Query psy11505
Match_columns 312
No_of_seqs 217 out of 1998
Neff 9.0
Searched_HMMs 46136
Date Fri Aug 16 20:07:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11505.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11505hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 100.0 3.8E-46 8.3E-51 322.9 6.9 254 1-308 53-350 (432)
2 KOG4217|consensus 100.0 5.7E-37 1.2E-41 273.1 13.2 262 1-309 303-601 (605)
3 KOG4218|consensus 100.0 2.1E-34 4.5E-39 247.8 8.8 166 103-310 274-473 (475)
4 cd06949 NR_LBD_ER Ligand bindi 100.0 5.8E-31 1.3E-35 227.7 13.6 194 74-310 3-235 (235)
5 cd06947 NR_LBD_GR_Like Ligand 100.0 6.6E-30 1.4E-34 221.5 13.6 192 77-310 2-231 (246)
6 cd06937 NR_LBD_RAR The ligand 100.0 5.8E-30 1.3E-34 220.9 11.3 167 100-309 35-231 (231)
7 cd06946 NR_LBD_ERR The ligand 100.0 9.8E-30 2.1E-34 218.9 12.6 189 78-309 2-221 (221)
8 cd06944 NR_LBD_Ftz-F1_like The 100.0 5.4E-30 1.2E-34 222.2 10.9 168 101-310 36-237 (237)
9 cd07076 NR_LBD_GR Ligand bindi 100.0 2E-29 4.4E-34 217.6 13.0 190 77-308 2-224 (247)
10 KOG4216|consensus 100.0 8.1E-31 1.8E-35 229.1 3.3 138 104-285 283-424 (479)
11 cd07348 NR_LBD_NGFI-B The liga 100.0 4.2E-29 9.1E-34 215.5 13.1 165 101-310 39-235 (238)
12 cd07073 NR_LBD_AR Ligand bindi 100.0 6E-29 1.3E-33 215.6 12.9 190 78-309 3-230 (246)
13 cd07069 NR_LBD_Lrh-1 The ligan 100.0 3.2E-29 7E-34 217.3 10.6 168 101-310 38-239 (241)
14 cd07070 NR_LBD_SF-1 The ligand 100.0 3E-29 6.5E-34 217.3 10.1 168 100-309 35-236 (237)
15 cd07068 NR_LBD_ER_like The lig 100.0 7.6E-29 1.6E-33 213.2 12.3 184 83-309 7-221 (221)
16 cd07072 NR_LBD_DHR38_like Liga 100.0 1.7E-28 3.7E-33 211.9 13.4 167 99-310 38-236 (239)
17 cd07071 NR_LBD_Nurr1 The ligan 100.0 1.8E-28 3.8E-33 211.8 12.3 165 101-310 39-235 (238)
18 cd06935 NR_LBD_TR The ligand b 100.0 2.1E-28 4.5E-33 212.8 10.1 164 100-306 49-243 (243)
19 cd06945 NR_LBD_Nurr1_like The 100.0 3.2E-28 7E-33 210.9 10.7 166 101-310 39-236 (239)
20 cd07075 NR_LBD_MR Ligand bindi 100.0 7.9E-28 1.7E-32 207.8 13.0 165 78-284 3-173 (248)
21 cd06948 NR_LBD_COUP-TF Ligand 100.0 4.2E-28 9E-33 210.4 11.1 167 101-309 28-225 (236)
22 cd07074 NR_LBD_PR Ligand bindi 99.9 2.1E-27 4.5E-32 205.0 12.7 167 77-285 2-174 (248)
23 cd07349 NR_LBD_SHP The ligand 99.9 1E-27 2.2E-32 205.1 7.4 164 101-307 17-222 (222)
24 cd06941 NR_LBD_DmE78_like The 99.9 7.4E-27 1.6E-31 197.2 10.5 162 104-308 3-195 (195)
25 cd06954 NR_LBD_LXR The ligand 99.9 3.1E-26 6.7E-31 199.1 10.8 164 101-308 41-235 (236)
26 cd07350 NR_LBD_Dax1 The ligand 99.9 1.5E-26 3.3E-31 199.0 7.5 162 101-305 17-232 (232)
27 cd06951 NR_LBD_Dax1_like The l 99.9 1.3E-26 2.7E-31 198.8 6.8 162 101-305 17-222 (222)
28 cd06931 NR_LBD_HNF4_like The l 99.9 1.2E-25 2.5E-30 193.8 11.1 163 100-306 29-222 (222)
29 cd06939 NR_LBD_ROR_like The li 99.9 1.2E-25 2.7E-30 194.9 10.6 163 101-307 46-241 (241)
30 cd06932 NR_LBD_PPAR The ligand 99.9 3.8E-25 8.2E-30 193.8 10.6 165 100-309 60-258 (259)
31 cd06940 NR_LBD_REV_ERB The lig 99.9 4.4E-25 9.5E-30 185.0 10.2 143 100-285 9-155 (189)
32 cd06933 NR_LBD_VDR The ligand 99.9 6.7E-25 1.5E-29 190.2 11.3 143 100-285 34-182 (238)
33 cd06938 NR_LBD_EcR The ligand 99.9 7.7E-25 1.7E-29 189.5 10.3 164 101-308 37-230 (231)
34 cd06950 NR_LBD_Tlx_PNR_like Th 99.9 8E-25 1.7E-29 186.0 8.8 143 100-285 23-169 (206)
35 cd06934 NR_LBD_PXR_like The li 99.9 1.4E-24 3.1E-29 186.7 7.8 140 102-285 34-178 (226)
36 cd06943 NR_LBD_RXR_like The li 99.9 2.5E-24 5.4E-29 183.6 8.3 140 103-285 30-174 (207)
37 cd06952 NR_LBD_TR2_like The li 99.9 5.7E-24 1.2E-28 183.2 9.7 171 96-308 14-221 (222)
38 cd06929 NR_LBD_F1 Ligand-bindi 99.9 2.8E-23 6.1E-28 172.4 8.0 139 104-285 3-145 (174)
39 cd06930 NR_LBD_F2 Ligand-bindi 99.9 3.4E-23 7.4E-28 170.4 8.4 138 106-285 2-144 (165)
40 cd06936 NR_LBD_Fxr The ligand 99.9 5.1E-23 1.1E-27 176.6 8.9 137 101-285 34-176 (221)
41 cd06953 NR_LBD_DHR4_like The l 99.9 4.6E-23 1E-27 176.0 8.5 146 97-285 21-174 (213)
42 cd06942 NR_LBD_Sex_1_like The 99.9 1.5E-21 3.3E-26 164.1 8.6 137 104-285 3-146 (191)
43 cd06157 NR_LBD The ligand bind 99.8 1.2E-18 2.6E-23 143.0 7.6 137 107-285 2-146 (168)
44 smart00430 HOLI Ligand binding 99.7 1.1E-18 2.4E-23 142.4 4.7 131 113-285 2-141 (163)
45 PF00104 Hormone_recep: Ligand 99.7 1.1E-17 2.3E-22 141.7 8.4 143 98-282 12-163 (203)
46 cd06961 NR_DBD_TR DNA-binding 99.5 1.6E-15 3.4E-20 109.5 2.2 51 1-51 33-83 (85)
47 cd07170 NR_DBD_ERR DNA-binding 99.5 2.9E-15 6.4E-20 110.4 3.3 52 2-53 39-90 (97)
48 KOG4846|consensus 99.5 3.9E-15 8.5E-20 132.1 3.2 48 1-48 166-214 (538)
49 cd07169 NR_DBD_GCNF_like DNA-b 99.5 4.5E-15 9.7E-20 108.2 2.1 49 2-50 41-89 (90)
50 cd07167 NR_DBD_Lrh-1_like The 99.5 5.8E-15 1.3E-19 107.9 2.2 52 1-52 32-83 (93)
51 cd07168 NR_DBD_DHR4_like DNA-b 99.5 6.6E-15 1.4E-19 107.4 2.2 50 1-50 40-89 (90)
52 cd06967 NR_DBD_TR2_like DNA-bi 99.5 9.1E-15 2E-19 105.9 2.1 46 2-47 38-83 (87)
53 cd07164 NR_DBD_PNR_like_1 DNA- 99.5 9.8E-15 2.1E-19 103.9 2.2 45 2-46 33-77 (78)
54 cd06964 NR_DBD_RAR DNA-binding 99.5 1.1E-14 2.4E-19 105.0 2.3 45 2-46 39-83 (85)
55 cd06956 NR_DBD_RXR DNA-binding 99.5 9.6E-15 2.1E-19 103.5 1.9 44 1-44 34-77 (77)
56 cd07155 NR_DBD_ER_like DNA-bin 99.5 1.4E-14 3E-19 102.3 2.1 43 2-44 33-75 (75)
57 cd07165 NR_DBD_DmE78_like DNA- 99.5 1.7E-14 3.7E-19 103.3 2.0 46 2-47 33-78 (81)
58 cd06960 NR_DBD_HNF4A DNA-bindi 99.5 1.9E-14 4.1E-19 102.0 2.1 44 2-45 33-76 (76)
59 cd06957 NR_DBD_PNR_like_2 DNA- 99.5 1.9E-14 4.2E-19 103.2 2.1 46 2-47 33-79 (82)
60 cd07171 NR_DBD_ER DNA-binding 99.4 2.7E-14 5.9E-19 102.2 1.9 43 2-44 38-80 (82)
61 cd07160 NR_DBD_LXR DNA-binding 99.4 3E-14 6.4E-19 105.7 1.8 45 2-46 53-97 (101)
62 cd07163 NR_DBD_TLX DNA-binding 99.4 3.8E-14 8.2E-19 103.8 2.2 46 2-47 41-88 (92)
63 cd06962 NR_DBD_FXR DNA-binding 99.4 3.7E-14 8E-19 102.0 1.9 46 1-46 35-80 (84)
64 cd07166 NR_DBD_REV_ERB DNA-bin 99.4 2.9E-14 6.4E-19 103.7 1.4 47 2-48 38-85 (89)
65 cd06970 NR_DBD_PNR DNA-binding 99.4 4.5E-14 9.8E-19 103.1 2.0 47 1-47 40-87 (92)
66 cd06968 NR_DBD_ROR DNA-binding 99.4 4.6E-14 9.9E-19 103.8 1.7 47 2-48 40-86 (95)
67 cd07161 NR_DBD_EcR DNA-binding 99.4 4.4E-14 9.5E-19 103.1 1.5 46 2-47 36-81 (91)
68 cd06966 NR_DBD_CAR DNA-binding 99.4 2.3E-14 5E-19 105.3 -0.3 49 2-50 35-83 (94)
69 cd06969 NR_DBD_NGFI-B DNA-bind 99.4 7.4E-14 1.6E-18 98.5 2.0 41 2-42 35-75 (75)
70 cd06958 NR_DBD_COUP_TF DNA-bin 99.4 1.2E-13 2.7E-18 96.9 2.3 40 2-41 33-72 (73)
71 cd06916 NR_DBD_like DNA-bindin 99.4 1.4E-13 3E-18 96.4 2.0 40 2-41 33-72 (72)
72 cd07179 2DBD_NR_DBD2 The secon 99.4 1.5E-13 3.3E-18 96.6 2.1 41 2-42 33-73 (74)
73 cd07157 2DBD_NR_DBD1 The first 99.4 2.1E-13 4.5E-18 98.6 2.8 45 2-46 37-81 (86)
74 cd07156 NR_DBD_VDR_like The DN 99.4 1.7E-13 3.7E-18 95.9 2.0 39 2-40 33-71 (72)
75 cd07162 NR_DBD_PXR DNA-binding 99.4 1E-13 2.3E-18 100.5 1.0 44 2-45 34-77 (87)
76 cd07154 NR_DBD_PNR_like The DN 99.4 1.8E-13 3.8E-18 96.2 2.0 41 1-41 32-73 (73)
77 cd06955 NR_DBD_VDR DNA-binding 99.4 1.3E-13 2.7E-18 103.4 1.1 42 2-43 41-82 (107)
78 cd06959 NR_DBD_EcR_like The DN 99.4 2.1E-13 4.6E-18 95.7 2.2 40 2-41 34-73 (73)
79 cd06963 NR_DBD_GR_like The DNA 99.4 2.7E-13 5.8E-18 95.0 2.6 40 2-41 33-72 (73)
80 cd07158 NR_DBD_Ppar_like The D 99.4 2.6E-13 5.5E-18 95.4 2.0 40 2-41 33-73 (73)
81 cd06965 NR_DBD_Ppar DNA-bindin 99.3 3.9E-13 8.5E-18 96.8 1.5 45 2-48 34-79 (84)
82 cd07172 NR_DBD_GR_PR DNA-bindi 99.3 7.6E-13 1.7E-17 93.8 2.9 40 2-41 37-76 (78)
83 cd07173 NR_DBD_AR DNA-binding 99.3 1.3E-12 2.8E-17 93.4 2.4 43 2-44 38-80 (82)
84 smart00399 ZnF_C4 c4 zinc fing 99.2 5.1E-12 1.1E-16 88.1 2.7 37 2-38 34-70 (70)
85 PF00105 zf-C4: Zinc finger, C 99.1 1.5E-11 3.1E-16 86.0 1.0 36 2-37 35-70 (70)
86 KOG4846|consensus 98.9 4.3E-10 9.4E-15 100.4 1.5 36 208-243 134-169 (538)
87 KOG4215|consensus 98.6 1E-08 2.3E-13 90.5 2.1 42 205-246 18-59 (432)
88 cd07161 NR_DBD_EcR DNA-binding 98.6 1.6E-08 3.4E-13 73.9 2.5 40 207-246 2-41 (91)
89 cd06956 NR_DBD_RXR DNA-binding 98.6 1.6E-08 3.4E-13 71.7 2.2 38 207-244 1-38 (77)
90 cd07170 NR_DBD_ERR DNA-binding 98.6 1.8E-08 3.9E-13 74.4 2.5 40 206-245 4-43 (97)
91 cd06959 NR_DBD_EcR_like The DN 98.6 1.9E-08 4.1E-13 70.6 2.0 36 208-243 1-36 (73)
92 cd07172 NR_DBD_GR_PR DNA-bindi 98.6 2E-08 4.4E-13 71.2 2.2 38 207-244 3-40 (78)
93 cd07173 NR_DBD_AR DNA-binding 98.6 2.7E-08 5.8E-13 71.2 2.6 38 207-244 4-41 (82)
94 cd07171 NR_DBD_ER DNA-binding 98.6 2.4E-08 5.2E-13 71.5 2.1 39 207-245 4-42 (82)
95 cd06963 NR_DBD_GR_like The DNA 98.6 2.5E-08 5.5E-13 69.8 1.8 36 209-244 1-36 (73)
96 cd07155 NR_DBD_ER_like DNA-bin 98.6 3E-08 6.4E-13 70.0 2.0 37 209-245 1-37 (75)
97 cd07179 2DBD_NR_DBD2 The secon 98.6 3.3E-08 7.2E-13 69.5 2.1 36 209-244 1-36 (74)
98 cd07168 NR_DBD_DHR4_like DNA-b 98.5 4.1E-08 8.8E-13 71.7 2.3 39 206-244 6-44 (90)
99 cd07156 NR_DBD_VDR_like The DN 98.5 2.4E-08 5.2E-13 69.9 1.0 36 209-244 1-36 (72)
100 cd07160 NR_DBD_LXR DNA-binding 98.5 2.7E-08 6E-13 73.9 1.3 40 206-245 18-57 (101)
101 cd07162 NR_DBD_PXR DNA-binding 98.5 3.9E-08 8.4E-13 71.4 2.0 38 208-245 1-38 (87)
102 cd07169 NR_DBD_GCNF_like DNA-b 98.5 5.3E-08 1.2E-12 71.0 2.5 39 206-244 6-44 (90)
103 cd06961 NR_DBD_TR DNA-binding 98.5 4.2E-08 9E-13 70.9 1.9 38 208-245 1-38 (85)
104 cd07167 NR_DBD_Lrh-1_like The 98.5 4.3E-08 9.2E-13 71.8 1.7 37 209-245 1-37 (93)
105 cd06958 NR_DBD_COUP_TF DNA-bin 98.5 4.2E-08 9.2E-13 68.8 1.5 36 209-244 1-36 (73)
106 cd07158 NR_DBD_Ppar_like The D 98.5 5.3E-08 1.1E-12 68.4 1.7 35 209-243 1-35 (73)
107 smart00399 ZnF_C4 c4 zinc fing 98.5 4.6E-08 1E-12 68.1 1.4 37 208-244 1-37 (70)
108 cd06962 NR_DBD_FXR DNA-binding 98.5 2E-08 4.3E-13 72.3 -1.0 38 207-244 2-39 (84)
109 cd06955 NR_DBD_VDR DNA-binding 98.4 3E-08 6.5E-13 74.4 -0.3 40 206-245 6-45 (107)
110 cd06964 NR_DBD_RAR DNA-binding 98.4 2E-08 4.4E-13 72.4 -1.3 39 206-244 4-42 (85)
111 cd06969 NR_DBD_NGFI-B DNA-bind 98.4 2E-08 4.3E-13 70.8 -1.4 38 207-244 1-38 (75)
112 cd06966 NR_DBD_CAR DNA-binding 98.4 4.1E-08 9E-13 72.2 0.1 38 208-245 2-39 (94)
113 cd06968 NR_DBD_ROR DNA-binding 98.4 9.4E-08 2E-12 70.4 2.0 40 206-245 5-44 (95)
114 cd07164 NR_DBD_PNR_like_1 DNA- 98.4 8E-08 1.7E-12 68.3 1.4 36 209-244 1-36 (78)
115 KOG4217|consensus 98.4 1E-07 2.2E-12 86.8 2.1 64 196-271 263-330 (605)
116 cd06970 NR_DBD_PNR DNA-binding 98.4 2.9E-08 6.3E-13 72.6 -1.2 39 207-245 7-45 (92)
117 cd07163 NR_DBD_TLX DNA-binding 98.4 2.4E-08 5.1E-13 73.2 -1.9 40 205-244 5-44 (92)
118 cd07154 NR_DBD_PNR_like The DN 98.4 2.6E-08 5.7E-13 69.9 -1.6 37 209-245 1-37 (73)
119 cd06965 NR_DBD_Ppar DNA-bindin 98.4 5.7E-08 1.2E-12 70.0 0.0 36 208-243 1-36 (84)
120 cd07165 NR_DBD_DmE78_like DNA- 98.4 1.6E-07 3.4E-12 67.3 2.1 36 209-244 1-36 (81)
121 cd06957 NR_DBD_PNR_like_2 DNA- 98.4 2.2E-08 4.7E-13 71.9 -2.4 38 209-246 1-38 (82)
122 cd06960 NR_DBD_HNF4A DNA-bindi 98.4 5.9E-08 1.3E-12 68.7 -0.6 36 209-244 1-36 (76)
123 cd07166 NR_DBD_REV_ERB DNA-bin 98.4 7E-08 1.5E-12 70.3 -0.3 38 206-243 3-40 (89)
124 cd06967 NR_DBD_TR2_like DNA-bi 98.3 5.9E-08 1.3E-12 70.4 -1.1 39 206-244 3-41 (87)
125 cd07157 2DBD_NR_DBD1 The first 98.3 5.5E-08 1.2E-12 70.3 -1.6 33 208-240 2-34 (86)
126 PF00105 zf-C4: Zinc finger, C 98.3 2E-07 4.3E-12 65.0 1.2 36 208-243 2-37 (70)
127 KOG4216|consensus 98.3 2.1E-07 4.5E-12 82.9 1.6 37 207-243 47-83 (479)
128 cd06916 NR_DBD_like DNA-bindin 98.3 4.8E-08 1E-12 68.3 -2.0 36 209-244 1-36 (72)
129 KOG4218|consensus 98.2 6.1E-07 1.3E-11 78.8 2.1 43 205-247 14-56 (475)
130 PF09289 FOLN: Follistatin/Ost 78.3 0.45 9.9E-06 24.7 -0.6 20 3-22 3-22 (22)
131 smart00274 FOLN Follistatin-N- 58.5 6 0.00013 21.5 1.1 20 3-22 4-23 (26)
132 PF12760 Zn_Tnp_IS1595: Transp 39.7 13 0.00028 23.1 0.6 18 11-28 29-46 (46)
133 PF03811 Zn_Tnp_IS1: InsA N-te 31.3 21 0.00046 21.0 0.5 10 17-26 27-36 (36)
134 smart00309 PAH Pancreatic horm 31.1 61 0.0013 19.1 2.4 22 262-284 9-30 (36)
135 cd00126 PAH Pancreatic Hormone 30.8 62 0.0013 19.1 2.4 22 262-284 9-30 (36)
136 PF00645 zf-PARP: Poly(ADP-rib 30.4 51 0.0011 23.1 2.5 21 123-143 60-80 (82)
137 PF01412 ArfGap: Putative GTPa 29.4 32 0.00069 26.1 1.4 36 206-242 13-51 (116)
138 PF01831 Peptidase_C16: Peptid 25.8 1.2E+02 0.0025 25.4 4.0 102 123-260 47-155 (249)
139 smart00453 WSN Worm-specific ( 25.6 46 0.001 22.8 1.5 17 292-308 26-42 (69)
140 PF00159 Hormone_3: Pancreatic 23.2 1E+02 0.0022 18.2 2.4 23 262-285 9-31 (36)
No 1
>KOG4215|consensus
Probab=100.00 E-value=3.8e-46 Score=322.91 Aligned_cols=254 Identities=26% Similarity=0.393 Sum_probs=201.2
Q ss_pred CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccccccCCCCCccCCCCCCCCCCchhHHHHHH-
Q psy11505 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLE- 79 (312)
Q Consensus 1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~- 79 (312)
+..|+|+++++|.|||..||.|||||||||+++||++||||.+|++++.++....... .. ......++.
T Consensus 53 ~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg~Rr~~~~~~n--------~~--~~~id~L~~a 122 (432)
T KOG4215|consen 53 NHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIGSRRPSYEAGN--------EN--SPSIDALVQA 122 (432)
T ss_pred cceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccccccccCCCCCCCC--------CC--chhHHHHHhH
Confidence 3579999999999999999999999999999999999999999999987543222111 00 111112211
Q ss_pred -----HHHh----cCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHH
Q psy11505 80 -----ALLL----CEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILT 150 (312)
Q Consensus 80 -----~l~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~ 150 (312)
.+.. ..+... .......++....+..++++...+++...|||||.+|.|.+|+.+||++|||+...++.+
T Consensus 123 E~~~~q~~~srs~~~~~~~-~d~r~~~~n~~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hll 201 (432)
T KOG4215|consen 123 EALVRQLRSSRSGGVPGID-GDIRQGPPNKKIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLL 201 (432)
T ss_pred HHHHhhhhccccccCcCcc-hhhhcCccccccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhh
Confidence 1111 001000 000011234456778899999999999999999999999999999999999999999999
Q ss_pred HhhhhhcccCCCCeeEecccchhhHHhhhhcc----cchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccc
Q psy11505 151 LTIAYRSLPHCAGKIRFASDLVLDERQARECG----FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASC 226 (312)
Q Consensus 151 L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~----~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~ 226 (312)
|..++||.-.++ .++++|+.+++++...... ..+++++++.++++|++|+.||
T Consensus 202 Lg~a~RSm~l~~-v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~Pmr~L~md~~Ey---------------------- 258 (432)
T KOG4215|consen 202 LGAAFRSMHLKD-VCLLNNTYVLHRHAPDLPEISRVAPRIIDELVNPMRRLQMDEIEY---------------------- 258 (432)
T ss_pred hhhhhccccccc-eEEecCceeeccCCCChHHHHHHHHHHHHHHhhHHHHhccchHHH----------------------
Confidence 999999999976 6778888887765443322 3678899999999999999999
Q ss_pred hhHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccchH--HHHHHHHHHHHHhHhHHHHH-------hh---------
Q psy11505 227 EACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEFS--SLKKFRNSILSSLGDCIYVL-------RF--------- 287 (312)
Q Consensus 227 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~--~~~~~~~~~~~~l~~~~~~~-------~~--------- 287 (312)
++||||++|+||++ |++++ .|+++|++++.+|.+||.-+ ||
T Consensus 259 --------------------~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~g~LLLllPs 318 (432)
T KOG4215|consen 259 --------------------VCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRFGNLLLLLPS 318 (432)
T ss_pred --------------------HHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccchhhHHHHHHH
Confidence 99999999999998 99999 79999999999999999765 33
Q ss_pred -----------hhccccCCccchhHHHHHHHh
Q psy11505 288 -----------WSTVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 288 -----------~~~~~~~~~~~~~~~~~~~~~ 308 (312)
..+.+++|.+.+++|+.||+.
T Consensus 319 LqsIt~qliE~iqlaklFGla~vDsll~e~~l 350 (432)
T KOG4215|consen 319 LQSITQQLIEQIQLAKLFGLAKVDSLLQEFLL 350 (432)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhc
Confidence 445699999999999999984
No 2
>KOG4217|consensus
Probab=100.00 E-value=5.7e-37 Score=273.14 Aligned_cols=262 Identities=30% Similarity=0.465 Sum_probs=202.0
Q ss_pred CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccccccCCCCCccCCCCCCCCCCchhHHHHHHH
Q psy11505 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYRRNPDLLSQQWPPNKSIPSLEENKMLEA 80 (312)
Q Consensus 1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 80 (312)
|.+|+|..+++|+|||..||+||||||||||+|||-+|.|+.+-.++++.+...++... .+.+|+++ ......++..
T Consensus 303 naKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLkGRRGRLpSKpKs~-q~sppSpP--i~LltalvrA 379 (605)
T KOG4217|consen 303 NAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRRGRLPSKPKSR-QPSPPSPP--ISLLTALVRA 379 (605)
T ss_pred CCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheeccccccccCCCCCCCCCC-CCCCCCCc--hHHHHHHHHH
Confidence 56899999999999999999999999999999999999999988777766655554443 11112111 1112334444
Q ss_pred HHhcCccccccc--CCCC----CCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhh
Q psy11505 81 LLLCEPEMLTVR--SETP----QSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIA 154 (312)
Q Consensus 81 l~~~~~~~~~~~--~~~~----~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a 154 (312)
+....+....+. ...+ ........+..+.++..-.+..+-.||.++|+|.+|+.+||..||..+++++++|+.|
T Consensus 380 h~Dstp~~~~ldys~~q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlA 459 (605)
T KOG4217|consen 380 HVDSTPSTMTLDYSRFQELVPHFSGTDALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLA 459 (605)
T ss_pred hhcCCCCcchhhHHHhccccccccccHHHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHH
Confidence 444444211111 1111 2223445567778888888999999999999999999999999999999999999999
Q ss_pred hhcccCCCCeeEecccchhhHHhhhhcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHH
Q psy11505 155 YRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKA 231 (312)
Q Consensus 155 ~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~ 231 (312)
||+.+..+ +++|++|.++++.+... ++++|++.|..+.+ .|++|-.-|
T Consensus 460 yRs~~~e~-kliFcsG~vlhr~qC~r-gfgewidsi~~FS~~l~~l~idi~Af--------------------------- 510 (605)
T KOG4217|consen 460 YRSNPSED-KLIFCSGLVLHRLQCLR-GFGEWIDSIREFSRSLHSLNIDISAF--------------------------- 510 (605)
T ss_pred HhcCCCCC-eEEEecchhhhHHHHHH-HHHHHHHHHHHHHHHhhhchhhHHHH---------------------------
Confidence 99999887 89999999999977644 66799999998877 677777777
Q ss_pred HHHHHhhhcccceecCCCCceeecCCCCcccchHHHHHHHHHHHHHhHhHHHHH--------------------hh----
Q psy11505 232 FFKRTIQVYSGYRQTGACGTLVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVL--------------------RF---- 287 (312)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~--------------------~~---- 287 (312)
+++.|+.+..---+|.++.+|+++|+++..+|++|+..+ |.
T Consensus 511 ---------------acL~aLa~iTErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr~l~tq 575 (605)
T KOG4217|consen 511 ---------------ACLSALALITERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELRTLCTQ 575 (605)
T ss_pred ---------------HHHHHHHhhhhhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHHHHHHH
Confidence 899999988876669999999999999999999999554 11
Q ss_pred ----hhccccCCccchhHHHHHHHhh
Q psy11505 288 ----WSTVHKDGKVLMNKLFVEMLEA 309 (312)
Q Consensus 288 ----~~~~~~~~~~~~~~~~~~~~~~ 309 (312)
++.-++.+.||.+.++..|+..
T Consensus 576 gLqrifyLklEdlvp~p~iidklf~d 601 (605)
T KOG4217|consen 576 GLQRIFYLKLEDLVPPPAIIDKLFLD 601 (605)
T ss_pred hhhhhhcccHhhccCchhhhhhhhhc
Confidence 2224778888888888888753
No 3
>KOG4218|consensus
Probab=100.00 E-value=2.1e-34 Score=247.78 Aligned_cols=166 Identities=25% Similarity=0.338 Sum_probs=136.9
Q ss_pred HHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC-CeeEecccchhhHHh-hhh
Q psy11505 103 QTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA-GKIRFASDLVLDERQ-ARE 180 (312)
Q Consensus 103 ~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~-~~l~~~~g~~~~~~~-~~~ 180 (312)
..+.-.+.+.+..+..+|+||++--.|.+|+.+||++||+++|.++.++...|+-..++. +.+.+.+|.-++-.. +..
T Consensus 274 ~~fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgkegsi~lvtGqeV~~~~vA~q 353 (475)
T KOG4218|consen 274 EKFGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKEGSIKLVTGQEVPVGLVALQ 353 (475)
T ss_pred hhhhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcccceEEecCCcccchhHhhh
Confidence 344555778889999999999999999999999999999999999999999999998876 567776665443221 112
Q ss_pred ccc--ch---hhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505 181 CGF--SE---IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA 255 (312)
Q Consensus 181 ~~~--~~---~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 255 (312)
+|. .. -.++++..++.|++|..|| +++|.|+||
T Consensus 354 ags~l~tlvs~aqelV~~Lr~lqfd~~ef------------------------------------------vclkFl~LF 391 (475)
T KOG4218|consen 354 AGSLLQTLVSSAQELVIRLRNLQFDNFEF------------------------------------------VCLKFLALF 391 (475)
T ss_pred hhhHHHHHHHHHHHHHHHHHhcCCccchh------------------------------------------hHHHHHHHH
Confidence 221 12 2355666677999999999 999999999
Q ss_pred CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505 256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~ 308 (312)
+-|.+ |++...|+++|++...+|.+|.... ++++.+++.+.+|-++|+.||+.
T Consensus 392 sld~kfLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF~qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~ 471 (475)
T KOG4218|consen 392 SLDMKFLENFELVRRLQEDSNAALLDYTSCCYPNWEQKFPQLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLT 471 (475)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhh
Confidence 99999 9999999999999999999986432 45778899999999999999998
Q ss_pred hh
Q psy11505 309 AY 310 (312)
Q Consensus 309 ~~ 310 (312)
|.
T Consensus 472 Ak 473 (475)
T KOG4218|consen 472 AK 473 (475)
T ss_pred cc
Confidence 84
No 4
>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. 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 doma
Probab=99.97 E-value=5.8e-31 Score=227.70 Aligned_cols=194 Identities=32% Similarity=0.486 Sum_probs=162.7
Q ss_pred HHHHHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhh
Q psy11505 74 ENKMLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTI 153 (312)
Q Consensus 74 ~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~ 153 (312)
.+.++..+...+|...........++.....+..++++.++.+..+|+|||++|+|.+|+.+||+.|+|++|+++++++.
T Consensus 3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~ 82 (235)
T cd06949 3 AEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGL 82 (235)
T ss_pred HHHHHHHHHHhCCCcCcCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHH
Confidence 34567788888887655554444566678889999999999999999999999999999999999999999999999999
Q ss_pred hhhcccCCCCeeEecccchhhHHhhh-hcccchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhH
Q psy11505 154 AYRSLPHCAGKIRFASDLVLDERQAR-ECGFSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEAC 229 (312)
Q Consensus 154 a~rs~~~~~~~l~~~~g~~~~~~~~~-~~~~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~ 229 (312)
||++.+..+ .+.+.+|..++..... ..+..++++.++.+ +.+|++|++||
T Consensus 83 a~rs~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~Ey------------------------- 136 (235)
T cd06949 83 VWRSMEHPG-KLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEY------------------------- 136 (235)
T ss_pred HHHhcCCCC-eEEeeCCceecHHHhhhcccHHHHHHHHHHHHHHHHHhCCCHHHH-------------------------
Confidence 999998866 7888888877766543 34445555555544 44999999999
Q ss_pred HHHHHHHhhhcccceecCCCCceeecCCCCc------ccchHHHHHHHHHHHHHhHhHHHHH------------------
Q psy11505 230 KAFFKRTIQVYSGYRQTGACGTLVLANSDVK------LDEFSSLKKFRNSILSSLGDCIYVL------------------ 285 (312)
Q Consensus 230 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~------l~~~~~~~~~~~~~~~~l~~~~~~~------------------ 285 (312)
+++|||+|||||++ ++++++|+++|++++.||.+|+..+
T Consensus 137 -----------------alLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~~~~Rf~~LLl~L 199 (235)
T cd06949 137 -----------------VCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLIL 199 (235)
T ss_pred -----------------HHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHHHhc
Confidence 99999999999985 5688999999999999999998743
Q ss_pred -----------hhhhccccCCccchhHHHHHHHhhh
Q psy11505 286 -----------RFWSTVHKDGKVLMNKLFVEMLEAY 310 (312)
Q Consensus 286 -----------~~~~~~~~~~~~~~~~~~~~~~~~~ 310 (312)
+++++++++|.+|+++|+.|||+||
T Consensus 200 p~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~~ 235 (235)
T cd06949 200 SHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235 (235)
T ss_pred hHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhcCC
Confidence 3467789999999999999999986
No 5
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in 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 use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=99.97 E-value=6.6e-30 Score=221.55 Aligned_cols=192 Identities=27% Similarity=0.460 Sum_probs=156.7
Q ss_pred HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR 156 (312)
Q Consensus 77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r 156 (312)
++..+...+|...........++.....+..+++|.++++..+|+|||++|+|.+|+.+||++|||++|+++++++.|||
T Consensus 2 ~~~~l~~~ep~~~~~~~~~~~p~~~~~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~r 81 (246)
T cd06947 2 LLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWR 81 (246)
T ss_pred HHHHHHhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHh
Confidence 45667777886655555555666677889999999999999999999999999999999999999999999999999999
Q ss_pred cccCCC-CeeEecccchhhHHhhhhcccchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505 157 SLPHCA-GKIRFASDLVLDERQARECGFSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF 232 (312)
Q Consensus 157 s~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~ 232 (312)
+++... +.+.+++|..++++.....+..++. .++...+++|++|++||
T Consensus 82 s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~L~ld~~E~---------------------------- 133 (246)
T cd06947 82 SYKHVNSQMLYFAPDLVFNEQRMHQSAMYSLCLGMRQISQEFVRLQVTYEEF---------------------------- 133 (246)
T ss_pred hccCCCCCeEEecCCeeecHHHhhhccHHHHHHHHHHHHHHHHhcCCCHHHH----------------------------
Confidence 998765 3477788888777665554544443 34455566999999999
Q ss_pred HHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh--------------
Q psy11505 233 FKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF-------------- 287 (312)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~-------------- 287 (312)
+|+|||+|||| |++ |+++++|+++|++++.||.+|+..+ ||
T Consensus 134 --------------acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~Rf~kLLllLp~Lr~i~ 199 (246)
T cd06947 134 --------------LCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQRFYQLTKLLDSMHDLV 199 (246)
T ss_pred --------------HHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHhhhhHHHHH
Confidence 99999999999 787 9999999999999999999999753 22
Q ss_pred ------hhcc---ccCCccchhHHHHHHHhhh
Q psy11505 288 ------WSTV---HKDGKVLMNKLFVEMLEAY 310 (312)
Q Consensus 288 ------~~~~---~~~~~~~~~~~~~~~~~~~ 310 (312)
++.. +..++|++++|+.||++++
T Consensus 200 ~~~~e~~~~~~~~~~~~~v~~~~ll~ei~~~~ 231 (246)
T cd06947 200 KNLLQFCFYTFIQSHALSVEFPEMLVEIISDQ 231 (246)
T ss_pred HHHHHHHHHHHhhcCCCccccHHHHHHHHHcc
Confidence 2222 3345689999999999976
No 6
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally 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. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=99.96 E-value=5.8e-30 Score=220.89 Aligned_cols=167 Identities=26% Similarity=0.380 Sum_probs=149.1
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR 179 (312)
Q Consensus 100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~ 179 (312)
.....+..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.++++++.|+++.+..+ .+.+.+|..+++....
T Consensus 35 ~~~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~-~l~~~~~~~~~~~~~~ 113 (231)
T cd06937 35 LDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQD-TMTFSDGLTLNRTQMH 113 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-eEEecCCceecHHHHh
Confidence 356778899999999999999999999999999999999999999999999999999988776 7899999888887776
Q ss_pred hcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505 180 ECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN 256 (312)
Q Consensus 180 ~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 256 (312)
..+.++++++++.+.. +|++|++|| +|+|||+||+
T Consensus 114 ~~~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------alLkAivLf~ 151 (231)
T cd06937 114 NAGFGPLTDLVFTFANQLLPLEMDDTEI------------------------------------------GLLSAICLIC 151 (231)
T ss_pred hcChHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcC
Confidence 6666666666666544 999999999 9999999999
Q ss_pred CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHHHhh
Q psy11505 257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEMLEA 309 (312)
Q Consensus 257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~~ 309 (312)
||++ +.++.+|+++||+++.||.+|+..+ ..++++++.|.+||++|+.|||+.
T Consensus 152 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~ 231 (231)
T cd06937 152 GDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEMLEN 231 (231)
T ss_pred CCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhcC
Confidence 9998 9999999999999999999999865 235667999999999999999973
No 7
>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-
Probab=99.96 E-value=9.8e-30 Score=218.87 Aligned_cols=189 Identities=46% Similarity=0.739 Sum_probs=155.9
Q ss_pred HHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhc
Q psy11505 78 LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRS 157 (312)
Q Consensus 78 l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs 157 (312)
+..+...+|...........+......+..++++..++++.+|+|||++|+|.+|+.+||++|+|++|+++++++.||++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s 81 (221)
T cd06946 2 LSHLLVAEPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRS 81 (221)
T ss_pred hHHHhhcCCccccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 34556667765544444444455677899999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCeeEecccchhhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHH
Q psy11505 158 LPHCAGKIRFASDLVLDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFK 234 (312)
Q Consensus 158 ~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (312)
++.++ .+.+++|...++......+..++.+ ++...+++|++|++||
T Consensus 82 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~l~~~E~------------------------------ 130 (221)
T cd06946 82 LPFNG-ELVFAEDFILDEELAREAGLLELYSACLQLVRRLQRLRLEKEEY------------------------------ 130 (221)
T ss_pred cCCCC-ceeecCCeEEcHHHHhhcCHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------
Confidence 99875 6778777766655544444444333 4455566999999999
Q ss_pred HHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH---------------------------h
Q psy11505 235 RTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL---------------------------R 286 (312)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------------------------~ 286 (312)
++++||+|||||+. +.+..+|+++|++|+.||.+||..+ .
T Consensus 131 ------------~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~LL~~l~~Lr~~~~~~~e 198 (221)
T cd06946 131 ------------VLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARR 198 (221)
T ss_pred ------------HHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHhhchhHHHHHHHHHH
Confidence 99999999999987 9999999999999999999999744 2
Q ss_pred hhhccccCCccchhHHHHHHHhh
Q psy11505 287 FWSTVHKDGKVLMNKLFVEMLEA 309 (312)
Q Consensus 287 ~~~~~~~~~~~~~~~~~~~~~~~ 309 (312)
+++.+++.|.+|+++|+.|||+|
T Consensus 199 ~l~~~~~~~~~~~~~Ll~eml~~ 221 (221)
T cd06946 199 FFYGVKREGKVPMHKLFLEMLEA 221 (221)
T ss_pred HHHHHHhcCCCCHHHHHHHHhcC
Confidence 35567899999999999999975
No 8
>cd06944 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors. The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not
Probab=99.96 E-value=5.4e-30 Score=222.21 Aligned_cols=168 Identities=27% Similarity=0.424 Sum_probs=145.0
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCC-CCeeEecccchhhHHhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQAR 179 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~-~~~l~~~~g~~~~~~~~~ 179 (312)
....+..++++..+.+..+|+|||++|+|.+|+.+||+.|+|++|+++++|+.+|+++..+ .+.+.+++|..++.....
T Consensus 36 ~~~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~ 115 (237)
T cd06944 36 ELDTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLA 115 (237)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhh
Confidence 4457789999999999999999999999999999999999999999999999999999886 568999999877665432
Q ss_pred h-cc--cchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505 180 E-CG--FSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV 253 (312)
Q Consensus 180 ~-~~--~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 (312)
. .+ ..++. .++...+++|++|++|| +++|||+
T Consensus 116 ~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lLkaIi 153 (237)
T cd06944 116 SQAGLGLSSLVDRAQELVNKLRELQFDRQEF------------------------------------------VCLKFLI 153 (237)
T ss_pred hhccccHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHH
Confidence 2 11 22333 44555566999999999 9999999
Q ss_pred ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHH
Q psy11505 254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEM 306 (312)
Q Consensus 254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~ 306 (312)
|||||++ +++++.|+++|++|..||.+|+..+ .+++++++.|.+|+++|+.||
T Consensus 154 L~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~em 233 (237)
T cd06944 154 LFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEM 233 (237)
T ss_pred HcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHH
Confidence 9999998 9999999999999999999999765 346778999999999999999
Q ss_pred Hhhh
Q psy11505 307 LEAY 310 (312)
Q Consensus 307 ~~~~ 310 (312)
|+|+
T Consensus 234 l~~~ 237 (237)
T cd06944 234 LHAK 237 (237)
T ss_pred HcCC
Confidence 9874
No 9
>cd07076 NR_LBD_GR Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. 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. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription
Probab=99.96 E-value=2e-29 Score=217.57 Aligned_cols=190 Identities=28% Similarity=0.416 Sum_probs=160.5
Q ss_pred HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR 156 (312)
Q Consensus 77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r 156 (312)
++..+...+|.......+...++.....+.++++..+++++.+|+|||++|+|.+|+.+||++|||++|.++++++.|||
T Consensus 2 ~~~~l~~~ep~~~~~~~d~~~p~~~~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~r 81 (247)
T cd07076 2 LVSLLEVIEPEVLYSGYDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWR 81 (247)
T ss_pred HHHHHHHcCCCcccCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHh
Confidence 35667777888777776777777778889999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCC-eeEecccchhhHHhhhhcccchh---hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505 157 SLPHCAG-KIRFASDLVLDERQARECGFSEI---YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF 232 (312)
Q Consensus 157 s~~~~~~-~l~~~~g~~~~~~~~~~~~~~~~---~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~ 232 (312)
+++..++ .+.+++|..+++......+..++ +.++...+++|++|++||
T Consensus 82 s~~~~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~l~e~~~~~r~L~ld~~Ef---------------------------- 133 (247)
T cd07076 82 SYRQSNGNLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEY---------------------------- 133 (247)
T ss_pred ccCCCCCceEEecCCeeecHHHHhhhhHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------
Confidence 9998663 47888999888776655444443 334555666999999999
Q ss_pred HHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hhh-------------
Q psy11505 233 FKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RFW------------- 288 (312)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~~------------- 288 (312)
+|+|||+|||| |++ |+++++|+++|++++.+|.+||..+ ||.
T Consensus 134 --------------acLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~RF~kLLllLp~Lr~i~ 199 (247)
T cd07076 134 --------------LCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVV 199 (247)
T ss_pred --------------HHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhHHHHHHHHHHHHHHHH
Confidence 99999999999 887 9999999999999999999999854 441
Q ss_pred -----hccccCCccchhHHHHHHHh
Q psy11505 289 -----STVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 289 -----~~~~~~~~~~~~~~~~~~~~ 308 (312)
++.+.+|.+|+..++.||+.
T Consensus 200 ~~~~ef~~~~~~~~~~~~~~~~ml~ 224 (247)
T cd07076 200 ENLLNFCFQTFLDKTMSIEFPEMLA 224 (247)
T ss_pred HHHHHHHHHHhcccchhhhhHHHHH
Confidence 33577899988888888875
No 10
>KOG4216|consensus
Probab=99.96 E-value=8.1e-31 Score=229.14 Aligned_cols=138 Identities=20% Similarity=0.247 Sum_probs=113.7
Q ss_pred HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhccc
Q psy11505 104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF 183 (312)
Q Consensus 104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~ 183 (312)
.|+....-....|..+|||||.+++|.+|+.+||+.|||...+|+.+.+.+..+..... .+.+.... .+.......+.
T Consensus 283 mWe~cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~n-tV~~e~~~-~g~~~f~a~~~ 360 (479)
T KOG4216|consen 283 MWELCAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNN-TVYFEGKY-AGPEVFYALGC 360 (479)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhccccc-ceeecccc-cchhheeccCh
Confidence 35555555567899999999999999999999999999999999999988866555544 55554443 33344445566
Q ss_pred chhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505 184 SEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK 260 (312)
Q Consensus 184 ~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 260 (312)
.+++++++.+.. .|++++.|+ +++.|+||.+||+.
T Consensus 361 ~elis~vf~~~ksL~~Lq~te~Ei------------------------------------------AL~~alVL~~~~r~ 398 (479)
T KOG4216|consen 361 EELISRVFEFGKSLCSLQLTEDEI------------------------------------------ALFSALVLMSADRS 398 (479)
T ss_pred HHHHHHHHhhhHHHHhhccCcHHH------------------------------------------HHHHHHHhhCCccc
Confidence 778899998876 899999999 99999999999998
Q ss_pred -ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 261 -LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 261 -l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
|.+..+|+++++.+..||++.+..+
T Consensus 399 gl~e~~ki~~lq~~~~~a~qhvl~kn 424 (479)
T KOG4216|consen 399 GLQEKVKIEKLQQKIQLALQHVLQKN 424 (479)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999987655
No 11
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): 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 the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=99.96 E-value=4.2e-29 Score=215.50 Aligned_cols=165 Identities=24% Similarity=0.373 Sum_probs=146.9
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~ 180 (312)
....+..+++.....+..+|+|||++|+|.+|+.+||++|||++|.++++|+.||++.+..+ .+++++|..+++.+. .
T Consensus 39 ~~~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~-~l~f~~~~~~~r~~~-~ 116 (238)
T cd07348 39 DASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEG-KLIFCNGVVLHRTQC-V 116 (238)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCC-eEEeeCCeeecHHHH-H
Confidence 34668999999999999999999999999999999999999999999999999999998866 799999998887664 4
Q ss_pred cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505 181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS 257 (312)
Q Consensus 181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 257 (312)
.+.+++++.++++.. +|++|++|| +|+|||+|| |
T Consensus 117 ~~~~~~~~~i~ef~~~l~~L~ld~~E~------------------------------------------a~LkAIvLf-~ 153 (238)
T cd07348 117 RGFGDWIDSILEFSQSLHRMNLDVSAF------------------------------------------SCLAALVII-T 153 (238)
T ss_pred hhHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHc-C
Confidence 566677777776655 999999999 999999999 7
Q ss_pred CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505 258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~ 308 (312)
|++ |+++++|+++||+++.||.+|+..+ +.+++.++.|.+||++|+.||++
T Consensus 154 Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl~Lp~LRsl~~~~~e~lf~~kl~~~~~~~pLl~e~~~ 233 (238)
T cd07348 154 DRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIVDKIFM 233 (238)
T ss_pred CCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHh
Confidence 998 9999999999999999999999763 23566799999999999999998
Q ss_pred hh
Q psy11505 309 AY 310 (312)
Q Consensus 309 ~~ 310 (312)
+-
T Consensus 234 ~~ 235 (238)
T cd07348 234 DT 235 (238)
T ss_pred cc
Confidence 64
No 12
>cd07073 NR_LBD_AR Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator. The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell funct
Probab=99.96 E-value=6e-29 Score=215.56 Aligned_cols=190 Identities=24% Similarity=0.409 Sum_probs=151.3
Q ss_pred HHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhc
Q psy11505 78 LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRS 157 (312)
Q Consensus 78 l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs 157 (312)
++.+...||...........++.....+.+++++.+++++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.||++
T Consensus 3 ~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs 82 (246)
T cd07073 3 LNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRS 82 (246)
T ss_pred HHHHhhcCCccccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44455566665544444444555667789999999999999999999999999999999999999999999999999999
Q ss_pred ccCC-CCeeEecccchhhHHhhhhcccchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHH
Q psy11505 158 LPHC-AGKIRFASDLVLDERQARECGFSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFF 233 (312)
Q Consensus 158 ~~~~-~~~l~~~~g~~~~~~~~~~~~~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~ 233 (312)
++.. .+.+.+++|..+++......+..+.. .++...+++|++|.+||
T Consensus 83 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~Ey----------------------------- 133 (246)
T cd07073 83 FTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEF----------------------------- 133 (246)
T ss_pred cccCCCCeEEecCCeeechhhhccccHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------
Confidence 9874 45688988887776654443433433 34445555899999999
Q ss_pred HHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH---------hh---------------
Q psy11505 234 KRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL---------RF--------------- 287 (312)
Q Consensus 234 ~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------~~--------------- 287 (312)
+|+|||+|||| |++ |+++++|+.+|++++.||.+|+..+ ||
T Consensus 134 -------------acLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp~LRsi~~ 200 (246)
T cd07073 134 -------------LCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIAR 200 (246)
T ss_pred -------------HHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHHHHHHHHHHHHHHHHH
Confidence 99999999999 887 9999999999999999999999653 33
Q ss_pred ---hhcccc-----CCccchhHHHHHHHhh
Q psy11505 288 ---WSTVHK-----DGKVLMNKLFVEMLEA 309 (312)
Q Consensus 288 ---~~~~~~-----~~~~~~~~~~~~~~~~ 309 (312)
+++.++ .|+++|++||.||++.
T Consensus 201 ~~~~~~~~l~~~~~~~~~~~~pll~ei~~~ 230 (246)
T cd07073 201 ELHQFTFDLLIKSHMVSVDFPEMMAEIISV 230 (246)
T ss_pred HHHHHHHHHhCccccCccCccHHHHHHHHh
Confidence 122333 4556899999999984
No 13
>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 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=99.96 E-value=3.2e-29 Score=217.31 Aligned_cols=168 Identities=27% Similarity=0.399 Sum_probs=143.4
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCC-CCeeEecccchhhHHhh-
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQA- 178 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~-~~~l~~~~g~~~~~~~~- 178 (312)
....+..++++.++.+..+|+|||++|+|.+|+.+||+.|||++|.++++++.+|++.++. .+.+.+++|..++....
T Consensus 38 ~~~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~ 117 (241)
T cd07069 38 KLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIA 117 (241)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhh
Confidence 4567789999999999999999999999999999999999999999999999999998765 35788888876553321
Q ss_pred --hhcccc---hhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505 179 --RECGFS---EIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV 253 (312)
Q Consensus 179 --~~~~~~---~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 (312)
...+.. +.+.++...+++|++|.+|| +++|||+
T Consensus 118 ~~~~~~~~~~~~~~~e~~~~lr~L~ld~~E~------------------------------------------a~LKaiv 155 (241)
T cd07069 118 SQAGATLNNLMSHAQELVAKLRSLQFDQREF------------------------------------------VCLKFLV 155 (241)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHH
Confidence 111222 33445666677999999999 9999999
Q ss_pred ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHH
Q psy11505 254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEM 306 (312)
Q Consensus 254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~ 306 (312)
|||||++ +.+.++|+++|++++.||.+|+..+ +.++++++.|.+|+++|+.||
T Consensus 156 Lfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Em 235 (241)
T cd07069 156 LFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEM 235 (241)
T ss_pred HcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHH
Confidence 9999998 9999999999999999999999765 336778999999999999999
Q ss_pred Hhhh
Q psy11505 307 LEAY 310 (312)
Q Consensus 307 ~~~~ 310 (312)
|+|+
T Consensus 236 l~~~ 239 (241)
T cd07069 236 LHAK 239 (241)
T ss_pred Hhcc
Confidence 9986
No 14
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 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=99.96 E-value=3e-29 Score=217.30 Aligned_cols=168 Identities=24% Similarity=0.380 Sum_probs=143.6
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCC-CCeeEecccchhhHHhh
Q psy11505 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHC-AGKIRFASDLVLDERQA 178 (312)
Q Consensus 100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~-~~~l~~~~g~~~~~~~~ 178 (312)
.....+..++++..+.++.+|+|||++|+|.+|+.+||+.|||++|.++++|..|||+++.. .+.+.+++|..+.....
T Consensus 35 ~~~~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~ 114 (237)
T cd07070 35 DQPAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTV 114 (237)
T ss_pred CcccHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHH
Confidence 34566889999999999999999999999999999999999999999999999999999765 35788888877664432
Q ss_pred h-hccc--chh---hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCce
Q psy11505 179 R-ECGF--SEI---YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTL 252 (312)
Q Consensus 179 ~-~~~~--~~~---~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 (312)
. ..+. ..+ +.++...+++|++|++|| +++|||
T Consensus 115 ~~~~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey------------------------------------------~~LkaI 152 (237)
T cd07070 115 AAQAGSLLHSLVLRAQELVLQLHALQLDRQEF------------------------------------------VCLKFL 152 (237)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHH
Confidence 2 2221 121 245666677999999999 999999
Q ss_pred eecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHH
Q psy11505 253 VLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVE 305 (312)
Q Consensus 253 ~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~ 305 (312)
+|||||++ ++++++|+++|++++.||.+||..+ +++++++++|.+|+++|+.|
T Consensus 153 iLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~kLLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~e 232 (237)
T cd07070 153 ILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIE 232 (237)
T ss_pred HhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHH
Confidence 99999998 9999999999999999999998764 44778899999999999999
Q ss_pred HHhh
Q psy11505 306 MLEA 309 (312)
Q Consensus 306 ~~~~ 309 (312)
||++
T Consensus 233 ml~~ 236 (237)
T cd07070 233 MLQA 236 (237)
T ss_pred HhcC
Confidence 9987
No 15
>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin
Probab=99.96 E-value=7.6e-29 Score=213.24 Aligned_cols=184 Identities=47% Similarity=0.711 Sum_probs=153.3
Q ss_pred hcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC
Q psy11505 83 LCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA 162 (312)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~ 162 (312)
..+|...........+......+..++++..+.+..+|+|+|++|+|.+|+.+||+.|+|++|++++++..||++++.+.
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~ 86 (221)
T cd07068 7 VAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPG 86 (221)
T ss_pred hhCCCcccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCC
Confidence 34443333333344556677889999999999999999999999999999999999999999999999999999998877
Q ss_pred CeeEecccchhhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhh
Q psy11505 163 GKIRFASDLVLDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQV 239 (312)
Q Consensus 163 ~~l~~~~g~~~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 239 (312)
.+.+++|.+++++.....+..++.+ ++...+++|++|++||
T Consensus 87 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~----------------------------------- 130 (221)
T cd07068 87 -KLVFAPDLLLDREQARVEGLLEIFDMLLQLVRRFRELGLQREEY----------------------------------- 130 (221)
T ss_pred -eEEeCCCceECHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------------
Confidence 7888888877766554445444333 4455566999999999
Q ss_pred cccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH---------------------------hhhhcc
Q psy11505 240 YSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL---------------------------RFWSTV 291 (312)
Q Consensus 240 ~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~---------------------------~~~~~~ 291 (312)
+++|||++||||++ |+++..|++.|++|+.+|.+|+..+ ++++.+
T Consensus 131 -------~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~LL~~l~~Lr~~~~~~~e~l~~~ 203 (221)
T cd07068 131 -------VCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHLYSV 203 (221)
T ss_pred -------HHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHHhccHHHHHHHHHHHHHHHH
Confidence 99999999999998 9999999999999999999998755 335567
Q ss_pred ccCCccchhHHHHHHHhh
Q psy11505 292 HKDGKVLMNKLFVEMLEA 309 (312)
Q Consensus 292 ~~~~~~~~~~~~~~~~~~ 309 (312)
++.|.+|+++|+.||++|
T Consensus 204 k~~~~~~~~~Ll~e~l~~ 221 (221)
T cd07068 204 KCEGKVPMYKLFLEMLEA 221 (221)
T ss_pred HHcCCccHHHHHHHHhcC
Confidence 999999999999999986
No 16
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 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=99.96 E-value=1.7e-28 Score=211.85 Aligned_cols=167 Identities=24% Similarity=0.335 Sum_probs=145.8
Q ss_pred CchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhh
Q psy11505 99 DPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQA 178 (312)
Q Consensus 99 ~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~ 178 (312)
......++.+.+.....+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.||++.+..+ .+.+++|..+++.+.
T Consensus 38 ~~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~-~l~~~~g~~~~~~~~ 116 (239)
T cd07072 38 MSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDT-KLTFCNGVVLHKQQC 116 (239)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCC-eEEeeCCeeecHHHH
Confidence 3456678999999999999999999999999999999999999999999999999999998865 799999988887765
Q ss_pred hhcccchhhhhhcccC---ccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505 179 RECGFSEIYQQVKHSG---SLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA 255 (312)
Q Consensus 179 ~~~~~~~~~~~i~~~~---~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 255 (312)
.. +++++++.++++. ++|++|++|| +|++||+||
T Consensus 117 ~~-~~~~~~~~i~ef~~~l~~L~ld~~E~------------------------------------------a~LkAivLf 153 (239)
T cd07072 117 QR-SFGDWLHAILEFSKSLHAMDIDISAF------------------------------------------ACLCALTLI 153 (239)
T ss_pred Hh-hHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHh
Confidence 43 5566666665554 4899999999 999999999
Q ss_pred CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHH
Q psy11505 256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEM 306 (312)
Q Consensus 256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~ 306 (312)
+ |++ |.++++|+++|++++.+|.+|+..+ +.+++.++.|.+|+++|+.||
T Consensus 154 ~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kLLl~Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em 232 (239)
T cd07072 154 T-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENM 232 (239)
T ss_pred C-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHH
Confidence 5 887 9999999999999999999999743 235667999999999999999
Q ss_pred Hhhh
Q psy11505 307 LEAY 310 (312)
Q Consensus 307 ~~~~ 310 (312)
+.+-
T Consensus 233 ~~~~ 236 (239)
T cd07072 233 FVAS 236 (239)
T ss_pred Hhcc
Confidence 9863
No 17
>cd07071 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 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=99.96 E-value=1.8e-28 Score=211.82 Aligned_cols=165 Identities=27% Similarity=0.381 Sum_probs=145.0
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~ 180 (312)
....+..+++.....+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.+..+ .+.+++|..+++.+. .
T Consensus 39 ~~~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~-~l~~~~g~~~~~~~~-~ 116 (238)
T cd07071 39 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEG-KLIFCNGVVLHRLQC-V 116 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCC-ceEeeCCceechhhh-h
Confidence 45678999999999999999999999999999999999999999999999999999998866 799999988876653 4
Q ss_pred cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505 181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS 257 (312)
Q Consensus 181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 257 (312)
.+.+++++.++++.. +|++|++|| +|++||+|| +
T Consensus 117 ~~~~~~~~~i~ef~~~l~~L~ld~~E~------------------------------------------alLkAIvLf-~ 153 (238)
T cd07071 117 RGFGEWIDSIVEFSSNLQNMNIDISAF------------------------------------------SCIAALAMV-T 153 (238)
T ss_pred hcHHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHc-C
Confidence 466667777766554 899999999 999999999 5
Q ss_pred CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505 258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~ 308 (312)
|++ |+++++|+++||+++.||.+|+..+ +.+++.++.|.+|+++|+.||+.
T Consensus 154 D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl~Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~~ 233 (238)
T cd07071 154 ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL 233 (238)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHH
Confidence 887 9999999999999999999999743 23556789999999999999997
Q ss_pred hh
Q psy11505 309 AY 310 (312)
Q Consensus 309 ~~ 310 (312)
+-
T Consensus 234 ~~ 235 (238)
T cd07071 234 DT 235 (238)
T ss_pred hh
Confidence 64
No 18
>cd06935 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors. The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), a
Probab=99.95 E-value=2.1e-28 Score=212.80 Aligned_cols=164 Identities=20% Similarity=0.347 Sum_probs=146.6
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR 179 (312)
Q Consensus 100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~ 179 (312)
.....+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.+++|..+.++...
T Consensus 49 ~~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~-~~~~~~~~~~~~~~~~ 127 (243)
T cd06935 49 VDLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESE-TLTLSGEMAVTREQLK 127 (243)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCC-eEEeeCCeEeeHHHHH
Confidence 356789999999999999999999999999999999999999999999999999999877765 7999999988888777
Q ss_pred hcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505 180 ECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN 256 (312)
Q Consensus 180 ~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 256 (312)
..+.+++.+.++.++. +|++|++|| ++++||+|||
T Consensus 128 ~~~~~~~~~~i~~f~~~l~~L~ld~~E~------------------------------------------alLkAivLf~ 165 (243)
T cd06935 128 NGGLGVVSDAIFDLGVSLSSFNLDDTEV------------------------------------------ALLQAVLLMS 165 (243)
T ss_pred hcChHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHhC
Confidence 7777777777776654 999999999 9999999999
Q ss_pred CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccch-hHHHHHH
Q psy11505 257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLM-NKLFVEM 306 (312)
Q Consensus 257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~-~~~~~~~ 306 (312)
||++ |+++++|+++|++++.||.+|+..+ +.+++.++.|..|+ ++|+.||
T Consensus 166 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~L~~LR~i~~~~~e~l~~~k~~~~~~~~~~L~~Em 243 (243)
T cd06935 166 SDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEV 243 (243)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChhhhcC
Confidence 9998 9999999999999999999999765 22455788999995 9999987
No 19
>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. 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
Probab=99.95 E-value=3.2e-28 Score=210.94 Aligned_cols=166 Identities=27% Similarity=0.343 Sum_probs=147.2
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~ 180 (312)
....+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+++.+..+ .+.+++|..+++.+. .
T Consensus 39 ~~~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~-~l~~~~~~~~~~~~~-~ 116 (239)
T cd06945 39 DSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDG-KLVFCNGLVLHRLQC-V 116 (239)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-ceEeeCCceecHHHH-H
Confidence 45678999999999999999999999999999999999999999999999999999998866 799999988877664 3
Q ss_pred cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505 181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS 257 (312)
Q Consensus 181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 257 (312)
.+..++++.++.+.. +|++|++|| ++++||+||+|
T Consensus 117 ~~~~~~~~~i~~f~~~l~~L~ld~~E~------------------------------------------~~LkaivL~~p 154 (239)
T cd06945 117 RGFGEWLDSILAFSSSLQSLLLDDISA------------------------------------------FCCLALLLLIT 154 (239)
T ss_pred HhHHHHHHHHHHHHHHHHHHhCChHHH------------------------------------------HHHHHHHHhCC
Confidence 456677787777544 799999999 99999999999
Q ss_pred CCc-ccchHHHHHHHHHHHHHhHhHHHHH----------------------------hhhhccccCCccchhHHHHHHHh
Q psy11505 258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL----------------------------RFWSTVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~----------------------------~~~~~~~~~~~~~~~~~~~~~~~ 308 (312)
|++ |.++++|+++|++++.+|.+|+..+ +.+++.++.|.+||++|+.||++
T Consensus 155 D~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl~Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~~ 234 (239)
T cd06945 155 ERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRFL 234 (239)
T ss_pred CccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHHH
Confidence 998 9999999999999999999999754 22556799999999999999997
Q ss_pred hh
Q psy11505 309 AY 310 (312)
Q Consensus 309 ~~ 310 (312)
.-
T Consensus 235 ~~ 236 (239)
T cd06945 235 DT 236 (239)
T ss_pred hc
Confidence 53
No 20
>cd07075 NR_LBD_MR Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR h
Probab=99.95 E-value=7.9e-28 Score=207.81 Aligned_cols=165 Identities=24% Similarity=0.427 Sum_probs=137.9
Q ss_pred HHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhc
Q psy11505 78 LEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRS 157 (312)
Q Consensus 78 l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs 157 (312)
+..+...++...........++.....+..+++..++.+..+|+|||++|+|.+|+.+||++|||++|.++++++.+||+
T Consensus 3 ~~~l~~~e~~~~~~~~~~~~p~~~~~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs 82 (248)
T cd07075 3 VMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRS 82 (248)
T ss_pred HHHHhhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34455566655555555555666677899999999999999999999999999999999999999999999999999999
Q ss_pred ccCCC-CeeEecccchhhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHH
Q psy11505 158 LPHCA-GKIRFASDLVLDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFF 233 (312)
Q Consensus 158 ~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~ 233 (312)
++... +.+.+++|..++.......+..++.+ ++...+++|++|++||
T Consensus 83 ~~~~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~L~Ld~~E~----------------------------- 133 (248)
T cd07075 83 YKHTNSQFLYFAPDLVFNEERMHQSAMYELCQGMHQISLQFVRLQLTFEEY----------------------------- 133 (248)
T ss_pred cCCCCCceEEecCCccccHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------
Confidence 98865 45888888888877766656555433 4444555999999999
Q ss_pred HHHhhhcccceecCCCCceeecCCC-Cc-ccchHHHHHHHHHHHHHhHhHHHH
Q psy11505 234 KRTIQVYSGYRQTGACGTLVLANSD-VK-LDEFSSLKKFRNSILSSLGDCIYV 284 (312)
Q Consensus 234 ~~~~~~~~~~~~~~~~~~~~l~~~~-~~-l~~~~~~~~~~~~~~~~l~~~~~~ 284 (312)
+|+|||+||||| ++ |+++++|+++|++++.||.+|+..
T Consensus 134 -------------acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~ 173 (248)
T cd07075 134 -------------TIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTK 173 (248)
T ss_pred -------------HHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999997 56 999999999999999999999984
No 21
>cd06948 NR_LBD_COUP-TF Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family. The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone
Probab=99.95 E-value=4.2e-28 Score=210.40 Aligned_cols=167 Identities=23% Similarity=0.359 Sum_probs=141.6
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~ 180 (312)
....++.++++..+.++.+|+|||++|+|.+|+.+||+.|||++|+++++|+.|+++.+...+.+.+++|..........
T Consensus 28 ~~~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~~~ 107 (236)
T cd06948 28 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSADR 107 (236)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccchhh
Confidence 34668999999999999999999999999999999999999999999999999999999887677777777554322111
Q ss_pred -ccc---chhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505 181 -CGF---SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN 256 (312)
Q Consensus 181 -~~~---~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 256 (312)
... .+.+.++...+++|++|++|| +++|||+|||
T Consensus 108 ~~~~~~~~~~~~~l~~~l~~L~ld~~E~------------------------------------------~lLkaiiL~n 145 (236)
T cd06948 108 VVAFMDHIRIFQEQVEKLKALHVDSAEF------------------------------------------SCLKAIVLFT 145 (236)
T ss_pred HhHHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcC
Confidence 111 122445566677999999999 9999999999
Q ss_pred CCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccchhHHHHHHHhh
Q psy11505 257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVLMNKLFVEMLEA 309 (312)
Q Consensus 257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~~~~~~~ 309 (312)
||++ |++.++|+++|++|+.||.+|+..+ ..+++++++|.+|+++|+.|||++
T Consensus 146 pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~ 225 (236)
T cd06948 146 SDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLS 225 (236)
T ss_pred cccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhC
Confidence 9997 9999999999999999999999865 236678999999999999999986
No 22
>cd07074 NR_LBD_PR Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor. The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues
Probab=99.95 E-value=2.1e-27 Score=204.99 Aligned_cols=167 Identities=25% Similarity=0.510 Sum_probs=140.2
Q ss_pred HHHHHHhcCcccccccCCCCCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhh
Q psy11505 77 MLEALLLCEPEMLTVRSETPQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYR 156 (312)
Q Consensus 77 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~r 156 (312)
+++.+...||...........++.....+..+++..+++++.+|+|||++|+|.+|+.+||++|+|++|++++++..|||
T Consensus 2 ~~~~l~~~ep~~~~~~~d~~~p~~~~~~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~r 81 (248)
T cd07074 2 LINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWR 81 (248)
T ss_pred HhHHHHHhCCCcccCCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46677888887777766666677777889999999999999999999999999999999999999999999999999999
Q ss_pred cccCCC-CeeEecccchhhHHhhhhcccchhh---hhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHH
Q psy11505 157 SLPHCA-GKIRFASDLVLDERQARECGFSEIY---QQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAF 232 (312)
Q Consensus 157 s~~~~~-~~l~~~~g~~~~~~~~~~~~~~~~~---~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~ 232 (312)
|++.+. +.+.+++|..+++......+..+.. .++...+.++++|++||
T Consensus 82 S~~~~~~~~l~fa~d~~~~~~~~~~~~~~~~~~~m~e~~~~~~~L~ld~~Ey---------------------------- 133 (248)
T cd07074 82 SYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEF---------------------------- 133 (248)
T ss_pred hhccCCCCeEEecCCcccchhhhhhccHHHHHHHHHHHHHHHHHcCCCHHHH----------------------------
Confidence 998864 4567877777776654333333322 23555666999999999
Q ss_pred HHHHhhhcccceecCCCCceeecCC-CCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 233 FKRTIQVYSGYRQTGACGTLVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~l~~~-~~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
+|+|||+|||| |++ |+++++|+++|++|..+|.+||..+
T Consensus 134 --------------~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~ 174 (248)
T cd07074 134 --------------LCMKALLLLNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLR 174 (248)
T ss_pred --------------HHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 99999999999 777 9999999999999999999997644
No 23
>cd07349 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.
Probab=99.94 E-value=1e-27 Score=205.09 Aligned_cols=164 Identities=18% Similarity=0.153 Sum_probs=132.0
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCe---------eEecccc
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGK---------IRFASDL 171 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~---------l~~~~g~ 171 (312)
....++.+++...+.++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.||++.+..... +.+. |.
T Consensus 17 ~~~~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~-~~ 95 (222)
T cd07349 17 CLCTPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLE-GQ 95 (222)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhc-cc
Confidence 3456788899999999999999999999999999999999999999999999999997765421 1122 11
Q ss_pred hhhHHh--hhhcc----cchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 172 VLDERQ--ARECG----FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 172 ~~~~~~--~~~~~----~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
...... ....+ ....+.++...+++|++|++||
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Ey----------------------------------------- 134 (222)
T cd07349 96 SSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEY----------------------------------------- 134 (222)
T ss_pred ccccccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------------------
Confidence 111000 00001 1123455666677999999999
Q ss_pred cCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccc
Q psy11505 246 TGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVL 298 (312)
Q Consensus 246 ~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~ 298 (312)
+++|||+|||||++ +++.++|+.+|++++.||.+|+... +.+++++++|.+|
T Consensus 135 -a~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~~~r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~ 213 (222)
T cd07349 135 -AYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDAD 213 (222)
T ss_pred -HHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCcccHHHHHHHHhHHHhcCCHHHHHHHhCccccCCCc
Confidence 99999999999998 9999999999999999999999765 3478889999999
Q ss_pred hhHHHHHHH
Q psy11505 299 MNKLFVEML 307 (312)
Q Consensus 299 ~~~~~~~~~ 307 (312)
|++|+.|||
T Consensus 214 i~~Ll~eml 222 (222)
T cd07349 214 IAELLGDML 222 (222)
T ss_pred HHHHHHHhC
Confidence 999999996
No 24
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: 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. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. 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. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=99.94 E-value=7.4e-27 Score=197.23 Aligned_cols=162 Identities=21% Similarity=0.266 Sum_probs=134.9
Q ss_pred HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhccc
Q psy11505 104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF 183 (312)
Q Consensus 104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~ 183 (312)
.|..+.+..+..+..+|+|||++|+|++|+.+||+.|+|++|+++++++.++++.+..+ .+.+.+|..++.+.....+.
T Consensus 3 ~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 81 (195)
T cd06941 3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSG-SITFDDGISISRQQLDIIYD 81 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCC-eEEecCCeEeeHHHHHhccc
Confidence 57888999999999999999999999999999999999999999999999987666544 79999998887665433222
Q ss_pred chhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505 184 SEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK 260 (312)
Q Consensus 184 ~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 260 (312)
.++.+.+.. .+++|++|++|| ++++||+||+||++
T Consensus 82 ~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------allkAi~Lf~pd~~ 119 (195)
T cd06941 82 SDFVKALFEFSDSFNSLGLSDTEV------------------------------------------ALFCAVVLLSPDRI 119 (195)
T ss_pred hHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHcCCCCC
Confidence 344444444 455999999999 99999999999997
Q ss_pred -ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hh-ccccCCccchhHHHHHHHh
Q psy11505 261 -LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WS-TVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 261 -l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~-~~~~~~~~~~~~~~~~~~~ 308 (312)
++++++|+++|++++.+|.+|+..+ || +. +++..+.+++++|+.||+|
T Consensus 120 gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~Lr~l~~~~~e~l~~~~~~~~~~~~p~L~~E~~~ 195 (195)
T cd06941 120 GLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPELRSIGAKHQMHLDWYRVNWPLLRLPPLFAEIYD 195 (195)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHhcC
Confidence 9999999999999999999998755 22 22 3455677899999999986
No 25
>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee
Probab=99.93 E-value=3.1e-26 Score=199.05 Aligned_cols=164 Identities=19% Similarity=0.279 Sum_probs=138.2
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~ 180 (312)
....+..+.+|....+..+|+|||++|+|..|+.+||+.|||++|+++++++.|+++.+..+ .+.+++|..++++....
T Consensus 41 ~~~~~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~~~-~~~~~~g~~~~~~~~~~ 119 (236)
T cd06954 41 RQQRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESE-AITFLKDFPYSRDDFAR 119 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCC-eEEeeCCccccHHHHHH
Confidence 34678899999999999999999999999999999999999999999999999988766654 89999998877765543
Q ss_pred ccc-chhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505 181 CGF-SEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN 256 (312)
Q Consensus 181 ~~~-~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 256 (312)
.+. .++.+.+. ..+++|++|++|| ++++||+|||
T Consensus 120 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~------------------------------------------~lL~aivLf~ 157 (236)
T cd06954 120 AGLQVEFINPIFEFSKSMRELQLDDAEY------------------------------------------ALLIAINIFS 157 (236)
T ss_pred hcChHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHhhcc
Confidence 332 34544444 4455999999999 9999999999
Q ss_pred CCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhccccCCccchhHHHHHHHh
Q psy11505 257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~~~~~~~~~~~~~~~~~~ 308 (312)
||++ |++.++|+++|++++.+|.+|+..+ | .++..++.+ .++++|+.||++
T Consensus 158 pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~L~~Lr~l~~~~~e~l~~~k~~~-~~~~~L~~El~~ 235 (236)
T cd06954 158 ADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWD 235 (236)
T ss_pred CCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCcHHHHHhc
Confidence 9998 9999999999999999999999755 2 234456655 689999999987
No 26
>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.
Probab=99.93 E-value=1.5e-26 Score=199.04 Aligned_cols=162 Identities=19% Similarity=0.226 Sum_probs=130.0
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccc----hhhHH
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDL----VLDER 176 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~----~~~~~ 176 (312)
+...++.+++...+.++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.|+++.+.....+ +.++. .....
T Consensus 17 ~l~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~-~~~~~~~~~l~~~~ 95 (232)
T cd07350 17 TLKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVET-SEPSMLQRILTTRP 95 (232)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccc-cchhHHHHHHhccc
Confidence 45567888999999999999999999999999999999999999999999999999988875221 21111 00000
Q ss_pred -----------------hhhhccc------chhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHH
Q psy11505 177 -----------------QARECGF------SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFF 233 (312)
Q Consensus 177 -----------------~~~~~~~------~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~ 233 (312)
.....+. .+.+.++...+++|++|++||
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~----------------------------- 146 (232)
T cd07350 96 PPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEY----------------------------- 146 (232)
T ss_pred ccccccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------
Confidence 0000010 123455556666999999999
Q ss_pred HHHhhhcccceecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------h
Q psy11505 234 KRTIQVYSGYRQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------R 286 (312)
Q Consensus 234 ~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~ 286 (312)
+++|||+|||||++ |.++++|+++|++++.+|.+|+... .
T Consensus 147 -------------a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~~~~iE 213 (232)
T cd07350 147 -------------AYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIA 213 (232)
T ss_pred -------------HHHHHHHHhCCCcccCCCHHHHHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHhHHHHccCHHHHH
Confidence 99999999999998 9999999999999999999999855 3
Q ss_pred hhhccccCCccchhHHHHH
Q psy11505 287 FWSTVHKDGKVLMNKLFVE 305 (312)
Q Consensus 287 ~~~~~~~~~~~~~~~~~~~ 305 (312)
.+++++++|.+||++|+.|
T Consensus 214 ~lff~~l~g~v~i~~ll~E 232 (232)
T cd07350 214 ELFFRPIIGTVNMDDMLLE 232 (232)
T ss_pred HHhccccCCCCcHHHHhcC
Confidence 4778899999999999875
No 27
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=99.93 E-value=1.3e-26 Score=198.82 Aligned_cols=162 Identities=18% Similarity=0.165 Sum_probs=129.0
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCC---------eeEecccc
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAG---------KIRFASDL 171 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~---------~l~~~~g~ 171 (312)
.....+.+++...+.+..+|+|||++|+|.+|+.+||+.|||++|.++++|+.|+++.+.+.. .+...++.
T Consensus 17 ~~~~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~ 96 (222)
T cd06951 17 QLCAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEM 96 (222)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhcccc
Confidence 345678899999999999999999999999999999999999999999999999999887542 11222222
Q ss_pred hhhHHhh--hhcc------cchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505 172 VLDERQA--RECG------FSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243 (312)
Q Consensus 172 ~~~~~~~--~~~~------~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (312)
....... ...+ ..+.+.++...+++|++|++||
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Ey--------------------------------------- 137 (222)
T cd06951 97 HWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEY--------------------------------------- 137 (222)
T ss_pred ccccccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHH---------------------------------------
Confidence 2211110 0001 1122445555666999999999
Q ss_pred eecCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCc
Q psy11505 244 RQTGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGK 296 (312)
Q Consensus 244 ~~~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~ 296 (312)
+++|||+|||||++ + ++++|+++|++++.+|.+|+..+ +.+++++++|.
T Consensus 138 ---a~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LRsl~~~~~e~lff~~~~g~ 213 (222)
T cd06951 138 ---AYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGN 213 (222)
T ss_pred ---HHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHhhcCCHHHHHHHhCccccCC
Confidence 99999999999998 9 99999999999999999999765 34778899999
Q ss_pred cchhHHHHH
Q psy11505 297 VLMNKLFVE 305 (312)
Q Consensus 297 ~~~~~~~~~ 305 (312)
+||++++.|
T Consensus 214 ~~i~~ll~~ 222 (222)
T cd06951 214 VSMDDVLLQ 222 (222)
T ss_pred CcHHHHhcC
Confidence 999999865
No 28
>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal lig
Probab=99.93 E-value=1.2e-25 Score=193.83 Aligned_cols=163 Identities=26% Similarity=0.385 Sum_probs=140.4
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR 179 (312)
Q Consensus 100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~ 179 (312)
.+..+..++++++..++..+++|+|+||+|+.|+.+||+.|+|++|++++++..||++++.++ .+++++|.+++.....
T Consensus 29 ~~~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~-~l~~~~g~~~~~~~~~ 107 (222)
T cd06931 29 KKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKD-ILLLGNDLIIPRHCPE 107 (222)
T ss_pred cccCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCC-eeeeCCCccccccccc
Confidence 467789999999999999999999999999999999999999999999999999999987655 7888988877654322
Q ss_pred hccc----chhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505 180 ECGF----SEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA 255 (312)
Q Consensus 180 ~~~~----~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 255 (312)
.+. .++++.+...+.+|++|++|| ++++||++|
T Consensus 108 -~~~~~~~~~~~~~~~~~l~~L~l~~~E~------------------------------------------~lLkaiil~ 144 (222)
T cd06931 108 -PEISRVANRILDELVLPLRDLNIDDNEY------------------------------------------ACLKAIVFF 144 (222)
T ss_pred -chHHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHc
Confidence 222 233455666777999999999 999999999
Q ss_pred CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------h--------------------hhhccccCCccchhHHHHHH
Q psy11505 256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------R--------------------FWSTVHKDGKVLMNKLFVEM 306 (312)
Q Consensus 256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~--------------------~~~~~~~~~~~~~~~~~~~~ 306 (312)
+||++ +++.++++++|++++.+|.+|+... | .+...+++|.+|+++|+.||
T Consensus 145 ~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e~ 222 (222)
T cd06931 145 DPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222 (222)
T ss_pred CCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhhC
Confidence 99998 9999999999999999999998543 2 34557999999999999986
No 29
>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely r
Probab=99.93 E-value=1.2e-25 Score=194.93 Aligned_cols=163 Identities=18% Similarity=0.254 Sum_probs=136.5
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~ 180 (312)
....|..+.+.....+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++.+... .+.+. |...+++....
T Consensus 46 ~~~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~-~~~~~-~~~~~~~~~~~ 123 (241)
T cd06939 46 REEMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNN-TVLFD-GKYAPIDLFKS 123 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCC-EEEEC-CccccHHHHHH
Confidence 55789999999999999999999999999999999999999999999999999977665544 66664 44566666666
Q ss_pred cccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505 181 CGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS 257 (312)
Q Consensus 181 ~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 257 (312)
.+.+++++.++.++. +|++|++|| ++++||+||+|
T Consensus 124 ~~~~~~~~~~~~f~~~l~~L~ld~~E~------------------------------------------all~AivL~~p 161 (241)
T cd06939 124 LGCDDLISAVFDFAKSLCELKLTEDEI------------------------------------------ALFSALVLISA 161 (241)
T ss_pred cCcHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHhcC
Confidence 666677777766655 899999999 99999999999
Q ss_pred CCc-ccchHHHHHHHHHHHHHhHhHHHHH-------------------------hhhhccccC----CccchhHHHHHHH
Q psy11505 258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL-------------------------RFWSTVHKD----GKVLMNKLFVEML 307 (312)
Q Consensus 258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~-------------------------~~~~~~~~~----~~~~~~~~~~~~~ 307 (312)
|++ |.++++|+++|++++.||.+|+..+ +.+...+.. +..++++|+.||+
T Consensus 162 Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~p~~~~~~~ppL~~Elf 241 (241)
T cd06939 162 DRPGLQEKRKVEKLQQKIELALRHVLQKNHGDDTILTKLLAKMPTLRALCSLHMEKLQKFKQSYPDIVHLEFPPLYKELF 241 (241)
T ss_pred CCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcccCCCCcHHHhhC
Confidence 998 9999999999999999999999764 223444555 3457899999985
No 30
>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): 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 element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, P
Probab=99.92 E-value=3.8e-25 Score=193.76 Aligned_cols=165 Identities=16% Similarity=0.194 Sum_probs=133.8
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEeccc-chhhHHhh
Q psy11505 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASD-LVLDERQA 178 (312)
Q Consensus 100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g-~~~~~~~~ 178 (312)
.....|..+.......+..+|+|||++|+|.+|+.+||++|||++|++++++..+.+... + .+++++| .+..++..
T Consensus 60 ~~~~~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~~--~-~~~~~~~~~~~~~~~~ 136 (259)
T cd06932 60 IRIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYNK--D-GLLFPEGNGYVTREFL 136 (259)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcCC--C-CeEEeCCCEEeeHHHH
Confidence 456678888888889999999999999999999999999999999999999999976432 2 4666554 44555554
Q ss_pred hhcc--cchhhhhhcccC---ccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCcee
Q psy11505 179 RECG--FSEIYQQVKHSG---SLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLV 253 (312)
Q Consensus 179 ~~~~--~~~~~~~i~~~~---~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 (312)
...+ ..++++.++.++ .+|++|++|| ++++||+
T Consensus 137 ~~~~~~~~~~~~~~~e~~~~l~~L~ld~~E~------------------------------------------alLkAiv 174 (259)
T cd06932 137 ESLRKPFCDIMEPKFEFAEKFNALELTDSEL------------------------------------------ALFCAVI 174 (259)
T ss_pred HHhcccHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHH
Confidence 4433 245666555544 4899999999 9999999
Q ss_pred ecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH------hh--------------------hhc-cccCCccchhHHHHH
Q psy11505 254 LANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL------RF--------------------WST-VHKDGKVLMNKLFVE 305 (312)
Q Consensus 254 l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~------~~--------------------~~~-~~~~~~~~~~~~~~~ 305 (312)
||+||++ |.++++|+++|++++.||.+|+..+ || +.. +...|.+++++|+.|
T Consensus 175 Lf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~kLLl~L~~LRsl~~~~~e~l~~~k~~~~~~~~~pLl~E 254 (259)
T cd06932 175 ILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQMVQQIKKTETDASLPPLLQE 254 (259)
T ss_pred HhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCcHHHH
Confidence 9999998 9999999999999999999999876 22 232 345678999999999
Q ss_pred HHhh
Q psy11505 306 MLEA 309 (312)
Q Consensus 306 ~~~~ 309 (312)
|++.
T Consensus 255 i~~~ 258 (259)
T cd06932 255 IYKD 258 (259)
T ss_pred Hhhc
Confidence 9975
No 31
>cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of
Probab=99.92 E-value=4.4e-25 Score=185.02 Aligned_cols=143 Identities=20% Similarity=0.290 Sum_probs=127.8
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR 179 (312)
Q Consensus 100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~ 179 (312)
.....|+.+.+..+..+..+|+|||++|+|.+|+.+||+.|||++|+++++++.++++....+ .+.+.+|..++++...
T Consensus 9 ~~~~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~-~l~~~~~~~~~~~~~~ 87 (189)
T cd06940 9 SGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKER-SVTFLSGQKYSVDDLH 87 (189)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCC-eEEecCCcEEcHHHHH
Confidence 355778999999999999999999999999999999999999999999999999998776655 7889899888877766
Q ss_pred hcccchhhhhhcccCc---cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505 180 ECGFSEIYQQVKHSGS---LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN 256 (312)
Q Consensus 180 ~~~~~~~~~~i~~~~~---~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 256 (312)
..+..++++.++.+.. +|++|++|| ++++||+|||
T Consensus 88 ~~~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------a~LkAivLf~ 125 (189)
T cd06940 88 SMGAGDLLNSMFDFSEKLNSLQLSDEEM------------------------------------------GLFTAVVLVS 125 (189)
T ss_pred HcCcHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHHhC
Confidence 6666677776666554 999999999 9999999999
Q ss_pred CCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
||++ +.++++|+++|++++.+|.+|+...
T Consensus 126 pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~ 155 (189)
T cd06940 126 ADRSGLENVNLVEALQETLIRALRTLIAKN 155 (189)
T ss_pred CCCcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9998 9999999999999999999999865
No 32
>cd06933 NR_LBD_VDR The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily. The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and
Probab=99.92 E-value=6.7e-25 Score=190.23 Aligned_cols=143 Identities=22% Similarity=0.311 Sum_probs=115.0
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecc-cchhhHHhh
Q psy11505 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFAS-DLVLDERQA 178 (312)
Q Consensus 100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~-g~~~~~~~~ 178 (312)
.+...+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.++. ++..+..+.+++ +..+.....
T Consensus 34 ~~~~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 112 (238)
T cd06933 34 VRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQS-FSLDDMSWTCGSPDFKYKVSDV 112 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHh-cCcCCCeeEecCCceeecHHHH
Confidence 356778899999999999999999999999999999999999999999999998875 444443455443 333344333
Q ss_pred hhcccc-hhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceee
Q psy11505 179 RECGFS-EIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVL 254 (312)
Q Consensus 179 ~~~~~~-~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 254 (312)
...+.. ++.+.+.. .+++|++|++|| +|++||+|
T Consensus 113 ~~~g~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------alLkAivL 150 (238)
T cd06933 113 TKAGHSLELLEPLVKFQVGLKKLNLHEEEH------------------------------------------VLLMAICI 150 (238)
T ss_pred HHccCcHHHHHHHHHHHHHHHhcCCCHHHH------------------------------------------HHHHHHHH
Confidence 333322 34444433 455999999999 99999999
Q ss_pred cCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 255 ANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 255 ~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
||||++ |.++++|+++||+++.||.+|+..+
T Consensus 151 f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 182 (238)
T cd06933 151 LSPDRPGVQDHALIEAIQDRLSDTLQTYIRCR 182 (238)
T ss_pred HCCCCCCCcchHHHHHHHHHHHHHHHHHHHhc
Confidence 999998 9999999999999999999999765
No 33
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=99.92 E-value=7.7e-25 Score=189.45 Aligned_cols=164 Identities=18% Similarity=0.260 Sum_probs=137.4
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARE 180 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~ 180 (312)
....+..++++....+..+|+|+|++|+|..|+.+||+.|+|++|+++++++.|+++... .+.+.+++|..+.++....
T Consensus 37 ~~~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~-~~~~~f~~g~~~~~~~~~~ 115 (231)
T cd06938 37 SDMRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAK-TDSIVFANNQPYTRDSYRK 115 (231)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCC-CCeEEeeCCEEecHHHHhh
Confidence 346788999999999999999999999999999999999999999999999999876554 4589999998877776555
Q ss_pred cccchhhhhhc---ccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505 181 CGFSEIYQQVK---HSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS 257 (312)
Q Consensus 181 ~~~~~~~~~i~---~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 257 (312)
.+.+++.+.++ ..+.+|++|++|| ++++||+||++
T Consensus 116 ~~~~~~~~~l~~~~~~l~~L~ld~~E~------------------------------------------~lL~AI~Lf~d 153 (231)
T cd06938 116 AGMGDSAEDLFRFCRAMCSMKVDNAEY------------------------------------------ALLTAIVIFSD 153 (231)
T ss_pred cCHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHccC
Confidence 56555555554 4455999999999 99999999985
Q ss_pred CCcccchHHHHHHHHHHHHHhHhHHHHH-------hh--------------------hhccccCCccchhHHHHHHHh
Q psy11505 258 DVKLDEFSSLKKFRNSILSSLGDCIYVL-------RF--------------------WSTVHKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 258 ~~~l~~~~~~~~~~~~~~~~l~~~~~~~-------~~--------------------~~~~~~~~~~~~~~~~~~~~~ 308 (312)
..+|+++..|+++|++|..+|.+|+..+ || ++..++. ..++++|+.|++|
T Consensus 154 ~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~~L~~Lr~l~~~~~e~~~~~k~~-~~~~~pl~~Ei~d 230 (231)
T cd06938 154 RPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSILTELRTLGNQNSEMCFSLKLK-NRKLPPFLAEIWD 230 (231)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHhC
Confidence 4449999999999999999999999765 22 3445667 5689999999986
No 34
>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge
Probab=99.91 E-value=8e-25 Score=186.01 Aligned_cols=143 Identities=23% Similarity=0.321 Sum_probs=117.1
Q ss_pred chhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh
Q psy11505 100 PTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR 179 (312)
Q Consensus 100 ~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~ 179 (312)
......+.+++++.+.++.+|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.....+..+++........
T Consensus 23 ~~~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~~~~~- 101 (206)
T cd06950 23 SYEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEA- 101 (206)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCcccccccch-
Confidence 3556788999999999999999999999999999999999999999999999999999887664344444443322111
Q ss_pred hcccc---hhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecC
Q psy11505 180 ECGFS---EIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLAN 256 (312)
Q Consensus 180 ~~~~~---~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 256 (312)
..... ..+.++...+++|++|++|| +++|||+|||
T Consensus 102 ~~~~~~~~~~i~~~~~~~~~L~ld~~Ey------------------------------------------alLKai~L~n 139 (206)
T cd06950 102 ERTFLSEVRALQETLSRFRQLRVDATEF------------------------------------------ACLKAIVLFK 139 (206)
T ss_pred hhHHHHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHhC
Confidence 11111 23445555667999999999 9999999999
Q ss_pred CCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 257 SDVK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 257 ~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
||++ +++.++|+++|++++.||.+|+..+
T Consensus 140 pd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~ 169 (206)
T cd06950 140 PETRGLKDPAQVEALQDQAQLMLNKHIRTR 169 (206)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9998 9999999999999999999999765
No 35
>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of
Probab=99.91 E-value=1.4e-24 Score=186.73 Aligned_cols=140 Identities=19% Similarity=0.239 Sum_probs=115.0
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhc
Q psy11505 102 LQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAREC 181 (312)
Q Consensus 102 ~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~ 181 (312)
...+..+++.....+..+|+|||++|+|.+|+.+||++|||++|+++++++.++++....+ .+.. +|..+........
T Consensus 34 ~~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~ 111 (226)
T cd06934 34 FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETG-TWEC-GPLTYCIEDAARA 111 (226)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhcccCC-eEee-CCEeecHHHHHHc
Confidence 5567888999999999999999999999999999999999999999999999988777543 4444 4444433334444
Q ss_pred ccch-hhhhh---cccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCC
Q psy11505 182 GFSE-IYQQV---KHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANS 257 (312)
Q Consensus 182 ~~~~-~~~~i---~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 257 (312)
++.. +.+.+ ...+++|++|++|| ++++||+||||
T Consensus 112 g~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------alLkAivLf~p 149 (226)
T cd06934 112 GFQQLLLEPLLRFHYTLRKLQLQEEEY------------------------------------------VLMQAMSLFSP 149 (226)
T ss_pred cchHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhCC
Confidence 5443 33333 34455999999999 99999999999
Q ss_pred CCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 258 DVK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 258 ~~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
|++ |.+.++|+++|++++.||.+|+..+
T Consensus 150 Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 178 (226)
T cd06934 150 DRPGVTQHDVIDQLQEKMALTLKSYIDSK 178 (226)
T ss_pred CCcCCcChHHHHHHHHHHHHHHHHHHHHc
Confidence 998 9999999999999999999999765
No 36
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=99.90 E-value=2.5e-24 Score=183.65 Aligned_cols=140 Identities=28% Similarity=0.466 Sum_probs=122.6
Q ss_pred HHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhcc
Q psy11505 103 QTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECG 182 (312)
Q Consensus 103 ~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~ 182 (312)
..+..++++....+..+|+|+|++|+|.+|+.+||+.|+|++|++++++..||+++...+ .+++++|..+.++.....+
T Consensus 30 ~~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~-~~~~~~~~~~~~~~~~~~~ 108 (207)
T cd06943 30 DPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKD-GILLATGLHLHRNSAHQAG 108 (207)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCC-eeEecCCceeccchhhhcc
Confidence 456799999999999999999999999999999999999999999999999999998866 6888888777665544444
Q ss_pred cchh----hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC
Q psy11505 183 FSEI----YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD 258 (312)
Q Consensus 183 ~~~~----~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 258 (312)
...+ ++++...+++|++|++|| +++|||+|||||
T Consensus 109 ~~~~~~~~~~~~~~~l~~L~ld~~E~------------------------------------------~lLkaI~L~~pd 146 (207)
T cd06943 109 VGAIFDRILTELVVKMRDLKMDRTEL------------------------------------------GCLRAIILFNPD 146 (207)
T ss_pred chHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHhcCCC
Confidence 4443 445555677999999999 999999999999
Q ss_pred Cc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 259 VK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 259 ~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
++ |++++.|+++|++|+.+|.+|+..+
T Consensus 147 ~~~L~~~~~v~~~q~~~~~aL~~y~~~~ 174 (207)
T cd06943 147 VKGLKSRQEVESLREKVYASLEEYCRQK 174 (207)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 97 9999999999999999999999765
No 37
>cd06952 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2. The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. 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. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D
Probab=99.90 E-value=5.7e-24 Score=183.23 Aligned_cols=171 Identities=20% Similarity=0.250 Sum_probs=134.4
Q ss_pred CCCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhH
Q psy11505 96 PQSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDE 175 (312)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~ 175 (312)
|...+....+..+++++.+++..+++|+|++|+|..|+.+||+.|+|++|.+++++..++++.+...+.+..+.+.+...
T Consensus 14 ~~~~~~~~~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~ 93 (222)
T cd06952 14 PSPMPSYLNVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQT 93 (222)
T ss_pred CCCCcccCCHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhh
Confidence 34445556688999999999999999999999999999999999999999999999999888766654333333222211
Q ss_pred H----hhhhcccchh------hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 176 R----QARECGFSEI------YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 176 ~----~~~~~~~~~~------~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
. .........+ +..+...+++|++|++||
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~----------------------------------------- 132 (222)
T cd06952 94 SIQQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEY----------------------------------------- 132 (222)
T ss_pred hHhcCCCchhhhHHHHHHHHHHHHHHHHHHHcCCCHHHH-----------------------------------------
Confidence 1 1111111111 234455666999999999
Q ss_pred cCCCCceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH--------------------------hhhhccccCCccc
Q psy11505 246 TGACGTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL--------------------------RFWSTVHKDGKVL 298 (312)
Q Consensus 246 ~~~~~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~--------------------------~~~~~~~~~~~~~ 298 (312)
+++|||+||+||++ +++.+.++++|++++.+|.+|+..+ +.+++.+++|.+|
T Consensus 133 -~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~ 211 (222)
T cd06952 133 -AYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQ 211 (222)
T ss_pred -HHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHhHHhhhcCHHHHHHHhcccccCCCc
Confidence 99999999999998 9999999999999999999999654 3366789999999
Q ss_pred hhHHHHHHHh
Q psy11505 299 MNKLFVEMLE 308 (312)
Q Consensus 299 ~~~~~~~~~~ 308 (312)
+++++..+|-
T Consensus 212 ~~~ll~~~~~ 221 (222)
T cd06952 212 IDSVIPYILR 221 (222)
T ss_pred HHHHHHHHHh
Confidence 9999999873
No 38
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.89 E-value=2.8e-23 Score=172.41 Aligned_cols=139 Identities=22% Similarity=0.341 Sum_probs=120.0
Q ss_pred HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhccc
Q psy11505 104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGF 183 (312)
Q Consensus 104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~ 183 (312)
.+..+++..+..+..+|+|||++|+|..|+.+||+.|+|++|+++++++.++++.+. .+.+.+++|...+.......+.
T Consensus 3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 81 (174)
T cd06929 3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPE-KNSLTFGDGKGNSRDVLLNGGF 81 (174)
T ss_pred HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhccc-CCeEEecCCceecHHHHHHccc
Confidence 578889999999999999999999999999999999999999999999999866554 4589999998766655444455
Q ss_pred chhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505 184 SEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK 260 (312)
Q Consensus 184 ~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 260 (312)
.++.+.+.. .+++|++|++|| ++++||+|||||+.
T Consensus 82 ~~~~~~~~~~~~~l~~L~l~~~E~------------------------------------------~llkai~l~~pd~~ 119 (174)
T cd06929 82 GEFIEPLFEFAEKMNKLQLDDNEY------------------------------------------ALLTAIVLFSPDRP 119 (174)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhCCCcc
Confidence 555555444 455999999999 99999999999997
Q ss_pred -ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 261 -LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 261 -l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
++++..|++.|+++..+|.+|+..+
T Consensus 120 ~l~~~~~v~~~q~~~~~aL~~y~~~~ 145 (174)
T cd06929 120 GLQDVDTVEKLQERLLEALQRYLKVN 145 (174)
T ss_pred cCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999765
No 39
>cd06930 NR_LBD_F2 Ligand-binding domain of nuclear receptor family 2. Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.89 E-value=3.4e-23 Score=170.37 Aligned_cols=138 Identities=28% Similarity=0.410 Sum_probs=118.8
Q ss_pred hhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCC-CeeEecccchhhHHhhhhcccc
Q psy11505 106 NSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCA-GKIRFASDLVLDERQARECGFS 184 (312)
Q Consensus 106 ~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~-~~l~~~~g~~~~~~~~~~~~~~ 184 (312)
+.++++..+.+..+|||||++|+|.+|+.+||+.|+|++|.+++++..||++++.+. +.+.+++|..++.......+..
T Consensus 2 ~~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (165)
T cd06930 2 ESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLA 81 (165)
T ss_pred hhHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHH
Confidence 467889999999999999999999999999999999999999999999999998853 5788888887776544332322
Q ss_pred h---hhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-
Q psy11505 185 E---IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK- 260 (312)
Q Consensus 185 ~---~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~- 260 (312)
+ .+..+...+.+|++|++|| ++++||++|+||++
T Consensus 82 ~~~~~~~~~~~~l~~L~l~~~E~------------------------------------------~lLkai~l~~p~~~~ 119 (165)
T cd06930 82 ELVQRLQELLSKLRSLQLDPKEY------------------------------------------ACLKAIVLFNPDLPG 119 (165)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcCCCCCC
Confidence 2 3345566667999999999 99999999999997
Q ss_pred ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 261 LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 261 l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
+++.+.+++.|++++.+|.+|+..+
T Consensus 120 l~~~~~v~~~q~~~~~aL~~~~~~~ 144 (165)
T cd06930 120 LKNQQQVEELQEKAQQALQEYIRKR 144 (165)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999754
No 40
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=99.88 E-value=5.1e-23 Score=176.65 Aligned_cols=137 Identities=18% Similarity=0.238 Sum_probs=109.4
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccc-hhhHHhhh
Q psy11505 101 TLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDL-VLDERQAR 179 (312)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~-~~~~~~~~ 179 (312)
....+..+++|....+..+|+|||++|+|.+|+.+||+.|||++|+++++++.|+.+... +++|. .+......
T Consensus 34 ~~~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~~------~~~~~~~~~~~~~~ 107 (221)
T cd06936 34 PEENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKK------LPAGHADLLEERIR 107 (221)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhccc------ccCCCchhhHHHHH
Confidence 357899999999999999999999999999999999999999999999999988554321 22222 11111112
Q ss_pred hcc-cchhhhhhccc---CccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeec
Q psy11505 180 ECG-FSEIYQQVKHS---GSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLA 255 (312)
Q Consensus 180 ~~~-~~~~~~~i~~~---~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 255 (312)
..+ ..++++.++.+ +.+|++|++|| ++++||++|
T Consensus 108 ~~~~~~e~~~~i~~~~~kl~~L~l~~~E~------------------------------------------~lLkaIvL~ 145 (221)
T cd06936 108 SSGISDEFITPMFNFYKSMGELKMTQEEY------------------------------------------ALLTAITIL 145 (221)
T ss_pred hccchHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHh
Confidence 222 23455555444 44999999999 999999999
Q ss_pred CCCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 256 NSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 256 ~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
|||++ |++++.|+.+|++|+.||.+||...
T Consensus 146 npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~ 176 (221)
T cd06936 146 FPDRPYLKDKEAVEKLQEPLLDLLQKFCKLY 176 (221)
T ss_pred cCCCcCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 99998 9999999999999999999999765
No 41
>cd06953 NR_LBD_DHR4_like The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4. The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.88 E-value=4.6e-23 Score=176.01 Aligned_cols=146 Identities=21% Similarity=0.215 Sum_probs=114.3
Q ss_pred CCCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeE----ecccch
Q psy11505 97 QSDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIR----FASDLV 172 (312)
Q Consensus 97 ~~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~----~~~g~~ 172 (312)
.+......+..+++...+.+..+|+|||++|+|.+|+.+||+.|+|++|+++++++.||++++.+...+. .+.|.-
T Consensus 21 ~~~~~~~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~ 100 (213)
T cd06953 21 ATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSE 100 (213)
T ss_pred CCcchhhHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCch
Confidence 3344567889999999999999999999999999999999999999999999999999999986532111 111110
Q ss_pred hhHHhhhhcccchhhh---hhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCC
Q psy11505 173 LDERQARECGFSEIYQ---QVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGAC 249 (312)
Q Consensus 173 ~~~~~~~~~~~~~~~~---~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 249 (312)
...... .....++.+ ++...+++|++|++|| +++
T Consensus 101 ~~~~~~-~~~~~~~~~~i~~l~~~l~~L~ld~eEy------------------------------------------~lL 137 (213)
T cd06953 101 DELERF-GDEGGEVVERLTYLLAKFRQLKVSNEEY------------------------------------------VCL 137 (213)
T ss_pred hhHHHH-HhhHHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHH
Confidence 000000 111223333 4445556999999999 999
Q ss_pred CceeecCCCCc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 250 GTLVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 250 ~~~~l~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
|||+|||||++ +++.++|+++|++|..+|.+|+..+
T Consensus 138 kAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~ 174 (213)
T cd06953 138 KVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELN 174 (213)
T ss_pred HHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999998 9999999999999999999999755
No 42
>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.85 E-value=1.5e-21 Score=164.15 Aligned_cols=137 Identities=14% Similarity=0.143 Sum_probs=112.8
Q ss_pred HHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh-hcc
Q psy11505 104 TINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR-ECG 182 (312)
Q Consensus 104 ~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~-~~~ 182 (312)
.|..+.+...+.+..+|+|+|++|+|..|+.+||+.|+|++|+++++++.++++.+. .+.+++|..+...... ..+
T Consensus 3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~---~~~~~~g~~~~~~~~~~~~~ 79 (191)
T cd06942 3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNE---GTVLCDFRPVEFASLLSQLL 79 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcC---CeEEeCCccccHHHHHHhcc
Confidence 578889999999999999999999999999999999999999999999877554444 3566667665544321 222
Q ss_pred cchhhhhhcc---cCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCC-
Q psy11505 183 FSEIYQQVKH---SGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSD- 258 (312)
Q Consensus 183 ~~~~~~~i~~---~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~- 258 (312)
..++++++.. .+.+|++|++|| ++++||++|+||
T Consensus 80 ~~~~~~~~~~~~~~l~~L~l~~~E~------------------------------------------~lL~Aivl~~pd~ 117 (191)
T cd06942 80 HGKLIDEMLQFANKILTLNLTNAEL------------------------------------------ALLCAAELLQPDS 117 (191)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHhCCCC
Confidence 3455554444 445999999999 999999999999
Q ss_pred -Cc-ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 259 -VK-LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 259 -~~-l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
++ ++++++|+.+|+.+..+|.+|+..+
T Consensus 118 ~~~~l~~~~~v~~~q~~l~~~L~~~~~~~ 146 (191)
T cd06942 118 LGIQLEETAKSNLQLSVLFQFLKSVLFKD 146 (191)
T ss_pred CCCCccchHHHHHHHHHHHHHHHHHHHhc
Confidence 87 9999999999999999999999754
No 43
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.76 E-value=1.2e-18 Score=143.04 Aligned_cols=137 Identities=28% Similarity=0.426 Sum_probs=113.5
Q ss_pred hHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccch---hhHHhhhh---
Q psy11505 107 SLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLV---LDERQARE--- 180 (312)
Q Consensus 107 ~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~---~~~~~~~~--- 180 (312)
.+.+++..++..+++|++++|+|+.|+.+||+.|+|++|+++++|+.+|+++..+......+++.. ........
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (168)
T cd06157 2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK 81 (168)
T ss_pred cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence 467899999999999999999999999999999999999999999999999999885555544432 11111111
Q ss_pred cccchhhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505 181 CGFSEIYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK 260 (312)
Q Consensus 181 ~~~~~~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 260 (312)
....+.+..+...+.+|++|++|| ++++||++|+|+.+
T Consensus 82 ~~~~~~~~~~~~~~~~L~l~~~E~------------------------------------------~~l~ai~l~~~~~~ 119 (168)
T cd06157 82 GELIRLLFEFVNPLRALKLDDEEY------------------------------------------ALLKAIVLFSPDRK 119 (168)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHH------------------------------------------HHHHHHHHhCCCCC
Confidence 112345566777777999999999 99999999999985
Q ss_pred --ccchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 261 --LDEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 261 --l~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
......+++.|+++..+|..|+...
T Consensus 120 ~s~~~~~~~~~~~~~~~~~L~~y~~~~ 146 (168)
T cd06157 120 ESLEDRKIVEELQERLLEALQDYLRKN 146 (168)
T ss_pred CCccCHHHHHHHHHHHHHHHHHHHHHh
Confidence 7888899999999999999999665
No 44
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=99.74 E-value=1.1e-18 Score=142.44 Aligned_cols=131 Identities=25% Similarity=0.348 Sum_probs=109.7
Q ss_pred HHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhh------hcccchh
Q psy11505 113 DRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQAR------ECGFSEI 186 (312)
Q Consensus 113 ~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~------~~~~~~~ 186 (312)
..++..+++|++++|+|.+|+.+||+.|+|++|.++++++.++++++.+.+.+.+++|......... .......
T Consensus 2 ~~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (163)
T smart00430 2 ERDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRI 81 (163)
T ss_pred hhHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999999999999999999988765666766655432211 1122345
Q ss_pred hhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc-ccch-
Q psy11505 187 YQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK-LDEF- 264 (312)
Q Consensus 187 ~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-l~~~- 264 (312)
++.+...+.+|++|++|| ++++|+++|+||.+ +++.
T Consensus 82 ~~~~~~~l~~L~l~~~E~------------------------------------------~~l~ai~l~~~~~~~l~~~~ 119 (163)
T smart00430 82 LQELVKPLRELKLDDEEY------------------------------------------ALLKAILLFNPAGPGLSEEG 119 (163)
T ss_pred HHHHHHHHHHcCCCHHHH------------------------------------------HHHHHHHHcChhhhhhChHH
Confidence 667777788999999999 99999999999987 8888
Q ss_pred -HHHHHHHHHHHHHhHhHHHHH
Q psy11505 265 -SSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 265 -~~~~~~~~~~~~~l~~~~~~~ 285 (312)
..++++|+.+..+|.+|+..+
T Consensus 120 ~~~~~~~~~~~~~~L~~y~~~~ 141 (163)
T smart00430 120 KEILEKLQEKLANALHDYYLKN 141 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc
Confidence 789999999999999999654
No 45
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 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 (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=99.73 E-value=1.1e-17 Score=141.74 Aligned_cols=143 Identities=29% Similarity=0.508 Sum_probs=119.4
Q ss_pred CCchhHHHhhHHHHHHHHHHHHHHHHhhCCccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHh
Q psy11505 98 SDPTLQTINSLSDLYDRELVCIIGWAKQIPGFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQ 177 (312)
Q Consensus 98 ~~~~~~~~~~~~~~~~~~l~~~iewak~lp~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~ 177 (312)
...+..++.++.+++...+..+++|++++|+|.+|+.+||+.|+|++|+++++|+.++++.....+.+.+++|...+...
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~ 91 (203)
T PF00104_consen 12 QELRPATFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDS 91 (203)
T ss_dssp SSSHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHH
T ss_pred CCCcHhhHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcccccccccccccccccccc
Confidence 44577889999999999999999999999999999999999999999999999999999995444689999998876554
Q ss_pred hhhc---ccch---hhhhhcccCccCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCc
Q psy11505 178 AREC---GFSE---IYQQVKHSGSLDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGT 251 (312)
Q Consensus 178 ~~~~---~~~~---~~~~i~~~~~~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (312)
.... ...+ .+..+...+.++++|++|| ++++|
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~------------------------------------------~~l~~ 129 (203)
T PF00104_consen 92 FDDFITGIFSEFIQYMNEVLRPFRRLKLDEEEF------------------------------------------ALLKA 129 (203)
T ss_dssp HHHTSTTTHHHHHHHHHHHHHHHHHTT-BHHHH------------------------------------------HHHHH
T ss_pred cccccccccccchhHHHHHHHHHHHhhhhhHHH------------------------------------------HHHHH
Confidence 4333 1222 3345555677999999999 99999
Q ss_pred eeecCCCCc-cc-chHH-HHHHHHHHHHHhHhHH
Q psy11505 252 LVLANSDVK-LD-EFSS-LKKFRNSILSSLGDCI 282 (312)
Q Consensus 252 ~~l~~~~~~-l~-~~~~-~~~~~~~~~~~l~~~~ 282 (312)
+++++||.. ++ +... +++.|+++..+|.+|+
T Consensus 130 l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~ 163 (203)
T PF00104_consen 130 LILFNPDYPGLSEETREIVEELRDRIIQALHSYY 163 (203)
T ss_dssp HHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhhcccccccccchhHHHHHHHHHHHHHHHHHH
Confidence 999999987 66 5555 9999999999999999
No 46
>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=99.55 E-value=1.6e-15 Score=109.51 Aligned_cols=51 Identities=45% Similarity=0.931 Sum_probs=46.6
Q ss_pred CceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccccc
Q psy11505 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQK 51 (312)
Q Consensus 1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~ 51 (312)
+..|.|..+++|.|+...|+.||+|||+||++|||++++||.+|++.++++
T Consensus 33 ~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~~ 83 (85)
T cd06961 33 KLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKRK 83 (85)
T ss_pred CCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCcccccc
Confidence 357999999999999999999999999999999999999999999876654
No 47
>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=99.54 E-value=2.9e-15 Score=110.37 Aligned_cols=52 Identities=83% Similarity=1.525 Sum_probs=47.1
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKYR 53 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~~ 53 (312)
..|.|.++++|.|++..|+.||+|||+|||+|||++++||.+|+..++++..
T Consensus 39 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~~~~~~~ 90 (97)
T cd07170 39 IEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYK 90 (97)
T ss_pred CceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCCCCCCcc
Confidence 5699999999999999999999999999999999999999999887765543
No 48
>KOG4846|consensus
Probab=99.52 E-value=3.9e-15 Score=132.08 Aligned_cols=48 Identities=40% Similarity=0.890 Sum_probs=43.2
Q ss_pred Ccee-EcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505 1 NIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 48 (312)
Q Consensus 1 ~~~Y-~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~ 48 (312)
|..| .|.+..+|.|.+..||+||+|||+|||+|||+++||+..+++..
T Consensus 166 kI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~r 214 (538)
T KOG4846|consen 166 KIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKFR 214 (538)
T ss_pred hhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhcccccc
Confidence 4578 69999999999999999999999999999999999998876543
No 49
>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=99.51 E-value=4.5e-15 Score=108.15 Aligned_cols=49 Identities=37% Similarity=0.888 Sum_probs=45.9
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ 50 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~ 50 (312)
..|.|..+++|.|+...|..||+|||+|||+|||++++||.+|++++++
T Consensus 41 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~ 89 (90)
T cd07169 41 RVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGRN 89 (90)
T ss_pred CceecCCCCcccccccccccccccchhhhccccCCHHHhccccCCCCCC
Confidence 5799999999999999999999999999999999999999999988765
No 50
>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=99.50 E-value=5.8e-15 Score=107.92 Aligned_cols=52 Identities=54% Similarity=1.059 Sum_probs=47.2
Q ss_pred CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccccc
Q psy11505 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQKY 52 (312)
Q Consensus 1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~~~ 52 (312)
+..|+|..+++|.|+...|+.|++|||+|||+|||++++||.+|.++++.+.
T Consensus 32 ~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~~~~ 83 (93)
T cd07167 32 KKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKF 83 (93)
T ss_pred CCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCcccc
Confidence 3579999999999999999999999999999999999999999987776553
No 51
>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=99.50 E-value=6.6e-15 Score=107.35 Aligned_cols=50 Identities=52% Similarity=1.028 Sum_probs=45.9
Q ss_pred CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ 50 (312)
Q Consensus 1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~ 50 (312)
+..|.|..+++|.|+...|..||+|||+|||+|||++++||.+|+++++.
T Consensus 40 ~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~~~ 89 (90)
T cd07168 40 KRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGGRN 89 (90)
T ss_pred CCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCCCCC
Confidence 35789999999999999999999999999999999999999999887653
No 52
>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=99.49 E-value=9.1e-15 Score=105.93 Aligned_cols=46 Identities=46% Similarity=0.884 Sum_probs=43.2
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~ 47 (312)
..|+|.++++|.|++..|..||+|||+|||+|||++++||.+|++.
T Consensus 38 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~ 83 (87)
T cd06967 38 LGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPI 83 (87)
T ss_pred CCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCC
Confidence 5789999999999999999999999999999999999999999764
No 53
>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=99.49 E-value=9.8e-15 Score=103.86 Aligned_cols=45 Identities=38% Similarity=0.910 Sum_probs=42.5
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~ 46 (312)
..|+|..+++|.|++..|..||+|||+|||+|||++++||.+|++
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 77 (78)
T cd07164 33 LAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP 77 (78)
T ss_pred CCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence 578999999999999999999999999999999999999999874
No 54
>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=99.48 E-value=1.1e-14 Score=105.03 Aligned_cols=45 Identities=51% Similarity=0.933 Sum_probs=42.4
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~ 46 (312)
..|.|..+++|.|++..|..||+|||+|||+|||++++||.+|++
T Consensus 39 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~ 83 (85)
T cd06964 39 MVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK 83 (85)
T ss_pred CCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence 569999999999999999999999999999999999999999865
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=99.48 E-value=9.6e-15 Score=103.54 Aligned_cols=44 Identities=50% Similarity=1.051 Sum_probs=41.1
Q ss_pred CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44 (312)
Q Consensus 1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r 44 (312)
+..|+|..+++|.|++..|+.||+|||+|||+|||++++||.+|
T Consensus 34 ~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 34 DLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred CCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 35799999999999999999999999999999999999999875
No 56
>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=99.47 E-value=1.4e-14 Score=102.29 Aligned_cols=43 Identities=67% Similarity=1.421 Sum_probs=40.7
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r 44 (312)
..|.|..+++|.|++..|..||+|||+|||+|||++++||.+|
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 33 LGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred CceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 5799999999999999999999999999999999999999875
No 57
>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=99.46 E-value=1.7e-14 Score=103.32 Aligned_cols=46 Identities=48% Similarity=0.957 Sum_probs=43.1
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~ 47 (312)
..|.|..+++|.|++..|..|++|||+|||+|||++++||.+|++.
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~ 78 (81)
T cd07165 33 IEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPN 78 (81)
T ss_pred CceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCc
Confidence 5799999999999999999999999999999999999999998763
No 58
>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=99.46 E-value=1.9e-14 Score=102.00 Aligned_cols=44 Identities=43% Similarity=0.887 Sum_probs=41.4
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~ 45 (312)
..|.|..+++|.|+...|..|++|||+|||+|||++++||.+|+
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 33 RTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred CceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 57899999999999999999999999999999999999999874
No 59
>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=99.46 E-value=1.9e-14 Score=103.18 Aligned_cols=46 Identities=39% Similarity=0.785 Sum_probs=42.1
Q ss_pred ceeEcC-CCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505 2 IEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47 (312)
Q Consensus 2 ~~Y~C~-~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~ 47 (312)
..|.|. .+++|.|+...|+.||+|||+||++|||++++||.+|++.
T Consensus 33 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~ 79 (82)
T cd06957 33 IIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPR 79 (82)
T ss_pred CceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcC
Confidence 579999 5789999999999999999999999999999999988654
No 60
>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=99.45 E-value=2.7e-14 Score=102.18 Aligned_cols=43 Identities=56% Similarity=1.200 Sum_probs=40.7
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r 44 (312)
..|+|.++++|.|+...|+.||+|||+|||+|||++++|+.+|
T Consensus 38 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~ 80 (82)
T cd07171 38 NDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER 80 (82)
T ss_pred CceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhh
Confidence 5799999999999999999999999999999999999999875
No 61
>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=99.44 E-value=3e-14 Score=105.73 Aligned_cols=45 Identities=29% Similarity=0.703 Sum_probs=42.2
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~ 46 (312)
..|.|..+++|.|+...|..||+|||+|||+|||++++||.+|+.
T Consensus 53 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~ 97 (101)
T cd07160 53 AQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI 97 (101)
T ss_pred CccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence 579999999999999999999999999999999999999998864
No 62
>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=99.44 E-value=3.8e-14 Score=103.82 Aligned_cols=46 Identities=35% Similarity=0.833 Sum_probs=41.9
Q ss_pred ceeEcCC--CCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505 2 IEYTCPA--SNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47 (312)
Q Consensus 2 ~~Y~C~~--~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~ 47 (312)
..|.|.. +++|.|++..|..||+|||+||++|||++++||.+|++.
T Consensus 41 ~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~ 88 (92)
T cd07163 41 RQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPR 88 (92)
T ss_pred CCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcC
Confidence 5789987 479999999999999999999999999999999988753
No 63
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=99.43 E-value=3.7e-14 Score=101.96 Aligned_cols=46 Identities=35% Similarity=0.732 Sum_probs=42.1
Q ss_pred CceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505 1 NIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46 (312)
Q Consensus 1 ~~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~ 46 (312)
+..|.|.++++|.|+...|+.||+|||+|||+|||++++|+.++..
T Consensus 35 ~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~ 80 (84)
T cd06962 35 NAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQC 80 (84)
T ss_pred CCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHH
Confidence 3579999999999999999999999999999999999999987653
No 64
>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=99.43 E-value=2.9e-14 Score=103.73 Aligned_cols=47 Identities=40% Similarity=0.910 Sum_probs=42.9
Q ss_pred cee-EcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505 2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 48 (312)
Q Consensus 2 ~~Y-~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~ 48 (312)
..| .|..+++|.|++..|..|++|||+|||+|||++++||.+|++..
T Consensus 38 ~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~ 85 (89)
T cd07166 38 IQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKR 85 (89)
T ss_pred CcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCCCCc
Confidence 568 59999999999999999999999999999999999999987643
No 65
>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=99.43 E-value=4.5e-14 Score=103.13 Aligned_cols=47 Identities=40% Similarity=0.858 Sum_probs=42.7
Q ss_pred CceeEcCCC-CCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505 1 NIEYTCPAS-NDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47 (312)
Q Consensus 1 ~~~Y~C~~~-~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~ 47 (312)
+..|+|..+ ++|.|+...|..||+|||+|||+|||++++||.+|++.
T Consensus 40 ~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~ 87 (92)
T cd06970 40 KLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR 87 (92)
T ss_pred CCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCcc
Confidence 357999985 89999999999999999999999999999999998754
No 66
>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=99.42 E-value=4.6e-14 Score=103.83 Aligned_cols=47 Identities=38% Similarity=0.950 Sum_probs=43.3
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 48 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~ 48 (312)
..|.|..+++|.|+...|+.||+|||+||++|||++++||.+|.+.+
T Consensus 40 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~~ 86 (95)
T cd06968 40 VSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK 86 (95)
T ss_pred CceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCChh
Confidence 57999999999999999999999999999999999999999886544
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=99.42 E-value=4.4e-14 Score=103.08 Aligned_cols=46 Identities=35% Similarity=0.686 Sum_probs=42.5
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 47 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~ 47 (312)
..|.|..+++|.|+...|+.||+|||+|||+|||++++||.+++..
T Consensus 36 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~ 81 (91)
T cd07161 36 AVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCA 81 (91)
T ss_pred CceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhh
Confidence 5799999999999999999999999999999999999999987543
No 68
>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=99.41 E-value=2.3e-14 Score=105.31 Aligned_cols=49 Identities=37% Similarity=0.778 Sum_probs=45.0
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGRQ 50 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~~~ 50 (312)
..|.|..+++|.|+...|..|++|||+|||+|||++++||.+|+..++.
T Consensus 35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~~r 83 (94)
T cd06966 35 KEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSEKR 83 (94)
T ss_pred CccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhHHH
Confidence 4799999999999999999999999999999999999999998776554
No 69
>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=99.41 E-value=7.4e-14 Score=98.47 Aligned_cols=41 Identities=56% Similarity=1.112 Sum_probs=38.4
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~ 42 (312)
..|+|..+++|.|++..|+.||+|||+|||+|||++++||.
T Consensus 35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~ 75 (75)
T cd06969 35 AKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75 (75)
T ss_pred CcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence 57899999999999999999999999999999999999873
No 70
>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=99.39 E-value=1.2e-13 Score=96.88 Aligned_cols=40 Identities=43% Similarity=1.036 Sum_probs=38.0
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq 41 (312)
..|+|..+++|.|++..|+.||+|||+|||+|||++++||
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (73)
T cd06958 33 LTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred CceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 5689999999999999999999999999999999999987
No 71
>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=99.38 E-value=1.4e-13 Score=96.43 Aligned_cols=40 Identities=63% Similarity=1.222 Sum_probs=37.7
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq 41 (312)
..|.|..+++|.|+...|..||+|||+|||+|||++++||
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 33 LEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred CCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 5789999999999999999999999999999999999886
No 72
>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=99.38 E-value=1.5e-13 Score=96.63 Aligned_cols=41 Identities=44% Similarity=1.058 Sum_probs=38.6
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRL 42 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~ 42 (312)
..|+|..+++|.|++..|+.||+|||+|||+|||++++|+.
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 73 (74)
T cd07179 33 NSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73 (74)
T ss_pred CcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence 57999999999999999999999999999999999999975
No 73
>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=99.38 E-value=2.1e-13 Score=98.62 Aligned_cols=45 Identities=42% Similarity=0.852 Sum_probs=41.5
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 46 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~ 46 (312)
..|.|..+++|.++...|+.||+|||+|||+|||++++++.+|+.
T Consensus 37 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~ 81 (86)
T cd07157 37 TISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS 81 (86)
T ss_pred ccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence 378999999999999999999999999999999999999988753
No 74
>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=99.37 E-value=1.7e-13 Score=95.91 Aligned_cols=39 Identities=54% Similarity=1.086 Sum_probs=37.0
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGV 40 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaV 40 (312)
..|+|..+++|.|++..|+.||+|||+|||+|||++++|
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (72)
T cd07156 33 ARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71 (72)
T ss_pred CccccCCCCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence 579999999999999999999999999999999999987
No 75
>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=99.37 E-value=1e-13 Score=100.55 Aligned_cols=44 Identities=43% Similarity=0.833 Sum_probs=40.9
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 45 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~ 45 (312)
..|.|..+++|.|+...|+.|++|||+|||++||++++|+.++.
T Consensus 34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~ 77 (87)
T cd07162 34 ARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA 77 (87)
T ss_pred ceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence 57999999999999999999999999999999999999998753
No 76
>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=99.37 E-value=1.8e-13 Score=96.15 Aligned_cols=41 Identities=46% Similarity=0.987 Sum_probs=37.7
Q ss_pred CceeEcC-CCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505 1 NIEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41 (312)
Q Consensus 1 ~~~Y~C~-~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq 41 (312)
+..|.|. ++++|.|++..|..||+|||+|||+|||++++||
T Consensus 32 ~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 32 NLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred CCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 3578999 7789999999999999999999999999999886
No 77
>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=99.37 E-value=1.3e-13 Score=103.38 Aligned_cols=42 Identities=45% Similarity=0.971 Sum_probs=39.0
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 43 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~ 43 (312)
..|.|..+++|.|+...|+.||+|||+|||+|||++++|+.+
T Consensus 41 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 82 (107)
T cd06955 41 ALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82 (107)
T ss_pred CccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence 578999999999999999999999999999999999888776
No 78
>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=99.37 E-value=2.1e-13 Score=95.68 Aligned_cols=40 Identities=35% Similarity=0.790 Sum_probs=37.4
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq 41 (312)
..|.|..+++|.|++..|..||+|||+|||+|||+++.|+
T Consensus 34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (73)
T cd06959 34 AVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73 (73)
T ss_pred CCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence 5799999999999999999999999999999999999873
No 79
>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=99.36 E-value=2.7e-13 Score=95.04 Aligned_cols=40 Identities=45% Similarity=0.924 Sum_probs=37.4
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq 41 (312)
..|.|..+++|.|++..|+.||+|||+|||++||+++++.
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 33 HNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred CceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 5799999999999999999999999999999999999864
No 80
>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=99.35 E-value=2.6e-13 Score=95.41 Aligned_cols=40 Identities=43% Similarity=0.998 Sum_probs=37.4
Q ss_pred cee-EcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505 2 IEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41 (312)
Q Consensus 2 ~~Y-~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq 41 (312)
..| .|..+++|.|++..|..||+|||+|||+|||++++|+
T Consensus 33 ~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 73 (73)
T cd07158 33 LTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred CCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence 468 7999999999999999999999999999999999885
No 81
>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=99.32 E-value=3.9e-13 Score=96.80 Aligned_cols=45 Identities=44% Similarity=0.935 Sum_probs=39.7
Q ss_pred ceeE-cCCCCCcccccccccccccCchhHHHHhccccccccccccccc
Q psy11505 2 IEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 48 (312)
Q Consensus 2 ~~Y~-C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r~~~~ 48 (312)
..|. |.++ |.|++..|+.||+|||+||++|||++++||.+|++..
T Consensus 34 ~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~ 79 (84)
T cd06965 34 LVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRV 79 (84)
T ss_pred CCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCch
Confidence 4674 9853 9999999999999999999999999999999987643
No 82
>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=99.32 E-value=7.6e-13 Score=93.84 Aligned_cols=40 Identities=48% Similarity=0.943 Sum_probs=37.4
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 41 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq 41 (312)
..|+|.++++|.|+...|+.||+|||+|||+|||++.++.
T Consensus 37 ~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 37 HNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred CceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence 5799999999999999999999999999999999998875
No 83
>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=99.29 E-value=1.3e-12 Score=93.43 Aligned_cols=43 Identities=42% Similarity=0.936 Sum_probs=38.4
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccccccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 44 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~eaVq~~r 44 (312)
..|.|..+++|.|++..|+.||+|||+|||+|||+++....++
T Consensus 38 ~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~~ 80 (82)
T cd07173 38 QKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKK 80 (82)
T ss_pred CceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhhc
Confidence 5789999999999999999999999999999999988765443
No 84
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.22 E-value=5.1e-12 Score=88.13 Aligned_cols=37 Identities=51% Similarity=1.011 Sum_probs=34.5
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhccccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 38 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~e 38 (312)
..|.|..+++|.|++..|+.||+|||+|||+|||+++
T Consensus 34 ~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 34 YKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 4689999999999999999999999999999999974
No 85
>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=99.12 E-value=1.5e-11 Score=85.97 Aligned_cols=36 Identities=47% Similarity=1.089 Sum_probs=29.6
Q ss_pred ceeEcCCCCCcccccccccccccCchhHHHHhcccc
Q psy11505 2 IEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 37 (312)
Q Consensus 2 ~~Y~C~~~~~C~i~~~~R~~Cr~CRf~KCl~vGM~~ 37 (312)
..|.|..+++|.+++..|..|++|||+|||+|||++
T Consensus 35 ~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 35 KPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp CG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred ccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence 458999999999999999999999999999999974
No 86
>KOG4846|consensus
Probab=98.90 E-value=4.3e-10 Score=100.39 Aligned_cols=36 Identities=67% Similarity=1.336 Sum_probs=33.5
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (312)
.|.||||.++||||||..|||||+||||+||--.+|
T Consensus 134 lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~Y 169 (538)
T KOG4846|consen 134 LCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDY 169 (538)
T ss_pred eehhhccccccceeceeecccchHHHHHHHHHhhhH
Confidence 799999999999999999999999999999766666
No 87
>KOG4215|consensus
Probab=98.65 E-value=1e-08 Score=90.52 Aligned_cols=42 Identities=40% Similarity=0.965 Sum_probs=38.1
Q ss_pred CCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceec
Q psy11505 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQT 246 (312)
Q Consensus 205 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 246 (312)
....|.||||++.|.|||+.+|.|||+||||+|.+...|+|+
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCR 59 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCR 59 (432)
T ss_pred ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeee
Confidence 455699999999999999999999999999999998888654
No 88
>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=98.64 E-value=1.6e-08 Score=73.86 Aligned_cols=40 Identities=50% Similarity=1.100 Sum_probs=35.4
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceec
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQT 246 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 246 (312)
+.|.||++.++|+|||+.+|++|++||+|++.....|++.
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~ 41 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCK 41 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecC
Confidence 5699999999999999999999999999999866666543
No 89
>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=98.63 E-value=1.6e-08 Score=71.70 Aligned_cols=38 Identities=58% Similarity=1.130 Sum_probs=34.2
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
+.|.||++.++|+|||+.+|++|++||+|++.....|.
T Consensus 1 ~~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~ 38 (77)
T cd06956 1 HICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYT 38 (77)
T ss_pred CCCcccCCcCcceEECceeehhHHHHHHHHhhCCCccc
Confidence 36999999999999999999999999999998666664
No 90
>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=98.63 E-value=1.8e-08 Score=74.39 Aligned_cols=40 Identities=78% Similarity=1.369 Sum_probs=35.1
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
...|.||++.++|+||||.+|++|++||+|+++....|.+
T Consensus 4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C 43 (97)
T cd07170 4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSC 43 (97)
T ss_pred CCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceee
Confidence 3569999999999999999999999999999977665543
No 91
>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=98.60 E-value=1.9e-08 Score=70.57 Aligned_cols=36 Identities=61% Similarity=1.244 Sum_probs=32.6
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (312)
+|.||++.++++|||+.+|++|++||+|++.....|
T Consensus 1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~ 36 (73)
T cd06959 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVY 36 (73)
T ss_pred CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCc
Confidence 589999999999999999999999999999755555
No 92
>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=98.60 E-value=2e-08 Score=71.22 Aligned_cols=38 Identities=53% Similarity=1.124 Sum_probs=34.6
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
..|.||++.++++||||.+|++|++||+|++.....|.
T Consensus 3 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~ 40 (78)
T cd07172 3 KICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYL 40 (78)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCcee
Confidence 57999999999999999999999999999998776664
No 93
>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=98.59 E-value=2.7e-08 Score=71.20 Aligned_cols=38 Identities=50% Similarity=1.064 Sum_probs=34.2
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
..|.||++.++++||||.+|++|++||+|+|.....|.
T Consensus 4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~ 41 (82)
T cd07173 4 KTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYL 41 (82)
T ss_pred CCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCcee
Confidence 46999999999999999999999999999997666554
No 94
>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=98.58 E-value=2.4e-08 Score=71.48 Aligned_cols=39 Identities=62% Similarity=1.125 Sum_probs=34.8
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
..|.||++.++++|||+.+|++|++||+|++.....|++
T Consensus 4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C 42 (82)
T cd07171 4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYIC 42 (82)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeC
Confidence 579999999999999999999999999999977666643
No 95
>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=98.56 E-value=2.5e-08 Score=69.84 Aligned_cols=36 Identities=56% Similarity=1.154 Sum_probs=32.7
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
|.||++.++++|||+.+|++|++||+|++.....|.
T Consensus 1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~ 36 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYL 36 (73)
T ss_pred CcccCccCcceEECceeehhhhHhHHHhhcCCCcee
Confidence 789999999999999999999999999997666564
No 96
>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=98.56 E-value=3e-08 Score=69.96 Aligned_cols=37 Identities=81% Similarity=1.441 Sum_probs=33.0
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
|.||++.++++|||+.+|++|++||+|++.....+++
T Consensus 1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C 37 (75)
T cd07155 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSC 37 (75)
T ss_pred CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeC
Confidence 7899999999999999999999999999976655643
No 97
>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=98.55 E-value=3.3e-08 Score=69.47 Aligned_cols=36 Identities=50% Similarity=1.099 Sum_probs=32.9
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
|.||++.++++|||+.+|++|++||+|++.....++
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~ 36 (74)
T cd07179 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYV 36 (74)
T ss_pred CcccCccCcceEECceeehhHHHHHHHHhhCCCccc
Confidence 789999999999999999999999999997766664
No 98
>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=98.53 E-value=4.1e-08 Score=71.67 Aligned_cols=39 Identities=51% Similarity=1.106 Sum_probs=35.0
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
...|.||++.++++|||+.+|++|++||+|++.....|.
T Consensus 6 ~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~ 44 (90)
T cd07168 6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYT 44 (90)
T ss_pred CCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCcc
Confidence 567999999999999999999999999999997666553
No 99
>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=98.53 E-value=2.4e-08 Score=69.85 Aligned_cols=36 Identities=42% Similarity=1.090 Sum_probs=32.7
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
|.||++.++++|||+.+|++|++||+|++.....++
T Consensus 1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~ 36 (72)
T cd07156 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFT 36 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCcCccc
Confidence 789999999999999999999999999997666554
No 100
>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=98.53 E-value=2.7e-08 Score=73.90 Aligned_cols=40 Identities=53% Similarity=1.048 Sum_probs=35.2
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
...|.||++.++|+|||+.+|++|++||+|++.....|.+
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C 57 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVC 57 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhhhhcccccCcccc
Confidence 3569999999999999999999999999999976666643
No 101
>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=98.53 E-value=3.9e-08 Score=71.38 Aligned_cols=38 Identities=39% Similarity=0.992 Sum_probs=33.7
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
.|.||++.++++|||+.+|++|++||+|++.....|.+
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C 38 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCC 38 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEc
Confidence 48999999999999999999999999999976655543
No 102
>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=98.52 E-value=5.3e-08 Score=70.99 Aligned_cols=39 Identities=59% Similarity=1.214 Sum_probs=34.7
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
...|.||++.++++|||+.+|++|++||+|++.....|+
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~ 44 (90)
T cd07169 6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYR 44 (90)
T ss_pred CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCcee
Confidence 357999999999999999999999999999997666554
No 103
>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=98.52 E-value=4.2e-08 Score=70.86 Aligned_cols=38 Identities=50% Similarity=1.093 Sum_probs=33.7
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
.|.||++.++++|||+.+|++|++||+|++.....|++
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C 38 (85)
T cd06961 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSC 38 (85)
T ss_pred CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCcccc
Confidence 38999999999999999999999999999976666643
No 104
>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=98.50 E-value=4.3e-08 Score=71.81 Aligned_cols=37 Identities=57% Similarity=1.186 Sum_probs=33.6
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
|.||++.++++||||.+|++|++||+|+|.....|++
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C 37 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTC 37 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCCcccc
Confidence 7899999999999999999999999999977766643
No 105
>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=98.50 E-value=4.2e-08 Score=68.79 Aligned_cols=36 Identities=53% Similarity=1.137 Sum_probs=32.5
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
|.||++.++++|||+.+|++|++||+|++.....|.
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~ 36 (73)
T cd06958 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYT 36 (73)
T ss_pred CCccCccCcceEEChhhhhhhhhhhhhhhcCCCcee
Confidence 789999999999999999999999999997665553
No 106
>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=98.49 E-value=5.3e-08 Score=68.38 Aligned_cols=35 Identities=71% Similarity=1.330 Sum_probs=32.0
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (312)
|.||++.++++|||+.+|++|++||+|++.....|
T Consensus 1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~ 35 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTY 35 (73)
T ss_pred CcccCccCcceEECcchhhHHHHHHhhhhcCCCCc
Confidence 78999999999999999999999999999766555
No 107
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=98.48 E-value=4.6e-08 Score=68.12 Aligned_cols=37 Identities=68% Similarity=1.338 Sum_probs=33.3
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
.|.||++.++++|||+.+|++|++||+|+|+....+.
T Consensus 1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~ 37 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYR 37 (70)
T ss_pred CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCee
Confidence 4899999999999999999999999999997666553
No 108
>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=98.46 E-value=2e-08 Score=72.27 Aligned_cols=38 Identities=53% Similarity=1.191 Sum_probs=34.1
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
..|.||++.++|+|||+.+|++|++||+|++.....|.
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~ 39 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYK 39 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCcee
Confidence 46999999999999999999999999999997665554
No 109
>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=98.45 E-value=3e-08 Score=74.45 Aligned_cols=40 Identities=43% Similarity=1.004 Sum_probs=35.4
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
...|.||++.++|+|||+.+|++|++||+|+|.....|++
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C 45 (107)
T cd06955 6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTC 45 (107)
T ss_pred CCCCeecCCcCcccEECcceeeeecceecceeccCCcccc
Confidence 4579999999999999999999999999999976666643
No 110
>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=98.44 E-value=2e-08 Score=72.42 Aligned_cols=39 Identities=51% Similarity=1.111 Sum_probs=34.4
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
...|.|||+.++++|||+.+|++|++||+|++.....|.
T Consensus 4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~ 42 (85)
T cd06964 4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYT 42 (85)
T ss_pred CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeE
Confidence 357999999999999999999999999999997655553
No 111
>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=98.44 E-value=2e-08 Score=70.82 Aligned_cols=38 Identities=58% Similarity=1.092 Sum_probs=33.8
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
+.|.||++.++++|||+.+|++|++||+|++.....|.
T Consensus 1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~ 38 (75)
T cd06969 1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYV 38 (75)
T ss_pred CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCccc
Confidence 36999999999999999999999999999997665553
No 112
>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=98.43 E-value=4.1e-08 Score=72.18 Aligned_cols=38 Identities=39% Similarity=0.949 Sum_probs=34.0
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
.|.||++.++|+|||+.+|++|++||+|++.....|++
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C 39 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKC 39 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehhcccCCCcccc
Confidence 59999999999999999999999999999976666643
No 113
>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=98.43 E-value=9.4e-08 Score=70.38 Aligned_cols=40 Identities=48% Similarity=0.981 Sum_probs=35.0
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
...|.|||+.++|+|||+.+|++|++||+|++.....+.+
T Consensus 5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C 44 (95)
T cd06968 5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSC 44 (95)
T ss_pred ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceec
Confidence 3579999999999999999999999999999976655543
No 114
>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=98.42 E-value=8e-08 Score=68.32 Aligned_cols=36 Identities=58% Similarity=1.173 Sum_probs=32.5
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
|.||++.++++|||+.+|++|++||+|++.....+.
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~ 36 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYV 36 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCcc
Confidence 789999999999999999999999999997655553
No 115
>KOG4217|consensus
Probab=98.41 E-value=1e-07 Score=86.77 Aligned_cols=64 Identities=44% Similarity=0.825 Sum_probs=49.2
Q ss_pred cCCCCccccCCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCccc----chHHHHHHH
Q psy11505 196 LDGIKEEELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVKLD----EFSSLKKFR 271 (312)
Q Consensus 196 ~L~ld~~E~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~----~~~~~~~~~ 271 (312)
+-.++.+ ..|.||||.+.=-||||-.|||||+||+|++||..+| +.|-|-+++++ +.-+--++|
T Consensus 263 rs~~~~e----~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKY--------vClanKnCPVDKRrRnRCQyCRfQ 330 (605)
T KOG4217|consen 263 RSSLSAE----GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKY--------VCLANKNCPVDKRRRNRCQYCRFQ 330 (605)
T ss_pred ccCCCcc----ceeeecCChHHhhhcCccccccchHHHHHHHhcCCee--------EeecCCCCCcchhhhhhchhhhHh
Confidence 4445554 4699999999999999999999999999999999999 44556666543 333444444
No 116
>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=98.41 E-value=2.9e-08 Score=72.58 Aligned_cols=39 Identities=49% Similarity=1.014 Sum_probs=34.5
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
..|.||++.++|+|||+.+|++|++||+|+|+....|.+
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C 45 (92)
T cd06970 7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRC 45 (92)
T ss_pred CCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCcee
Confidence 469999999999999999999999999999976655543
No 117
>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=98.40 E-value=2.4e-08 Score=73.23 Aligned_cols=40 Identities=45% Similarity=0.934 Sum_probs=35.4
Q ss_pred CCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 205 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
+...|.||++.++|+|||+.+|++|++||+|++.....|.
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~ 44 (92)
T cd07163 5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYV 44 (92)
T ss_pred cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcC
Confidence 3568999999999999999999999999999997666554
No 118
>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=98.40 E-value=2.6e-08 Score=69.87 Aligned_cols=37 Identities=51% Similarity=1.025 Sum_probs=33.0
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhccccee
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQ 245 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (312)
|.||++.++++|||+.+|++|++||+|+++....|.+
T Consensus 1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C 37 (73)
T cd07154 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTC 37 (73)
T ss_pred CcccCccCcceEECcceeeeeeeEeeeeecCCCCccc
Confidence 7899999999999999999999999999976655543
No 119
>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=98.39 E-value=5.7e-08 Score=69.97 Aligned_cols=36 Identities=64% Similarity=1.254 Sum_probs=32.7
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (312)
.|.||++.++|+|||+.+|++|++||+|++.....|
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~ 36 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVY 36 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCc
Confidence 389999999999999999999999999999766555
No 120
>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=98.39 E-value=1.6e-07 Score=67.30 Aligned_cols=36 Identities=67% Similarity=1.328 Sum_probs=32.5
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
|.||++.++++|||+.+|++|++||+|++.....+.
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~ 36 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYR 36 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCcee
Confidence 789999999999999999999999999997665553
No 121
>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=98.38 E-value=2.2e-08 Score=71.87 Aligned_cols=38 Identities=45% Similarity=0.925 Sum_probs=33.9
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccceec
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQT 246 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 246 (312)
|.||++.++|+|||+.+|++|++||+|+|+....|.+.
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~ 38 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCI 38 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEcc
Confidence 78999999999999999999999999999876666443
No 122
>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=98.36 E-value=5.9e-08 Score=68.68 Aligned_cols=36 Identities=53% Similarity=1.159 Sum_probs=32.5
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
|.||++.++++|||+.+|++|++||+|++.....++
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~ 36 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYT 36 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCcee
Confidence 789999999999999999999999999997665554
No 123
>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=98.35 E-value=7e-08 Score=70.26 Aligned_cols=38 Identities=63% Similarity=1.209 Sum_probs=33.9
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (312)
...|.||++.++|+|||+.+|++|++||+|++.....|
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~ 40 (89)
T cd07166 3 VVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQY 40 (89)
T ss_pred CCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcc
Confidence 35799999999999999999999999999999755555
No 124
>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=98.33 E-value=5.9e-08 Score=70.35 Aligned_cols=39 Identities=62% Similarity=1.192 Sum_probs=34.5
Q ss_pred CceeeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 206 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 206 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
...|.||++.++++|||+.+|++|++||+|+|.....+.
T Consensus 3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~ 41 (87)
T cd06967 3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYS 41 (87)
T ss_pred CCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcc
Confidence 357999999999999999999999999999997665553
No 125
>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=98.32 E-value=5.5e-08 Score=70.33 Aligned_cols=33 Identities=52% Similarity=1.052 Sum_probs=30.9
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhc
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVY 240 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (312)
.|.||++.++++|||+.+|++|++||+|++...
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~ 34 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAI 34 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecC
Confidence 599999999999999999999999999999754
No 126
>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=98.31 E-value=2e-07 Score=64.98 Aligned_cols=36 Identities=58% Similarity=1.217 Sum_probs=32.8
Q ss_pred eeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505 208 LCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243 (312)
Q Consensus 208 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (312)
.|.||++.++++|||+.+|++|+.||+|++.....+
T Consensus 2 ~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~ 37 (70)
T PF00105_consen 2 KCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPY 37 (70)
T ss_dssp BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-
T ss_pred CCeECCCccCcccccccccccceeeeeecccccccc
Confidence 599999999999999999999999999999876665
No 127
>KOG4216|consensus
Probab=98.31 E-value=2.1e-07 Score=82.95 Aligned_cols=37 Identities=51% Similarity=1.131 Sum_probs=33.7
Q ss_pred ceeeeeCCCCcccccccccchhHHHHHHHHhhhcccc
Q psy11505 207 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGY 243 (312)
Q Consensus 207 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (312)
--|.||||.+||+||||..|||||+||||+=+-...|
T Consensus 47 IPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~Y 83 (479)
T KOG4216|consen 47 IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANY 83 (479)
T ss_pred EeeeeccCCCCcceeeeEeeccchHhhhhhhhccccc
Confidence 3699999999999999999999999999998766666
No 128
>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=98.31 E-value=4.8e-08 Score=68.34 Aligned_cols=36 Identities=56% Similarity=1.246 Sum_probs=32.5
Q ss_pred eeeeCCCCcccccccccchhHHHHHHHHhhhcccce
Q psy11505 209 CLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYR 244 (312)
Q Consensus 209 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (312)
|.||++.++++|||+.+|++|++||+|++.....+.
T Consensus 1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~ 36 (72)
T cd06916 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYT 36 (72)
T ss_pred CCccCccCcccEECcceeeeeeeeEeEeecCCCCcc
Confidence 789999999999999999999999999997665553
No 129
>KOG4218|consensus
Probab=98.20 E-value=6.1e-07 Score=78.79 Aligned_cols=43 Identities=51% Similarity=1.040 Sum_probs=38.4
Q ss_pred CCceeeeeCCCCcccccccccchhHHHHHHHHhhhcccceecC
Q psy11505 205 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQVYSGYRQTG 247 (312)
Q Consensus 205 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 (312)
+.+.|.||||.-||+|||.-.||.||+||+|++|.-+-|+|.+
T Consensus 14 l~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e 56 (475)
T KOG4218|consen 14 LGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSE 56 (475)
T ss_pred cccccccccCccccceeeeeehhhhhhHHHHHhhcCcceeccc
Confidence 3566999999999999999999999999999999888886543
No 130
>PF09289 FOLN: Follistatin/Osteonectin-like EGF domain; InterPro: IPR015369 This domain is predominantly found in osteonectin and follistatin. They adopt an EGF-like structure [, ]. Follistatin is involved in diverse activities from embryonic development to cell secretion. ; GO: 0005515 protein binding; PDB: 1LR7_A 1LR8_A 1LR9_A 2ARP_F 3B4V_H 2KCX_A 3SEK_C 2P6A_D 3HH2_C 2B0U_D ....
Probab=78.27 E-value=0.45 Score=24.71 Aligned_cols=20 Identities=15% Similarity=0.780 Sum_probs=14.8
Q ss_pred eeEcCCCCCccccccccccc
Q psy11505 3 EYTCPASNDCEINKRRRKAC 22 (312)
Q Consensus 3 ~Y~C~~~~~C~i~~~~R~~C 22 (312)
.|.|+.++-|.+|...+..|
T Consensus 3 n~~Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 3 NFHCKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp T---BTTEEEEEETTTCEEE
T ss_pred CcccCCCCEeeeCCCCCcCC
Confidence 47899999999999888776
No 131
>smart00274 FOLN Follistatin-N-terminal domain-like. Follistatin-N-terminal domain-like, EGF-like. Region distinct from the kazal-like sequence
Probab=58.49 E-value=6 Score=21.50 Aligned_cols=20 Identities=25% Similarity=0.697 Sum_probs=16.8
Q ss_pred eeEcCCCCCccccccccccc
Q psy11505 3 EYTCPASNDCEINKRRRKAC 22 (312)
Q Consensus 3 ~Y~C~~~~~C~i~~~~R~~C 22 (312)
...|..+..|.+|+..+.+|
T Consensus 4 ~v~C~~G~~C~~d~~g~p~C 23 (26)
T smart00274 4 NVQCPFGKVCVVDKGGNARC 23 (26)
T ss_pred CEECCCCCEEEeCCCCCEEE
Confidence 46799999999998877776
No 132
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=39.67 E-value=13 Score=23.07 Aligned_cols=18 Identities=39% Similarity=0.754 Sum_probs=12.6
Q ss_pred CcccccccccccccCchh
Q psy11505 11 DCEINKRRRKACQACRFQ 28 (312)
Q Consensus 11 ~C~i~~~~R~~Cr~CRf~ 28 (312)
-..+....+.+|+.||.|
T Consensus 29 ~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 29 HYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred eEEeCCCCeEECCCCCCc
Confidence 344545567899999975
No 133
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=31.26 E-value=21 Score=21.03 Aligned_cols=10 Identities=40% Similarity=1.099 Sum_probs=8.1
Q ss_pred ccccccccCc
Q psy11505 17 RRRKACQACR 26 (312)
Q Consensus 17 ~~R~~Cr~CR 26 (312)
..|.+|+.||
T Consensus 27 ~qryrC~~C~ 36 (36)
T PF03811_consen 27 HQRYRCKDCR 36 (36)
T ss_pred CEeEecCcCC
Confidence 3488999997
No 134
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=31.12 E-value=61 Score=19.13 Aligned_cols=22 Identities=23% Similarity=0.350 Sum_probs=16.6
Q ss_pred cchHHHHHHHHHHHHHhHhHHHH
Q psy11505 262 DEFSSLKKFRNSILSSLGDCIYV 284 (312)
Q Consensus 262 ~~~~~~~~~~~~~~~~l~~~~~~ 284 (312)
.+....++++ +|+.+|.+|+..
T Consensus 9 g~~a~~e~l~-~Y~~~L~~Yinl 30 (36)
T smart00309 9 GDDASPEDLR-QYLAALREYINL 30 (36)
T ss_pred CCCCCHHHHH-HHHHHHHHHHHH
Confidence 4445566777 999999999864
No 135
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=30.85 E-value=62 Score=19.11 Aligned_cols=22 Identities=23% Similarity=0.360 Sum_probs=16.9
Q ss_pred cchHHHHHHHHHHHHHhHhHHHH
Q psy11505 262 DEFSSLKKFRNSILSSLGDCIYV 284 (312)
Q Consensus 262 ~~~~~~~~~~~~~~~~l~~~~~~ 284 (312)
.+....++++ +|+.+|.+|+..
T Consensus 9 g~~a~~eel~-~Y~~~L~~Yinl 30 (36)
T cd00126 9 GDDASPEELR-QYLAALREYINL 30 (36)
T ss_pred CCCCCHHHHH-HHHHHHHHHHHH
Confidence 4445577787 999999999864
No 136
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=30.38 E-value=51 Score=23.07 Aligned_cols=21 Identities=29% Similarity=0.518 Sum_probs=16.6
Q ss_pred HhhCCccccCChHHHHHHHHH
Q psy11505 123 AKQIPGFTDLSLNDQMRLLQS 143 (312)
Q Consensus 123 ak~lp~F~~L~~~DQi~LLK~ 143 (312)
+..+++|..|..+||..+.+.
T Consensus 60 ~~~i~G~~~L~~~Dq~~i~~~ 80 (82)
T PF00645_consen 60 IEEIKGFDELKPEDQEKIRKL 80 (82)
T ss_dssp GGGCETCCCS-HHHHHHHHHH
T ss_pred HHHCCChHHCCHHHHHHHHHH
Confidence 456999999999999988763
No 137
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=29.44 E-value=32 Score=26.11 Aligned_cols=36 Identities=22% Similarity=0.637 Sum_probs=23.1
Q ss_pred CceeeeeCCCCcc---cccccccchhHHHHHHHHhhhccc
Q psy11505 206 RRLCLVCGDVASG---FHYGVASCEACKAFFKRTIQVYSG 242 (312)
Q Consensus 206 ~~~c~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~ 242 (312)
+..|.-||..... ..||+..|..|++.-|. ++++.+
T Consensus 13 N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~-lg~~is 51 (116)
T PF01412_consen 13 NKVCADCGAPNPTWASLNYGIFLCLECAGIHRS-LGVHIS 51 (116)
T ss_dssp CTB-TTT-SBS--EEETTTTEEE-HHHHHHHHH-HTTTT-
T ss_pred cCcCCCCCCCCCCEEEeecChhhhHHHHHHHHH-hcccch
Confidence 5678889876544 78999999999988554 554333
No 138
>PF01831 Peptidase_C16: Peptidase C16 family; InterPro: IPR002705 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry contains coronavirus cysteine endopeptidases that belong to MEROPS peptidase families C30 (clan PA) and C16 (subfamiles C16A and C16B, clan CA). These peptidase are involved in viral polyprotein processing. All coronaviruses encodes between one and two accessory cysteine proteinases that recognise and process one or two sites in the amino-terminal half of the replicase polyprotein during assembly of the viral replication complex. MHV, HCoV and TGEV encode two accesssory proteinases, called coronavirus papain-like proteinase 1 and 2 (PL1-PRO and PL2-PRO). IBV and SARS encodes only one called PL-PRO []. Coronavirus papain-like proteinases 1 and 2 have restricted specificities, cleaving respectively two and one bond(s)in the polyprotein. This restricted activity may be due to extended specificity sites: Arg or Lys at the cleavage site position P5 are required for PL1-PRO [], and Phe at the cleavage site position P6 is required for PL2-PRO []. PL1-PRO releases p28 and p65 from the N terminus of the polyprotein; PL2-PRO cleaves between p210 and p150. ; GO: 0003968 RNA-directed RNA polymerase activity, 0008234 cysteine-type peptidase activity, 0006508 proteolysis
Probab=25.76 E-value=1.2e+02 Score=25.36 Aligned_cols=102 Identities=17% Similarity=0.273 Sum_probs=60.0
Q ss_pred HhhCC-ccccCChHHHHHHHHHHHHHHHHHhhhhhcccCCCCeeEecccchhhHHhhhhcccchhhhhhcccCccCCCCc
Q psy11505 123 AKQIP-GFTDLSLNDQMRLLQSTWAEILTLTIAYRSLPHCAGKIRFASDLVLDERQARECGFSEIYQQVKHSGSLDGIKE 201 (312)
Q Consensus 123 ak~lp-~F~~L~~~DQi~LLK~~~~~~~~L~~a~rs~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~L~ld~ 201 (312)
+.++| .|+.+..++-+...|......+ ..--....+. .++.+.|.++..-..+.. -+.+-
T Consensus 47 mqklp~~fkd~~~q~lwlsyk~gy~Q~F-VD~lv~~Ip~---~IV~pqgGyVADfaywfl---------------s~Cd~ 107 (249)
T PF01831_consen 47 MQKLPCQFKDKNLQNLWLSYKQGYMQEF-VDKLVIGIPK---NIVDPQGGYVADFAYWFL---------------SQCDW 107 (249)
T ss_pred HHhCCcccccchHHHHHHHHHhchhHHH-HHHHHhhCcH---heEcCCCCEEeeeHHHHH---------------Hhcch
Confidence 45566 5888999998988888888776 3333333333 344444433321111110 01123
Q ss_pred cccCCceeeeeC------CCCcccccccccchhHHHHHHHHhhhcccceecCCCCceeecCCCCc
Q psy11505 202 EELPRRLCLVCG------DVASGFHYGVASCEACKAFFKRTIQVYSGYRQTGACGTLVLANSDVK 260 (312)
Q Consensus 202 ~E~~~~~c~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 260 (312)
.-|.+..|+-|+ ++-..|-||+.-|..|+ +=...+|+..|.+
T Consensus 108 qaya~w~ClkC~~el~lngLDa~ffyGDivshvCK-----------------cG~sm~l~~~d~p 155 (249)
T PF01831_consen 108 QAYANWRCLKCQMELRLNGLDAMFFYGDIVSHVCK-----------------CGNSMTLISADVP 155 (249)
T ss_pred hhhhhhhHhhcCceeeeccchheeeeccEEEEEec-----------------cCCceEEEecCCc
Confidence 334455666665 23456889998888888 6666777777776
No 139
>smart00453 WSN Worm-specific (usually) N-terminal domain.
Probab=25.56 E-value=46 Score=22.77 Aligned_cols=17 Identities=18% Similarity=0.493 Sum_probs=15.5
Q ss_pred ccCCccchhHHHHHHHh
Q psy11505 292 HKDGKVLMNKLFVEMLE 308 (312)
Q Consensus 292 ~~~~~~~~~~~~~~~~~ 308 (312)
-..|.+|.++++.|+|+
T Consensus 26 l~~gsi~~~~vI~ELL~ 42 (69)
T smart00453 26 LINGSIPIDDVIAELLN 42 (69)
T ss_pred HHcCCCCHHHHHHHHHc
Confidence 46899999999999997
No 140
>PF00159 Hormone_3: Pancreatic hormone peptide; InterPro: IPR001955 Pancreatic hormone (PP) [] is a peptide synthesized in pancreatic islets of Langherhans, which acts as a regulator of pancreatic and gastrointestinal functions. The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length [] and has an amidated C terminus []. The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a beta turn, and 14-32 an alpha-helix,held close to the first helix by hydrophobic interactions []. Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution []. Both N and C termini are required for activity: receptor binding and activation functions may reside in the N and C termini respectively []. Pancreatic hormone is part of a wider family of active peptides that includes: Neuropeptide Y (NPY) [], one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotrophin-releasing hormone. Peptide YY (PYY) []. PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictory action and inhibits jejunal and colonic mobility. Various NPY and PYY-like polypeptides from fish and amphibians [, ]. Neuropeptide F (NPF) from invertebrates such as worms and snail. Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity. All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesized as larger protein precursors.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1LJV_A 1BBA_A 1V1D_A 1PPT_A 2H3T_A 2H4B_A 2BF9_A 2H3S_B 1K8V_A 2DF0_A ....
Probab=23.20 E-value=1e+02 Score=18.19 Aligned_cols=23 Identities=17% Similarity=0.369 Sum_probs=17.5
Q ss_pred cchHHHHHHHHHHHHHhHhHHHHH
Q psy11505 262 DEFSSLKKFRNSILSSLGDCIYVL 285 (312)
Q Consensus 262 ~~~~~~~~~~~~~~~~l~~~~~~~ 285 (312)
.+....++++ +|+.+|.+|+...
T Consensus 9 ~~~aspeel~-~Y~~~L~~Y~~lv 31 (36)
T PF00159_consen 9 GDFASPEELA-QYYAALRHYINLV 31 (36)
T ss_dssp STTSSHHHHH-HHHHHHHHHHHHH
T ss_pred CCCCCHHHHH-HHHHHHHHHHHHH
Confidence 5555677777 8999999998643
Done!