Query psy1615
Match_columns 295
No_of_seqs 283 out of 1944
Neff 9.0
Searched_HMMs 46136
Date Fri Aug 16 22:07:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1615.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1615hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07076 NR_LBD_GR Ligand bindi 100.0 3.6E-34 7.8E-39 244.4 17.6 174 3-181 30-224 (247)
2 cd07069 NR_LBD_Lrh-1 The ligan 100.0 5.6E-34 1.2E-38 244.4 17.3 178 2-183 41-239 (241)
3 cd06948 NR_LBD_COUP-TF Ligand 100.0 9.2E-34 2E-38 243.1 17.6 186 2-192 31-234 (236)
4 cd07349 NR_LBD_SHP The ligand 100.0 5.9E-34 1.3E-38 241.0 15.3 174 2-180 20-222 (222)
5 cd07070 NR_LBD_SF-1 The ligand 100.0 1.6E-33 3.6E-38 241.2 17.2 177 2-182 39-236 (237)
6 cd06937 NR_LBD_RAR The ligand 100.0 3.4E-33 7.4E-38 238.4 17.5 172 3-180 40-229 (231)
7 cd06951 NR_LBD_Dax1_like The l 100.0 1.3E-33 2.7E-38 239.5 14.6 155 2-161 20-192 (222)
8 cd06949 NR_LBD_ER Ligand bindi 100.0 4.5E-33 9.9E-38 238.2 16.9 179 2-181 33-233 (235)
9 cd06944 NR_LBD_Ftz-F1_like The 100.0 6.5E-33 1.4E-37 237.8 16.9 177 2-182 39-236 (237)
10 cd06950 NR_LBD_Tlx_PNR_like Th 100.0 1E-32 2.2E-37 231.9 15.7 168 2-176 27-199 (206)
11 cd07348 NR_LBD_NGFI-B The liga 100.0 1.9E-32 4.2E-37 233.7 17.3 167 3-178 43-216 (238)
12 cd07350 NR_LBD_Dax1 The ligand 100.0 8.8E-33 1.9E-37 235.1 14.4 171 2-176 20-230 (232)
13 cd07075 NR_LBD_MR Ligand bindi 100.0 1.7E-32 3.6E-37 234.4 15.6 174 3-182 30-213 (248)
14 cd07073 NR_LBD_AR Ligand bindi 100.0 4.4E-32 9.4E-37 232.6 16.9 155 2-161 29-193 (246)
15 cd07071 NR_LBD_Nurr1 The ligan 100.0 7.3E-32 1.6E-36 230.4 17.6 170 3-180 43-232 (238)
16 cd06947 NR_LBD_GR_Like Ligand 100.0 4.7E-32 1E-36 232.4 14.9 156 2-162 29-194 (246)
17 cd06945 NR_LBD_Nurr1_like The 100.0 1.4E-31 3E-36 229.5 17.8 172 2-180 42-233 (239)
18 cd07072 NR_LBD_DHR38_like Liga 100.0 1.7E-31 3.6E-36 228.1 17.7 172 3-182 44-235 (239)
19 cd06935 NR_LBD_TR The ligand b 100.0 7.4E-32 1.6E-36 231.9 14.8 174 3-183 54-232 (243)
20 cd07074 NR_LBD_PR Ligand bindi 100.0 9.9E-32 2.1E-36 229.3 14.7 155 3-162 30-194 (248)
21 cd06940 NR_LBD_REV_ERB The lig 100.0 1.7E-31 3.6E-36 221.4 14.3 168 3-177 14-186 (189)
22 cd06941 NR_LBD_DmE78_like The 100.0 5.1E-31 1.1E-35 220.2 15.3 172 2-180 3-179 (195)
23 cd06933 NR_LBD_VDR The ligand 100.0 5.3E-31 1.1E-35 225.9 14.8 173 3-181 39-219 (238)
24 cd06946 NR_LBD_ERR The ligand 100.0 2E-30 4.4E-35 220.7 16.8 173 2-180 28-219 (221)
25 cd06954 NR_LBD_LXR The ligand 100.0 1.7E-30 3.6E-35 223.3 15.6 173 3-181 45-222 (236)
26 cd07068 NR_LBD_ER_like The lig 100.0 3.2E-30 7E-35 219.3 17.1 173 2-180 28-219 (221)
27 cd06943 NR_LBD_RXR_like The li 100.0 1.8E-30 3.9E-35 219.0 14.4 166 2-174 31-202 (207)
28 cd06953 NR_LBD_DHR4_like The l 100.0 2.3E-30 5E-35 218.6 14.4 159 2-164 28-193 (213)
29 cd06939 NR_LBD_ROR_like The li 100.0 4.3E-30 9.3E-35 220.4 15.3 170 3-181 50-224 (241)
30 cd06952 NR_LBD_TR2_like The li 100.0 4.9E-30 1.1E-34 218.5 15.4 176 2-181 22-221 (222)
31 cd06934 NR_LBD_PXR_like The li 100.0 6.3E-30 1.4E-34 217.6 15.1 172 2-181 36-215 (226)
32 cd06936 NR_LBD_Fxr The ligand 100.0 5.1E-30 1.1E-34 217.5 14.4 176 2-188 37-218 (221)
33 cd06942 NR_LBD_Sex_1_like The 100.0 7.5E-30 1.6E-34 212.3 14.8 179 2-188 3-189 (191)
34 cd06930 NR_LBD_F2 Ligand-bindi 100.0 2.9E-29 6.4E-34 204.2 16.0 156 3-163 1-162 (165)
35 cd06932 NR_LBD_PPAR The ligand 100.0 2.4E-29 5.1E-34 217.9 15.3 169 3-179 65-240 (259)
36 cd06929 NR_LBD_F1 Ligand-bindi 100.0 3.5E-29 7.6E-34 205.6 14.1 157 2-164 3-164 (174)
37 KOG4215|consensus 100.0 1.2E-28 2.5E-33 212.3 13.8 179 1-185 154-354 (432)
38 cd06938 NR_LBD_EcR The ligand 100.0 2.2E-28 4.8E-33 209.2 15.4 177 3-187 41-223 (231)
39 cd06931 NR_LBD_HNF4_like The l 100.0 1.6E-27 3.5E-32 203.1 16.2 171 1-178 32-221 (222)
40 cd06157 NR_LBD The ligand bind 99.9 8.4E-23 1.8E-27 165.9 15.5 155 5-162 2-164 (168)
41 smart00430 HOLI Ligand binding 99.9 6.3E-22 1.4E-26 159.9 13.2 149 11-163 2-160 (163)
42 PF00104 Hormone_recep: Ligand 99.9 1.4E-21 3E-26 163.7 13.5 158 2-163 18-186 (203)
43 KOG4218|consensus 99.8 4.9E-19 1.1E-23 151.7 12.8 175 3-181 276-471 (475)
44 KOG4215|consensus 99.7 6.9E-19 1.5E-23 152.2 3.1 123 160-293 54-190 (432)
45 KOG4217|consensus 99.7 2.4E-17 5.2E-22 146.7 3.6 127 161-292 305-443 (605)
46 KOG4216|consensus 99.6 5.2E-16 1.1E-20 135.4 4.1 136 3-145 284-419 (479)
47 KOG4217|consensus 99.5 2.3E-13 5E-18 121.6 14.5 145 3-155 410-561 (605)
48 cd07076 NR_LBD_GR Ligand bindi 99.4 1.5E-13 3.3E-18 117.8 4.5 62 232-293 2-64 (247)
49 cd07075 NR_LBD_MR Ligand bindi 99.3 1.4E-12 2.9E-17 111.9 4.6 62 232-293 2-64 (248)
50 KOG4216|consensus 99.3 2.3E-13 5E-18 119.0 -0.2 40 161-203 82-121 (479)
51 cd07074 NR_LBD_PR Ligand bindi 99.3 1.9E-12 4.1E-17 111.0 4.7 62 232-293 2-64 (248)
52 cd06949 NR_LBD_ER Ligand bindi 99.3 2.4E-12 5.3E-17 110.3 4.9 65 229-293 3-68 (235)
53 cd07073 NR_LBD_AR Ligand bindi 99.3 2.7E-12 5.8E-17 110.4 4.5 62 232-293 2-64 (246)
54 KOG4218|consensus 99.3 6E-13 1.3E-17 114.6 0.0 41 161-204 51-91 (475)
55 cd06947 NR_LBD_GR_Like Ligand 99.3 3.6E-12 7.8E-17 109.6 4.6 62 232-293 2-64 (246)
56 cd06948 NR_LBD_COUP-TF Ligand 99.1 1E-10 2.2E-15 100.5 5.1 64 230-293 3-66 (236)
57 cd07072 NR_LBD_DHR38_like Liga 99.0 1.5E-10 3.2E-15 99.3 4.4 40 254-293 39-78 (239)
58 cd06945 NR_LBD_Nurr1_like The 99.0 2.6E-10 5.6E-15 98.0 4.9 39 255-293 39-77 (239)
59 cd06933 NR_LBD_VDR The ligand 99.0 1.3E-10 2.8E-15 99.8 2.5 66 228-293 4-73 (238)
60 cd07348 NR_LBD_NGFI-B The liga 99.0 3E-10 6.6E-15 97.3 4.4 39 255-293 39-77 (238)
61 cd07071 NR_LBD_Nurr1 The ligan 99.0 5E-10 1.1E-14 96.0 4.3 39 255-293 39-77 (238)
62 cd06946 NR_LBD_ERR The ligand 99.0 5.2E-10 1.1E-14 95.2 4.1 61 233-293 2-63 (221)
63 cd07070 NR_LBD_SF-1 The ligand 98.9 5.1E-10 1.1E-14 96.1 1.8 41 253-293 34-74 (237)
64 cd06950 NR_LBD_Tlx_PNR_like Th 98.9 1.8E-09 3.9E-14 90.9 4.2 40 254-293 23-62 (206)
65 cd07069 NR_LBD_Lrh-1 The ligan 98.9 1.3E-09 2.7E-14 93.9 2.9 40 254-293 37-76 (241)
66 cd06953 NR_LBD_DHR4_like The l 98.8 1.6E-09 3.5E-14 91.6 3.2 43 251-293 21-63 (213)
67 cd06937 NR_LBD_RAR The ligand 98.8 9.3E-10 2E-14 94.1 1.7 39 255-293 36-74 (231)
68 cd06935 NR_LBD_TR The ligand b 98.8 3.3E-09 7.1E-14 91.5 2.8 39 255-293 50-88 (243)
69 cd06931 NR_LBD_HNF4_like The l 98.8 1E-08 2.2E-13 87.3 5.8 65 229-293 2-68 (222)
70 cd06934 NR_LBD_PXR_like The li 98.8 4.5E-09 9.7E-14 89.6 3.0 38 256-293 34-71 (226)
71 cd07068 NR_LBD_ER_like The lig 98.7 9.1E-09 2E-13 87.6 4.2 60 234-293 3-63 (221)
72 cd06944 NR_LBD_Ftz-F1_like The 98.7 1E-08 2.2E-13 88.1 2.3 39 255-293 36-74 (237)
73 cd06939 NR_LBD_ROR_like The li 98.6 1.6E-08 3.4E-13 87.0 2.7 39 255-293 46-84 (241)
74 cd06943 NR_LBD_RXR_like The li 98.6 8.1E-08 1.7E-12 80.9 5.8 37 257-293 30-66 (207)
75 cd06954 NR_LBD_LXR The ligand 98.6 3.4E-08 7.4E-13 84.9 3.3 37 257-293 43-79 (236)
76 cd06936 NR_LBD_Fxr The ligand 98.4 1E-07 2.2E-12 81.1 2.8 38 256-293 35-72 (221)
77 cd06932 NR_LBD_PPAR The ligand 98.4 8.7E-08 1.9E-12 83.3 2.3 39 255-293 61-99 (259)
78 KOG4846|consensus 98.4 2.5E-07 5.5E-12 82.2 3.5 36 164-202 172-207 (538)
79 cd06938 NR_LBD_EcR The ligand 98.4 2E-07 4.2E-12 79.9 2.7 38 256-293 38-75 (231)
80 cd07166 NR_DBD_REV_ERB DNA-bin 97.8 6.6E-06 1.4E-10 59.3 1.2 46 161-209 39-85 (89)
81 cd07164 NR_DBD_PNR_like_1 DNA- 97.8 4.2E-06 9.1E-11 58.9 0.2 43 161-206 34-76 (78)
82 cd06961 NR_DBD_TR DNA-binding 97.8 4.8E-06 1E-10 59.5 0.4 44 161-207 35-78 (85)
83 cd07171 NR_DBD_ER DNA-binding 97.8 2.7E-06 5.8E-11 60.3 -1.1 43 161-206 39-81 (82)
84 cd06957 NR_DBD_PNR_like_2 DNA- 97.8 7.6E-06 1.7E-10 58.1 1.0 46 160-208 33-79 (82)
85 cd06964 NR_DBD_RAR DNA-binding 97.8 5.2E-06 1.1E-10 59.3 0.1 45 160-207 39-83 (85)
86 cd07165 NR_DBD_DmE78_like DNA- 97.8 7.4E-06 1.6E-10 58.0 0.7 44 161-207 34-77 (81)
87 cd07155 NR_DBD_ER_like DNA-bin 97.8 5.7E-06 1.2E-10 57.7 -0.1 40 161-203 34-73 (75)
88 cd06956 NR_DBD_RXR DNA-binding 97.7 4.7E-06 1E-10 58.5 -0.7 41 160-203 35-75 (77)
89 cd06967 NR_DBD_TR2_like DNA-bi 97.7 7.4E-06 1.6E-10 58.8 0.1 45 160-207 38-82 (87)
90 cd06968 NR_DBD_ROR DNA-binding 97.7 1E-05 2.2E-10 59.0 0.5 44 160-206 40-83 (95)
91 cd07170 NR_DBD_ERR DNA-binding 97.7 1.3E-05 2.8E-10 58.6 1.0 42 161-205 40-81 (97)
92 cd07158 NR_DBD_Ppar_like The D 97.6 1.2E-05 2.5E-10 55.9 0.0 39 161-202 34-73 (73)
93 cd07168 NR_DBD_DHR4_like DNA-b 97.6 1.5E-05 3.3E-10 57.5 0.6 44 161-207 42-85 (90)
94 cd07157 2DBD_NR_DBD1 The first 97.6 1.3E-05 2.9E-10 57.4 0.2 42 161-205 38-79 (86)
95 cd07167 NR_DBD_Lrh-1_like The 97.6 1.7E-05 3.6E-10 57.6 0.7 42 161-205 34-75 (93)
96 cd07179 2DBD_NR_DBD2 The secon 97.6 8.5E-06 1.8E-10 56.7 -0.9 39 161-202 34-72 (74)
97 cd06960 NR_DBD_HNF4A DNA-bindi 97.6 1.4E-05 3E-10 55.9 0.2 41 161-204 34-74 (76)
98 cd07160 NR_DBD_LXR DNA-binding 97.6 8.2E-06 1.8E-10 60.1 -1.1 43 160-205 53-95 (101)
99 cd06963 NR_DBD_GR_like The DNA 97.6 9.3E-06 2E-10 56.3 -0.8 38 161-201 34-71 (73)
100 cd06970 NR_DBD_PNR DNA-binding 97.6 1.2E-05 2.7E-10 58.2 -0.3 46 160-208 41-87 (92)
101 cd06969 NR_DBD_NGFI-B DNA-bind 97.6 9.4E-06 2E-10 56.6 -0.9 40 160-202 35-74 (75)
102 cd07163 NR_DBD_TLX DNA-binding 97.6 1.8E-05 3.9E-10 57.4 0.5 45 160-207 41-87 (92)
103 cd07156 NR_DBD_VDR_like The DN 97.6 1E-05 2.3E-10 55.9 -0.8 39 160-201 33-71 (72)
104 cd07169 NR_DBD_GCNF_like DNA-b 97.6 2.1E-05 4.6E-10 56.8 0.7 42 161-205 42-83 (90)
105 cd06958 NR_DBD_COUP_TF DNA-bin 97.6 1.3E-05 2.8E-10 55.6 -0.6 39 161-202 34-72 (73)
106 cd06962 NR_DBD_FXR DNA-binding 97.6 1.1E-05 2.5E-10 57.4 -0.9 41 160-203 36-76 (84)
107 cd07161 NR_DBD_EcR DNA-binding 97.5 1.5E-05 3.2E-10 57.7 -0.6 41 161-204 37-77 (91)
108 cd06916 NR_DBD_like DNA-bindin 97.5 1.6E-05 3.5E-10 55.0 -0.4 39 160-201 33-71 (72)
109 cd06966 NR_DBD_CAR DNA-binding 97.5 2.4E-05 5.1E-10 57.0 0.3 43 160-205 35-77 (94)
110 cd07173 NR_DBD_AR DNA-binding 97.5 2.2E-05 4.7E-10 55.7 -0.1 39 161-202 39-77 (82)
111 cd06959 NR_DBD_EcR_like The DN 97.5 1.9E-05 4.2E-10 54.7 -0.5 39 160-201 34-72 (73)
112 cd07154 NR_DBD_PNR_like The DN 97.5 2E-05 4.4E-10 54.6 -0.5 39 160-201 33-72 (73)
113 cd07172 NR_DBD_GR_PR DNA-bindi 97.4 2.9E-05 6.4E-10 54.5 -0.8 39 161-202 38-76 (78)
114 cd07162 NR_DBD_PXR DNA-binding 97.4 2.8E-05 6.1E-10 55.8 -1.0 40 161-203 35-74 (87)
115 cd06955 NR_DBD_VDR DNA-binding 97.3 3.9E-05 8.4E-10 57.1 -0.6 40 160-202 41-80 (107)
116 smart00399 ZnF_C4 c4 zinc fing 97.2 8.6E-05 1.9E-09 51.1 0.1 36 161-199 35-70 (70)
117 cd06965 NR_DBD_Ppar DNA-bindin 97.1 0.00015 3.4E-09 51.6 0.6 39 164-207 39-77 (84)
118 PF00105 zf-C4: Zinc finger, C 96.5 0.00012 2.6E-09 50.3 -3.6 35 161-198 36-70 (70)
119 KOG4846|consensus 94.4 0.042 9.1E-07 49.7 3.7 138 4-151 365-504 (538)
120 PF00645 zf-PARP: Poly(ADP-rib 39.0 28 0.00061 24.2 2.3 21 21-41 60-80 (82)
121 PF10330 Stb3: Putative Sin3 b 35.8 42 0.0009 24.1 2.7 23 20-42 30-52 (92)
122 COG3795 Uncharacterized protei 25.7 47 0.001 25.3 1.6 15 268-282 87-101 (123)
123 KOG2631|consensus 24.1 2.1E+02 0.0045 24.1 5.2 55 51-105 175-229 (238)
No 1
>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=100.00 E-value=3.6e-34 Score=244.43 Aligned_cols=174 Identities=22% Similarity=0.305 Sum_probs=146.2
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 81 (295)
++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++++.|||+++.... .+++.+|........ ...+
T Consensus 30 ~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~-~~~~ 108 (247)
T cd07076 30 MSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRM-TLPC 108 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHH-hhhh
Confidence 57899999999999999999999999999999999999999999999999999987655 367777777665443 4455
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCC---c
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKR---M 152 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~---R 152 (295)
+.+.++.+.+++.+|++|++|++||+|||||+|||| |++ |+++...|+++|++++.+ |+. +++.|. |
T Consensus 109 ~~~~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~----GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~R 184 (247)
T cd07076 109 MYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKD----GLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQR 184 (247)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhH
Confidence 666667889999999999999999999999999999 999 899999999999998555 444 565555 9
Q ss_pred ccccccccc-----------hhhhhhcCCCccchhhhhhh
Q psy1615 153 FGKPLPLNQ-----------HYTATISNVPLSSSLSTAVQ 181 (295)
Q Consensus 153 f~~lLl~~~-----------y~~r~~~~c~id~l~r~~~q 181 (295)
||+||++++ ++.+++++.++...+.+++-
T Consensus 185 F~kLLllLp~Lr~i~~~~~ef~~~~~~~~~~~~~~~~ml~ 224 (247)
T cd07076 185 FYQLTKLLDSMHEVVENLLNFCFQTFLDKTMSIEFPEMLA 224 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccchhhhhHHHHH
Confidence 999888874 23466777777777777754
No 2
>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=100.00 E-value=5.6e-34 Score=244.35 Aligned_cols=178 Identities=27% Similarity=0.421 Sum_probs=148.8
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhH--HH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAA--DR 78 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~--~~ 78 (295)
.++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.... .+.+++.+|........ ..
T Consensus 41 ~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~~~ 120 (241)
T cd07069 41 TFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQA 120 (241)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhhhh
Confidence 4689999999999999999999999999999999999999999999999999988653 44566667765443221 11
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcc
Q psy1615 79 VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMF 153 (295)
Q Consensus 79 ~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf 153 (295)
..++.+.++.+++++.+|++|++|.+||+|||||+|||||++ |+++...|+.+|++++.++ +. ||++|.||
T Consensus 121 ~~~~~~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf 196 (241)
T cd07069 121 GATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK----NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKF 196 (241)
T ss_pred hhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHH
Confidence 223445567788999999999999999999999999999999 8999999999999985554 43 89999999
Q ss_pred cccccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615 154 GKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRG 183 (295)
Q Consensus 154 ~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~ 183 (295)
|+||++++ ++.+..++.+++.++.+++.+.
T Consensus 197 ~kLLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Eml~~~ 239 (241)
T cd07069 197 GQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK 239 (241)
T ss_pred HHHHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHHHhcc
Confidence 99888873 4567788888999998887764
No 3
>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=100.00 E-value=9.2e-34 Score=243.06 Aligned_cols=186 Identities=64% Similarity=0.937 Sum_probs=158.8
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
+++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++++.+.+.++..+|.............
T Consensus 31 ~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~~~~~~ 110 (236)
T cd06948 31 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSADRVVA 110 (236)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccchhhHhH
Confidence 57999999999999999999999999999999999999999999999999999998887777777777665444334444
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCCCccccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGKRMFGKP 156 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~~Rf~~l 156 (295)
+.+.++.+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|++++.++.. |+++|.||++|
T Consensus 111 ~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~----~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~L 186 (236)
T cd06948 111 FMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDAC----GLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKL 186 (236)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCcccc----cccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHH
Confidence 555566778999999999999999999999999999999 788899999999998666443 78999999998
Q ss_pred cccc-------------chhhhhhcCCCccchhhhhhhcCCCCCCCCCC
Q psy1615 157 LPLN-------------QHYTATISNVPLSSSLSTAVQRGRVPPNQSCL 192 (295)
Q Consensus 157 Ll~~-------------~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~ 192 (295)
|+++ +++.+..|+.+++.++.+++.. ..++...|+
T Consensus 187 Ll~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~-~~~~~~~~~ 234 (236)
T cd06948 187 LLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLS-GSSFVWPYL 234 (236)
T ss_pred HHHHHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhC-CCCCcccCC
Confidence 8876 3566788999999999999975 455555553
No 4
>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=100.00 E-value=5.9e-34 Score=240.95 Aligned_cols=174 Identities=24% Similarity=0.358 Sum_probs=141.1
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc---------eeecCCcccC
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP---------LLAAAGLHAS 72 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~---------~~~~~~~~~~ 72 (295)
+++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.+.+... ++.. +....
T Consensus 20 ~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~-~~~~~ 98 (222)
T cd07349 20 TPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLE-GQSSS 98 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhc-ccccc
Confidence 6789999999999999999999999999999999999999999999999999998765432 2222 21111
Q ss_pred hhh--HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--
Q psy1615 73 PMA--ADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL-- 145 (295)
Q Consensus 73 ~~~--~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~-- 145 (295)
... ..........++.+++++.+|++|++|.+||+|||||+|||||++ |+++...|+.+|++++.+ |+.
T Consensus 99 ~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~----gl~~~~~V~~lqe~~~~aL~~~~~~~ 174 (222)
T cd07349 99 GGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVP----GLTASSHVGHLQQEAQWALCEVLEPL 174 (222)
T ss_pred cccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcc----cCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 100 111122334456788999999999999999999999999999999 899999999999987555 443
Q ss_pred CCCCCCccccccccc-------------chhhhhhcCCCccchhhhhh
Q psy1615 146 FTTGKRMFGKPLPLN-------------QHYTATISNVPLSSSLSTAV 180 (295)
Q Consensus 146 ~~~~~~Rf~~lLl~~-------------~y~~r~~~~c~id~l~r~~~ 180 (295)
||++|.||++||+++ +++.+.+|+.+|+.++.+++
T Consensus 175 ~p~~~~r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~i~~Ll~eml 222 (222)
T cd07349 175 HPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML 222 (222)
T ss_pred CCCcccHHHHHHHHhHHHhcCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence 899999999988886 46678888889988887763
No 5
>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=100.00 E-value=1.6e-33 Score=241.22 Aligned_cols=177 Identities=25% Similarity=0.347 Sum_probs=147.5
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAADRVV 80 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ 80 (295)
.+..+|+++++.++.+|+|||++|+|..|+.+||++|||++|+|+++|+.||++++.. .+.+.+.+|..+.........
T Consensus 39 ~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~ 118 (237)
T cd07070 39 PFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAAQA 118 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHHHHH
Confidence 4678999999999999999999999999999999999999999999999999998653 455777777765543322222
Q ss_pred H--HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcc
Q psy1615 81 A--FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMF 153 (295)
Q Consensus 81 ~--~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf 153 (295)
+ +...+..+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|++++.+ |+. ||+.+.||
T Consensus 119 ~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~----gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf 194 (237)
T cd07070 119 GSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVK----FLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKF 194 (237)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCcc----CCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHH
Confidence 2 223445567999999999999999999999999999999 899999999999998555 443 89999999
Q ss_pred ccccccc-------------chhhhhhcCCCccchhhhhhhc
Q psy1615 154 GKPLPLN-------------QHYTATISNVPLSSSLSTAVQR 182 (295)
Q Consensus 154 ~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~ 182 (295)
++||+++ +++.+..|+.+++.++.+++.+
T Consensus 195 ~kLLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~eml~~ 236 (237)
T cd07070 195 QQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA 236 (237)
T ss_pred HHHHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHHHhcC
Confidence 9988876 3566788888888888888764
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=100.00 E-value=3.4e-33 Score=238.39 Aligned_cols=172 Identities=21% Similarity=0.268 Sum_probs=139.7
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
++++|+.+++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++.+.. +.+.+.+|..+..... ...++
T Consensus 40 ~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~-~~l~~~~~~~~~~~~~-~~~~~ 117 (231)
T cd06937 40 WDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQ-DTMTFSDGLTLNRTQM-HNAGF 117 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CeEEecCCceecHHHH-hhcCh
Confidence 578999999999999999999999999999999999999999999999999987655 4466667765544322 22234
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKPL 157 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~lL 157 (295)
.+.+..+.+++.+|++|++|++||+|||||+||+||++ |+.+..+|+.+|++++.++ +. ||++|.||++||
T Consensus 118 ~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLL 193 (231)
T cd06937 118 GPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQ----DLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKML 193 (231)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCc----cCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHH
Confidence 45556677999999999999999999999999999999 8999999999999985554 43 899999999977
Q ss_pred cccc-------------hhhhhhcCCCccchhhhhh
Q psy1615 158 PLNQ-------------HYTATISNVPLSSSLSTAV 180 (295)
Q Consensus 158 l~~~-------------y~~r~~~~c~id~l~r~~~ 180 (295)
++++ ++.+..+..+++.++.+++
T Consensus 194 l~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml 229 (231)
T cd06937 194 MKITDLRSISAKGAERVITLKMEIPGPMPPLISEML 229 (231)
T ss_pred HHhHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHh
Confidence 7663 3334555556666655553
No 7
>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=100.00 E-value=1.3e-33 Score=239.46 Aligned_cols=155 Identities=23% Similarity=0.363 Sum_probs=125.4
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc---------eeecCCcccC
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP---------LLAAAGLHAS 72 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~---------~~~~~~~~~~ 72 (295)
+++++|++|++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.+.+... ++...+....
T Consensus 20 ~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~ 99 (222)
T cd06951 20 APQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMHWG 99 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhccccccc
Confidence 5789999999999999999999999999999999999999999999999999998775431 1222222221
Q ss_pred hhh----HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh
Q psy1615 73 PMA----ADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL 145 (295)
Q Consensus 73 ~~~----~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~ 145 (295)
... ..+.....+.++.+++++.+|++|++|++||+|||||+|||||++ |+ +..+|+++|++++.++ +.
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~----gl-~~~~Ve~lQe~~~~aL~~yi~ 174 (222)
T cd06951 100 GTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPP----LL-CPHYIEALQKEAQQALNEHTM 174 (222)
T ss_pred cccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCC----cc-CHHHHHHHHHHHHHHHHHHHH
Confidence 111 011122223457889999999999999999999999999999999 89 9999999999985554 43
Q ss_pred --CCCCCCcccccccccc
Q psy1615 146 --FTTGKRMFGKPLPLNQ 161 (295)
Q Consensus 146 --~~~~~~Rf~~lLl~~~ 161 (295)
||++|.||++||++++
T Consensus 175 ~~~p~~~~Rf~kLLl~Lp 192 (222)
T cd06951 175 MTRPLEQLRSARLLLMLS 192 (222)
T ss_pred hhCCCcccHHHHHHHHhH
Confidence 8999999999777663
No 8
>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=100.00 E-value=4.5e-33 Score=238.20 Aligned_cols=179 Identities=26% Similarity=0.317 Sum_probs=143.1
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
.+..+|+++++.++.+|+|||++|||.+|+.+||++|||++|.|+++|+.||++++.+.. +++.+|............+
T Consensus 33 ~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~-~~~~~~~~~~~~~~~~~~~ 111 (235)
T cd06949 33 LMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGK-LLFAPDLLLDRNQGSCVEG 111 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCe-EEeeCCceecHHHhhhccc
Confidence 367899999999999999999999999999999999999999999999999999987554 5555555444332221234
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccc-cchhHHHHHHHHHHHHHHHh---h--C---CCCCCc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTG-VLLKALHVDSAEYSCLKAIV---L--F---TTGKRM 152 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~-~l~~~~~i~~~q~~~l~~l~---~--~---~~~~~R 152 (295)
+.+..+.+.+++.+|++|++|++||+|||||+|||||+++++. ++++..+|+.+|++++.++. . | |++|.|
T Consensus 112 ~~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~~~~R 191 (235)
T cd06949 112 MVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQQSRR 191 (235)
T ss_pred HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccH
Confidence 5555667889999999999999999999999999999993220 18899999999999855543 3 5 889999
Q ss_pred ccccccccc-------------hhhhhhcCCCccchhhhhhh
Q psy1615 153 FGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQ 181 (295)
Q Consensus 153 f~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q 181 (295)
|++||+.++ ++.+..++.+++.++.+++.
T Consensus 192 f~~LLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~ 233 (235)
T cd06949 192 LAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLD 233 (235)
T ss_pred HHHHHHhchHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhc
Confidence 999777663 44566666777777776654
No 9
>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=100.00 E-value=6.5e-33 Score=237.85 Aligned_cols=177 Identities=29% Similarity=0.441 Sum_probs=149.2
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhHHHH-
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAADRV- 79 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~- 79 (295)
.++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|+++++|+.||++++.+ .+.+.+.+|..+.+......
T Consensus 39 ~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~ 118 (237)
T cd06944 39 TFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLASQA 118 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhhhc
Confidence 4688999999999999999999999999999999999999999999999999999876 66677788876554432221
Q ss_pred -HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcc
Q psy1615 80 -VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMF 153 (295)
Q Consensus 80 -~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf 153 (295)
.+..+.+..+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|+++..++ +. |+++|.||
T Consensus 119 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~----gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf 194 (237)
T cd06944 119 GLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVK----GLENRQLVESVQEQVNAALLDYTLCNYPQQTDKF 194 (237)
T ss_pred cccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHH
Confidence 12344556788999999999999999999999999999999 8889999999999986554 33 88999999
Q ss_pred ccccccc-------------chhhhhhcCCCccchhhhhhhc
Q psy1615 154 GKPLPLN-------------QHYTATISNVPLSSSLSTAVQR 182 (295)
Q Consensus 154 ~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~ 182 (295)
++||+++ +++.+.+|..+++.++.+++.+
T Consensus 195 ~~LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~eml~~ 236 (237)
T cd06944 195 GQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHA 236 (237)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHHHcC
Confidence 9988876 3456778888888888887643
No 10
>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=100.00 E-value=1e-32 Score=231.92 Aligned_cols=168 Identities=39% Similarity=0.642 Sum_probs=135.9
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
+++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++.+.+...++...+......... ..
T Consensus 27 ~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~~~~~~--~~ 104 (206)
T cd06950 27 SPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAE--RT 104 (206)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCcccccccchh--hH
Confidence 6789999999999999999999999999999999999999999999999999998876665665555433222111 13
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCccccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKP 156 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~l 156 (295)
..+.++.+.+++.+|++|++|++||+|||||+|||||++ |+++...|+++|++++.++ +. |+++|.||++|
T Consensus 105 ~~~~~~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~----~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf~kL 180 (206)
T cd06950 105 FLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETR----GLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKL 180 (206)
T ss_pred HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHH
Confidence 444457788999999999999999999999999999999 8889999999999885554 43 78999999996
Q ss_pred ccccchhhhhhcCCCccchh
Q psy1615 157 LPLNQHYTATISNVPLSSSL 176 (295)
Q Consensus 157 Ll~~~y~~r~~~~c~id~l~ 176 (295)
|+.+ ...|..+...++.++
T Consensus 181 Ll~L-p~lr~ls~~~~e~l~ 199 (206)
T cd06950 181 LLLL-PSLRFISSSTIEELF 199 (206)
T ss_pred HHHH-HHHHhhhHHHHHHHh
Confidence 6554 444445544444443
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=100.00 E-value=1.9e-32 Score=233.70 Aligned_cols=167 Identities=24% Similarity=0.291 Sum_probs=136.4
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
++++++++++.++.+|+|||++|||.+|+.+||++|||++|.|+++|+.||++.+.++ .+.+.+|..+.... ...++
T Consensus 43 ~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~-~l~f~~~~~~~r~~--~~~~~ 119 (238)
T cd07348 43 IQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEG-KLIFCNGVVLHRTQ--CVRGF 119 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCC-eEEeeCCeeecHHH--HHhhH
Confidence 6899999999999999999999999999999999999999999999999999987754 46666776665433 23456
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh----CCCCCCcccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL----FTTGKRMFGK 155 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~----~~~~~~Rf~~ 155 (295)
.+.+..+.+++.+|++|++|.+||+|||||+|| ||++ |+++..+|+.+|++++.+ |+. +|++|.||++
T Consensus 120 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~k 194 (238)
T cd07348 120 GDWIDSILEFSQSLHRMNLDVSAFSCLAALVII-TDRH----GLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSR 194 (238)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCc----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHH
Confidence 677778889999999999999999999999999 7999 899999999999997444 543 4889999999
Q ss_pred cccccchhhhhhcCCCccchhhh
Q psy1615 156 PLPLNQHYTATISNVPLSSSLST 178 (295)
Q Consensus 156 lLl~~~y~~r~~~~c~id~l~r~ 178 (295)
||+++ ...|..+..+++.++..
T Consensus 195 LLl~L-p~LRsl~~~~~e~lf~~ 216 (238)
T cd07348 195 LLGKL-PELRTLCTQGLQRIFYL 216 (238)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHH
Confidence 66655 33333444444443333
No 12
>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=100.00 E-value=8.8e-33 Score=235.13 Aligned_cols=171 Identities=20% Similarity=0.327 Sum_probs=133.1
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCccee--------ecCCccc--
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL--------AAAGLHA-- 71 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~--------~~~~~~~-- 71 (295)
+++++|++|++.|+.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++++.+..... ..++...
T Consensus 20 ~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~~~~~ 99 (232)
T cd07350 20 SPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPPPTS 99 (232)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhccccccc
Confidence 578999999999999999999999999999999999999999999999999999877654221 1111100
Q ss_pred ----------ChhhHH--HHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHH
Q psy1615 72 ----------SPMAAD--RVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSC 139 (295)
Q Consensus 72 ----------~~~~~~--~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~ 139 (295)
...... ........++.+++++.+|++|++|++||+|||||+|||||++ |+++...|+.+|+++
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~----~L~~~~~Ve~lQe~~ 175 (232)
T cd07350 100 GAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLP----GLQCVQYIQGLQWEA 175 (232)
T ss_pred ccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcc----cCCCHHHHHHHHHHH
Confidence 000001 1111223457789999999999999999999999999999999 899999999999998
Q ss_pred HHHH---hh--CCCCCCcccccccccc-------------hhhhhhcCCCccchh
Q psy1615 140 LKAI---VL--FTTGKRMFGKPLPLNQ-------------HYTATISNVPLSSSL 176 (295)
Q Consensus 140 l~~l---~~--~~~~~~Rf~~lLl~~~-------------y~~r~~~~c~id~l~ 176 (295)
+.+| +. ||++|.||++||++++ ++.+.+|+.+|+.++
T Consensus 176 ~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll 230 (232)
T cd07350 176 QQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDML 230 (232)
T ss_pred HHHHHHHHHhhCCChhhHHHHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHh
Confidence 5554 43 8899999999887763 444555666665544
No 13
>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=100.00 E-value=1.7e-32 Score=234.35 Aligned_cols=174 Identities=19% Similarity=0.223 Sum_probs=139.5
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 81 (295)
++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++++.|||+++.... .+++.+|..+...... ..+
T Consensus 30 ~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~~-~~~ 108 (248)
T cd07075 30 LSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMH-QSA 108 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHHh-hcc
Confidence 78999999999999999999999999999999999999999999999999999987554 4677777766543322 234
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCC-cccccccchhHHHHHHHHHHHHHH---Hhh--CC---CCCCc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG-KRIFTGVLLKALHVDSAEYSCLKA---IVL--FT---TGKRM 152 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd-~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~---~~~~R 152 (295)
+.+.++.+.+++.+|++|++|++||+|||||+||||| ++ |+++...|+.+|++++.+ |+. ++ +.+.|
T Consensus 109 ~~~~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~----gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~~R 184 (248)
T cd07075 109 MYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKD----GLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSWQR 184 (248)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccchhH
Confidence 5666678889999999999999999999999999997 78 899999999999988555 443 23 45689
Q ss_pred ccccccccchhhhhhcCCCccchhhhhhhc
Q psy1615 153 FGKPLPLNQHYTATISNVPLSSSLSTAVQR 182 (295)
Q Consensus 153 f~~lLl~~~y~~r~~~~c~id~l~r~~~q~ 182 (295)
||+|+++++. .|....-.++.++-...+.
T Consensus 185 F~~LLllLp~-Lr~i~~k~iE~lff~~~~~ 213 (248)
T cd07075 185 FYQLTKLLDS-MHDLVSDLLEFCFYTFRES 213 (248)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHccc
Confidence 9997766543 4444444555555554444
No 14
>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=100.00 E-value=4.4e-32 Score=232.62 Aligned_cols=155 Identities=23% Similarity=0.325 Sum_probs=128.9
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCC-CCcceeecCCcccChhhHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPL-HVAPLLAAAGLHASPMAADRVV 80 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 80 (295)
.++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++++. +.+.+.+.+|..+..... ...
T Consensus 29 ~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~~-~~~ 107 (246)
T cd07073 29 LLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRM-HKS 107 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhhh-ccc
Confidence 367899999999999999999999999999999999999999999999999999976 444577777765543321 122
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHHHhh-----C---CCCCC
Q psy1615 81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKAIVL-----F---TTGKR 151 (295)
Q Consensus 81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~---~~~~~ 151 (295)
++.+.+..+.+++.+|++|++|.+||+|||||+|||| |++ |+++...|+.+|++++.++.. + +++|.
T Consensus 108 ~~~~~~~~l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~ 183 (246)
T cd07073 108 RMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVD----GLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSR 183 (246)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcc----cccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccch
Confidence 3444445567999999999999999999999999999 998 899999999999998555433 2 35689
Q ss_pred cccccccccc
Q psy1615 152 MFGKPLPLNQ 161 (295)
Q Consensus 152 Rf~~lLl~~~ 161 (295)
|||+||++++
T Consensus 184 Rf~kLLl~Lp 193 (246)
T cd07073 184 RFYQLTKLLD 193 (246)
T ss_pred HHHHHHHHHH
Confidence 9999888764
No 15
>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=100.00 E-value=7.3e-32 Score=230.35 Aligned_cols=170 Identities=24% Similarity=0.314 Sum_probs=137.7
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
++++++.+++.+..+|+|||++|||.+|+.+||++|||++|.|+++|+.|+++.+.+ +.+++.+|..+.... ...++
T Consensus 43 ~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~-~~l~~~~g~~~~~~~--~~~~~ 119 (238)
T cd07071 43 IQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVE-GKLIFCNGVVLHRLQ--CVRGF 119 (238)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCC-CceEeeCCceechhh--hhhcH
Confidence 679999999999999999999999999999999999999999999999999998765 446666776655433 12345
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHH---HHHhh----CCCCCCcccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCL---KAIVL----FTTGKRMFGK 155 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l---~~l~~----~~~~~~Rf~~ 155 (295)
.+.+..+.+++.+|++|++|++||+|||||+|| +|++ |+++...|+++|++++ +.|+. +|++|.||++
T Consensus 120 ~~~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf-~D~~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~k 194 (238)
T cd07071 120 GEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV-TERH----GLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSK 194 (238)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc-CCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHH
Confidence 556677889999999999999999999999999 5999 8999999999999974 44543 4689999999
Q ss_pred cccccc-------------hhhhhhcCCCccchhhhhh
Q psy1615 156 PLPLNQ-------------HYTATISNVPLSSSLSTAV 180 (295)
Q Consensus 156 lLl~~~-------------y~~r~~~~c~id~l~r~~~ 180 (295)
||++++ ++.+..+..++..++.+++
T Consensus 195 LLl~Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~ 232 (238)
T cd07071 195 LLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLF 232 (238)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHH
Confidence 776653 2334445555555555554
No 16
>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=99.98 E-value=4.7e-32 Score=232.39 Aligned_cols=156 Identities=22% Similarity=0.305 Sum_probs=129.5
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc-eeecCCcccChhhHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP-LLAAAGLHASPMAADRVV 80 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 80 (295)
.++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++++...+. +++.+|..+.... ....
T Consensus 29 ~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~-~~~~ 107 (246)
T cd06947 29 LLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQR-MHQS 107 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHH-hhhc
Confidence 3579999999999999999999999999999999999999999999999999999765543 6666666554432 2223
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHHHh---h--C---CCCCC
Q psy1615 81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKAIV---L--F---TTGKR 151 (295)
Q Consensus 81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~---~~~~~ 151 (295)
++.+.++.+.+++.+|++|++|++||+|||||+|||| |++ |+++...|+++|++++.++. . + ++.|.
T Consensus 108 ~~~~~~~~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~----gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~ 183 (246)
T cd06947 108 AMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKD----GLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQ 183 (246)
T ss_pred cHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccc----cccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccch
Confidence 4555556778999999999999999999999999999 788 89999999999999855543 3 3 46688
Q ss_pred cccccccccch
Q psy1615 152 MFGKPLPLNQH 162 (295)
Q Consensus 152 Rf~~lLl~~~y 162 (295)
|||+||++++-
T Consensus 184 Rf~kLLllLp~ 194 (246)
T cd06947 184 RFYQLTKLLDS 194 (246)
T ss_pred HHHHHHHhhhh
Confidence 99997776643
No 17
>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=99.98 E-value=1.4e-31 Score=229.48 Aligned_cols=172 Identities=22% Similarity=0.279 Sum_probs=142.9
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
.++++|+++++.++.+|+|||++|||.+|+.+||++|||++|.|+++|+.|+++.+.++ .+.+.+|..+..... ..+
T Consensus 42 ~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~-~l~~~~~~~~~~~~~--~~~ 118 (239)
T cd06945 42 QVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDG-KLVFCNGLVLHRLQC--VRG 118 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-ceEeeCCceecHHHH--HHh
Confidence 36889999999999999999999999999999999999999999999999999987644 466666765554332 234
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC--CCCCccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT--TGKRMFG 154 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~--~~~~Rf~ 154 (295)
+.+.++.+.+++.+|++|++|++||+|||||+||+||++ |+++..+|+++|++++.+ |.. || ++|.||+
T Consensus 119 ~~~~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~----gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~ 194 (239)
T cd06945 119 FGEWLDSILAFSSSLQSLLLDDISAFCCLALLLLITERH----GLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLS 194 (239)
T ss_pred HHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCcc----ccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHH
Confidence 556667888999999999999999999999999999999 899999999999998555 433 78 8999999
Q ss_pred ccccccc-------------hhhhhhcCCCccchhhhhh
Q psy1615 155 KPLPLNQ-------------HYTATISNVPLSSSLSTAV 180 (295)
Q Consensus 155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~ 180 (295)
+||++++ ++.+..++.+++.+++++.
T Consensus 195 kLLl~Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~ 233 (239)
T cd06945 195 KLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRF 233 (239)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHH
Confidence 9777663 3445566666666666654
No 18
>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=99.98 E-value=1.7e-31 Score=228.08 Aligned_cols=172 Identities=22% Similarity=0.298 Sum_probs=141.1
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
++++++++++.+..+|+|||++|||.+|+.+||++|||++|.|+++|+.||++.+.++ .+.+.+|..+...... .++
T Consensus 44 ~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~-~l~~~~g~~~~~~~~~--~~~ 120 (239)
T cd07072 44 VQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDT-KLTFCNGVVLHKQQCQ--RSF 120 (239)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCC-eEEeeCCeeecHHHHH--hhH
Confidence 6889999999999999999999999999999999999999999999999999987654 4666677655543322 255
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh----CCCCCCcccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL----FTTGKRMFGK 155 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~----~~~~~~Rf~~ 155 (295)
.+.++.+.+++.+|++|++|++||+|||||+||+ |++ |+++..+|+.+|++++.++ +. ++++|.||++
T Consensus 121 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAivLf~-dr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~k 195 (239)
T cd07072 121 GDWLHAILEFSKSLHAMDIDISAFACLCALTLIT-ERH----GLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSR 195 (239)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhC-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHH
Confidence 5667788999999999999999999999999995 999 8999999999999985554 33 3478899999
Q ss_pred cccccc-------------hhhhhhcCCCccchhhhhhhc
Q psy1615 156 PLPLNQ-------------HYTATISNVPLSSSLSTAVQR 182 (295)
Q Consensus 156 lLl~~~-------------y~~r~~~~c~id~l~r~~~q~ 182 (295)
||++++ ++.+..+..+++.++.+++..
T Consensus 196 LLl~Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em~~~ 235 (239)
T cd07072 196 LLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMFVA 235 (239)
T ss_pred HHHHhHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHHHhc
Confidence 777653 344556666677777666543
No 19
>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=99.98 E-value=7.4e-32 Score=231.86 Aligned_cols=174 Identities=17% Similarity=0.197 Sum_probs=146.8
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
+.++++++++.+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.+. .+.+.+.+|..+.... ....++
T Consensus 54 ~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~ 131 (243)
T cd06935 54 FSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPE-SETLTLSGEMAVTREQ-LKNGGL 131 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcC-CCeEEeeCCeEeeHHH-HHhcCh
Confidence 67899999999999999999999999999999999999999999999999997655 4456667776655432 223455
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKPL 157 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~lL 157 (295)
.+.++.+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|+.++.+| +. +|+.|.||++||
T Consensus 132 ~~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL 207 (243)
T cd06935 132 GVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRP----GLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLL 207 (243)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHH
Confidence 56667888999999999999999999999999999999 8999999999999875554 43 789999999954
Q ss_pred cccchhhhhhcCCCccchhhhhhhcC
Q psy1615 158 PLNQHYTATISNVPLSSSLSTAVQRG 183 (295)
Q Consensus 158 l~~~y~~r~~~~c~id~l~r~~~q~~ 183 (295)
+++...|..+..+++.+..-+++..
T Consensus 208 -~~L~~LR~i~~~~~e~l~~~k~~~~ 232 (243)
T cd06935 208 -MKVTDLRMIGACHASRFLHMKVECP 232 (243)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 5556788888888888887777653
No 20
>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=99.98 E-value=9.9e-32 Score=229.33 Aligned_cols=155 Identities=21% Similarity=0.359 Sum_probs=129.9
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 81 (295)
+..+|+++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||++++.+.+ .+.+.+|....+... ...+
T Consensus 30 ~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~-~~~~ 108 (248)
T cd07074 30 LTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM-KESS 108 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhh-hhcc
Confidence 68899999999999999999999999999999999999999999999999999977544 455666655554332 1223
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHHHhhC--------CCCCCc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKAIVLF--------TTGKRM 152 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~l~~~--------~~~~~R 152 (295)
+.+.+..+.+++.+|++|++|++||+|||||+|||| |++ |++++..|+++|+++.++|.+| .++|.|
T Consensus 109 ~~~~~~~m~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~----gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~R 184 (248)
T cd07074 109 FYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLE----GLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQR 184 (248)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCC----CCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcHH
Confidence 445556677899999999999999999999999999 798 8999999999999986665442 478999
Q ss_pred ccccccccch
Q psy1615 153 FGKPLPLNQH 162 (295)
Q Consensus 153 f~~lLl~~~y 162 (295)
|++|++++..
T Consensus 185 F~~Ll~ll~~ 194 (248)
T cd07074 185 FYQLTKLMDN 194 (248)
T ss_pred HHHHHHHHHH
Confidence 9998877643
No 21
>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=99.97 E-value=1.7e-31 Score=221.44 Aligned_cols=168 Identities=20% Similarity=0.205 Sum_probs=137.8
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
++++++.++..+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.++++.... +.+.+.+|..+...... ..++
T Consensus 14 ~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~-~~l~~~~~~~~~~~~~~-~~~~ 91 (189)
T cd06940 14 WEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKE-RSVTFLSGQKYSVDDLH-SMGA 91 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCC-CeEEecCCcEEcHHHHH-HcCc
Confidence 678999999999999999999999999999999999999999999999999875543 44666667655443322 2234
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHh---h--CCCCCCcccccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIV---L--FTTGKRMFGKPL 157 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~~~~~~Rf~~lL 157 (295)
.+.++.+.+++.+|++|++|++||+|||||+|||||++ |+++..+|+++|++++.++. . ||++|.||++||
T Consensus 92 ~~~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~----~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL 167 (189)
T cd06940 92 GDLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRS----GLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLL 167 (189)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCc----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHH
Confidence 45567788999999999999999999999999999999 89999999999999855543 3 899999999955
Q ss_pred cccchhhhhhcCCCccchhh
Q psy1615 158 PLNQHYTATISNVPLSSSLS 177 (295)
Q Consensus 158 l~~~y~~r~~~~c~id~l~r 177 (295)
+ ++...|..+..+++.++.
T Consensus 168 ~-~L~~LR~l~~~~~e~l~~ 186 (189)
T cd06940 168 L-KLPDLRTLNNLHSEKLLA 186 (189)
T ss_pred H-HHHHHHHHHHHHHHHHHH
Confidence 4 455566677666666543
No 22
>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=99.97 E-value=5.1e-31 Score=220.16 Aligned_cols=172 Identities=19% Similarity=0.191 Sum_probs=138.9
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
-+.++++.+++.++.+|+|||++|+|.+|+.+||++|||++|+|+++++.++++.. ..+.+.+.+|........ ....
T Consensus 3 ~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~ 80 (195)
T cd06941 3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINS-KSGSITFDDGISISRQQL-DIIY 80 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcC-CCCeEEecCCeEeeHHHH-Hhcc
Confidence 36889999999999999999999999999999999999999999999999986644 445677777766554332 2122
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCccccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKP 156 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~l 156 (295)
..+.++.+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|++++.++ +. ||++|.||++|
T Consensus 81 ~~~~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~----gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~L 156 (195)
T cd06941 81 DSDFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRI----GLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASL 156 (195)
T ss_pred chHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHH
Confidence 234557889999999999999999999999999999999 8999999999999875554 33 89999999996
Q ss_pred ccccchhhhhhcCCCccchhhhhh
Q psy1615 157 LPLNQHYTATISNVPLSSSLSTAV 180 (295)
Q Consensus 157 Ll~~~y~~r~~~~c~id~l~r~~~ 180 (295)
|++++ ..|..+..+++.+...+.
T Consensus 157 l~~Lp-~Lr~l~~~~~e~l~~~~~ 179 (195)
T cd06941 157 LMKIP-ELRSIGAKHQMHLDWYRV 179 (195)
T ss_pred HHHhH-HHHHHHHHHHHHHHHHHh
Confidence 65554 455566666666544333
No 23
>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=99.97 E-value=5.3e-31 Score=225.89 Aligned_cols=173 Identities=15% Similarity=0.198 Sum_probs=134.4
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecC-CcccChhhHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAA-GLHASPMAADRVVA 81 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 81 (295)
+.++++++++.+..+|+|||++|||.+|+.+||++|||++|.|+++++.++. ++.+...+...+ +..+........+.
T Consensus 39 ~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~g~ 117 (238)
T cd06933 39 LPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQS-FSLDDMSWTCGSPDFKYKVSDVTKAGH 117 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHh-cCcCCCeeEecCCceeecHHHHHHccC
Confidence 5789999999999999999999999999999999999999999999998875 444444334333 23332222222111
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC--CCCCccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT--TGKRMFG 154 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~--~~~~Rf~ 154 (295)
..+.++.+.+++.+|++|++|++||+|||||+|||||++ |+.+...|+.+|++++.+ |+. || +++.||+
T Consensus 118 ~~~~~~~l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~~~~f~ 193 (238)
T cd06933 118 SLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRP----GVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYA 193 (238)
T ss_pred cHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCC----CCcchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHH
Confidence 224567888999999999999999999999999999999 899999999999998544 444 55 4556799
Q ss_pred ccccccchhhhhhcCCCccchhhhhhh
Q psy1615 155 KPLPLNQHYTATISNVPLSSSLSTAVQ 181 (295)
Q Consensus 155 ~lLl~~~y~~r~~~~c~id~l~r~~~q 181 (295)
+|| +++...|.++..|...++...++
T Consensus 194 kLL-l~L~~LRsi~~~h~~~~~~~~~~ 219 (238)
T cd06933 194 KMI-QKLADLRSLNEEHSKQYRSLSFQ 219 (238)
T ss_pred HHH-HHhHHHHhhhHHHHHHHHHHHhc
Confidence 955 45566788888888776554444
No 24
>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=99.97 E-value=2e-30 Score=220.66 Aligned_cols=173 Identities=23% Similarity=0.330 Sum_probs=141.3
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
.++++|+++++.++.+|+|||++|+|..|+.+||+.|+|++|+++++|+.||++++.+.. +.+.++....... ....+
T Consensus 28 ~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~-~~~~~~~~~~~~~-~~~~~ 105 (221)
T cd06946 28 ALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGE-LVFAEDFILDEEL-AREAG 105 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCc-eeecCCeEEcHHH-HhhcC
Confidence 368899999999999999999999999999999999999999999999999999987644 4545554433322 22334
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC-CCCCcccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT-TGKRMFGK 155 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~-~~~~Rf~~ 155 (295)
..+..+.+.+++.+|++|++|++||+|||||+|||||++ |+++...|++.|++++.+ |+. |+ ++|.||++
T Consensus 106 ~~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~----~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~ 181 (221)
T cd06946 106 LLELYSACLQLVRRLQRLRLEKEEYVLLKALALANSDSV----HIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQ 181 (221)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHH
Confidence 445557778999999999999999999999999999998 788999999999987544 443 77 89999999
Q ss_pred cccccch-------------hhhhhcCCCccchhhhhh
Q psy1615 156 PLPLNQH-------------YTATISNVPLSSSLSTAV 180 (295)
Q Consensus 156 lLl~~~y-------------~~r~~~~c~id~l~r~~~ 180 (295)
||+.++. ..+..+..+++.++.++.
T Consensus 182 LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml 219 (221)
T cd06946 182 LLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEML 219 (221)
T ss_pred HHhhchhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHh
Confidence 8877642 345566777777777765
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=99.97 E-value=1.7e-30 Score=223.33 Aligned_cols=173 Identities=22% Similarity=0.255 Sum_probs=141.4
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
+.++++++...+..+|+|||++|+|..|+.+||+.|||++|+|+++|+.|+++... .+.+.+.+|..+.+.........
T Consensus 45 ~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~ 123 (236)
T cd06954 45 FAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPE-SEAITFLKDFPYSRDDFARAGLQ 123 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCC-CCeEEeeCCccccHHHHHHhcCh
Confidence 67899999999999999999999999999999999999999999999999887544 55677788876655432221222
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL 157 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL 157 (295)
.+.++.+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|+++..+ |+. ||++|.||+++|
T Consensus 124 ~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~----gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL 199 (236)
T cd06954 124 VEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRP----NVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRML 199 (236)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCcc----cCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence 35567888999999999999999999999999999999 888999999999998544 554 899999999966
Q ss_pred cccchhhhhhcCCCccchhhhhhh
Q psy1615 158 PLNQHYTATISNVPLSSSLSTAVQ 181 (295)
Q Consensus 158 l~~~y~~r~~~~c~id~l~r~~~q 181 (295)
+.++ ..|..+..+++.++.-++.
T Consensus 200 ~~L~-~Lr~l~~~~~e~l~~~k~~ 222 (236)
T cd06954 200 MKLV-SLRTLSSVHSEQVFALRLQ 222 (236)
T ss_pred HHHH-HHHHHHHHHHHHHHHHHhc
Confidence 6654 5566666666666555554
No 26
>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=99.97 E-value=3.2e-30 Score=219.31 Aligned_cols=173 Identities=28% Similarity=0.416 Sum_probs=139.8
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
.++++|+++.+.++.+|+|||++|+|.+|+.+||+.|+|++|.++++++.||+++..+. .+.+.+|........ ...+
T Consensus 28 ~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~-~~~~~~~~~~~~~~~-~~~~ 105 (221)
T cd07068 28 LLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPG-KLVFAPDLLLDREQA-RVEG 105 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCC-eEEeCCCceECHHHH-hhcc
Confidence 47899999999999999999999999999999999999999999999999999987765 566666654433221 2234
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHh---h--CC-CCCCcccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIV---L--FT-TGKRMFGK 155 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~~-~~~~Rf~~ 155 (295)
+.+..+.+.+++.+|++|++|++||++||||+|||||++ |+++...|+..|++++.++. . |+ ++|.||++
T Consensus 106 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~----~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~ 181 (221)
T cd07068 106 LLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVR----HLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQ 181 (221)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcc----CccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHH
Confidence 445556778999999999999999999999999999999 78899999999999865544 3 77 89999999
Q ss_pred cccccchh-------------hhhhcCCCccchhhhhh
Q psy1615 156 PLPLNQHY-------------TATISNVPLSSSLSTAV 180 (295)
Q Consensus 156 lLl~~~y~-------------~r~~~~c~id~l~r~~~ 180 (295)
||++++.. .+..+..+++.++.+++
T Consensus 182 LL~~l~~Lr~~~~~~~e~l~~~k~~~~~~~~~Ll~e~l 219 (221)
T cd07068 182 LLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEML 219 (221)
T ss_pred HHHhccHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHh
Confidence 88776432 34455555555555544
No 27
>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=99.97 E-value=1.8e-30 Score=219.01 Aligned_cols=166 Identities=31% Similarity=0.479 Sum_probs=132.3
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
+++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.++++++.||+++..++. +++.+|..+.+..... .+
T Consensus 31 ~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~-~~~~~~~~~~~~~~~~-~~ 108 (207)
T cd06943 31 PVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDG-ILLATGLHLHRNSAHQ-AG 108 (207)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCe-eEecCCceeccchhhh-cc
Confidence 578999999999999999999999999999999999999999999999999999887655 4455665544332211 12
Q ss_pred HHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccc
Q psy1615 82 FMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGK 155 (295)
Q Consensus 82 ~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~ 155 (295)
..+.. +.+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|++++.+| +. |+++|.||++
T Consensus 109 ~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~----~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~ 184 (207)
T cd06943 109 VGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVK----GLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAK 184 (207)
T ss_pred chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHH
Confidence 22222 4567899999999999999999999999999999 7888999999999985554 43 7899999999
Q ss_pred cccccchhhhhhcCCCccc
Q psy1615 156 PLPLNQHYTATISNVPLSS 174 (295)
Q Consensus 156 lLl~~~y~~r~~~~c~id~ 174 (295)
||++++. .|..+...++.
T Consensus 185 LLl~L~~-lr~l~~~~~e~ 202 (207)
T cd06943 185 LLLRLPA-LRSIGLKCLEH 202 (207)
T ss_pred HHHHHHH-HHhHhHHHHHH
Confidence 7766554 44444444433
No 28
>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=99.97 E-value=2.3e-30 Score=218.57 Aligned_cols=159 Identities=21% Similarity=0.351 Sum_probs=125.1
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccC-hhhHHH-H
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHAS-PMAADR-V 79 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~-~ 79 (295)
.++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|++++..+...+....+.... ...... .
T Consensus 28 ~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~~~~~ 107 (213)
T cd06953 28 LFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELERFG 107 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhHHHHH
Confidence 36789999999999999999999999999999999999999999999999999987543321111111111 111111 1
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccc
Q psy1615 80 VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFG 154 (295)
Q Consensus 80 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~ 154 (295)
....+.++.+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|+++..+ |+. |+++|.||+
T Consensus 108 ~~~~~~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~----gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf~ 183 (213)
T cd06953 108 DEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDID----GLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFS 183 (213)
T ss_pred hhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHHH
Confidence 12334556778999999999999999999999999999999 888999999999997555 443 799999999
Q ss_pred ccccccchhh
Q psy1615 155 KPLPLNQHYT 164 (295)
Q Consensus 155 ~lLl~~~y~~ 164 (295)
+||++++...
T Consensus 184 ~LL~~L~~Lr 193 (213)
T cd06953 184 DLLSCLPEIR 193 (213)
T ss_pred HHHHHhHHHH
Confidence 9777665443
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=99.97 E-value=4.3e-30 Score=220.37 Aligned_cols=170 Identities=18% Similarity=0.169 Sum_probs=139.7
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
++++.+..+..+..+|+|||++|||.+|+.+||++|||++|+|++++++|+++.. ....+++. |..... ......++
T Consensus 50 ~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~-~~~~~~~~-~~~~~~-~~~~~~~~ 126 (241)
T cd06939 50 WQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNP-SNNTVLFD-GKYAPI-DLFKSLGC 126 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCC-CCCEEEEC-CccccH-HHHHHcCc
Confidence 5678899999999999999999999999999999999999999999999966544 44555554 332322 22222344
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHh---h--CCCCCCcccccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIV---L--FTTGKRMFGKPL 157 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~~~~~~Rf~~lL 157 (295)
.+.++.+.+++.+|++|++|++||+|||||+||+||++ |+.+...|+.+|++++.++. . | ++|.||++ |
T Consensus 127 ~~~~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~k-L 200 (241)
T cd06939 127 DDLISAVFDFAKSLCELKLTEDEIALFSALVLISADRP----GLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTK-L 200 (241)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCc----CCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHH-H
Confidence 56667889999999999999999999999999999999 89999999999999855544 3 6 89999999 5
Q ss_pred cccchhhhhhcCCCccchhhhhhh
Q psy1615 158 PLNQHYTATISNVPLSSSLSTAVQ 181 (295)
Q Consensus 158 l~~~y~~r~~~~c~id~l~r~~~q 181 (295)
|+++...|..+..+++.+..-+..
T Consensus 201 L~~Lp~LR~l~~~~~e~l~~~k~~ 224 (241)
T cd06939 201 LAKMPTLRALCSLHMEKLQKFKQS 224 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 566666788888888888777766
No 30
>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=99.97 E-value=4.9e-30 Score=218.53 Aligned_cols=176 Identities=34% Similarity=0.529 Sum_probs=142.2
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCccc------Chhh
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHA------SPMA 75 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~------~~~~ 75 (295)
+++++|+++++.++.+|+|||++|+|..|+.+||++|+|++|.|+++++.++++.+.+...++...+... ....
T Consensus 22 ~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 (222)
T cd06952 22 NVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQDKLS 101 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhhhHhcCCCc
Confidence 5789999999999999999999999999999999999999999999999998886655554443322111 1111
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCC
Q psy1615 76 ADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGK 150 (295)
Q Consensus 76 ~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~ 150 (295)
......+.+.+..+.+++.+|++|++|++||++||||+||+||++ |+++...++.+|+++++++.. +|+++
T Consensus 102 ~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~----~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~ 177 (222)
T cd06952 102 ADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHP----GQELRQQIEKLQEKALMELRDYVGKTYPEDE 177 (222)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCc----CCcCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 223334555556678999999999999999999999999999999 889999999999998655433 78999
Q ss_pred Cccccccccc-------------chhhhhhcCCCccchhhhhhh
Q psy1615 151 RMFGKPLPLN-------------QHYTATISNVPLSSSLSTAVQ 181 (295)
Q Consensus 151 ~Rf~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q 181 (295)
.||+++|+++ +++++.+|+.+++.++...++
T Consensus 178 ~R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~~~~ll~~~~~ 221 (222)
T cd06952 178 YRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSVIPYILR 221 (222)
T ss_pred cHHHHHHHHhHHhhhcCHHHHHHHhcccccCCCcHHHHHHHHHh
Confidence 9999988876 356788888888888766543
No 31
>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=99.97 E-value=6.3e-30 Score=217.55 Aligned_cols=172 Identities=15% Similarity=0.172 Sum_probs=132.2
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
.+.++++.+.+.+..+|+|||++|||.+|+.+||++|||++|+|+++++.++++... .+.+.. ++..+...... ..+
T Consensus 36 ~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~-~~~~~~-~~~~~~~~~~~-~~g 112 (226)
T cd06934 36 LLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEE-TGTWEC-GPLTYCIEDAA-RAG 112 (226)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhccc-CCeEee-CCEeecHHHHH-Hcc
Confidence 367899999999999999999999999999999999999999999999999887653 333433 33333322211 122
Q ss_pred HHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCc--c
Q psy1615 82 FMD-HIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRM--F 153 (295)
Q Consensus 82 ~~~-~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~R--f 153 (295)
+.. .++.+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|++++.+ |+. ||..+.| |
T Consensus 113 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r~~f 188 (226)
T cd06934 113 FQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRP----GVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFLY 188 (226)
T ss_pred chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCc----CCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcccHH
Confidence 332 447788999999999999999999999999999999 899999999999997544 443 6554455 9
Q ss_pred cccccccchhhhhhcCCCccchhhhhhh
Q psy1615 154 GKPLPLNQHYTATISNVPLSSSLSTAVQ 181 (295)
Q Consensus 154 ~~lLl~~~y~~r~~~~c~id~l~r~~~q 181 (295)
++|| +++...|..+..+++.+.+-...
T Consensus 189 ~kLL-l~L~~LRsl~~~~~~~~~~~~~~ 215 (226)
T cd06934 189 PKIL-ACLTELRTINEEYTKQILHIQDI 215 (226)
T ss_pred HHHH-HHhHHHhcchHHHHHHHHHHhcc
Confidence 9955 55566666766666666554333
No 32
>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=99.97 E-value=5.1e-30 Score=217.53 Aligned_cols=176 Identities=19% Similarity=0.169 Sum_probs=140.9
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
.+.++++++.+.++.+|+|||++|||..|+.+||+.|||++|+|+++|+.|+++.. + .+.|............+
T Consensus 37 ~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~-~-----~~~~~~~~~~~~~~~~~ 110 (221)
T cd06936 37 NFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNK-K-----LPAGHADLLEERIRSSG 110 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhcc-c-----ccCCCchhhHHHHHhcc
Confidence 35789999999999999999999999999999999999999999999999865432 1 12222111111111112
Q ss_pred -HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccc
Q psy1615 82 -FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGK 155 (295)
Q Consensus 82 -~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~ 155 (295)
..+.+..+.+++.+|++|++|++||+|||||+|||||++ |+++...|+.+|++++.+ |+. ||++|.||++
T Consensus 111 ~~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~----gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~ 186 (221)
T cd06936 111 ISDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRP----YLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFAC 186 (221)
T ss_pred chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCc----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHH
Confidence 234556778999999999999999999999999999999 888999999999998555 443 8999999999
Q ss_pred cccccchhhhhhcCCCccchhhhhhhcCCCCCC
Q psy1615 156 PLPLNQHYTATISNVPLSSSLSTAVQRGRVPPN 188 (295)
Q Consensus 156 lLl~~~y~~r~~~~c~id~l~r~~~q~~r~~~~ 188 (295)
||+++...|..+..+++.+..-++..-.+||.
T Consensus 187 -LL~~L~~LR~l~~~~~e~l~~~k~~~~~~~pl 218 (221)
T cd06936 187 -LLGRLTELRTLNHHHAEMLMSWKVNDHKFTPL 218 (221)
T ss_pred -HHHHhHHHHHHHHHHHHHHHHHHccCCCCCcc
Confidence 66777788889999999999888876556553
No 33
>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=99.97 E-value=7.5e-30 Score=212.30 Aligned_cols=179 Identities=13% Similarity=0.047 Sum_probs=140.4
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
-++++++.+++.+..+|+|||++|||..|+.+||++|||++|+|++++++++++.. + ..++.+|....+.......+
T Consensus 3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~-~--~~~~~~g~~~~~~~~~~~~~ 79 (191)
T cd06942 3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNN-E--GTVLCDFRPVEFASLLSQLL 79 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCc-C--CeEEeCCccccHHHHHHhcc
Confidence 37899999999999999999999999999999999999999999999988865543 3 34555666555432211112
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCC--cccccccchhHHHHHHHHHHHHHHHh---h--CCCCCCccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG--KRIFTGVLLKALHVDSAEYSCLKAIV---L--FTTGKRMFG 154 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd--~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~~~~~~Rf~ 154 (295)
..+.+..+.+++.+|++|++|++||+||+||+||+|| ++ ++++...|+.+|+.+.+++. . |++.+.||+
T Consensus 80 ~~~~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~----~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~ 155 (191)
T cd06942 80 HGKLIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLGI----QLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQ 155 (191)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCC----CccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHH
Confidence 2344556789999999999999999999999999999 99 89999999999998865544 3 799999999
Q ss_pred ccccccchhhhhhcCCCccchhh-hhhhcCCCCCC
Q psy1615 155 KPLPLNQHYTATISNVPLSSSLS-TAVQRGRVPPN 188 (295)
Q Consensus 155 ~lLl~~~y~~r~~~~c~id~l~r-~~~q~~r~~~~ 188 (295)
+|| .++...|.....+.+.+.. ...+...+||.
T Consensus 156 kLL-~~l~~Lr~~~~~~~~~l~~~~~~~~~~~ppl 189 (191)
T cd06942 156 KLF-DILNRLRNMNKEHQNILADRDKRSNLQLPPL 189 (191)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHccccCccCCCCCc
Confidence 954 5555666666666666554 45555666664
No 34
>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=99.96 E-value=2.9e-29 Score=204.24 Aligned_cols=156 Identities=31% Similarity=0.516 Sum_probs=131.6
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
.+++|+++++.++.+|+|||++|+|.+|+.+||+.|+|++|.++++|..||++++.+ .+.+.+++|.......... ..
T Consensus 1 ~~~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~-~~ 79 (165)
T cd06930 1 PESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREAL-LG 79 (165)
T ss_pred ChhHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhh-hh
Confidence 368999999999999999999999999999999999999999999999999998775 4456777776655433221 23
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCCCccccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGKRMFGKP 156 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~~Rf~~l 156 (295)
..+..+.+.+++.+|++|++|++||++||||++|+||++ |+++...++..|++++++|.. ++++|.||++|
T Consensus 80 ~~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~----~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~l 155 (165)
T cd06930 80 LAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLP----GLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKL 155 (165)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC----CCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHH
Confidence 445567788999999999999999999999999999999 788899999999998666543 68899999998
Q ss_pred ccccchh
Q psy1615 157 LPLNQHY 163 (295)
Q Consensus 157 Ll~~~y~ 163 (295)
|+.++..
T Consensus 156 l~~l~~l 162 (165)
T cd06930 156 LLRLPEL 162 (165)
T ss_pred HHHhHhh
Confidence 8776543
No 35
>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=99.96 E-value=2.4e-29 Score=217.86 Aligned_cols=169 Identities=18% Similarity=0.210 Sum_probs=130.4
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcc-cChhhHHHHH-
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLH-ASPMAADRVV- 80 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~-~~~~~~~~~~- 80 (295)
+.++.......+..+|+|||++|||.+|+.+||++|||++|+|+++++.|.++. .+ .+++..|.. ..........
T Consensus 65 ~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~--~~-~~~~~~~~~~~~~~~~~~~~~ 141 (259)
T cd06932 65 FQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYN--KD-GLLFPEGNGYVTREFLESLRK 141 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcC--CC-CeEEeCCCEEeeHHHHHHhcc
Confidence 455667778899999999999999999999999999999999999999996642 22 344444432 2332221111
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccc
Q psy1615 81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGK 155 (295)
Q Consensus 81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~ 155 (295)
++.+.++.+.+++.+|++|++|++||+|||||+||+||++ |+.+...|+.+|++++.+| +. ||+.|.||++
T Consensus 142 ~~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~k 217 (259)
T cd06932 142 PFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRP----GLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAK 217 (259)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcc----cCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHH
Confidence 2345556678999999999999999999999999999999 8999999999999985554 43 8999999999
Q ss_pred cccccchhhhhhcCCCccchhhhh
Q psy1615 156 PLPLNQHYTATISNVPLSSSLSTA 179 (295)
Q Consensus 156 lLl~~~y~~r~~~~c~id~l~r~~ 179 (295)
|| +++...|..+..+++.+..-+
T Consensus 218 LL-l~L~~LRsl~~~~~e~l~~~k 240 (259)
T cd06932 218 LL-QKMVDLRQLVTDHVQMVQQIK 240 (259)
T ss_pred HH-HHHHHHHHHHHHHHHHHHHHH
Confidence 55 445556666666666655443
No 36
>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=99.96 E-value=3.5e-29 Score=205.62 Aligned_cols=157 Identities=27% Similarity=0.326 Sum_probs=131.1
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA 81 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (295)
.++++|+.+++.++.+|+|||++|+|..|+.+||+.|+|++|.++++++.|+++.+ +.+.+.+++|...... .....+
T Consensus 3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~-~~~~~~~~~~~~~~~~-~~~~~~ 80 (174)
T cd06929 3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDP-EKNSLTFGDGKGNSRD-VLLNGG 80 (174)
T ss_pred HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcc-cCCeEEecCCceecHH-HHHHcc
Confidence 47899999999999999999999999999999999999999999999999986654 5566777777654332 222223
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCccccc
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKP 156 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~l 156 (295)
..+.++.+.+++.+|++|++|++||+|||||+|||||++ |+++...|++.|+++..++ +. |+++|.||++|
T Consensus 81 ~~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~----~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~L 156 (174)
T cd06929 81 FGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRP----GLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKL 156 (174)
T ss_pred cHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcc----cCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHH
Confidence 445667788999999999999999999999999999999 7889999999999885554 43 78999999997
Q ss_pred ccccchhh
Q psy1615 157 LPLNQHYT 164 (295)
Q Consensus 157 Ll~~~y~~ 164 (295)
|+.++...
T Consensus 157 l~~l~~lr 164 (174)
T cd06929 157 LKKLTELR 164 (174)
T ss_pred HHHhHHHH
Confidence 76665543
No 37
>KOG4215|consensus
Probab=99.96 E-value=1.2e-28 Score=212.30 Aligned_cols=179 Identities=27% Similarity=0.370 Sum_probs=146.9
Q ss_pred CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHH
Q psy1615 1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVV 80 (295)
Q Consensus 1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (295)
+|..++|+...+.|..+|||||.||.|.+|+.+||++|||+...+.++|+.++|++..++-.++ ++........ ..+.
T Consensus 154 at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll-~N~~v~~~~~-~~~~ 231 (432)
T KOG4215|consen 154 ATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLL-NNTYVLHRHA-PDLP 231 (432)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEe-cCceeeccCC-CChH
Confidence 5788999999999999999999999999999999999999999999999999999987655444 3433332211 1222
Q ss_pred HHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHH--HHHHHHHHHHHHHhhC------CCCCC
Q psy1615 81 AFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKAL--HVDSAEYSCLKAIVLF------TTGKR 151 (295)
Q Consensus 81 ~~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~--~i~~~q~~~l~~l~~~------~~~~~ 151 (295)
.+.... |.+.+++.+||+|++|+.||+|||||+||+||.. |+++.. .|+++++++++.+..| .+.+.
T Consensus 232 eis~v~~RIiDElv~Pmr~L~md~~Ey~cLKAi~FfdP~ak----Gis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~ 307 (432)
T KOG4215|consen 232 EISRVAPRIIDELVNPMRRLQMDEIEYVCLKAIAFFDPDAK----GLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPG 307 (432)
T ss_pred HHHHHHHHHHHHHhhHHHHhccchHHHHHHHHHHhcCcccc----ccCCchHhHHHHHHHHHHHHHHHHHhhcCcccccc
Confidence 222222 7899999999999999999999999999999999 788888 8999999997776552 46778
Q ss_pred cccccccccch-------------hhhhhcCCCccchhhhhhhcCCC
Q psy1615 152 MFGKPLPLNQH-------------YTATISNVPLSSSLSTAVQRGRV 185 (295)
Q Consensus 152 Rf~~lLl~~~y-------------~~r~~~~c~id~l~r~~~q~~r~ 185 (295)
|||+|||+++. +.+.+|-..||.++.++...+..
T Consensus 308 R~g~LLLllPsLqsIt~qliE~iqlaklFGla~vDsll~e~~l~~~~ 354 (432)
T KOG4215|consen 308 RFGNLLLLLPSLQSITQQLIEQIQLAKLFGLAKVDSLLQEFLLGGEP 354 (432)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhcCCCC
Confidence 99999888743 45788999999999998887543
No 38
>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=99.96 E-value=2.2e-28 Score=209.20 Aligned_cols=177 Identities=23% Similarity=0.281 Sum_probs=142.6
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
+.++++++...+..+|+|||++|+|..|+.+||+.|||++|+|+++|+.|+++. .+.+.+.+++|..+..... ...++
T Consensus 41 ~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~-~~~~~~~f~~g~~~~~~~~-~~~~~ 118 (231)
T cd06938 41 FRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYD-AKTDSIVFANNQPYTRDSY-RKAGM 118 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhC-CCCCeEEeeCCEEecHHHH-hhcCH
Confidence 578999999999999999999999999999999999999999999999998764 4566677888876655332 22344
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCC-CCCccccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTT-GKRMFGKP 156 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~-~~~Rf~~l 156 (295)
.+.++.+.+++.+|++|++|++||+|||||+||+ |++ |+++...|+.+|+.++.+ |+. ||. +|.||++|
T Consensus 119 ~~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d~~----~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kL 193 (231)
T cd06938 119 GDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRP----GLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKL 193 (231)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcc-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHH
Confidence 4556778899999999999999999999999997 678 788999999999988555 443 666 89999995
Q ss_pred ccccchhhhhhcCCCccchhhhhhhcCCCCC
Q psy1615 157 LPLNQHYTATISNVPLSSSLSTAVQRGRVPP 187 (295)
Q Consensus 157 Ll~~~y~~r~~~~c~id~l~r~~~q~~r~~~ 187 (295)
|.++...|..+.-+++.++.-++..-++||
T Consensus 194 -L~~L~~Lr~l~~~~~e~~~~~k~~~~~~~p 223 (231)
T cd06938 194 -LSILTELRTLGNQNSEMCFSLKLKNRKLPP 223 (231)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHhCCCCCc
Confidence 455566677777777777666665444444
No 39
>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=99.95 E-value=1.6e-27 Score=203.11 Aligned_cols=171 Identities=28% Similarity=0.429 Sum_probs=135.1
Q ss_pred CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHH
Q psy1615 1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVV 80 (295)
Q Consensus 1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (295)
++.+.+|+.+.+.++.+|+|||.+|+|..|+.+||++|+|++|++++++..|++++..+ +.+++.+|..+...... .
T Consensus 32 ~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~-~~l~~~~g~~~~~~~~~--~ 108 (222)
T cd06931 32 ASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYK-DILLLGNDLIIPRHCPE--P 108 (222)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCC-CeeeeCCCccccccccc--c
Confidence 47899999999999999999999999999999999999999999999999999998654 44555666544332211 1
Q ss_pred HHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCCCccc
Q psy1615 81 AFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGKRMFG 154 (295)
Q Consensus 81 ~~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~~Rf~ 154 (295)
++...+ +.+.+++.+|++|++|++||++||||++|+||++ |+++...++.+|++++.+|.. ++++|.||+
T Consensus 109 ~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~----~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~ 184 (222)
T cd06931 109 EISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAK----GLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFG 184 (222)
T ss_pred hHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcc----CCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHH
Confidence 222222 4466899999999999999999999999999999 788899999999987555433 678899999
Q ss_pred ccccccchh-------------hhhhcCCCccchhhh
Q psy1615 155 KPLPLNQHY-------------TATISNVPLSSSLST 178 (295)
Q Consensus 155 ~lLl~~~y~-------------~r~~~~c~id~l~r~ 178 (295)
+||+.++.. .+.++..+++.++.+
T Consensus 185 ~LL~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e 221 (222)
T cd06931 185 ELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQE 221 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhh
Confidence 988876433 344555555555543
No 40
>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=99.90 E-value=8.4e-23 Score=165.90 Aligned_cols=155 Identities=35% Similarity=0.488 Sum_probs=125.0
Q ss_pred HHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccC--hhhHHHHHHH
Q psy1615 5 NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHAS--PMAADRVVAF 82 (295)
Q Consensus 5 ~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 82 (295)
++++++.+.+..+++|+|++|+|..|+.+||+.|+|++|.++++|+.++++........+..++.... ..........
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (168)
T cd06157 2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK 81 (168)
T ss_pred cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence 58899999999999999999999999999999999999999999999999998877766655554211 1111111222
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CC-CCCCccccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FT-TGKRMFGKP 156 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~-~~~~Rf~~l 156 (295)
....+.+.+++.+|++|++|++||++||||++|+|+.++ +..+...++..|+.+.+++.. ++ +.+.||++|
T Consensus 82 ~~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~---s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~l 158 (168)
T cd06157 82 GELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE---SLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKL 158 (168)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCC---CccCHHHHHHHHHHHHHHHHHHHHHhCCccchhHHHHH
Confidence 234477889999999999999999999999999999984 367888899999888555443 44 888899998
Q ss_pred ccccch
Q psy1615 157 LPLNQH 162 (295)
Q Consensus 157 Ll~~~y 162 (295)
|+.+..
T Consensus 159 l~~l~~ 164 (168)
T cd06157 159 LLLLPS 164 (168)
T ss_pred HHhchh
Confidence 876654
No 41
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=99.88 E-value=6.3e-22 Score=159.91 Aligned_cols=149 Identities=28% Similarity=0.385 Sum_probs=118.4
Q ss_pred HHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHH--HHHHHHHHHH
Q psy1615 11 ARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADR--VVAFMDHIRV 88 (295)
Q Consensus 11 ~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 88 (295)
.+.+..+|+|+|++|+|.+|+.+||+.|+|++|.++++|..++++...+...+++++|.......... ........+.
T Consensus 2 ~~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (163)
T smart00430 2 ERDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRI 81 (163)
T ss_pred hhHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHH
Confidence 45788999999999999999999999999999999999999999998777666666665444322211 1112233477
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhH--HHHHHHHHHHHHHHhh-----CC-CCCCccccccccc
Q psy1615 89 FQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKA--LHVDSAEYSCLKAIVL-----FT-TGKRMFGKPLPLN 160 (295)
Q Consensus 89 l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~--~~i~~~q~~~l~~l~~-----~~-~~~~Rf~~lLl~~ 160 (295)
+.+++.+|++|++|++||++|+||++|+|+.+ ++++. ..+++.|+.+..+|.. ++ +.+.||++||+.+
T Consensus 82 ~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~~----~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l 157 (163)
T smart00430 82 LQELVKPLRELKLDDEEYALLKAILLFNPAGP----GLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGRFGELLLIL 157 (163)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcChhhh----hhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHH
Confidence 88999999999999999999999999999999 67777 8899999887555433 44 5678999988776
Q ss_pred chh
Q psy1615 161 QHY 163 (295)
Q Consensus 161 ~y~ 163 (295)
...
T Consensus 158 ~~i 160 (163)
T smart00430 158 NAI 160 (163)
T ss_pred HHh
Confidence 543
No 42
>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=99.87 E-value=1.4e-21 Score=163.69 Aligned_cols=158 Identities=27% Similarity=0.428 Sum_probs=124.1
Q ss_pred cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHH--
Q psy1615 2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRV-- 79 (295)
Q Consensus 2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~-- 79 (295)
+++++++++.+.+..+|+|||++|+|.+|+.+||..|+|++|.++++|..++++...+.+.+.+.+|...........
T Consensus 18 ~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (203)
T PF00104_consen 18 TFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDSFDDFIT 97 (203)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHHHHHTST
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcccccccccccccccccccccccccc
Confidence 578899999999999999999999999999999999999999999999999999854555677777776544333332
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccch-hHHH-HHHHHHHHHHH---Hh-h--CCCC-C
Q psy1615 80 VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLL-KALH-VDSAEYSCLKA---IV-L--FTTG-K 150 (295)
Q Consensus 80 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~-~~~~-i~~~q~~~l~~---l~-~--~~~~-~ 150 (295)
....+.++.+.+++.+|+++++|++||++|+|++||+||.+ +++ +... ++..|+++++. |+ . ++.+ +
T Consensus 98 ~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~----~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~~ 173 (203)
T PF00104_consen 98 GIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYP----GLSEETREIVEELRDRIIQALHSYYNQSKGPEDYA 173 (203)
T ss_dssp TTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTST----THS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTHT
T ss_pred cccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhccccc----ccccchhHHHHHHHHHHHHHHHHHHhccCCCccHH
Confidence 23345556888999999999999999999999999999999 454 4444 78888876444 44 2 3333 7
Q ss_pred Ccccccccccchh
Q psy1615 151 RMFGKPLPLNQHY 163 (295)
Q Consensus 151 ~Rf~~lLl~~~y~ 163 (295)
.|||+|++++...
T Consensus 174 ~R~~~ll~ll~~l 186 (203)
T PF00104_consen 174 QRFGKLLLLLPSL 186 (203)
T ss_dssp THHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 8999987666544
No 43
>KOG4218|consensus
Probab=99.80 E-value=4.9e-19 Score=151.75 Aligned_cols=175 Identities=23% Similarity=0.300 Sum_probs=137.0
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHH-
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVV- 80 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~- 80 (295)
..-.|++|++.++.+|+|||+--.|++|+.+||++||+++|.|++++++.|+.+..+.. .+...+|..+.-.......
T Consensus 276 fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgkegsi~lvtGqeV~~~~vA~qag 355 (475)
T KOG4218|consen 276 FGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKEGSIKLVTGQEVPVGLVALQAG 355 (475)
T ss_pred hhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcccceEEecCCcccchhHhhhhh
Confidence 44578999999999999999999999999999999999999999999999999866543 3555566544322222211
Q ss_pred -HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCCCccc
Q psy1615 81 -AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGKRMFG 154 (295)
Q Consensus 81 -~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~~Rf~ 154 (295)
-....+...++++.+++.|++|..||+|||.++||+-|.. .|++-..|+.+|++...++.. ||+....|+
T Consensus 356 s~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LFsld~k----fLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF~ 431 (475)
T KOG4218|consen 356 SLLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALFSLDMK----FLENFELVRRLQEDSNAALLDYTSCCYPNWEQKFP 431 (475)
T ss_pred hHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHHhhhHH----HHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHH
Confidence 1334456778999999999999999999999999999999 899999999999998777643 888889999
Q ss_pred ccccccc-------------hhhhhhcCCCccchhhhhhh
Q psy1615 155 KPLPLNQ-------------HYTATISNVPLSSSLSTAVQ 181 (295)
Q Consensus 155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~q 181 (295)
+++|.+. |+....+..+-..+.-++++
T Consensus 432 qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~ 471 (475)
T KOG4218|consen 432 QLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLT 471 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhh
Confidence 9888763 33444444554444444444
No 44
>KOG4215|consensus
Probab=99.74 E-value=6.9e-19 Score=152.23 Aligned_cols=123 Identities=23% Similarity=0.271 Sum_probs=89.9
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCCCCchhhHHHhhhcCCCCCCChHHHHHHHHhc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRA 239 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~a 239 (295)
..|.||...+|.+|+-.|++|..||+ +||+++||++++++.++++-..+.+... ++ .+-...++.|+++
T Consensus 54 ~~YtCRF~k~C~VDKdkRNaCRyCRf---qKC~~aGMK~eAiQnERDrIg~Rr~~~~---~~-----n~~~~~id~L~~a 122 (432)
T KOG4215|consen 54 HQYTCRFNKQCVVDKDKRNACRYCRF---QKCVRAGMKREAIQNERDRIGSRRPSYE---AG-----NENSPSIDALVQA 122 (432)
T ss_pred ceeeeeccccccccchhhhhhhHhhH---HHHHHhcccHHhhhcccccccccCCCCC---CC-----CCCchhHHHHHhH
Confidence 47999999999999999999999999 9999999999999888775443222110 11 1222334444444
Q ss_pred CC----CCCC-----cC---C--CCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 240 EP----YPTA-----RY---S--QCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 240 e~----~~~~-----~~---~--~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
|. ...+ .+ + ...+.....+.+++||...++|..+|||||.||+|.+|+++|||+
T Consensus 123 E~~~~q~~~srs~~~~~~~~d~r~~~~n~~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~Dqva 190 (432)
T KOG4215|consen 123 EALVRQLRSSRSGGVPGIDGDIRQGPPNKKIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVA 190 (432)
T ss_pred HHHHhhhhccccccCcCcchhhhcCccccccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHH
Confidence 43 2111 11 1 112233457789999999999999999999999999999999986
No 45
>KOG4217|consensus
Probab=99.67 E-value=2.4e-17 Score=146.72 Aligned_cols=127 Identities=20% Similarity=0.239 Sum_probs=92.2
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc-CCCCCchhhHHHhhhcCCCCCCChHHHHHHHHhc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT-NGDSASAASAAIAAAGLNGHSSYLSSYISLLLRA 239 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~a 239 (295)
-|+|-.+.+||||+.+|++||.||+ ||||.|||.+|-||... .|++.+.++.. ...+.... ++.-.++.++.+|
T Consensus 305 KYvClanKnCPVDKRrRnRCQyCRf---QKCL~VGMVKEVVRtdSLkGRRGRLpSKp-Ks~q~spp-SpPi~LltalvrA 379 (605)
T KOG4217|consen 305 KYVCLANKNCPVDKRRRNRCQYCRF---QKCLAVGMVKEVVRTDSLKGRRGRLPSKP-KSRQPSPP-SPPISLLTALVRA 379 (605)
T ss_pred eeEeecCCCCCcchhhhhhchhhhH---hHHHHhhhhhhheeccccccccCCCCCCC-CCCCCCCC-CCchHHHHHHHHH
Confidence 3889999999999999999999999 99999999999987432 22222222111 11111122 4456788888888
Q ss_pred CCCCCC--------cC---CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCccc
Q psy1615 240 EPYPTA--------RY---SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGV 292 (295)
Q Consensus 240 e~~~~~--------~~---~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv 292 (295)
+-.... .+ .....+++...+..|+++.+-.|..+-+||.+||||.+|+.+||-
T Consensus 380 h~Dstp~~~~ldys~~q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~ 443 (605)
T KOG4217|consen 380 HVDSTPSTMTLDYSRFQELVPHFSGTDALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQD 443 (605)
T ss_pred hhcCCCCcchhhHHHhccccccccccHHHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHH
Confidence 653322 11 122344455678999999999999999999999999999999994
No 46
>KOG4216|consensus
Probab=99.60 E-value=5.2e-16 Score=135.37 Aligned_cols=136 Identities=15% Similarity=0.128 Sum_probs=108.4
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
+++...-....+..+|||||.|+||.+|+++||+.|||.+.+|+.+.+++..+ +...+.+++..... +.......+.
T Consensus 284 We~cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~-~v~~ntV~~e~~~~--g~~~f~a~~~ 360 (479)
T KOG4216|consen 284 WELCAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAF-DVDNNTVYFEGKYA--GPEVFYALGC 360 (479)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhh-cccccceeeccccc--chhheeccCh
Confidence 34445556678999999999999999999999999999999999999988555 45555666544322 1112222344
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL 145 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~ 145 (295)
.+.+...+++...+-.|++++.|++|+.|+||.+||++ |+.+..+|+.+|++...+|..
T Consensus 361 ~elis~vf~~~ksL~~Lq~te~EiAL~~alVL~~~~r~----gl~e~~ki~~lq~~~~~a~qh 419 (479)
T KOG4216|consen 361 EELISRVFEFGKSLCSLQLTEDEIALFSALVLMSADRS----GLQEKVKIEKLQQKIQLALQH 419 (479)
T ss_pred HHHHHHHHhhhHHHHhhccCcHHHHHHHHHHhhCCccc----cccchHHHHHHHHHHHHHHHH
Confidence 45666778999999999999999999999999999999 899999999999887665554
No 47
>KOG4217|consensus
Probab=99.53 E-value=2.3e-13 Score=121.57 Aligned_cols=145 Identities=25% Similarity=0.365 Sum_probs=123.1
Q ss_pred HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615 3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF 82 (295)
Q Consensus 3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (295)
+++++++.+-.+-.+-.||.+||+|.+|+.+||-.|+.++++|+++|+.|||+-+. .+.++|-+|..+.. ...+.++
T Consensus 410 vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~-e~kliFcsG~vlhr--~qC~rgf 486 (605)
T KOG4217|consen 410 VQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPS-EDKLIFCSGLVLHR--LQCLRGF 486 (605)
T ss_pred HHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCC-CCeEEEecchhhhH--HHHHHHH
Confidence 57788889999999999999999999999999999999999999999999999654 45677778876655 4566688
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hhC----CCCCCcccc
Q psy1615 83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VLF----TTGKRMFGK 155 (295)
Q Consensus 83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~~----~~~~~Rf~~ 155 (295)
++.++.+.+|...+..|.+|-.-|+||.|+++.. ++. ||+++.+||++|.+....| +.+ ...+.++.+
T Consensus 487 gewidsi~~FS~~l~~l~idi~AfacL~aLa~iT-Erh----GL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSr 561 (605)
T KOG4217|consen 487 GEWIDSIREFSRSLHSLNIDISAFACLSALALIT-ERH----GLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSR 561 (605)
T ss_pred HHHHHHHHHHHHHhhhchhhHHHHHHHHHHHhhh-hhh----cCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHH
Confidence 8888999999999999999999999999999877 666 8999999999999975544 432 244556766
No 48
>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=99.41 E-value=1.5e-13 Score=117.75 Aligned_cols=62 Identities=26% Similarity=0.400 Sum_probs=55.2
Q ss_pred HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+++.+..+||... ..++++.+++....++++|++|+|+|+.+|+|||+||||++|+++|||+
T Consensus 2 ~~~~l~~~ep~~~~~~~d~~~p~~~~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~ 64 (247)
T cd07076 2 LVSLLEVIEPEVLYSGYDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMT 64 (247)
T ss_pred HHHHHHHcCCCcccCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence 5788889999765 4457777888888899999999999999999999999999999999985
No 49
>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=99.31 E-value=1.4e-12 Score=111.94 Aligned_cols=62 Identities=21% Similarity=0.339 Sum_probs=53.0
Q ss_pred HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+++.+..+||.+. ..+++..+++....++++|++|+++|+.+|+|||+||||++|+.+|||+
T Consensus 2 ~~~~l~~~e~~~~~~~~~~~~p~~~~~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~ 64 (248)
T cd07075 2 PVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQIT 64 (248)
T ss_pred HHHHHhhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHH
Confidence 4667778888764 4456666777777899999999999999999999999999999999985
No 50
>KOG4216|consensus
Probab=99.31 E-value=2.3e-13 Score=118.97 Aligned_cols=40 Identities=18% Similarity=0.213 Sum_probs=37.5
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA 203 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~ 203 (295)
-|.|+...+|.||+..|++||+||+ +||+..||+|++|+.
T Consensus 82 ~YsCpRqknC~iDRtnRNRCQ~CRL---qKClaLGMSRDAVKF 121 (479)
T KOG4216|consen 82 NYSCPRQKNCLIDRTNRNRCQHCRL---QKCLALGMSRDAVKF 121 (479)
T ss_pred cccCCcccCCcccccccchhhHHHH---HHHHHhccchhhHHh
Confidence 4889999999999999999999999 999999999998863
No 51
>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=99.30 E-value=1.9e-12 Score=110.96 Aligned_cols=62 Identities=26% Similarity=0.461 Sum_probs=54.4
Q ss_pred HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+++.|..+||... .++++..++++...++++|++|+|+|+.+|||||++|||.+|+.+|||+
T Consensus 2 ~~~~l~~~ep~~~~~~~d~~~p~~~~~~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~ 64 (248)
T cd07074 2 LINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQIT 64 (248)
T ss_pred HhHHHHHhCCCcccCCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence 5788999999654 4446777777778899999999999999999999999999999999985
No 52
>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=99.29 E-value=2.4e-12 Score=110.33 Aligned_cols=65 Identities=31% Similarity=0.398 Sum_probs=57.7
Q ss_pred hHHHHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 229 LSSYISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 229 ~~~l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
...+++.+..+||... ..+++..+++....++++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus 3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~ 68 (235)
T cd06949 3 AEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVH 68 (235)
T ss_pred HHHHHHHHHHhCCCcCcCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence 4568999999999764 5556677788888999999999999999999999999999999999985
No 53
>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=99.28 E-value=2.7e-12 Score=110.42 Aligned_cols=62 Identities=23% Similarity=0.352 Sum_probs=51.2
Q ss_pred HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+++.+..+||... +.+++..+.+....++++|++|+++|+.+|+|||+||||++|+.+|||+
T Consensus 2 ~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~ 64 (246)
T cd07073 2 FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMA 64 (246)
T ss_pred hHHHHhhcCCccccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHH
Confidence 4677778899654 3345555555667789999999999999999999999999999999985
No 54
>KOG4218|consensus
Probab=99.27 E-value=6e-13 Score=114.64 Aligned_cols=41 Identities=20% Similarity=0.183 Sum_probs=37.7
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL 204 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~ 204 (295)
.|.|-...+|+||+-.|.+|..||+ +||+.|||+-|+||+.
T Consensus 51 ~YtC~e~qnC~iDkTqRKRCP~CRF---QKCLtvGMklEAVRAD 91 (475)
T KOG4218|consen 51 QYTCSEEQNCHIDKTQRKRCPSCRF---QKCLTVGMKLEAVRAD 91 (475)
T ss_pred ceecccccccccchHhhccCCchhH---HHHhhhhhhHHHHHHh
Confidence 5889999999999999999999999 9999999998887643
No 55
>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=99.27 E-value=3.6e-12 Score=109.65 Aligned_cols=62 Identities=26% Similarity=0.413 Sum_probs=54.1
Q ss_pred HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+++++..+||... ..++++.+++....++++|++|+++|+.+|+|||+||||.+|+.+|||+
T Consensus 2 ~~~~l~~~ep~~~~~~~~~~~p~~~~~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~ 64 (246)
T cd06947 2 LLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMT 64 (246)
T ss_pred HHHHHHhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHH
Confidence 6788999999654 4446667777778899999999999999999999999999999999985
No 56
>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=99.09 E-value=1e-10 Score=100.50 Aligned_cols=64 Identities=84% Similarity=1.309 Sum_probs=53.2
Q ss_pred HHHHHHHHhcCCCCCCcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 230 SSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 230 ~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+.+++.+..+||++....+...++.....++++|++|+++|+.+|+|||++|||.+|+.+||++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~ 66 (236)
T cd06948 3 SSYISLLLRAEPYPTSRYGSQCQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVA 66 (236)
T ss_pred hhHHHHHHhcccCccccCCCcCCccccchHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHH
Confidence 4578888999997655543333555567799999999999999999999999999999999985
No 57
>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=99.05 E-value=1.5e-10 Score=99.27 Aligned_cols=40 Identities=20% Similarity=0.252 Sum_probs=36.7
Q ss_pred CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
.+...+.++++++++.++.+|+|||+||||.+|+.+||++
T Consensus 39 ~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~ 78 (239)
T cd07072 39 SEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQEL 78 (239)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHH
Confidence 3446689999999999999999999999999999999985
No 58
>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=99.02 E-value=2.6e-10 Score=98.03 Aligned_cols=39 Identities=21% Similarity=0.324 Sum_probs=36.5
Q ss_pred CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+...++++|++++++|+.+|+|||+||||++|+.+||++
T Consensus 39 ~~~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~ 77 (239)
T cd06945 39 DSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDL 77 (239)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence 356789999999999999999999999999999999985
No 59
>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=99.01 E-value=1.3e-10 Score=99.82 Aligned_cols=66 Identities=18% Similarity=0.300 Sum_probs=51.2
Q ss_pred ChHHHHHHHHhcCCCCCC----cCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 228 YLSSYISLLLRAEPYPTA----RYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 228 ~~~~l~~~l~~ae~~~~~----~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
....+++.+..|++.... .+....++.+...+.+++++++++|+.+|+|||+||||.+|+.+|||+
T Consensus 4 ~q~~li~~l~~a~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~ 73 (238)
T cd06933 4 EQQKIIDILLEAHHKTYDTTYSDFNKFRPPVRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIA 73 (238)
T ss_pred HHHHHHHHHHHHHHHhcccchhHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHH
Confidence 356788888888873211 112233344566789999999999999999999999999999999985
No 60
>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=99.00 E-value=3e-10 Score=97.27 Aligned_cols=39 Identities=23% Similarity=0.339 Sum_probs=36.3
Q ss_pred CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+...++++||++++.|+.+|+|||+||||++|+.+||++
T Consensus 39 ~~~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~ 77 (238)
T cd07348 39 DASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQEL 77 (238)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHH
Confidence 346689999999999999999999999999999999985
No 61
>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=98.96 E-value=5e-10 Score=95.97 Aligned_cols=39 Identities=23% Similarity=0.309 Sum_probs=36.3
Q ss_pred CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+...+.++||++++.|+.+|+|||+||||.+|+.+|||+
T Consensus 39 ~~~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~ 77 (238)
T cd07071 39 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDL 77 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHH
Confidence 346689999999999999999999999999999999985
No 62
>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=98.96 E-value=5.2e-10 Score=95.24 Aligned_cols=61 Identities=28% Similarity=0.442 Sum_probs=50.9
Q ss_pred HHHHHhcCCCCCCc-CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 233 ISLLLRAEPYPTAR-YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 233 ~~~l~~ae~~~~~~-~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
++++..+||..... ..+..+++....+.++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~ 63 (221)
T cd06946 2 LSHLLVAEPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMS 63 (221)
T ss_pred hHHHhhcCCccccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence 56788899965432 24455556678899999999999999999999999999999999985
No 63
>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=98.89 E-value=5.1e-10 Score=96.13 Aligned_cols=41 Identities=24% Similarity=0.532 Sum_probs=37.7
Q ss_pred CCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 253 PNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 253 ~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
.++...++++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus 34 ~~~~~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~ 74 (237)
T cd07070 34 PDQPAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMT 74 (237)
T ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHH
Confidence 34567799999999999999999999999999999999985
No 64
>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=98.87 E-value=1.8e-09 Score=90.88 Aligned_cols=40 Identities=43% Similarity=0.752 Sum_probs=36.7
Q ss_pred CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
.+...++++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus 23 ~~~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~ 62 (206)
T cd06950 23 SYEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLI 62 (206)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHH
Confidence 3456689999999999999999999999999999999985
No 65
>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=98.85 E-value=1.3e-09 Score=93.86 Aligned_cols=40 Identities=33% Similarity=0.670 Sum_probs=37.0
Q ss_pred CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
.....+..+|++|++.|+.+|+|||+||||.+|+.+||++
T Consensus 37 ~~~~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~ 76 (241)
T cd07069 37 EKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMK 76 (241)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHH
Confidence 3456789999999999999999999999999999999985
No 66
>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=98.84 E-value=1.6e-09 Score=91.62 Aligned_cols=43 Identities=23% Similarity=0.617 Sum_probs=38.8
Q ss_pred CCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 251 MQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 251 ~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
.+++....++++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus 21 ~~~~~~~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~ 63 (213)
T cd06953 21 ATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTH 63 (213)
T ss_pred CCcchhhHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHH
Confidence 3445567899999999999999999999999999999999985
No 67
>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=98.84 E-value=9.3e-10 Score=94.13 Aligned_cols=39 Identities=23% Similarity=0.406 Sum_probs=36.6
Q ss_pred CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+...+.++||+++++|+.+|+|||+||||.+|+.+||++
T Consensus 36 ~~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~ 74 (231)
T cd06937 36 DLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQIT 74 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHH
Confidence 456789999999999999999999999999999999985
No 68
>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=98.77 E-value=3.3e-09 Score=91.47 Aligned_cols=39 Identities=13% Similarity=0.423 Sum_probs=36.5
Q ss_pred CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+...|.++|++++++|+.+|+|||+||||++|+.+|||+
T Consensus 50 ~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~ 88 (243)
T cd06935 50 DLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQII 88 (243)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHH
Confidence 456799999999999999999999999999999999985
No 69
>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=98.77 E-value=1e-08 Score=87.35 Aligned_cols=65 Identities=26% Similarity=0.425 Sum_probs=56.1
Q ss_pred hHHHHHHHHhcCCCCCCcC--CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 229 LSSYISLLLRAEPYPTARY--SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 229 ~~~l~~~l~~ae~~~~~~~--~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
++.+++++.++++.+.+.+ ......+...+.+.+|+.+.+.++.+|+|||++|+|.+|+.+||++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~ 68 (222)
T cd06931 2 ISVLLQAEALSRQQSSPIPTCSGDIRPKKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVA 68 (222)
T ss_pred HHHHHHHHHhhcCCCCCCCCCCCCCCccccCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHH
Confidence 6788999999999887765 2334456678899999999999999999999999999999999985
No 70
>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=98.75 E-value=4.5e-09 Score=89.65 Aligned_cols=38 Identities=13% Similarity=0.435 Sum_probs=35.6
Q ss_pred cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
...+.++++++++.++.+|+|||+||||.+|+.+|||+
T Consensus 34 ~~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~ 71 (226)
T cd06934 34 FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQIS 71 (226)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHH
Confidence 45688999999999999999999999999999999985
No 71
>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=98.73 E-value=9.1e-09 Score=87.60 Aligned_cols=60 Identities=30% Similarity=0.421 Sum_probs=48.5
Q ss_pred HHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 234 SLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 234 ~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+.+..+||... ..++...+.+....++++|++|++.++.+|+|||++|+|.+|+.+||++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~ 63 (221)
T cd07068 3 SALLVAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMH 63 (221)
T ss_pred HHHHhhCCCcccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence 44556677543 2234556666778899999999999999999999999999999999985
No 72
>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=98.66 E-value=1e-08 Score=88.14 Aligned_cols=39 Identities=36% Similarity=0.701 Sum_probs=36.4
Q ss_pred CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+...++.+|++|++.|+.+|+|||++|||.+|+.+||++
T Consensus 36 ~~~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~ 74 (237)
T cd06944 36 ELDTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMK 74 (237)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHH
Confidence 446789999999999999999999999999999999985
No 73
>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=98.63 E-value=1.6e-08 Score=87.04 Aligned_cols=39 Identities=21% Similarity=0.172 Sum_probs=36.5
Q ss_pred CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
....|.++.+..+..+..+|+|||+||||.+|+.+|||+
T Consensus 46 ~~~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~ 84 (241)
T cd06939 46 REEMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIV 84 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence 446799999999999999999999999999999999985
No 74
>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=98.59 E-value=8.1e-08 Score=80.94 Aligned_cols=37 Identities=41% Similarity=0.741 Sum_probs=35.2
Q ss_pred ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
..++++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus 30 ~~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~ 66 (207)
T cd06943 30 DPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVI 66 (207)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHH
Confidence 5689999999999999999999999999999999985
No 75
>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=98.58 E-value=3.4e-08 Score=84.92 Aligned_cols=37 Identities=22% Similarity=0.328 Sum_probs=35.2
Q ss_pred ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
..+.++++.++..++.+|+|||+||||.+|+.+||++
T Consensus 43 ~~~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~ 79 (236)
T cd06954 43 QRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIA 79 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHH
Confidence 4689999999999999999999999999999999985
No 76
>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=98.44 E-value=1e-07 Score=81.07 Aligned_cols=38 Identities=21% Similarity=0.316 Sum_probs=35.8
Q ss_pred cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
...+.++++.+++.++.+|+|||+||||.+|+.+||++
T Consensus 35 ~~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~ 72 (221)
T cd06936 35 EENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIA 72 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHH
Confidence 36799999999999999999999999999999999985
No 77
>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=98.44 E-value=8.7e-08 Score=83.32 Aligned_cols=39 Identities=18% Similarity=0.210 Sum_probs=35.6
Q ss_pred CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
+...|..+.+..+..+..+|+|||+||||.+|+.+|||+
T Consensus 61 ~~~~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~ 99 (259)
T cd06932 61 RIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVT 99 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHH
Confidence 345688899999999999999999999999999999985
No 78
>KOG4846|consensus
Probab=98.37 E-value=2.5e-07 Score=82.21 Aligned_cols=36 Identities=14% Similarity=0.175 Sum_probs=34.0
Q ss_pred hhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615 164 TATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA 202 (295)
Q Consensus 164 ~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~ 202 (295)
|-...+|.|-+..|++||.||+ +|||.|||+|++||
T Consensus 172 Clk~e~C~I~R~nRNRCQ~CRf---KKCL~vGMSrDaVR 207 (538)
T KOG4846|consen 172 CLKQEVCEIKRENRNRCQYCRF---KKCLDVGMSRDAVR 207 (538)
T ss_pred HhhhhceehhhhccchhhhhhH---HHHHhcccchhhhh
Confidence 6668899999999999999999 99999999999987
No 79
>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=98.37 E-value=2e-07 Score=79.93 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=35.8
Q ss_pred cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615 256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR 293 (295)
Q Consensus 256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~ 293 (295)
...+.++|++++..++.+|+|||+||||.+|+.+||++
T Consensus 38 ~~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~ 75 (231)
T cd06938 38 DMRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQIT 75 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHH
Confidence 36689999999999999999999999999999999985
No 80
>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=97.83 E-value=6.6e-06 Score=59.33 Aligned_cols=46 Identities=13% Similarity=0.061 Sum_probs=39.8
Q ss_pred ch-hhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCCC
Q psy1615 161 QH-YTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDS 209 (295)
Q Consensus 161 ~y-~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~~ 209 (295)
.| .|...++|.|+...+..|+.||+ +||+++||.++.++..+.+..
T Consensus 39 ~~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~~~r~~~~ 85 (89)
T cd07166 39 QYRKCTKNETCSIMRINRNRCQYCRF---KKCLAVGMSRDAVRFGRIPKR 85 (89)
T ss_pred cchhhccCCcccccccccccccchhh---hhcccccCCHHHhcCCCCCCc
Confidence 46 48888999999999999999999 999999999999876665543
No 81
>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=97.83 E-value=4.2e-06 Score=58.87 Aligned_cols=43 Identities=9% Similarity=0.075 Sum_probs=38.2
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN 206 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~ 206 (295)
.|.|...++|.|+...+..|+.||+ +||++|||.++.++..+.
T Consensus 34 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~r~ 76 (78)
T cd07164 34 AYVCKENGSCVVDVARRNQCQACRF---KKCLQVNMNRDAVQHERA 76 (78)
T ss_pred CccCCCCCcccccCcccccCccchh---hhhhHhcCCHHHhccCCC
Confidence 5778888999999999999999999 999999999998865543
No 82
>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=97.82 E-value=4.8e-06 Score=59.53 Aligned_cols=44 Identities=9% Similarity=0.109 Sum_probs=39.0
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG 207 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~ 207 (295)
.|.|...++|.++...+..|+.||+ +||++|||+++.++..+.+
T Consensus 35 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~r~~ 78 (85)
T cd06961 35 SYSCKGEGKCEIDKVTRNQCQECRF---KKCIAVGMAKDLVLDDRKR 78 (85)
T ss_pred ccccCCCCccccCccccccCccchh---hhhhhccCCHHHcccccCc
Confidence 5788888999999999999999999 9999999999988655543
No 83
>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=97.80 E-value=2.7e-06 Score=60.33 Aligned_cols=43 Identities=12% Similarity=0.207 Sum_probs=38.3
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN 206 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~ 206 (295)
.|.|...++|.|+...+..|+.||+ +||+++||.+++++.++.
T Consensus 39 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~~~ 81 (82)
T cd07171 39 DYICPATNQCTIDKNRRKSCQACRL---RKCYEVGMMKGGIRRERR 81 (82)
T ss_pred ceeCCCCCccccCCcccccCccchh---HHHhHhcCCHHHHHHhhc
Confidence 5778888999999999999999999 999999999999865543
No 84
>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=97.79 E-value=7.6e-06 Score=58.09 Aligned_cols=46 Identities=11% Similarity=0.042 Sum_probs=39.1
Q ss_pred cchhhh-hhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCC
Q psy1615 160 NQHYTA-TISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGD 208 (295)
Q Consensus 160 ~~y~~r-~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~ 208 (295)
..|.|. ..++|.|+...+..|+.||+ +||+++||.++.++..+.+.
T Consensus 33 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~r~p~ 79 (82)
T cd06957 33 IIYTCIAGNGNCVVDKARRNWCPFCRL---QKCFAVGMNRAAVQEERGPR 79 (82)
T ss_pred CceEccCccCCCccCCCccCcccCcch---hhcccccCCHHHhccccCcC
Confidence 357887 46899999999999999999 99999999999987655443
No 85
>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=97.78 E-value=5.2e-06 Score=59.31 Aligned_cols=45 Identities=16% Similarity=0.103 Sum_probs=39.5
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG 207 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~ 207 (295)
..|.|...++|.|+...+..|+.||+ +||+++||.++.++..+.+
T Consensus 39 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~R~~ 83 (85)
T cd06964 39 MVYTCHRDKNCIINKVTRNRCQYCRL---QKCFEVGMSKESVRNDRNK 83 (85)
T ss_pred CCeECCCCCccccCCcccccCccchh---hhhhhhCCCHHHhhccccC
Confidence 45789888999999999999999999 9999999999998665543
No 86
>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=97.77 E-value=7.4e-06 Score=58.05 Aligned_cols=44 Identities=11% Similarity=0.059 Sum_probs=38.9
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG 207 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~ 207 (295)
.|.|...++|.++...+..|+.||+ +||+++||.++.++..+.+
T Consensus 34 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~V~~~r~~ 77 (81)
T cd07165 34 EYRCLRDGKCEIIRLNRNRCQYCRF---KKCLAAGMSKDSVRYGRIP 77 (81)
T ss_pred ceeCCCCCCccccccccccccchhh---hhcccccCCHHHcccCCCC
Confidence 5778888999999999999999999 9999999999998765544
No 87
>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=97.75 E-value=5.7e-06 Score=57.74 Aligned_cols=40 Identities=18% Similarity=0.180 Sum_probs=36.4
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA 203 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~ 203 (295)
.|.|...++|.|+...+..|+.||+ +||+++||.+++++.
T Consensus 34 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~ 73 (75)
T cd07155 34 GYSCPSTSECEVDKKRRKSCQACRL---QKCLKVGMLKEGVRL 73 (75)
T ss_pred ceeCCcCCCcccCCcccccCccchh---hhhhHhCCCHHHccc
Confidence 5778888999999999999999999 999999999998753
No 88
>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=97.74 E-value=4.7e-06 Score=58.47 Aligned_cols=41 Identities=15% Similarity=0.118 Sum_probs=36.9
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA 203 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~ 203 (295)
..|.|+..++|.++...+..|+.||+ +||+++||.++.++.
T Consensus 35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~ 75 (77)
T cd06956 35 LTYTCRDNKDCLIDKRQRNRCQYCRY---QKCLAMGMKREAVQE 75 (77)
T ss_pred CccccCCCCccccCCCccccCccchh---HHHhHhCCCHHHhcc
Confidence 35778888999999999999999999 999999999998754
No 89
>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=97.72 E-value=7.4e-06 Score=58.79 Aligned_cols=45 Identities=13% Similarity=0.120 Sum_probs=39.7
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG 207 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~ 207 (295)
..|.|...++|.|+...+..|+.||+ +||+++||+++.++..+.+
T Consensus 38 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~Vq~~R~~ 82 (87)
T cd06967 38 LGYSCRGSKDCVINKHHRNRCQYCRL---QKCLAMGMKSDSVQCERKP 82 (87)
T ss_pred CCcccCCCCccccCccccccCccchh---hhhhHcCCCHHHhccccCC
Confidence 35778888999999999999999999 9999999999998766554
No 90
>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=97.70 E-value=1e-05 Score=59.00 Aligned_cols=44 Identities=16% Similarity=0.123 Sum_probs=38.4
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN 206 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~ 206 (295)
..|.|...++|.++...+..|+.||+ +||+++||.+++++..+.
T Consensus 40 ~~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~V~~~r~ 83 (95)
T cd06968 40 VSYSCPRQKNCLIDRTNRNRCQHCRL---QKCLALGMSRDAVKFGRM 83 (95)
T ss_pred CceecCCCcccccccCCceeccccch---hhcccccCChhhcccCcC
Confidence 35778888999999999999999999 999999999998865443
No 91
>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=97.69 E-value=1.3e-05 Score=58.65 Aligned_cols=42 Identities=12% Similarity=0.113 Sum_probs=37.5
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT 205 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~ 205 (295)
.|.|...++|.|+...+..|+.||+ +||++|||.++.++..+
T Consensus 40 ~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~vq~~r 81 (97)
T cd07170 40 EYSCPATNECEITKRRRKSCQACRF---MKCLKVGMLKEGVRLDR 81 (97)
T ss_pred ceeecCCCccccCcccCccCCcccc---chhhhcCCCHHHccccc
Confidence 5778888999999999999999999 99999999999886543
No 92
>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=97.63 E-value=1.2e-05 Score=55.88 Aligned_cols=39 Identities=13% Similarity=0.137 Sum_probs=35.1
Q ss_pred ch-hhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615 161 QH-YTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA 202 (295)
Q Consensus 161 ~y-~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~ 202 (295)
.| .|+..++|.++...+..|+.||+ +||+++||.+++++
T Consensus 34 ~~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~ 73 (73)
T cd07158 34 TYRRCLNGGKCVIQRKNRNRCQYCRF---KKCLSVGMSRNAVR 73 (73)
T ss_pred CcccCCCCCCcCCCccccccCccchh---hhhhHccCChHHcC
Confidence 46 68888999999999999999999 99999999988763
No 93
>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=97.63 E-value=1.5e-05 Score=57.54 Aligned_cols=44 Identities=9% Similarity=0.047 Sum_probs=38.7
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG 207 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~ 207 (295)
.|.|...++|.|+...+..|+.||+ +||+++||.++.++..+.+
T Consensus 42 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~~R~~ 85 (90)
T cd07168 42 VYTCVGDGRCEITKAQRNRCQYCRF---RKCIRKGMMLAAVREDRMP 85 (90)
T ss_pred CccCCCCCCccccccccccccccch---hhhhhcCCCHHHhhcccCC
Confidence 5778888999999999999999999 9999999999988655543
No 94
>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=97.63 E-value=1.3e-05 Score=57.35 Aligned_cols=42 Identities=17% Similarity=0.086 Sum_probs=37.1
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT 205 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~ 205 (295)
.|.|...++|.++...+..|+.||+ +||++|||..+.++..+
T Consensus 38 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~~~~~~ 79 (86)
T cd07157 38 ISECPNGGKCIIDKKNRTKCQACRY---RKCLNVGMSLGGPRYGR 79 (86)
T ss_pred cccCCCCCccccCccccccCccchh---hHHhHcCCCcccccccc
Confidence 6779888999999999999999999 99999999988875433
No 95
>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=97.62 E-value=1.7e-05 Score=57.59 Aligned_cols=42 Identities=17% Similarity=0.149 Sum_probs=37.8
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT 205 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~ 205 (295)
.|.|...++|.++...+..|+.||+ +||+++||.++.++..+
T Consensus 34 ~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~Vq~~r 75 (93)
T cd07167 34 RYTCIENQNCQIDKTQRKRCPYCRF---QKCLSVGMKLEAVRADR 75 (93)
T ss_pred ccccCCCCccccCccccCcCCCccc---chhhhccCCHHHhhhcc
Confidence 5778888999999999999999999 99999999999886544
No 96
>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=97.62 E-value=8.5e-06 Score=56.68 Aligned_cols=39 Identities=15% Similarity=0.209 Sum_probs=35.8
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA 202 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~ 202 (295)
.|.|...++|.++...+..|+.||+ +||+++||++++++
T Consensus 34 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~ 72 (74)
T cd07179 34 SYVCPGGQNCAITPATRNACKSCRF---RRCLAVGMSKTGSR 72 (74)
T ss_pred cccCCCCCccccCCcccccCccchh---HHHHHhCCCHhHee
Confidence 5778888899999999999999999 99999999999874
No 97
>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=97.61 E-value=1.4e-05 Score=55.93 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=36.8
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL 204 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~ 204 (295)
.|.|...++|.++...+..|+.||+ +||+++||.++.++..
T Consensus 34 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~~~ 74 (76)
T cd06960 34 TYTCRFGGNCVVDKDKRNACRYCRF---KKCLEVGMDPEAVQNE 74 (76)
T ss_pred ceeCCCCCcccccCcccccCccchh---hhhhhcCCCHHHcccC
Confidence 5778888999999999999999999 9999999999987543
No 98
>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=97.61 E-value=8.2e-06 Score=60.11 Aligned_cols=43 Identities=12% Similarity=0.136 Sum_probs=38.4
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT 205 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~ 205 (295)
..|.|...++|.|+...+..|+.||+ +||+++||++++++..+
T Consensus 53 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~~~ 95 (101)
T cd07160 53 AQYVCKNGGKCQMDMYMRRKCQECRL---RKCREAGMREQCVLSEE 95 (101)
T ss_pred CccccCCCCccccCCcccccCccchh---HHHHHhCCCHHHhcChh
Confidence 46788888999999999999999999 99999999999986544
No 99
>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=97.61 E-value=9.3e-06 Score=56.30 Aligned_cols=38 Identities=13% Similarity=0.201 Sum_probs=35.0
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF 201 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~ 201 (295)
.|.|+..++|.|+...+..|+.||+ +||+++||.++++
T Consensus 34 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~a~ 71 (73)
T cd06963 34 NYLCAGRNDCIIDKIRRKNCPACRL---RKCYQAGMTLGAR 71 (73)
T ss_pred ceeCCCCCccccCCcccccCccchh---hHHHHcCCChhhc
Confidence 4778889999999999999999999 9999999998876
No 100
>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=97.59 E-value=1.2e-05 Score=58.16 Aligned_cols=46 Identities=13% Similarity=0.165 Sum_probs=39.5
Q ss_pred cchhhhhh-cCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCC
Q psy1615 160 NQHYTATI-SNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGD 208 (295)
Q Consensus 160 ~~y~~r~~-~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~ 208 (295)
..|.|... ++|.++...+.+|+.||+ +||+++||.++.++..+.+.
T Consensus 41 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~~R~~~ 87 (92)
T cd06970 41 LIYRCQAGTGMCPVDKAHRNQCQACRL---KKCLQAGMNKDAVQNERQPR 87 (92)
T ss_pred CCceeecCCCcCccCCCccccCccchh---hHhhHhCCCHHHcccccCcc
Confidence 45788774 899999999999999999 99999999999987666544
No 101
>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=97.59 E-value=9.4e-06 Score=56.61 Aligned_cols=40 Identities=20% Similarity=0.222 Sum_probs=36.2
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA 202 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~ 202 (295)
..|.|...++|.++...+..|+.||+ +||+++||++++++
T Consensus 35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~ 74 (75)
T cd06969 35 AKYVCLANKNCPVDKRRRNRCQYCRF---QKCLQVGMVKEVVR 74 (75)
T ss_pred CcccCCcCCccccCCcccccCcccHh---HHHHHhCCCHHHcc
Confidence 35778888999999999999999999 99999999998764
No 102
>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=97.59 E-value=1.8e-05 Score=57.45 Aligned_cols=45 Identities=11% Similarity=0.221 Sum_probs=38.2
Q ss_pred cchhhhh--hcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615 160 NQHYTAT--ISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG 207 (295)
Q Consensus 160 ~~y~~r~--~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~ 207 (295)
..|.|.. .++|.++...|..|+.||+ +||+++||+++.++..+.+
T Consensus 41 ~~~~C~~~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~Vq~~r~p 87 (92)
T cd07163 41 RQYVCKSKGQGGCPVDKTHRNQCRACRL---KKCFEVGMNKDAVQHERGP 87 (92)
T ss_pred CCcCCCCCCCCCCccCCCccccCccchh---hhhhhhcCCHHHhhcccCc
Confidence 3577876 3789999999999999999 9999999999998765544
No 103
>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=97.58 E-value=1e-05 Score=55.92 Aligned_cols=39 Identities=13% Similarity=0.192 Sum_probs=35.4
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF 201 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~ 201 (295)
..|.|...++|.++...+..|+.||+ +||+++||+++.+
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v 71 (72)
T cd07156 33 ARFTCPFNGDCEITKDNRRHCQACRL---KKCLDIGMKKEMI 71 (72)
T ss_pred CccccCCCCccccCCcccccCccchh---HHHHHhCCCHHHc
Confidence 35778888999999999999999999 9999999998875
No 104
>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=97.58 E-value=2.1e-05 Score=56.80 Aligned_cols=42 Identities=17% Similarity=0.120 Sum_probs=37.5
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT 205 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~ 205 (295)
.|.|...++|.|+...+..|+.||+ +||+++||.++.++..+
T Consensus 42 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~r 83 (90)
T cd07169 42 VYRCSRDKNCVMSRKQRNRCQYCRL---LKCLQMGMNRKAIREDG 83 (90)
T ss_pred ceecCCCCcccccccccccccccch---hhhccccCCHHHhcccc
Confidence 5778888999999999999999999 99999999999886544
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=97.56 E-value=1.3e-05 Score=55.60 Aligned_cols=39 Identities=18% Similarity=0.246 Sum_probs=35.3
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA 202 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~ 202 (295)
.|.|...++|.++...+..|+.||+ +||+++||+++.++
T Consensus 34 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~ 72 (73)
T cd06958 34 TYTCRGNRNCPIDQHHRNQCQYCRL---KKCLKVGMRREAVQ 72 (73)
T ss_pred ceeCCCCCcCccCCcccccCccchh---hHhhHhCCCHHHcc
Confidence 4678888999999999999999999 99999999998763
No 106
>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=97.55 E-value=1.1e-05 Score=57.39 Aligned_cols=41 Identities=12% Similarity=0.106 Sum_probs=37.2
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA 203 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~ 203 (295)
..|.|+..++|.++...+..|+.||+ +||+++||++++++.
T Consensus 36 ~~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~~ 76 (84)
T cd06962 36 AVYKCKNGGNCEMDMYMRRKCQECRL---RKCKEMGMLAECLLT 76 (84)
T ss_pred CceecCCCCcCccCccccccCccchh---hHHHHhCCChHHccC
Confidence 46789888999999999999999999 999999999998754
No 107
>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=97.53 E-value=1.5e-05 Score=57.68 Aligned_cols=41 Identities=15% Similarity=0.165 Sum_probs=36.9
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL 204 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~ 204 (295)
.|.|...++|.|+...+..|+.||+ +||+++||.++.++.+
T Consensus 37 ~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~~~ 77 (91)
T cd07161 37 VYHCKYGRACEMDMYMRRKCQECRL---KKCLSVGMRPECVVPE 77 (91)
T ss_pred ceecCCCCccccCccccccCccchh---hHHhHcCCCHHHcCch
Confidence 5778888999999999999999999 9999999999987543
No 108
>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=97.53 E-value=1.6e-05 Score=54.97 Aligned_cols=39 Identities=15% Similarity=0.176 Sum_probs=35.3
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF 201 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~ 201 (295)
..|.|...++|.++...+..|+.||+ +||+++||.++.+
T Consensus 33 ~~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v 71 (72)
T cd06916 33 LEYTCPAGGNCVIDKRNRNRCQACRL---KKCLAVGMRKEAV 71 (72)
T ss_pred CCccCCCCCccccCCcccccCccchh---hHhhHhCCChHHc
Confidence 35778888999999999999999999 9999999998875
No 109
>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=97.52 E-value=2.4e-05 Score=57.01 Aligned_cols=43 Identities=9% Similarity=0.128 Sum_probs=38.0
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT 205 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~ 205 (295)
..|.|...++|.++...+..|+.||+ +||+++||.++.++..+
T Consensus 35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~~r 77 (94)
T cd06966 35 KEFKCPFNESCEINVVTRRFCQKCRL---DKCFAIGMKKEWIMSEE 77 (94)
T ss_pred CccccCCCCccccCccccccCccchh---hhCcccCCCHHHccchh
Confidence 35788888999999999999999999 99999999999876443
No 110
>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=97.50 E-value=2.2e-05 Score=55.67 Aligned_cols=39 Identities=13% Similarity=0.254 Sum_probs=34.9
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA 202 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~ 202 (295)
.|.|...++|.|+...+..|+.||+ +||++|||.+...+
T Consensus 39 ~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~~~ 77 (82)
T cd07173 39 KYLCASRNDCTIDKFRRKNCPSCRL---RKCFEAGMTLGARK 77 (82)
T ss_pred ceecCCCCccccCCCccCcCcchhh---hhhhhcCCCcChHH
Confidence 4678888999999999999999999 99999999987654
No 111
>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=97.48 E-value=1.9e-05 Score=54.73 Aligned_cols=39 Identities=13% Similarity=0.211 Sum_probs=35.2
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF 201 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~ 201 (295)
..|.|+..++|.++...+..|+.||+ +||+++||+++.+
T Consensus 34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v 72 (73)
T cd06959 34 AVYACKFGNKCEMDMYMRRKCQECRL---RKCKAAGMRPDCL 72 (73)
T ss_pred CCccCCCCCcCCcCCcccccCccchh---HHHHHhCCChhhc
Confidence 35778888999999999999999999 9999999998765
No 112
>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=97.48 E-value=2e-05 Score=54.63 Aligned_cols=39 Identities=10% Similarity=0.090 Sum_probs=34.7
Q ss_pred cchhhh-hhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615 160 NQHYTA-TISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF 201 (295)
Q Consensus 160 ~~y~~r-~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~ 201 (295)
..|.|+ ..++|.++...+..|+.||+ +||+++||+++.+
T Consensus 33 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v 72 (73)
T cd07154 33 LLYTCKAGNGSCVVDKARRNQCQACRL---KKCLEVSMNKDAV 72 (73)
T ss_pred CCcccCCCCCCCccCCcccccCccchh---hHhhHhCCChHHC
Confidence 357787 67899999999999999999 9999999998875
No 113
>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=97.37 E-value=2.9e-05 Score=54.48 Aligned_cols=39 Identities=15% Similarity=0.239 Sum_probs=35.1
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA 202 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~ 202 (295)
.|.|...++|.++...+..|+.||+ +||+++||...+++
T Consensus 38 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~~~ 76 (78)
T cd07172 38 NYLCAGRNDCIIDKIRRKNCPACRL---RKCLQAGMNLGARK 76 (78)
T ss_pred ceeCCCCCccccCCcccccCccchh---HHHHHhCCCccccc
Confidence 4678888999999999999999999 99999999987763
No 114
>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=97.36 E-value=2.8e-05 Score=55.85 Aligned_cols=40 Identities=15% Similarity=0.192 Sum_probs=35.9
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA 203 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~ 203 (295)
.|.|...++|.++...+..|+.||+ +||+++||.++.++.
T Consensus 35 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~ 74 (87)
T cd07162 35 RLCCPFQKGCVITKSNRRQCQACRL---RKCLSIGMKKELIMS 74 (87)
T ss_pred eeEcCCCCceecCCcccccCccchh---hHHhHhCCCHHHccC
Confidence 4678878899999999999999999 999999999998753
No 115
>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=97.32 E-value=3.9e-05 Score=57.11 Aligned_cols=40 Identities=10% Similarity=0.094 Sum_probs=36.2
Q ss_pred cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615 160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA 202 (295)
Q Consensus 160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~ 202 (295)
..|.|...++|.++...+..|+.||+ +||+++||.++.+.
T Consensus 41 ~~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~ 80 (107)
T cd06955 41 ALFTCPFNGDCRITKDNRRHCQACRL---KRCVDIGMMKEFIL 80 (107)
T ss_pred CccccCCCCccccccCCccccccchh---HHHHHcCCCchhcc
Confidence 46789889999999999999999999 99999999998764
No 116
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=97.20 E-value=8.6e-05 Score=51.07 Aligned_cols=36 Identities=17% Similarity=0.332 Sum_probs=32.9
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPG 199 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~ 199 (295)
.|.|...++|.++...+..|+.||+ +||+++||.++
T Consensus 35 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~~GM~~~ 70 (70)
T smart00399 35 KYRCDRKNNCSINKRYRCRCRACRL---KKCLGVGMDPE 70 (70)
T ss_pred CeecCCCcccccCCCccccCccCcC---hhHhhccCcCC
Confidence 5778888899999999999999999 99999999864
No 117
>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=97.11 E-value=0.00015 Score=51.62 Aligned_cols=39 Identities=15% Similarity=0.132 Sum_probs=33.1
Q ss_pred hhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615 164 TATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG 207 (295)
Q Consensus 164 ~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~ 207 (295)
|.. .|.++...+..|+.||+ +||+++||.+++++..+.+
T Consensus 39 C~~--~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~~~r~~ 77 (84)
T cd06965 39 CDL--SCKIHKKSRNKCQYCRF---QKCLNVGMSHNAIRFGRMP 77 (84)
T ss_pred ccc--CCCcCccccccccchhh---hhhhhccCCHHHcccCCCC
Confidence 653 49999999999999999 9999999999988655443
No 118
>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=96.52 E-value=0.00012 Score=50.34 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=28.3
Q ss_pred chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCc
Q psy1615 161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGP 198 (295)
Q Consensus 161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~ 198 (295)
.|.|+..++|.++.-.+..|+.||+ +||+++||.+
T Consensus 36 ~~~C~~~~~C~i~~~~~~~C~~CRf---~KCl~~GM~k 70 (70)
T PF00105_consen 36 PYKCKKNGNCKIDKDNRRKCRSCRF---QKCLEVGMKK 70 (70)
T ss_dssp G-STSSSST---STTTTTTSHHHHH---HHHHHTTBSG
T ss_pred cccccccccccccccCCCEeCcchH---HHHHHHCCcC
Confidence 4778888999999999999999999 9999999985
No 119
>KOG4846|consensus
Probab=94.44 E-value=0.042 Score=49.74 Aligned_cols=138 Identities=12% Similarity=-0.066 Sum_probs=89.8
Q ss_pred HHHHHHHHHHHHHHHhHhhcCCCCCCCC-HHHHHHHHHHHHHHHHHHHhhHhhcCCCCcce-eecCCcccChhhHHHHHH
Q psy1615 4 DNICELAARLLFSAVEWARNIPFFPDLQ-VTDQVALLRLVWSELFVLNASQCSMPLHVAPL-LAAAGLHASPMAADRVVA 81 (295)
Q Consensus 4 ~~~~~~~~~~l~~~v~waK~lp~F~~L~-~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 81 (295)
+++.-+....+-.+++||+.+++|..++ .-|++.+|+.+-.+...-..+-.. .....++ ++...+.... ....-..
T Consensus 365 ~~~~ll~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f-~~~~Q~~~mfl~~~~~~~-Q~~~~~~ 442 (538)
T KOG4846|consen 365 KSLQLLYGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNF-KSQLQLLEMFLFYKKVLF-QKMTCRI 442 (538)
T ss_pred chhhhhhhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHH-HHHHHHHHHHHHHHHHHH-HHHHhhh
Confidence 3444555666778899999999999999 679999999987776665554221 1111111 1100000000 0011123
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhhCCCCCC
Q psy1615 82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKR 151 (295)
Q Consensus 82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~~~~~~~ 151 (295)
.++.+..+..++.++..|...++|. +.++-+-++. +.+....||.+|+..++....+.++|.
T Consensus 443 ~gd~~~a~~~~~~~ln~L~~~~~~~----~~~l~s~~s~----~~e~~~sVe~lqe~~lr~~~~~~n~pl 504 (538)
T KOG4846|consen 443 DGDTYKALMKCIHELNRLNELHKQQ----LNILRSNLSF----LNEPPLSVEMLQESTLRLPVNHNNQPL 504 (538)
T ss_pred chHHHHHHHHhhcchhhcCchHHHH----HHHHHHhhhh----hccCCchHHHHHhhhhhccccccCCcc
Confidence 3455677788999999999988887 4455555555 778889999999999998877777774
No 120
>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=38.97 E-value=28 Score=24.16 Aligned_cols=21 Identities=29% Similarity=0.377 Sum_probs=16.8
Q ss_pred hhcCCCCCCCCHHHHHHHHHH
Q psy1615 21 ARNIPFFPDLQVTDQVALLRL 41 (295)
Q Consensus 21 aK~lp~F~~L~~~Dq~~LLk~ 41 (295)
+..|+||..|+.+||..+.+.
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 567999999999999887653
No 121
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=35.75 E-value=42 Score=24.06 Aligned_cols=23 Identities=26% Similarity=0.388 Sum_probs=19.8
Q ss_pred HhhcCCCCCCCCHHHHHHHHHHH
Q psy1615 20 WARNIPFFPDLQVTDQVALLRLV 42 (295)
Q Consensus 20 waK~lp~F~~L~~~Dq~~LLk~~ 42 (295)
-++.+|+|..|+..-|-.|+-++
T Consensus 30 Lt~~vPgF~~ls~sKqRRLi~~A 52 (92)
T PF10330_consen 30 LTTSVPGFSDLSPSKQRRLIMAA 52 (92)
T ss_pred HhccCCCcccCCHHHHHHHHHHH
Confidence 35789999999999999988764
No 122
>COG3795 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.75 E-value=47 Score=25.27 Aligned_cols=15 Identities=47% Similarity=0.733 Sum_probs=12.1
Q ss_pred HHHHHHHhHhhhCCC
Q psy1615 268 RLLFSAVEWARNIPF 282 (295)
Q Consensus 268 ~~l~~~V~WAK~iP~ 282 (295)
+-|-..|+|||.+|.
T Consensus 87 ~dLdeA~e~A~~~P~ 101 (123)
T COG3795 87 RDLDEALEWAARCPL 101 (123)
T ss_pred CCHHHHHHHHhcCCC
Confidence 346778999999993
No 123
>KOG2631|consensus
Probab=24.06 E-value=2.1e+02 Score=24.12 Aligned_cols=55 Identities=15% Similarity=0.103 Sum_probs=37.8
Q ss_pred hhHhhcCCCCcceeecCCcccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCHHH
Q psy1615 51 ASQCSMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAE 105 (295)
Q Consensus 51 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E 105 (295)
-|..-++.....++-..|...-...-++..-+.+.++.++++..+|++++++++-
T Consensus 175 ~aie~YP~tcAVLVR~HGvyvWG~TWekaKt~~EcydYLfelaikm~klgipp~~ 229 (238)
T KOG2631|consen 175 KAIELYPDTCAVLVRRHGVYVWGPTWEKAKTMTECYDYLFELAIKMKKLGIPPEQ 229 (238)
T ss_pred HHHHhCCcceEEEEecCcEEEecCcHHHHHHHHHHHHHHHHHHHHHHHcCCChhh
Confidence 3444456555556656665554445555566777788999999999999999653
Done!