (93)
T ss_pred ECchhhhhHH-------HHHHHHeeCCCc-----cccCC--CCccccCccccCcCCCcccchhhhccCCHHHh
Confidence 3456899998 888888876554 78875 48899999999999999999999999998765
No 83
>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=98.95 E-value=1.1e-10 Score=73.90 Aligned_cols=59 Identities=31% Similarity=0.693 Sum_probs=50.0
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++..+..... |.|.. +++|.|+...+..|++|||+|||++||++++|
T Consensus 15 yGv~sC~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 73 (94)
T cd06966 15 FNAITCESCK-------AFFRRNALKNKE-----FKCPF--NESCEINVVTRRFCQKCRLDKCFAIGMKKEWI 73 (94)
T ss_pred ECcceeeeeh-------heehhcccCCCc-----cccCC--CCccccCccccccCccchhhhCcccCCCHHHc
Confidence 4457899999 999888875544 77874 58899999999999999999999999998765
No 84
>KOG4218|consensus
Probab=98.93 E-value=1.5e-10 Score=87.44 Aligned_cols=57 Identities=35% Similarity=0.884 Sum_probs=52.9
Q ss_pred cccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 48 RNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 48 r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
-.-|.+|. |++.+.||++.+ |+|.+ +.+|.||+..|..|++||++|||.+||..+||
T Consensus 32 LLTCESCK-------GFFKRTVQNnK~-----YtC~e--~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAV 88 (475)
T KOG4218|consen 32 LLTCESCK-------GFFKRTVQNNKQ-----YTCSE--EQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAV 88 (475)
T ss_pred eeehhhhh-------hHHHHHhhcCcc-----eeccc--ccccccchHhhccCCchhHHHHhhhhhhHHHH
Confidence 46899999 999999999988 99985 68999999999999999999999999998776
No 85
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=98.93 E-value=3.4e-10 Score=67.98 Aligned_cols=57 Identities=32% Similarity=0.751 Sum_probs=47.7
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCCcC
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKD 116 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~ 116 (120)
.+-..|.+|. ++++++++.+.. +.|.. +++|.|+...+..|++|||+|||++||+++
T Consensus 14 ygv~~C~aC~-------~FFRR~v~~~~~-----~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 14 FGVCSCRACK-------AFFRRTVNLRYK-----YRCDR--KNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred eCCcEechhh-------hhhhhheeCCCC-----eecCC--CcccccCCCccccCccCcChhHhhccCcCC
Confidence 3456899999 888888876654 77874 467999999999999999999999999864
No 86
>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=98.93 E-value=1.2e-10 Score=73.06 Aligned_cols=59 Identities=34% Similarity=0.805 Sum_probs=49.3
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. ++++..++.... | .|.. +++|.|+..++..|++|||+|||++||++++|
T Consensus 18 yGv~sC~aCk-------~FFRR~v~~~~~-----~~~C~~--~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 77 (89)
T cd07166 18 YGVHACEGCK-------GFFRRSIQQKIQ-----YRKCTK--NETCSIMRINRNRCQYCRFKKCLAVGMSRDAV 77 (89)
T ss_pred EChhhhhhHh-------hEecceeEcCCc-----chhhcc--CCcccccccccccccchhhhhcccccCCHHHh
Confidence 4457899999 888888876644 6 4764 47899999999999999999999999998776
No 87
>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=98.88 E-value=3.6e-10 Score=70.23 Aligned_cols=57 Identities=32% Similarity=0.767 Sum_probs=47.2
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhc-ccccccccceeccccccccChhhhHHHHHHhcCCcCCc
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEF-ACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMNKDGK 118 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~-~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~~~~~ 118 (120)
.+...|.+|. +++++++..... | .|.. .|.|+..+++.|++|||+|||++||++++|
T Consensus 14 yGv~sC~aCk-------~FFRR~v~~~~~-----~~~C~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 71 (84)
T cd06965 14 YGVHACEGCK-------GFFRRTIRLKLV-----YKPCDL----SCKIHKKSRNKCQYCRFQKCLNVGMSHNAI 71 (84)
T ss_pred EChhhhhhhh-------hheeeeeecCCC-----cccccc----CCCcCccccccccchhhhhhhhccCCHHHc
Confidence 4457899999 898888876544 6 3753 399999999999999999999999998876
No 88
>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=98.77 E-value=2e-09 Score=64.53 Aligned_cols=55 Identities=31% Similarity=0.782 Sum_probs=41.2
Q ss_pred cccccccccccchhhhcccCchhhhhhhhccchhcccccccccceeccccccccChhhhHHHHHHhcCC
Q psy13208 46 AHRNQCQACRLKKCLNMGMNKDDAQHLKNSLLYEFACTNLVELRCIVDKAHRNQCQACRLKKCLNMGMN 114 (120)
Q Consensus 46 ~~r~~C~~CR~~kCl~~gm~~~~v~~~r~~~~~~~~c~~~~~~~c~i~~~~r~~C~~CRl~Kcl~~gm~ 114 (120)
.+...|.+|+ .++.+.+..... +.|.. +++|.|+...+..|++|||+|||++||+
T Consensus 15 ygv~sC~~C~-------~FFrR~~~~~~~-----~~C~~--~~~C~i~~~~~~~C~~CRf~KCl~~GM~ 69 (70)
T PF00105_consen 15 YGVLSCNACK-------MFFRRSVKKKKP-----YKCKK--NGNCKIDKDNRRKCRSCRFQKCLEVGMK 69 (70)
T ss_dssp TTEEEEHHHH-------HHHHHHHHTTCG------STSS--SST---STTTTTTSHHHHHHHHHHTTBS
T ss_pred ccccccccce-------eeeeeccccccc-----ccccc--cccccccccCCCEeCcchHHHHHHHCCc
Confidence 4456888888 667666665544 78864 5889999999999999999999999996
No 89
>PF07699 GCC2_GCC3: GCC2 and GCC3; InterPro: IPR011641 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups []: Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis []. RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction []. Cytoplasmic / non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases []. This entry represents various ephrin type A and B receptors, which have tyrosine kinase activity.
Probab=30.47 E-value=44 Score=17.80 Aligned_cols=31 Identities=16% Similarity=0.524 Sum_probs=21.0
Q ss_pred CccCCccCChhhhhcccceeeeccccCcceeccC
Q psy13208 3 FRHDGMTDHPTCQAGTERCIVDKAHRNQCQACQA 36 (120)
Q Consensus 3 ~~hygv~~C~~C~~ff~~ff~rsi~~~~~~~C~~ 36 (120)
|+.-+...|..|. +++|+..........|..
T Consensus 3 y~~~~~~~C~~Cp---~GtYq~~~g~~~C~~Cp~ 33 (48)
T PF07699_consen 3 YSDSGNNKCQPCP---KGTYQDEEGQTSCTPCPP 33 (48)
T ss_pred eCCCCCCccCCCC---CCccCCccCCccCccCcC
Confidence 4445667899998 468887766655666664
No 90
>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=22.79 E-value=64 Score=14.40 Aligned_cols=11 Identities=36% Similarity=0.821 Sum_probs=7.8
Q ss_pred HHHHHHhcCCc
Q psy13208 105 LKKCLNMGMNK 115 (120)
Q Consensus 105 l~Kcl~~gm~~ 115 (120)
|++|+.+.|..
T Consensus 6 L~~CI~sAmPk 16 (20)
T PF05924_consen 6 LQECIGSAMPK 16 (20)
T ss_dssp HHHHHHCTS--
T ss_pred HHHHHHHhccc
Confidence 68899988853
No 91
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=22.24 E-value=43 Score=17.02 Aligned_cols=13 Identities=8% Similarity=0.263 Sum_probs=7.3
Q ss_pred CccCCccCChhhh
Q psy13208 3 FRHDGMTDHPTCQ 15 (120)
Q Consensus 3 ~~hygv~~C~~C~ 15 (120)
+.||+..+|..|+
T Consensus 19 ~~~F~~~VCD~CR 31 (34)
T PF01286_consen 19 LNNFDLPVCDKCR 31 (34)
T ss_dssp CCCTS-S--TTT-
T ss_pred HHhCCcccccccc
Confidence 4688999999884
Done!