Query psy6602
Match_columns 367
No_of_seqs 293 out of 1529
Neff 8.5
Searched_HMMs 46136
Date Fri Aug 16 22:19:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6602.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6602hhsearch_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 7.8E-41 1.7E-45 302.6 20.9 210 64-278 9-224 (247)
2 cd06949 NR_LBD_ER Ligand bindi 100.0 2.8E-40 6.1E-45 299.7 23.2 213 64-279 13-234 (235)
3 cd06937 NR_LBD_RAR The ligand 100.0 4E-40 8.7E-45 297.9 20.0 194 85-278 37-230 (231)
4 cd07348 NR_LBD_NGFI-B The liga 100.0 1.5E-39 3.2E-44 294.1 20.4 193 86-280 41-235 (238)
5 cd06947 NR_LBD_GR_Like Ligand 100.0 9.1E-39 2E-43 290.4 23.1 223 64-289 9-240 (246)
6 cd07071 NR_LBD_Nurr1 The ligan 100.0 7.8E-39 1.7E-43 289.7 22.4 192 86-279 41-234 (238)
7 cd06935 NR_LBD_TR The ligand b 100.0 1.9E-39 4.1E-44 295.7 18.3 203 74-276 40-243 (243)
8 cd06945 NR_LBD_Nurr1_like The 100.0 1.8E-38 3.9E-43 288.4 21.8 193 86-279 41-235 (239)
9 cd07073 NR_LBD_AR Ligand bindi 100.0 3.7E-38 7.9E-43 286.4 22.8 220 64-288 9-239 (246)
10 cd07075 NR_LBD_MR Ligand bindi 100.0 3.7E-38 8E-43 285.3 22.3 198 64-264 9-212 (248)
11 cd07069 NR_LBD_Lrh-1 The ligan 100.0 6E-38 1.3E-42 285.1 21.8 197 85-281 39-240 (241)
12 cd07349 NR_LBD_SHP The ligand 100.0 4.7E-38 1E-42 281.9 19.9 193 85-277 18-222 (222)
13 cd07072 NR_LBD_DHR38_like Liga 100.0 5.7E-38 1.2E-42 284.0 20.4 193 86-280 42-236 (239)
14 cd06950 NR_LBD_Tlx_PNR_like Th 100.0 3.8E-37 8.2E-42 274.2 22.6 189 78-266 18-206 (206)
15 cd06946 NR_LBD_ERR The ligand 100.0 4.2E-37 9.1E-42 277.3 22.5 212 64-278 8-220 (221)
16 cd07070 NR_LBD_SF-1 The ligand 100.0 1.9E-37 4.2E-42 281.4 20.4 195 85-279 37-236 (237)
17 cd06944 NR_LBD_Ftz-F1_like The 100.0 3.7E-37 8E-42 279.9 21.5 195 85-279 37-236 (237)
18 cd07068 NR_LBD_ER_like The lig 100.0 7.1E-37 1.5E-41 275.7 22.7 212 64-278 8-220 (221)
19 cd06941 NR_LBD_DmE78_like The 100.0 3.1E-37 6.7E-42 273.0 19.9 192 87-278 3-195 (195)
20 cd07350 NR_LBD_Dax1 The ligand 100.0 3.2E-37 6.8E-42 278.2 19.5 193 83-275 16-232 (232)
21 cd06951 NR_LBD_Dax1_like The l 100.0 3.3E-37 7.2E-42 277.1 19.3 189 85-274 18-221 (222)
22 cd06948 NR_LBD_COUP-TF Ligand 100.0 1.9E-36 4.1E-41 275.2 21.5 201 86-286 30-232 (236)
23 cd07074 NR_LBD_PR Ligand bindi 100.0 5.7E-36 1.2E-40 270.8 22.0 215 64-281 9-232 (248)
24 cd06940 NR_LBD_REV_ERB The lig 100.0 2.7E-36 5.8E-41 265.1 18.5 177 86-262 12-188 (189)
25 cd06939 NR_LBD_ROR_like The li 100.0 2.8E-36 6.1E-41 274.2 19.0 190 86-277 48-241 (241)
26 cd06954 NR_LBD_LXR The ligand 100.0 1E-35 2.3E-40 270.9 19.5 193 85-278 42-235 (236)
27 cd06938 NR_LBD_EcR The ligand 100.0 1.5E-35 3.2E-40 268.7 19.4 194 84-279 37-231 (231)
28 cd06932 NR_LBD_PPAR The ligand 100.0 2E-35 4.4E-40 271.1 20.3 196 81-278 58-257 (259)
29 cd06933 NR_LBD_VDR The ligand 100.0 2E-35 4.4E-40 268.4 18.8 193 86-279 37-236 (238)
30 cd06934 NR_LBD_PXR_like The li 100.0 3.6E-35 7.8E-40 264.7 17.1 188 86-276 35-226 (226)
31 cd06943 NR_LBD_RXR_like The li 100.0 2.8E-34 6.1E-39 256.6 19.6 176 87-262 31-207 (207)
32 cd06952 NR_LBD_TR2_like The li 100.0 4.1E-34 9E-39 258.1 19.9 195 84-278 19-221 (222)
33 cd06936 NR_LBD_Fxr The ligand 100.0 1.4E-33 2.9E-38 253.8 17.2 184 86-274 36-220 (221)
34 cd06953 NR_LBD_DHR4_like The l 100.0 6.9E-33 1.5E-37 248.0 19.0 175 86-260 27-205 (213)
35 cd06931 NR_LBD_HNF4_like The l 100.0 2.6E-32 5.7E-37 246.5 21.6 193 83-276 29-222 (222)
36 cd06929 NR_LBD_F1 Ligand-bindi 100.0 6.9E-33 1.5E-37 241.0 16.7 170 87-257 3-173 (174)
37 KOG4215|consensus 100.0 1.2E-31 2.5E-36 244.3 19.1 206 82-287 150-359 (432)
38 cd06942 NR_LBD_Sex_1_like The 100.0 8.8E-32 1.9E-36 237.2 17.9 171 88-260 4-177 (191)
39 cd06930 NR_LBD_F2 Ligand-bindi 100.0 2.2E-31 4.7E-36 229.5 18.2 162 89-250 2-165 (165)
40 cd06157 NR_LBD The ligand bind 99.9 9.6E-26 2.1E-30 193.7 15.7 161 90-250 2-168 (168)
41 PF00104 Hormone_recep: Ligand 99.9 5.4E-25 1.2E-29 195.0 15.6 181 83-263 14-202 (203)
42 smart00430 HOLI Ligand binding 99.9 1.1E-24 2.4E-29 186.2 14.7 154 96-249 2-162 (163)
43 KOG4218|consensus 99.9 1.3E-24 2.8E-29 196.4 14.8 196 86-364 274-474 (475)
44 KOG4217|consensus 99.9 3E-22 6.5E-27 187.9 14.0 190 87-278 409-600 (605)
45 KOG4216|consensus 99.8 3.1E-21 6.7E-26 177.4 10.2 189 88-278 284-475 (479)
46 cd07069 NR_LBD_Lrh-1 The ligan 99.8 9.4E-19 2E-23 159.3 10.2 111 240-365 131-241 (241)
47 cd07349 NR_LBD_SHP The ligand 99.8 1E-18 2.2E-23 156.9 9.1 107 239-360 116-222 (222)
48 cd06937 NR_LBD_RAR The ligand 99.8 1.3E-17 2.8E-22 151.1 13.8 109 238-361 122-230 (231)
49 cd07070 NR_LBD_SF-1 The ligand 99.8 4.1E-18 8.8E-23 154.9 10.3 107 242-363 131-237 (237)
50 cd07348 NR_LBD_NGFI-B The liga 99.7 9.8E-17 2.1E-21 145.4 14.1 108 239-362 125-234 (238)
51 cd06944 NR_LBD_Ftz-F1_like The 99.7 2.6E-17 5.6E-22 149.8 10.3 109 240-363 129-237 (237)
52 cd06949 NR_LBD_ER Ligand bindi 99.7 2.9E-17 6.3E-22 149.1 10.5 113 236-363 115-235 (235)
53 cd07350 NR_LBD_Dax1 The ligand 99.7 1.6E-17 3.5E-22 150.1 7.6 106 238-358 127-232 (232)
54 cd06945 NR_LBD_Nurr1_like The 99.7 6.1E-17 1.3E-21 147.3 9.6 110 239-363 125-236 (239)
55 cd06951 NR_LBD_Dax1_like The l 99.7 4.5E-17 9.7E-22 146.6 8.3 104 239-358 119-222 (222)
56 cd07071 NR_LBD_Nurr1 The ligan 99.7 1.6E-16 3.4E-21 144.2 10.1 109 238-362 124-234 (238)
57 cd07072 NR_LBD_DHR38_like Liga 99.7 4E-15 8.7E-20 135.0 19.2 107 240-362 127-235 (239)
58 cd06932 NR_LBD_PPAR The ligand 99.6 1.8E-15 3.8E-20 139.2 13.3 107 240-361 150-257 (259)
59 cd06948 NR_LBD_COUP-TF Ligand 99.6 5.7E-16 1.2E-20 140.9 9.2 108 242-364 120-227 (236)
60 cd06935 NR_LBD_TR The ligand b 99.6 2.9E-15 6.3E-20 136.7 12.8 106 239-359 137-243 (243)
61 cd06941 NR_LBD_DmE78_like The 99.6 1.7E-14 3.8E-19 127.6 13.6 109 238-361 86-195 (195)
62 cd07068 NR_LBD_ER_like The lig 99.6 5.8E-15 1.3E-19 133.1 10.5 110 238-362 111-221 (221)
63 cd06946 NR_LBD_ERR The ligand 99.6 1.1E-14 2.4E-19 131.4 10.2 110 238-362 111-221 (221)
64 cd06939 NR_LBD_ROR_like The li 99.6 3.3E-14 7.2E-19 129.5 12.5 106 239-360 132-241 (241)
65 cd07076 NR_LBD_GR Ligand bindi 99.6 1.3E-14 2.9E-19 131.7 9.7 105 240-361 116-224 (247)
66 cd06952 NR_LBD_TR2_like The li 99.6 1.4E-14 3E-19 130.8 9.5 108 239-361 114-221 (222)
67 cd07073 NR_LBD_AR Ligand bindi 99.6 1.4E-14 3E-19 132.0 9.5 107 240-363 116-231 (246)
68 cd06954 NR_LBD_LXR The ligand 99.5 3.1E-14 6.7E-19 129.7 9.7 106 240-361 130-235 (236)
69 cd06947 NR_LBD_GR_Like Ligand 99.5 5E-14 1.1E-18 128.4 10.3 107 242-363 118-231 (246)
70 cd06933 NR_LBD_VDR The ligand 99.5 4E-14 8.8E-19 128.8 9.4 109 239-362 124-236 (238)
71 cd06950 NR_LBD_Tlx_PNR_like Th 99.5 9.8E-14 2.1E-18 123.7 8.3 95 240-349 112-206 (206)
72 cd06936 NR_LBD_Fxr The ligand 99.5 4.6E-13 9.9E-18 120.6 11.4 103 240-358 119-221 (221)
73 cd06938 NR_LBD_EcR The ligand 99.5 1.1E-12 2.3E-17 119.2 13.6 105 240-361 125-230 (231)
74 cd06940 NR_LBD_REV_ERB The lig 99.5 9.4E-13 2E-17 115.7 12.5 95 237-346 95-189 (189)
75 cd06934 NR_LBD_PXR_like The li 99.4 4.1E-13 8.8E-18 121.3 7.6 103 240-359 121-226 (226)
76 cd07075 NR_LBD_MR Ligand bindi 99.3 4.5E-12 9.7E-17 115.3 8.2 104 242-362 118-226 (248)
77 KOG4215|consensus 99.3 9.6E-12 2.1E-16 114.6 8.4 107 243-364 244-353 (432)
78 cd06943 NR_LBD_RXR_like The li 99.3 9.7E-12 2.1E-16 111.0 8.2 89 242-345 119-207 (207)
79 cd06931 NR_LBD_HNF4_like The l 99.3 9.1E-12 2E-16 112.5 8.1 102 243-359 121-222 (222)
80 cd06953 NR_LBD_DHR4_like The l 99.2 1E-10 2.2E-15 104.8 8.2 94 238-346 115-209 (213)
81 cd06929 NR_LBD_F1 Ligand-bindi 98.9 2.2E-09 4.8E-14 93.0 7.0 90 236-340 84-173 (174)
82 cd06942 NR_LBD_Sex_1_like The 98.9 1E-08 2.2E-13 90.3 11.0 89 240-343 87-177 (191)
83 KOG4217|consensus 98.7 2.9E-07 6.3E-12 87.8 12.7 123 238-360 474-599 (605)
84 cd06930 NR_LBD_F2 Ligand-bindi 98.6 1.5E-07 3.3E-12 80.6 7.1 80 239-333 86-165 (165)
85 cd07074 NR_LBD_PR Ligand bindi 98.3 5E-06 1.1E-10 75.8 9.8 105 243-362 119-230 (248)
86 KOG4216|consensus 98.0 4.1E-05 9E-10 71.8 10.4 196 114-361 265-475 (479)
87 PF00104 Hormone_recep: Ligand 97.9 3E-05 6.5E-10 68.1 7.5 94 239-347 106-203 (203)
88 smart00430 HOLI Ligand binding 97.7 6.2E-05 1.3E-09 63.6 5.5 76 243-333 85-163 (163)
89 cd06157 NR_LBD The ligand bind 97.6 0.00013 2.7E-09 62.0 6.2 77 242-333 90-168 (168)
90 KOG4846|consensus 96.9 0.0036 7.7E-08 59.6 7.4 158 165-345 371-534 (538)
91 KOG4218|consensus 96.0 0.021 4.7E-07 53.2 6.8 72 209-280 402-473 (475)
92 KOG4846|consensus 94.8 0.0064 1.4E-07 57.9 -0.5 163 88-258 364-530 (538)
93 PF00645 zf-PARP: Poly(ADP-rib 35.9 32 0.00069 25.3 2.3 23 104-126 58-80 (82)
94 PF10330 Stb3: Putative Sin3 b 35.7 40 0.00086 25.6 2.7 22 106-127 31-52 (92)
95 PF04048 Sec8_exocyst: Sec8 ex 24.3 1.8E+02 0.0038 24.0 5.1 90 168-261 5-98 (142)
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=7.8e-41 Score=302.60 Aligned_cols=210 Identities=20% Similarity=0.253 Sum_probs=182.3
Q ss_pred CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143 (367)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~ 143 (367)
.+|..++++|++..|++.... +..+|+++++.++.+|+|||++|||.+|+.+||++|||+||+|++++++|||+.+.
T Consensus 9 ~ep~~~~~~~d~~~p~~~~~~---~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~ 85 (247)
T cd07076 9 IEPEVLYSGYDSSVPDSTWRI---MSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQ 85 (247)
T ss_pred cCCCcccCCCCCCCCCcHHHH---HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCC
Confidence 577889999999999998666 45699999999999999999999999999999999999999999999999999986
Q ss_pred CCc-eE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602 144 DLS-LL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC 220 (367)
Q Consensus 144 ~~~-~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~ 220 (367)
.+. .+ +.++...++......+..+.++.+.+++.+|++|++|.+||+|||||+||+| |++|++++..|+++|++|..
T Consensus 86 ~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~ 165 (247)
T cd07076 86 SNGNLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIK 165 (247)
T ss_pred CCCceEEecCCeeecHHHHhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHH
Confidence 654 34 4455555544434445666678899999999999999999999999999999 99999999999999999999
Q ss_pred HHHHHHHhhCCCcc---hHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602 221 ILGDYVRGRYSRQP---TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278 (367)
Q Consensus 221 ~L~~y~~~~~~~~~---~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~ 278 (367)
+|.+|+..++++.+ .|||+|+++|+++|+++....| |+.+.+++.++..++.+|+.
T Consensus 166 aL~~yi~~~~p~~~~~~~RF~kLLllLp~Lr~i~~~~~e--f~~~~~~~~~~~~~~~~ml~ 224 (247)
T cd07076 166 ELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLN--FCFQTFLDKTMSIEFPEMLA 224 (247)
T ss_pred HHHHHHHhcCCCcchhhhHHHHHHHHHHHHHHHHHHHHH--HHHHHhcccchhhhhHHHHH
Confidence 99999999987654 4999999999999999999999 66667777777666666654
No 2
>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=2.8e-40 Score=299.66 Aligned_cols=213 Identities=24% Similarity=0.329 Sum_probs=192.4
Q ss_pred CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143 (367)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~ 143 (367)
.+|..+++.|+|..+++.... ++.+++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.|||+...
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~---~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~ 89 (235)
T cd06949 13 AEPPHIYSEYDPTRPFTEASL---MMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEH 89 (235)
T ss_pred hCCCcCcCCCCCCCCCChHHH---HHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCC
Confidence 466777788887777776555 77899999999999999999999999999999999999999999999999999988
Q ss_pred CCceEecCCccccCCCCC-ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCC-----CCChhHHHHHHHH
Q psy6602 144 DLSLLINCEKARERLPPD-DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG-----LVDAQPVEMLQDQ 217 (367)
Q Consensus 144 ~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~-----L~~~~~v~~~q~~ 217 (367)
++..++.++......... ..+..+..+.+.+++.+|++|++|.+||+|||||+|||||++| +.++.+|+++|++
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~ 169 (235)
T cd06949 90 PGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDK 169 (235)
T ss_pred CCeEEeeCCceecHHHhhhcccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHH
Confidence 777777777665544332 3345667788999999999999999999999999999999999 8899999999999
Q ss_pred HHHHHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602 218 AQCILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 279 (367)
Q Consensus 218 ~~~~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~ 279 (367)
+..+|++||..++ ++++.||++|+++++.+|+++..+.|.+++.+.++..++++++.||++.
T Consensus 170 ~~~aL~~y~~~~~~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~ 234 (235)
T cd06949 170 ITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDA 234 (235)
T ss_pred HHHHHHHHHHhcCCCCCCcccHHHHHHHhchHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhcC
Confidence 9999999999998 8999999999999999999999999999999999999999999999974
No 3
>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=4e-40 Score=297.90 Aligned_cols=194 Identities=21% Similarity=0.301 Sum_probs=178.0
Q ss_pred ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR 164 (367)
Q Consensus 85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~ 164 (367)
...++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++.+.++...+.++....+......+
T Consensus 37 ~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~ 116 (231)
T cd06937 37 LGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAG 116 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhhcC
Confidence 34488999999999999999999999999999999999999999999999999999887777666665444444333344
Q ss_pred hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602 165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML 244 (367)
Q Consensus 165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l 244 (367)
....++.+.+|+.+|++|++|.+||+|||||+||+||++|+.+..+|+++|+++.++|+.|+..+||+.+.||++||++|
T Consensus 117 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~L 196 (231)
T cd06937 117 FGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKI 196 (231)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHh
Confidence 56677889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602 245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278 (367)
Q Consensus 245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~ 278 (367)
+.||+++..++|.+++.+..+..++++++.||++
T Consensus 197 p~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~ 230 (231)
T cd06937 197 TDLRSISAKGAERVITLKMEIPGPMPPLISEMLE 230 (231)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhc
Confidence 9999999999999999999999999999999986
No 4
>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=1.5e-39 Score=294.11 Aligned_cols=193 Identities=24% Similarity=0.367 Sum_probs=177.8
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV 165 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 165 (367)
..++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+.+.++..++.++...++... ..+.
T Consensus 41 ~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~~-~~~~ 119 (238)
T cd07348 41 SDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQC-VRGF 119 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHHH-HhhH
Confidence 448999999999999999999999999999999999999999999999999999999887777777665555442 3456
Q ss_pred HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHh
Q psy6602 166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLM 243 (367)
Q Consensus 166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~ 243 (367)
.+.++.+.+|+.+|++|++|.+||+|||||+|| ||++|+++..+|+++|+++.++|+.|+..++ |+.+.||++||++
T Consensus 120 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl~ 198 (238)
T cd07348 120 GDWIDSILEFSQSLHRMNLDVSAFSCLAALVII-TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGK 198 (238)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHHH
Confidence 778889999999999999999999999999999 7999999999999999999999999999864 8999999999999
Q ss_pred hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602 244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 280 (367)
Q Consensus 244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~ 280 (367)
|+.||+++..+.|.+++.+..+..++++++.|||...
T Consensus 199 Lp~LRsl~~~~~e~lf~~kl~~~~~~~pLl~e~~~~~ 235 (238)
T cd07348 199 LPELRTLCTQGLQRIFYLKLEDLVPPPPIVDKIFMDT 235 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHhcc
Confidence 9999999999999999999999999999999999743
No 5
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=100.00 E-value=9.1e-39 Score=290.38 Aligned_cols=223 Identities=18% Similarity=0.233 Sum_probs=188.2
Q ss_pred CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143 (367)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~ 143 (367)
.+|..++++|++..|++.... ++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.|||+...
T Consensus 9 ~ep~~~~~~~~~~~p~~~~~~---~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~ 85 (246)
T cd06947 9 IEPEVVYAGYDNSQPDTTARL---LSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKH 85 (246)
T ss_pred cCCCcccCCCCCCCCCchhHH---HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccC
Confidence 455667788888888876544 67799999999999999999999999999999999999999999999999998875
Q ss_pred CCc-eE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602 144 DLS-LL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC 220 (367)
Q Consensus 144 ~~~-~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~ 220 (367)
.+. .+ +.++...++......+..+.+..+.+++.+|++|++|.+||+|||||+|||| |++|+.++..|+++|+++..
T Consensus 86 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~ 165 (246)
T cd06947 86 VNSQMLYFAPDLVFNEQRMHQSAMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIK 165 (246)
T ss_pred CCCCeEEecCCeeecHHHhhhccHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHH
Confidence 543 34 4455555544433444566667788999999999999999999999999999 89999999999999999999
Q ss_pred HHHHHHHhhCC---CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccC---CchhHhHHHHHHcccCCCCCCCCC
Q psy6602 221 ILGDYVRGRYS---RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIG---DIPIQRLLGDMYTMEKSYETPGLV 289 (367)
Q Consensus 221 ~L~~y~~~~~~---~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~---~~~~~~Ll~eml~~~~s~d~~gl~ 289 (367)
+|.+|+.++++ +.+.|||+|+++|+.+|+++....|+++...... .+++++++.|||+.....-..|..
T Consensus 166 AL~~yi~~~~~~~~~~~~Rf~kLLllLp~Lr~i~~~~~e~~~~~~~~~~~~~v~~~~ll~ei~~~~~~~~~~~~~ 240 (246)
T cd06947 166 ELRKAIVKREKNSSQSWQRFYQLTKLLDSMHDLVKNLLQFCFYTFIQSHALSVEFPEMLVEIISDQLPKVLSGNV 240 (246)
T ss_pred HHHHHHHHhCCCCcccchHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcCCCccccHHHHHHHHHcccchhhcCCc
Confidence 99999998863 5689999999999999999999999998774433 368999999999977654455543
No 6
>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=7.8e-39 Score=289.69 Aligned_cols=192 Identities=24% Similarity=0.334 Sum_probs=176.2
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV 165 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 165 (367)
..++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++++.++..++.++..+.+... ..++
T Consensus 41 ~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~~-~~~~ 119 (238)
T cd07071 41 QHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC-VRGF 119 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhhh-hhcH
Confidence 448899999999999999999999999999999999999999999999999999998887777766655555442 3456
Q ss_pred HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHh
Q psy6602 166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLM 243 (367)
Q Consensus 166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~ 243 (367)
.+.++.+.+|+.+|++|++|.+||+|||||+|| +|++|+.+..+|+++|+++..+|++|+..++ ++.+.||++||++
T Consensus 120 ~~~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf-~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl~ 198 (238)
T cd07071 120 GEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGK 198 (238)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHH
Confidence 777888999999999999999999999999999 5999999999999999999999999999774 5899999999999
Q ss_pred hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602 244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 279 (367)
Q Consensus 244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~ 279 (367)
|+.||+++..+.|.+++.+..+..++++++.+||..
T Consensus 199 Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~~~ 234 (238)
T cd07071 199 LPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFLD 234 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHh
Confidence 999999999999999999999999999999999863
No 7
>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=100.00 E-value=1.9e-39 Score=295.70 Aligned_cols=203 Identities=20% Similarity=0.239 Sum_probs=180.4
Q ss_pred CCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc
Q psy6602 74 QPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK 153 (367)
Q Consensus 74 ~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~ 153 (367)
.++.+++.......|.++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++...++...+.++.
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~ 119 (243)
T cd06935 40 IVSAPDGDKVDLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEM 119 (243)
T ss_pred CCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCe
Confidence 33445545555666999999999999999999999999999999999999999999999999999998776666666655
Q ss_pred cccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCc
Q psy6602 154 ARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ 233 (367)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~ 233 (367)
.+.+......+....++.+.+|+.+|++|++|++||+|||||+||+||++|+.+..+|+++|+.+..+|+.|+..++|+.
T Consensus 120 ~~~~~~~~~~~~~~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~ 199 (243)
T cd06935 120 AVTREQLKNGGLGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHV 199 (243)
T ss_pred EeeHHHHHhcChHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCC
Confidence 44554443445667788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchh-HhHHHHH
Q psy6602 234 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI-QRLLGDM 276 (367)
Q Consensus 234 ~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~-~~Ll~em 276 (367)
+.||++||++++.||+++..+.|.+++.+..+..++ ++|+.||
T Consensus 200 ~~rf~kLL~~L~~LR~i~~~~~e~l~~~k~~~~~~~~~~L~~Em 243 (243)
T cd06935 200 PHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEV 243 (243)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChhhhcC
Confidence 999999999999999999999999999999988775 8888775
No 8
>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=100.00 E-value=1.8e-38 Score=288.40 Aligned_cols=193 Identities=26% Similarity=0.384 Sum_probs=178.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV 165 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 165 (367)
..++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+++.++..++.++....+... ..+.
T Consensus 41 ~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~~-~~~~ 119 (239)
T cd06945 41 QQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQC-VRGF 119 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHHH-HHhH
Confidence 348899999999999999999999999999999999999999999999999999998877766766655544332 2346
Q ss_pred HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHHHHh
Q psy6602 166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRLLLM 243 (367)
Q Consensus 166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~LL~~ 243 (367)
.+.++.+.+|+.+|++|++|++||+|||||+||+||++|+.+..+|+++|+++.++|++|+..++| +.+.||++||++
T Consensus 120 ~~~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl~ 199 (239)
T cd06945 120 GEWLDSILAFSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLK 199 (239)
T ss_pred HHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHH
Confidence 677889999999999999999999999999999999999999999999999999999999999999 899999999999
Q ss_pred hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602 244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 279 (367)
Q Consensus 244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~ 279 (367)
|+.||+++..+.|.+++.+.++..++++++.+||..
T Consensus 200 Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~~~ 235 (239)
T cd06945 200 LPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRFLD 235 (239)
T ss_pred hHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHHHh
Confidence 999999999999999999999999999999999974
No 9
>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=3.7e-38 Score=286.43 Aligned_cols=220 Identities=18% Similarity=0.266 Sum_probs=181.0
Q ss_pred CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143 (367)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~ 143 (367)
.+|..+++++++..+++. ...++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+.+.
T Consensus 9 ~ep~~~~~~~~~~~~~~~---~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~ 85 (246)
T cd07073 9 IEPGVVCAGHDNNQPDSF---AALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTN 85 (246)
T ss_pred cCCccccCCCCCCCCCch---hHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 466677788777766663 34478899999999999999999999999999999999999999999999999999875
Q ss_pred -CCceE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602 144 -DLSLL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC 220 (367)
Q Consensus 144 -~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~ 220 (367)
+...+ +.++...++......+..+.+..+.+++.+|++|++|.+||+|||||+|||| |++|+.++..|+.+|+++..
T Consensus 86 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~ 165 (246)
T cd07073 86 VNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIK 165 (246)
T ss_pred CCCCeEEecCCeeechhhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHH
Confidence 44434 4444444443333334555666678999999999999999999999999999 99999999999999999999
Q ss_pred HHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCc-----hhHhHHHHHHcccCCCCCCCC
Q psy6602 221 ILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI-----PIQRLLGDMYTMEKSYETPGL 288 (367)
Q Consensus 221 ~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~-----~~~~Ll~eml~~~~s~d~~gl 288 (367)
+|.+|+..++ +..+.||++||++|+.+|+++... .+++.++++.. .+++++.||++.....-..|.
T Consensus 166 aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp~LRsi~~~~--~~~~~~l~~~~~~~~~~~~pll~ei~~~~~~~~~~~~ 239 (246)
T cd07073 166 ELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIAREL--HQFTFDLLIKSHMVSVDFPEMMAEIISVQVPKILSGK 239 (246)
T ss_pred HHHHHHHhcCCCCcccchHHHHHHHHHHHHHHHHHHH--HHHHHHHhCccccCccCccHHHHHHHHhccchhhcCC
Confidence 9999999874 366899999999999999999988 55666666554 689999999996654333343
No 10
>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=3.7e-38 Score=285.33 Aligned_cols=198 Identities=19% Similarity=0.213 Sum_probs=170.8
Q ss_pred CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143 (367)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~ 143 (367)
.++..+++++++..|++.... +.++|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.|||+.+.
T Consensus 9 ~e~~~~~~~~~~~~p~~~~~~---~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~ 85 (248)
T cd07075 9 IEPEIVYAGYDSSKPDTAENL---LSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKH 85 (248)
T ss_pred cCCCcccCCCCCCCCCchhHH---HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 455666678888888776544 67799999999999999999999999999999999999999999999999999876
Q ss_pred CCc-eE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCC-CCCCCChhHHHHHHHHHHH
Q psy6602 144 DLS-LL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPE-TPGLVDAQPVEMLQDQAQC 220 (367)
Q Consensus 144 ~~~-~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd-~~~L~~~~~v~~~q~~~~~ 220 (367)
++. .+ +.++..++.......+..+.++.+.+++.+|++|++|.+||+|||||+||||| ++|++++..|+++|++|..
T Consensus 86 ~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~ 165 (248)
T cd07075 86 TNSQFLYFAPDLVFNEERMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIK 165 (248)
T ss_pred CCCceEEecCCccccHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHH
Confidence 544 34 44555455544334456677788999999999999999999999999999996 7999999999999999999
Q ss_pred HHHHHHHhhCC---CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhcc
Q psy6602 221 ILGDYVRGRYS---RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETI 264 (367)
Q Consensus 221 ~L~~y~~~~~~---~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~ 264 (367)
+|.+|+.++++ ..+.|||+|+++|+.+|+++....|++||....
T Consensus 166 aL~~yi~~~~~~~~~~~~RF~~LLllLp~Lr~i~~k~iE~lff~~~~ 212 (248)
T cd07075 166 ELRKMVTKAPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRE 212 (248)
T ss_pred HHHHHHHHcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 99999996654 456899999999999999999999999887553
No 11
>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=6e-38 Score=285.10 Aligned_cols=197 Identities=30% Similarity=0.473 Sum_probs=173.1
Q ss_pred ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC--CceEecCCccccCCC---
Q psy6602 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD--LSLLINCEKARERLP--- 159 (367)
Q Consensus 85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~--~~~l~~~~~~~~~~~--- 159 (367)
...+..+|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++.... +..++.++.......
T Consensus 39 ~~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~ 118 (241)
T cd07069 39 LSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIAS 118 (241)
T ss_pred cchHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhh
Confidence 445788999999999999999999999999999999999999999999999999987542 334444433222211
Q ss_pred CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602 160 PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR 239 (367)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~ 239 (367)
....+....++.+.+++.+|++|++|.+||||||||+|||||++|+.+..+|+.+|+++..+|++|+..+||+.+.||++
T Consensus 119 ~~~~~~~~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~k 198 (241)
T cd07069 119 QAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQ 198 (241)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHH
Confidence 11223445567889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccC
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK 281 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~ 281 (367)
|+++|++||+++....|.+++++.++..++++++.||+....
T Consensus 199 LLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Eml~~~~ 240 (241)
T cd07069 199 LLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKR 240 (241)
T ss_pred HHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHHHhccc
Confidence 999999999999999999999999999999999999998653
No 12
>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=4.7e-38 Score=281.95 Aligned_cols=193 Identities=32% Similarity=0.494 Sum_probs=168.0
Q ss_pred ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCce---------EecCCccc
Q psy6602 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSL---------LINCEKAR 155 (367)
Q Consensus 85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~---------l~~~~~~~ 155 (367)
+.+++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.+.+... ++..+...
T Consensus 18 ~~~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~~~~~ 97 (222)
T cd07349 18 LCTPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQSS 97 (222)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhccccc
Confidence 345888999999999999999999999999999999999999999999999999997765432 22222111
Q ss_pred cCCCC---CccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC
Q psy6602 156 ERLPP---DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR 232 (367)
Q Consensus 156 ~~~~~---~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~ 232 (367)
..... ........++.+.+++.+|++|++|.+||+|||||+||+||++|+.+...|+.+|+++..+|++|+..+||+
T Consensus 98 ~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~ 177 (222)
T cd07349 98 SGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQ 177 (222)
T ss_pred ccccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 11110 111123445678899999999999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHH
Q psy6602 233 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 277 (367)
Q Consensus 233 ~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml 277 (367)
.+.||++|+++|+.+|+++...+|.+||.+.+|..++++++.||+
T Consensus 178 ~~~r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~i~~Ll~eml 222 (222)
T cd07349 178 DQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML 222 (222)
T ss_pred cccHHHHHHHHhHHHhcCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence 999999999999999999999999999999999999999999985
No 13
>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=100.00 E-value=5.7e-38 Score=283.97 Aligned_cols=193 Identities=25% Similarity=0.329 Sum_probs=174.6
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV 165 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 165 (367)
..++++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+.+.++..++.++....+.... .+.
T Consensus 42 ~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~~g~~~~~~~~~-~~~ 120 (239)
T cd07072 42 EKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQ-RSF 120 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEeeCCeeecHHHHH-hhH
Confidence 3489999999999999999999999999999999999999999999999999999988777666665544444322 246
Q ss_pred HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHh
Q psy6602 166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLM 243 (367)
Q Consensus 166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~ 243 (367)
++.++.+++|+.+|++|++|.+||+|||||+||+ |++|+.+..+|+++|+++..+|++|+..++ ++.+.||++||++
T Consensus 121 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAivLf~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kLLl~ 199 (239)
T cd07072 121 GDWLHAILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGK 199 (239)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHH
Confidence 6777889999999999999999999999999995 999999999999999999999999999765 4788999999999
Q ss_pred hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602 244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 280 (367)
Q Consensus 244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~ 280 (367)
|+.||+++..+.|.+++.+..+..++++++.|||..+
T Consensus 200 Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em~~~~ 236 (239)
T cd07072 200 LPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMFVAS 236 (239)
T ss_pred hHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHHHhcc
Confidence 9999999999999999999999999999999999753
No 14
>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=3.8e-37 Score=274.24 Aligned_cols=189 Identities=50% Similarity=0.799 Sum_probs=169.1
Q ss_pred CCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccC
Q psy6602 78 HPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER 157 (367)
Q Consensus 78 ~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~ 157 (367)
+++......+.+++|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.||++...+...++.+++....
T Consensus 18 ~~~~~~~~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~ 97 (206)
T cd06950 18 YGTISSYEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPD 97 (206)
T ss_pred cccccccccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCccccc
Confidence 45666778889999999999999999999999999999999999999999999999999999988777777776554333
Q ss_pred CCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHH
Q psy6602 158 LPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF 237 (367)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf 237 (367)
...........++.+.+++.+|++|++|++||+|||||+||+||++|+++...|+++|+++..+|++|+..+|+.++.||
T Consensus 98 ~~~~~~~~~~~~~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf 177 (206)
T cd06950 98 NTEAERTFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARF 177 (206)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHH
Confidence 22222234455577899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCC
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGD 266 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~ 266 (367)
++|+++|+.+|+++..+.|.+++.+++|+
T Consensus 178 ~kLLl~Lp~lr~ls~~~~e~l~~~~~~g~ 206 (206)
T cd06950 178 GKLLLLLPSLRFISSSTIEELFFKKTIGN 206 (206)
T ss_pred HHHHHHHHHHHhhhHHHHHHHhccCcCCC
Confidence 99999999999999999999999988763
No 15
>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=100.00 E-value=4.2e-37 Score=277.32 Aligned_cols=212 Identities=23% Similarity=0.381 Sum_probs=185.5
Q ss_pred CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143 (367)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~ 143 (367)
.+|.+..++|.|..+++.... ++++++++++.++.+|+|||++|||..|+.+||++|||++|+++++++.||++++.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~ 84 (221)
T cd06946 8 AEPDKLFAMPDPALPDSDIKA---LTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPF 84 (221)
T ss_pred cCCccccCCCCCCCCCCchHH---HHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence 445555556565555554433 78899999999999999999999999999999999999999999999999999988
Q ss_pred CCceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHH
Q psy6602 144 DLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223 (367)
Q Consensus 144 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~ 223 (367)
++..++.++....+......+.....+.+.+++.+|++|++|.+||+|||||+||+||+.|+.+...|+++|++|.++|.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~ 164 (221)
T cd06946 85 NGELVFAEDFILDEELAREAGLLELYSACLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALS 164 (221)
T ss_pred CCceeecCCeEEcHHHHhhcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 76666656554443332333455666788899999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhCC-CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602 224 DYVRGRYS-RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278 (367)
Q Consensus 224 ~y~~~~~~-~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~ 278 (367)
+||..+|+ ++|.||++|+++++.+|+++..+.|++++.+..+..++++++.||+.
T Consensus 165 ~y~~~~~~~~~p~Rf~~LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~ 220 (221)
T cd06946 165 DYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLE 220 (221)
T ss_pred HHHHHhCCCcchhHHHHHHhhchhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHhc
Confidence 99999988 89999999999999999999999999999999999999999999986
No 16
>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=1.9e-37 Score=281.44 Aligned_cols=195 Identities=24% Similarity=0.317 Sum_probs=169.4
Q ss_pred ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCcc-ccCCCCC-
Q psy6602 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEKA-RERLPPD- 161 (367)
Q Consensus 85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~~-~~~~~~~- 161 (367)
...+..+|+++++.++.+|+|||++|||.+|+.+||++|||+||+|+++|+.|||+.... .+.+.++++. +......
T Consensus 37 ~~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~ 116 (237)
T cd07070 37 PAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAA 116 (237)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHHH
Confidence 344788999999999999999999999999999999999999999999999999998543 3334444433 2222111
Q ss_pred ccc--hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602 162 DVR--VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR 239 (367)
Q Consensus 162 ~~~--~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~ 239 (367)
..+ ....+..+.+++.+|++|++|.+||+|||||+|||||++|+++...|+++|++|..+|.+||..+||..+.||++
T Consensus 117 ~~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~k 196 (237)
T cd07070 117 QAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQ 196 (237)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHH
Confidence 111 123334567899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 279 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~ 279 (367)
||++|+.||+++....|++++.+.++..++++++.||++.
T Consensus 197 LLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~eml~~ 236 (237)
T cd07070 197 LLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA 236 (237)
T ss_pred HHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999874
No 17
>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=3.7e-37 Score=279.94 Aligned_cols=195 Identities=30% Similarity=0.476 Sum_probs=173.9
Q ss_pred ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCcc-ccCCCC--
Q psy6602 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEKA-RERLPP-- 160 (367)
Q Consensus 85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~~-~~~~~~-- 160 (367)
...++.+++++.+.++.+|+|||++|+|.+|+.+||++|||++|+++++|+.||++...+ .+.+...++. ......
T Consensus 37 ~~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~ 116 (237)
T cd06944 37 LDTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLAS 116 (237)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhh
Confidence 345788999999999999999999999999999999999999999999999999998765 4445444443 222221
Q ss_pred -CccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHH
Q psy6602 161 -DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR 239 (367)
Q Consensus 161 -~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~ 239 (367)
...+..+.++.+.+++.+|++|++|++||+|||||+|||||++|++++..|+++|++|.++|.+||..+++.++.||++
T Consensus 117 ~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~ 196 (237)
T cd06944 117 QAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQ 196 (237)
T ss_pred hccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHH
Confidence 1123455677889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 279 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~ 279 (367)
|+++++.+|+++....|++++++.++..++++++.||++.
T Consensus 197 LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~eml~~ 236 (237)
T cd06944 197 LLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHA 236 (237)
T ss_pred HHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHHHcC
Confidence 9999999999999999999999999999999999999874
No 18
>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=100.00 E-value=7.1e-37 Score=275.74 Aligned_cols=212 Identities=26% Similarity=0.420 Sum_probs=185.0
Q ss_pred CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143 (367)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~ 143 (367)
.+|...++++++..+++.. ..++++|+++.+.++.+|+|||++|+|..|+.+||++|+|++|++++++..||+++..
T Consensus 8 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~ 84 (221)
T cd07068 8 AEPDKLYAMNDPTGPDTEV---SLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPH 84 (221)
T ss_pred hCCCcccCCCCCCCCCCch---HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCC
Confidence 3455555554444444443 3488999999999999999999999999999999999999999999999999999887
Q ss_pred CCceEecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHH
Q psy6602 144 DLSLLINCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILG 223 (367)
Q Consensus 144 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~ 223 (367)
+....+.++....+......+..+..+.+.+++.+|++|++|++||+|||||+||+||++|+.++..|++.|++|.++|.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~ 164 (221)
T cd07068 85 PGKLVFAPDLLLDREQARVEGLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALV 164 (221)
T ss_pred CCeEEeCCCceECHHHHhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHH
Confidence 77555555555444333334455666788999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhCC-CcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602 224 DYVRGRYS-RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278 (367)
Q Consensus 224 ~y~~~~~~-~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~ 278 (367)
+||..+++ .++.||++|+++++.+|+++..++|++++.+..+..++++++.||+.
T Consensus 165 ~y~~~~~~~~~~~Rf~~LL~~l~~Lr~~~~~~~e~l~~~k~~~~~~~~~Ll~e~l~ 220 (221)
T cd07068 165 DVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLE 220 (221)
T ss_pred HHHHHhCCCccccHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHhc
Confidence 99999999 99999999999999999999999999999999999999999999986
No 19
>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=100.00 E-value=3.1e-37 Score=273.01 Aligned_cols=192 Identities=21% Similarity=0.304 Sum_probs=169.0
Q ss_pred CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602 87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN 166 (367)
Q Consensus 87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 166 (367)
-|.++++.+++.++.+|+|||++|||++|+.+||++|||+||+|++++++++++...++...+.++..+.+......+..
T Consensus 3 ~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (195)
T cd06941 3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDS 82 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCeEEecCCeEeeHHHHHhccch
Confidence 37899999999999999999999999999999999999999999999999998877655555555444443322222234
Q ss_pred HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602 167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS 246 (367)
Q Consensus 167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~ 246 (367)
+..+.+.+|+.+|++|++|++||+|||||+||+||++|+.+...|+++|+++.++|++|+..++|+.+.||++|+++++.
T Consensus 83 ~~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~ 162 (195)
T cd06941 83 DFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPE 162 (195)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHH
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhhhhhHHHHHH-hhhccCCchhHhHHHHHHc
Q psy6602 247 LRAVRQSTIERLF-FKETIGDIPIQRLLGDMYT 278 (367)
Q Consensus 247 Lr~l~~~~~e~l~-~~~~~~~~~~~~Ll~eml~ 278 (367)
||+++..+.|.+. ++...+..++++|+.|||+
T Consensus 163 Lr~l~~~~~e~l~~~~~~~~~~~~p~L~~E~~~ 195 (195)
T cd06941 163 LRSIGAKHQMHLDWYRVNWPLLRLPPLFAEIYD 195 (195)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCcHHHHhcC
Confidence 9999999999997 4445566789999999986
No 20
>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=3.2e-37 Score=278.17 Aligned_cols=193 Identities=28% Similarity=0.438 Sum_probs=166.0
Q ss_pred hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc---------
Q psy6602 83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK--------- 153 (367)
Q Consensus 83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~--------- 153 (367)
.++.+++++|+++++.++.+|+|||++|+|.+|+.+||++|||+||.|+++|+.||++.+.+....+.++.
T Consensus 16 ~~l~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~ 95 (232)
T cd07350 16 VTLKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRP 95 (232)
T ss_pred cccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhccc
Confidence 34566899999999999999999999999999999999999999999999999999998766543221111
Q ss_pred ccc------------CCCCCc---cchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHH
Q psy6602 154 ARE------------RLPPDD---VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQA 218 (367)
Q Consensus 154 ~~~------------~~~~~~---~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~ 218 (367)
... ...... ......++.+.+|+.+|++|++|.+||||||||+||+||++|+.+..+|+++|+++
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~ 175 (232)
T cd07350 96 PPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEA 175 (232)
T ss_pred ccccccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHH
Confidence 000 000000 01123457799999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHH
Q psy6602 219 QCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 275 (367)
Q Consensus 219 ~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~e 275 (367)
..+|++|+..+||+++.||++|+++|+.||+++...+|.+||++.+|.+++++++.|
T Consensus 176 ~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll~E 232 (232)
T cd07350 176 QQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDMLLE 232 (232)
T ss_pred HHHHHHHHHhhCCChhhHHHHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHhcC
Confidence 999999999999999999999999999999999999999999999999999988753
No 21
>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=3.3e-37 Score=277.06 Aligned_cols=189 Identities=31% Similarity=0.456 Sum_probs=163.8
Q ss_pred ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEe---------cCCccc
Q psy6602 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLI---------NCEKAR 155 (367)
Q Consensus 85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~---------~~~~~~ 155 (367)
+..++++|+++++.++.+|+|||++|||.+|+.+||++|||++|+|+++|+.||++.+.+..... ..++..
T Consensus 18 ~~~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~ 97 (222)
T cd06951 18 LCAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMH 97 (222)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhccccc
Confidence 55688999999999999999999999999999999999999999999999999999876543221 112111
Q ss_pred -cCCCC----Ccc-chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhh
Q psy6602 156 -ERLPP----DDV-RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGR 229 (367)
Q Consensus 156 -~~~~~----~~~-~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~ 229 (367)
..... ... .....++.+++|+.+|++|++|.+||||||||+||+||++|+ +...|+++|+++..+|++|+..+
T Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~ 176 (222)
T cd06951 98 WGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMT 176 (222)
T ss_pred cccccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhh
Confidence 11110 011 122346789999999999999999999999999999999999 99999999999999999999999
Q ss_pred CCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHH
Q psy6602 230 YSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLG 274 (367)
Q Consensus 230 ~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~ 274 (367)
||+.+.||++||++|+.||+++...+|.+++.+.+|..++++++.
T Consensus 177 ~p~~~~Rf~kLLl~Lp~LRsl~~~~~e~lff~~~~g~~~i~~ll~ 221 (222)
T cd06951 177 RPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLL 221 (222)
T ss_pred CCCcccHHHHHHHHhHHhhcCCHHHHHHHhCccccCCCcHHHHhc
Confidence 999999999999999999999999999999999999999998875
No 22
>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=1.9e-36 Score=275.24 Aligned_cols=201 Identities=41% Similarity=0.718 Sum_probs=177.6
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccC-CCCCc-c
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARER-LPPDD-V 163 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~-~~~~~-~ 163 (367)
+.++++|+++++.++.+|+|||++|||..|+.+||++|||+||+|+++|+.|+++.+.+.+.++.+++.... ..... .
T Consensus 30 ~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~~~~~ 109 (236)
T cd06948 30 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSADRVV 109 (236)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccchhhHh
Confidence 448899999999999999999999999999999999999999999999999999988777766666554321 11111 1
Q ss_pred chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHh
Q psy6602 164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLM 243 (367)
Q Consensus 164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~ 243 (367)
...+.++.+.+++.+|++|++|++||+|||||+||+||++|+++..+|+++|++|.++|++||..++++++.||++|+++
T Consensus 110 ~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~ 189 (236)
T cd06948 110 AFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLR 189 (236)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHH
Confidence 12334456778999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCC
Q psy6602 244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETP 286 (367)
Q Consensus 244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~ 286 (367)
++.+|+++..+.|.+++.+.++..++++++.+|+....+++.+
T Consensus 190 Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~~~~~~~~ 232 (236)
T cd06948 190 LPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFVWP 232 (236)
T ss_pred HHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhCCCCCccc
Confidence 9999999999999999999999999999999999876665543
No 23
>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=100.00 E-value=5.7e-36 Score=270.77 Aligned_cols=215 Identities=16% Similarity=0.200 Sum_probs=180.4
Q ss_pred CCCcccccCCCCCCCCChhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy6602 64 HHPSMFLATHQPPPHPGLLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPW 143 (367)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~ 143 (367)
.+|..++++|++..|++.... +..+++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.|||+...
T Consensus 9 ~ep~~~~~~~d~~~p~~~~~~---~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~ 85 (248)
T cd07074 9 IEPDVVYAGYDNTKPETPSSL---LTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKH 85 (248)
T ss_pred hCCCcccCCCCCCCCCCchhh---HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 577888999999999887666 45599999999999999999999999999999999999999999999999999876
Q ss_pred CC-ceE-ecCCccccCCCCCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCC-CCCCCCChhHHHHHHHHHHH
Q psy6602 144 DL-SLL-INCEKARERLPPDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTP-ETPGLVDAQPVEMLQDQAQC 220 (367)
Q Consensus 144 ~~-~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~p-d~~~L~~~~~v~~~q~~~~~ 220 (367)
.. +.+ +.+|+..++......+..+.+..+.+++.+|++|++|.+||+|||||+|||| |++||+++..|+++|++|.+
T Consensus 86 ~~~~~l~fa~d~~~~~~~~~~~~~~~~~~~m~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~ 165 (248)
T cd07074 86 VSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMRSSYIR 165 (248)
T ss_pred CCCCeEEecCCcccchhhhhhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHH
Confidence 43 333 5566666655433334556667788999999999999999999999999999 89999999999999999999
Q ss_pred HHHHHHHhhC---CCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhc---cCCchhHhHHHHHHcccC
Q psy6602 221 ILGDYVRGRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKET---IGDIPIQRLLGDMYTMEK 281 (367)
Q Consensus 221 ~L~~y~~~~~---~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~---~~~~~~~~Ll~eml~~~~ 281 (367)
+|.+|+..++ .+++.||++|+.+++.++.+..+...+++.... ...+.++.++.|+.....
T Consensus 166 aL~~yi~~~~~~~~~~~~RF~~Ll~ll~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 (248)
T cd07074 166 ELIKAIGLRQKGVVASSQRFYQLTKLMDNMHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQL 232 (248)
T ss_pred HHHHHHHHcCCCCccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeecHHHHHHHHHhcc
Confidence 9999977664 378999999999999999888888777754432 335667777877776433
No 24
>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=100.00 E-value=2.7e-36 Score=265.06 Aligned_cols=177 Identities=20% Similarity=0.268 Sum_probs=159.2
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV 165 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 165 (367)
.-|+++++.++..|+.+|+|||++|||.+|+.+||++|||+||+|+++++.++++....+...+.++..+++......+.
T Consensus 12 ~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 91 (189)
T cd06940 12 EIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLHSMGA 91 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCcEEcHHHHHHcCc
Confidence 33889999999999999999999999999999999999999999999999999988766665555544444333223345
Q ss_pred HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602 166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP 245 (367)
Q Consensus 166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~ 245 (367)
.+.++.+.+++.+|++|++|.+||+|||||+||+||++|+.++.+|+++|+++.++|++|+..++|+++.||++|+++++
T Consensus 92 ~~~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL~~L~ 171 (189)
T cd06940 92 GDLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLP 171 (189)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHH
Confidence 67788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHhhhhhHHHHHHhhh
Q psy6602 246 SLRAVRQSTIERLFFKE 262 (367)
Q Consensus 246 ~Lr~l~~~~~e~l~~~~ 262 (367)
.+|+++..+.|.+++.+
T Consensus 172 ~LR~l~~~~~e~l~~~~ 188 (189)
T cd06940 172 DLRTLNNLHSEKLLAFK 188 (189)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 99999999999998865
No 25
>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=100.00 E-value=2.8e-36 Score=274.16 Aligned_cols=190 Identities=19% Similarity=0.269 Sum_probs=168.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV 165 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 165 (367)
.-|.++++..+..|+.+|+|||++|||.+|+.+||++|||+||+|++++++|++++..++.. ++++....+......+.
T Consensus 48 ~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 126 (241)
T cd06939 48 EMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTV-LFDGKYAPIDLFKSLGC 126 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCEE-EECCccccHHHHHHcCc
Confidence 44899999999999999999999999999999999999999999999999998887655554 44444333332222345
Q ss_pred HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602 166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP 245 (367)
Q Consensus 166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~ 245 (367)
.+.++.+++|+.+|+.|++|++||+|||||+||+||++|+.+..+|+++|+++..+|+.|+..+| +.+.||++||++++
T Consensus 127 ~~~~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~kLL~~Lp 205 (241)
T cd06939 127 DDLISAVFDFAKSLCELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTKLLAKMP 205 (241)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHHHHHHHH
Confidence 67788999999999999999999999999999999999999999999999999999999999998 89999999999999
Q ss_pred HhHhhhhhHHHHHHhhhccCC----chhHhHHHHHH
Q psy6602 246 SLRAVRQSTIERLFFKETIGD----IPIQRLLGDMY 277 (367)
Q Consensus 246 ~Lr~l~~~~~e~l~~~~~~~~----~~~~~Ll~eml 277 (367)
.||+++..+.|.+++.+..+. ..+++|+.|||
T Consensus 206 ~LR~l~~~~~e~l~~~k~~~p~~~~~~~ppL~~Elf 241 (241)
T cd06939 206 TLRALCSLHMEKLQKFKQSYPDIVHLEFPPLYKELF 241 (241)
T ss_pred HHHHHHHHHHHHHHHHhccCCCcccCCCCcHHHhhC
Confidence 999999999999999988743 35889998885
No 26
>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=100.00 E-value=1e-35 Score=270.86 Aligned_cols=193 Identities=23% Similarity=0.265 Sum_probs=170.7
Q ss_pred ccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc
Q psy6602 85 LMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR 164 (367)
Q Consensus 85 ~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~ 164 (367)
...+.++++++.+.++.+|+|||++|||..|+.+||++|||++|+|+++|+.||++....+...+.++..+.+......+
T Consensus 42 ~~~~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~ 121 (236)
T cd06954 42 QQRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFARAG 121 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCccccHHHHHHhc
Confidence 35588999999999999999999999999999999999999999999999999998876555555444333332211112
Q ss_pred -hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHh
Q psy6602 165 -VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLM 243 (367)
Q Consensus 165 -~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~ 243 (367)
..+..+.+.+|+.+|++|++|++||+|||||+||+||++|+++...|+++|++|..+|++||..+||+.+.||++++++
T Consensus 122 ~~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~ 201 (236)
T cd06954 122 LQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMK 201 (236)
T ss_pred ChHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Confidence 3456788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602 244 LPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278 (367)
Q Consensus 244 l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~ 278 (367)
|+.||+++..+.|.+++.+..+ .++++++.|||+
T Consensus 202 L~~Lr~l~~~~~e~l~~~k~~~-~~~~~L~~El~~ 235 (236)
T cd06954 202 LVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWD 235 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHhcC-CCCCcHHHHHhc
Confidence 9999999999999999888764 689999999987
No 27
>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=100.00 E-value=1.5e-35 Score=268.75 Aligned_cols=194 Identities=21% Similarity=0.308 Sum_probs=172.3
Q ss_pred hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCcc
Q psy6602 84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDV 163 (367)
Q Consensus 84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~ 163 (367)
....+.++++++...++.+|+|||++|||..|+.+||++|||+||+|+++|+.||++....+...+.++..+.+......
T Consensus 37 ~~~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~~~~~~f~~g~~~~~~~~~~~ 116 (231)
T cd06938 37 SDMRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYRKA 116 (231)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEeeCCEEecHHHHhhc
Confidence 44668999999999999999999999999999999999999999999999999999877666555555443444332233
Q ss_pred chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC-cchHHHHHHH
Q psy6602 164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR-QPTRFGRLLL 242 (367)
Q Consensus 164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~-~~~Rf~~LL~ 242 (367)
+.....+.+.+|+.+|++|++|++||+|||||+||+ |++|+++...|+.+|++|.++|+.||..+|+. ++.||++||+
T Consensus 117 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~ 195 (231)
T cd06938 117 GMGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLS 195 (231)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHH
Confidence 455667889999999999999999999999999998 77899999999999999999999999999986 8999999999
Q ss_pred hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcc
Q psy6602 243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 279 (367)
Q Consensus 243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~ 279 (367)
+++.||+++..+.|.+++.+.. ...+++++.|+++.
T Consensus 196 ~L~~Lr~l~~~~~e~~~~~k~~-~~~~~pl~~Ei~d~ 231 (231)
T cd06938 196 ILTELRTLGNQNSEMCFSLKLK-NRKLPPFLAEIWDV 231 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHhCC
Confidence 9999999999999999999988 67899999999873
No 28
>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=100.00 E-value=2e-35 Score=271.08 Aligned_cols=196 Identities=21% Similarity=0.294 Sum_probs=168.9
Q ss_pred hhhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc-cCCC
Q psy6602 81 LLQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR-ERLP 159 (367)
Q Consensus 81 ~~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~-~~~~ 159 (367)
......-|.++.......++.+|+|||++|||.+|+.+||++|||++|+|+++++.|++++ .+..++..++.+ .+..
T Consensus 58 ~~~~~~~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~--~~~~~~~~~~~~~~~~~ 135 (259)
T cd06932 58 KTIRIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYN--KDGLLFPEGNGYVTREF 135 (259)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcC--CCCeEEeCCCEEeeHHH
Confidence 3334445888999999999999999999999999999999999999999999999998764 334455544332 2222
Q ss_pred CCc--cchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHH
Q psy6602 160 PDD--VRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF 237 (367)
Q Consensus 160 ~~~--~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf 237 (367)
... .+..+.++.+++|+.+|++|++|++||+|||||+||+||++|+.++..|+++|+++..+|+.|+..+||+.+.||
T Consensus 136 ~~~~~~~~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf 215 (259)
T cd06932 136 LESLRKPFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLF 215 (259)
T ss_pred HHHhcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHH
Confidence 111 123466788899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhc-cCCchhHhHHHHHHc
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKET-IGDIPIQRLLGDMYT 278 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~-~~~~~~~~Ll~eml~ 278 (367)
++||++|+.||+++..+.|.+++.+. .+..++++|+.|||+
T Consensus 216 ~kLLl~L~~LRsl~~~~~e~l~~~k~~~~~~~~~pLl~Ei~~ 257 (259)
T cd06932 216 AKLLQKMVDLRQLVTDHVQMVQQIKKTETDASLPPLLQEIYK 257 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCcHHHHHhh
Confidence 99999999999999999999997764 557889999999986
No 29
>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=100.00 E-value=2e-35 Score=268.39 Aligned_cols=193 Identities=15% Similarity=0.205 Sum_probs=160.5
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCc-eEecCCcc-ccCCCCCcc
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLS-LLINCEKA-RERLPPDDV 163 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~-~l~~~~~~-~~~~~~~~~ 163 (367)
.-+.++++++++.++.+|+|||++|||.+|+.+||++|||+||+|+++++.++++.. ++. ..+.+... +........
T Consensus 37 ~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 115 (238)
T cd06933 37 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQSFSL-DDMSWTCGSPDFKYKVSDVTKA 115 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHhcCc-CCCeeEecCCceeecHHHHHHc
Confidence 336889999999999999999999999999999999999999999999999986543 443 33333221 222111111
Q ss_pred c-hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHH
Q psy6602 164 R-VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQPTRFGRL 240 (367)
Q Consensus 164 ~-~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~--~~~~Rf~~L 240 (367)
+ ..+.++.+.+|..+|++|++|.+||+|||||+||+||++|+.+...|+.+|+++.++|++|+..+|| ..+.||++|
T Consensus 116 g~~~~~~~~l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~~~~f~kL 195 (238)
T cd06933 116 GHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYAKM 195 (238)
T ss_pred cCcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCCCCcchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHH
Confidence 2 2356788999999999999999999999999999999999999999999999999999999999986 456689999
Q ss_pred HHhhhHhHhhhhhHHHHHHhhhccC--CchhHhHHHHHHcc
Q psy6602 241 LLMLPSLRAVRQSTIERLFFKETIG--DIPIQRLLGDMYTM 279 (367)
Q Consensus 241 L~~l~~Lr~l~~~~~e~l~~~~~~~--~~~~~~Ll~eml~~ 279 (367)
|++|+.||+++..+.|.+...+... ...+++|+.|+|+.
T Consensus 196 Ll~L~~LRsi~~~h~~~~~~~~~~~~~~~~~~pL~~Ei~~~ 236 (238)
T cd06933 196 IQKLADLRSLNEEHSKQYRSLSFQPEHSMKLTPLVLEVFGN 236 (238)
T ss_pred HHHhHHHHhhhHHHHHHHHHHHhccCCCCCCCcHHHHHhcc
Confidence 9999999999999999876544432 33589999999973
No 30
>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=100.00 E-value=3.6e-35 Score=264.73 Aligned_cols=188 Identities=15% Similarity=0.224 Sum_probs=157.3
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccch
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRV 165 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 165 (367)
..+.++++.+.+.++.+|+|||++|||.+|+.+||++|||+||+|+++++.+++++.. ...+++++..+........+.
T Consensus 35 ~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~-~~~~~~~~~~~~~~~~~~~g~ 113 (226)
T cd06934 35 SLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEE-TGTWECGPLTYCIEDAARAGF 113 (226)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhccc-CCeEeeCCEeecHHHHHHccc
Confidence 3478999999999999999999999999999999999999999999999999988764 344555554433222222233
Q ss_pred HH-HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcc--hHHHHHHH
Q psy6602 166 NN-EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP--TRFGRLLL 242 (367)
Q Consensus 166 ~~-~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~--~Rf~~LL~ 242 (367)
.. ..+.+.+|+.+|++|++|++||+|||||+||+||++|+.+...|+++|+++.++|++|+..+||..+ .||++||+
T Consensus 114 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r~~f~kLLl 193 (226)
T cd06934 114 QQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFLYPKILA 193 (226)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHH
Confidence 33 4578999999999999999999999999999999999999999999999999999999999987544 45999999
Q ss_pred hhhHhHhhhhhHHHHHHhhhccCCch-hHhHHHHH
Q psy6602 243 MLPSLRAVRQSTIERLFFKETIGDIP-IQRLLGDM 276 (367)
Q Consensus 243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~-~~~Ll~em 276 (367)
+|+.||+++..+.|.+...+ +..+ +++|+.|+
T Consensus 194 ~L~~LRsl~~~~~~~~~~~~--~~~~~~~pl~~Ei 226 (226)
T cd06934 194 CLTELRTINEEYTKQILHIQ--DIQPMATPLMQEI 226 (226)
T ss_pred HhHHHhcchHHHHHHHHHHh--ccCCCCCchhhcC
Confidence 99999999999999875433 3334 47777664
No 31
>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=100.00 E-value=2.8e-34 Score=256.62 Aligned_cols=176 Identities=31% Similarity=0.578 Sum_probs=157.2
Q ss_pred CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602 87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN 166 (367)
Q Consensus 87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 166 (367)
+++++|+++.+.++.+|+|||++|+|.+|+.+||++|+|++|+++++++.||++....+..++.++....+......+..
T Consensus 31 ~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 (207)
T cd06943 31 PVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQAGVG 110 (207)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCceeccchhhhccch
Confidence 47889999999999999999999999999999999999999999999999999998777777776655444332233334
Q ss_pred HHHHH-HHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602 167 NEIKL-IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP 245 (367)
Q Consensus 167 ~~~~~-~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~ 245 (367)
..... +.+++.+|++|++|++||+|||||+||+||++|+++...|+++|++|.++|++||..++++++.||++|+++++
T Consensus 111 ~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L~ 190 (207)
T cd06943 111 AIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLP 190 (207)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHHH
Confidence 44444 56899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHhhhhhHHHHHHhhh
Q psy6602 246 SLRAVRQSTIERLFFKE 262 (367)
Q Consensus 246 ~Lr~l~~~~~e~l~~~~ 262 (367)
.+|+++..+.|.+++.+
T Consensus 191 ~lr~l~~~~~e~l~~~~ 207 (207)
T cd06943 191 ALRSIGLKCLEHLFFFK 207 (207)
T ss_pred HHHhHhHHHHHHHhhcC
Confidence 99999999999998853
No 32
>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=100.00 E-value=4.1e-34 Score=258.09 Aligned_cols=195 Identities=31% Similarity=0.526 Sum_probs=168.4
Q ss_pred hccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCcccc-----CC
Q psy6602 84 ILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARE-----RL 158 (367)
Q Consensus 84 ~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~-----~~ 158 (367)
...+++++++++.+.++.+|+|||++|+|..|+.+||++|+|++|.|+++++.+|++...+...++...+.+. ..
T Consensus 19 ~~~~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 98 (222)
T cd06952 19 SYLNVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQD 98 (222)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhhhHhcC
Confidence 3445888999999999999999999999999999999999999999999999998887655554443321110 11
Q ss_pred CCCcc---chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcch
Q psy6602 159 PPDDV---RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 235 (367)
Q Consensus 159 ~~~~~---~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~ 235 (367)
..... ...+.+..+.+++.+|++|++|..||+|||||+||+||++|+.+...|+++|+++.++|.+|+..++++.+.
T Consensus 99 ~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~ 178 (222)
T cd06952 99 KLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEY 178 (222)
T ss_pred CCchhhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCccc
Confidence 11111 122334557889999999999999999999999999999999999999999999999999999998999999
Q ss_pred HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602 236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278 (367)
Q Consensus 236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~ 278 (367)
||++|+++|+.+|+++..+.|.+++.+.+|..+++.++..++.
T Consensus 179 R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~~~~ll~~~~~ 221 (222)
T cd06952 179 RLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSVIPYILR 221 (222)
T ss_pred HHHHHHHHhHHhhhcCHHHHHHHhcccccCCCcHHHHHHHHHh
Confidence 9999999999999999999999999999999999999998874
No 33
>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=100.00 E-value=1.4e-33 Score=253.79 Aligned_cols=184 Identities=22% Similarity=0.206 Sum_probs=156.6
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccc-
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVR- 164 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~- 164 (367)
..+.++++++.+.++.+|+|||++|||..|+.+||++|||+||+|+++++.|++++.. ...+............+
T Consensus 36 ~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~~----~~~~~~~~~~~~~~~~~~ 111 (221)
T cd06936 36 ENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKK----LPAGHADLLEERIRSSGI 111 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhccc----ccCCCchhhHHHHHhccc
Confidence 4488899999999999999999999999999999999999999999999999776531 10011011110001112
Q ss_pred hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602 165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML 244 (367)
Q Consensus 165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l 244 (367)
..+.++.+++|+.+|++|++|.+||+|||||+||+||++|++++..|+.+|++|.++|++||..+||+.+.||++||+++
T Consensus 112 ~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~LL~~L 191 (221)
T cd06936 112 SDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLLGRL 191 (221)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHh
Confidence 34567888899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhHhhhhhHHHHHHhhhccCCchhHhHHH
Q psy6602 245 PSLRAVRQSTIERLFFKETIGDIPIQRLLG 274 (367)
Q Consensus 245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~ 274 (367)
+.||+++..+.|.+++.+... ..+++|+.
T Consensus 192 ~~LR~l~~~~~e~l~~~k~~~-~~~~pl~~ 220 (221)
T cd06936 192 TELRTLNHHHAEMLMSWKVND-HKFTPLLC 220 (221)
T ss_pred HHHHHHHHHHHHHHHHHHccC-CCCCcccc
Confidence 999999999999999998875 46777764
No 34
>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=100.00 E-value=6.9e-33 Score=247.96 Aligned_cols=175 Identities=28% Similarity=0.421 Sum_probs=147.6
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCc-cccCCC---CC
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEK-ARERLP---PD 161 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~-~~~~~~---~~ 161 (367)
..+..+++++++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.||+++..+...+....+ ...... ..
T Consensus 27 ~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~~~~ 106 (213)
T cd06953 27 ELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELERF 106 (213)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhHHHH
Confidence 34788999999999999999999999999999999999999999999999999998644322111000 000100 00
Q ss_pred ccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHH
Q psy6602 162 DVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLL 241 (367)
Q Consensus 162 ~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL 241 (367)
.....+.++.+.+++.+|++|++|.+||+|||||+||+||++|+++...|+++|++|.++|++||..++++++.||++||
T Consensus 107 ~~~~~~~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf~~LL 186 (213)
T cd06953 107 GDEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFSDLL 186 (213)
T ss_pred HhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHH
Confidence 11234566788899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhHhHhhhhhHHHHHHh
Q psy6602 242 LMLPSLRAVRQSTIERLFF 260 (367)
Q Consensus 242 ~~l~~Lr~l~~~~~e~l~~ 260 (367)
++++.+|+++....|.-.+
T Consensus 187 ~~L~~Lr~l~~~~~e~~~~ 205 (213)
T cd06953 187 SCLPEIRAAAGKLLHSKLF 205 (213)
T ss_pred HHhHHHHHHHHHHHHHHHH
Confidence 9999999999988876543
No 35
>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=100.00 E-value=2.6e-32 Score=246.46 Aligned_cols=193 Identities=31% Similarity=0.536 Sum_probs=171.3
Q ss_pred hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCc
Q psy6602 83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD 162 (367)
Q Consensus 83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~ 162 (367)
.+.++++++++.+.+.++.+|+|||++|+|..|+.+||++|+|++|++++++..||++...++..++.++..+......
T Consensus 29 ~~~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~l~~~~g~~~~~~~~~- 107 (222)
T cd06931 29 KKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHCPE- 107 (222)
T ss_pred cccCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCCeeeeCCCccccccccc-
Confidence 5677799999999999999999999999999999999999999999999999999999876666566655544443322
Q ss_pred cchHHHH-HHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHH
Q psy6602 163 VRVNNEI-KLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLL 241 (367)
Q Consensus 163 ~~~~~~~-~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL 241 (367)
.+..... +.+.+++.+|++|++|++||+|||||++|+||++|+++...++++|+++.++|.+|+..++++++.||++|+
T Consensus 108 ~~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL 187 (222)
T cd06931 108 PEISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELL 187 (222)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHH
Confidence 2233334 345689999999999999999999999999999999999999999999999999999888889999999999
Q ss_pred HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHH
Q psy6602 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 276 (367)
Q Consensus 242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~em 276 (367)
.+++.+++++....|.+++.++++..++++++.+|
T Consensus 188 ~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e~ 222 (222)
T cd06931 188 LLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222 (222)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhhC
Confidence 99999999999999999999999999999999875
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=100.00 E-value=6.9e-33 Score=240.99 Aligned_cols=170 Identities=25% Similarity=0.333 Sum_probs=150.2
Q ss_pred CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc-cCCCCCccch
Q psy6602 87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR-ERLPPDDVRV 165 (367)
Q Consensus 87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~-~~~~~~~~~~ 165 (367)
.++++++.+++.++.+|+|||++|+|..|+.+||++|+|++|+++++++.||++....+ .+.++++.. ........+.
T Consensus 3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 81 (174)
T cd06929 3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKN-SLTFGDGKGNSRDVLLNGGF 81 (174)
T ss_pred HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcccCC-eEEecCCceecHHHHHHccc
Confidence 37889999999999999999999999999999999999999999999999998876444 455555443 2222122234
Q ss_pred HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhh
Q psy6602 166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLP 245 (367)
Q Consensus 166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~ 245 (367)
....+.+.+++.+|++|++|.+||+|||||+||+||++|++++..|++.|++|.++|++||..++++++.||++|+.+++
T Consensus 82 ~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~Ll~~l~ 161 (174)
T cd06929 82 GEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLT 161 (174)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHhH
Confidence 56778899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHhhhhhHHHH
Q psy6602 246 SLRAVRQSTIER 257 (367)
Q Consensus 246 ~Lr~l~~~~~e~ 257 (367)
.+|.++..+.|.
T Consensus 162 ~lr~l~~~~~e~ 173 (174)
T cd06929 162 ELRTLNELHAEL 173 (174)
T ss_pred HHHHHHHHHHhc
Confidence 999999998874
No 37
>KOG4215|consensus
Probab=100.00 E-value=1.2e-31 Score=244.25 Aligned_cols=206 Identities=26% Similarity=0.433 Sum_probs=183.9
Q ss_pred hhhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCC
Q psy6602 82 LQILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPD 161 (367)
Q Consensus 82 ~~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~ 161 (367)
....++..++++...+++...|||||.||+|.+|+.+||++|||+...+.++|..++|+...++-.++.++++..+....
T Consensus 150 n~~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~N~~v~~~~~~~ 229 (432)
T KOG4215|consen 150 NKKIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLNNTYVLHRHAPD 229 (432)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEecCceeeccCCCC
Confidence 34677889999999999999999999999999999999999999999999999999999988777777777776655544
Q ss_pred ccchHHH-HHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChh--HHHHHHHHHHHHHHHHHHhhCC-CcchHH
Q psy6602 162 DVRVNNE-IKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQ--PVEMLQDQAQCILGDYVRGRYS-RQPTRF 237 (367)
Q Consensus 162 ~~~~~~~-~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~--~v~~~q~~~~~~L~~y~~~~~~-~~~~Rf 237 (367)
....... .+.+.+++.+|++|++|+.||+|||||++|+||..|+++.. .|+++|++++.+|..|+..+.+ +.+.||
T Consensus 230 ~~eis~v~~RIiDElv~Pmr~L~md~~Ey~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~ 309 (432)
T KOG4215|consen 230 LPEISRVAPRIIDELVNPMRRLQMDEIEYVCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRF 309 (432)
T ss_pred hHHHHHHHHHHHHHHhhHHHHhccchHHHHHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccch
Confidence 3323333 37888999999999999999999999999999999999966 9999999999999999999985 778999
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCC
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPG 287 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~g 287 (367)
|+||+++|.|+.++.+.+|++.+.++||...++.++.+++.-....|.+.
T Consensus 310 g~LLLllPsLqsIt~qliE~iqlaklFGla~vDsll~e~~l~~~~~d~~~ 359 (432)
T KOG4215|consen 310 GNLLLLLPSLQSITQQLIEQIQLAKLFGLAKVDSLLQEFLLGGEPNDHSH 359 (432)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhcCCCCccCCC
Confidence 99999999999999999999999999999999999999998766555443
No 38
>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=100.00 E-value=8.8e-32 Score=237.22 Aligned_cols=171 Identities=16% Similarity=0.120 Sum_probs=148.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCC-CccchH
Q psy6602 88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPP-DDVRVN 166 (367)
Q Consensus 88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~ 166 (367)
|.++++.+++.++.+|+|||++|||.+|+.+||++|||++|+|+++++.+++++.. ..++.++........ ...+..
T Consensus 4 w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~--~~~~~~g~~~~~~~~~~~~~~~ 81 (191)
T cd06942 4 WGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNE--GTVLCDFRPVEFASLLSQLLHG 81 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcC--CeEEeCCccccHHHHHHhcchH
Confidence 88999999999999999999999999999999999999999999999998877654 334433322222111 111234
Q ss_pred HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCC--CCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhh
Q psy6602 167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPE--TPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLML 244 (367)
Q Consensus 167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd--~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l 244 (367)
+.++.+.+++.+|++|++|++||+||+||+||+|| ++|+++..+|+.+|+.+.++|.+||..+|++.+.||++|+.++
T Consensus 82 ~~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~kLL~~l 161 (191)
T cd06942 82 KLIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFDIL 161 (191)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence 66777889999999999999999999999999999 9999999999999999999999999999999999999999999
Q ss_pred hHhHhhhhhHHHHHHh
Q psy6602 245 PSLRAVRQSTIERLFF 260 (367)
Q Consensus 245 ~~Lr~l~~~~~e~l~~ 260 (367)
+.+|+++..+.+.+..
T Consensus 162 ~~Lr~~~~~~~~~l~~ 177 (191)
T cd06942 162 NRLRNMNKEHQNILAD 177 (191)
T ss_pred HHHHHHHHHHHHHHHc
Confidence 9999999999997665
No 39
>cd06930 NR_LBD_F2 Ligand-binding domain of nuclear receptor family 2. Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.98 E-value=2.2e-31 Score=229.46 Aligned_cols=162 Identities=41% Similarity=0.691 Sum_probs=141.9
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC-CceEecCCc-cccCCCCCccchH
Q psy6602 89 EKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD-LSLLINCEK-ARERLPPDDVRVN 166 (367)
Q Consensus 89 ~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~-~~~l~~~~~-~~~~~~~~~~~~~ 166 (367)
+++++++++.++.+|+|||++|+|..|+.+||++|+|++|++++++..||++.... ...+..+++ ..........+..
T Consensus 2 ~~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (165)
T cd06930 2 ESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLA 81 (165)
T ss_pred hhHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHH
Confidence 46899999999999999999999999999999999999999999999999998763 334444443 3333322223355
Q ss_pred HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhH
Q psy6602 167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPS 246 (367)
Q Consensus 167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~ 246 (367)
+..+.+.+++.+|++|++|++||+|||||++|+||++|+++...|++.|++|.++|..||..++++++.||++|+.+++.
T Consensus 82 ~~~~~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~ll~~l~~ 161 (165)
T cd06930 82 ELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPE 161 (165)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHh
Confidence 66788899999999999999999999999999999999999999999999999999999999989999999999999999
Q ss_pred hHhh
Q psy6602 247 LRAV 250 (367)
Q Consensus 247 Lr~l 250 (367)
+|++
T Consensus 162 lr~~ 165 (165)
T cd06930 162 LRSI 165 (165)
T ss_pred hccC
Confidence 9864
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=99.94 E-value=9.6e-26 Score=193.71 Aligned_cols=161 Identities=35% Similarity=0.548 Sum_probs=138.7
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc----cCCCCCccch
Q psy6602 90 KCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR----ERLPPDDVRV 165 (367)
Q Consensus 90 ~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~----~~~~~~~~~~ 165 (367)
++++++.+.+..+++|||++|+|..|+.+||+.|+|++|+++++|+.+|++........+..++.. ..........
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (168)
T cd06157 2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK 81 (168)
T ss_pred cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence 478999999999999999999999999999999999999999999999999987776666554432 1111111223
Q ss_pred HHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCC-CCCChhHHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHh
Q psy6602 166 NNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETP-GLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLM 243 (367)
Q Consensus 166 ~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~-~L~~~~~v~~~q~~~~~~L~~y~~~~~~-~~~~Rf~~LL~~ 243 (367)
....+.+.+++.+|.+|++|++||++||||++|+|+.+ +......+++.|++|.++|+.|+..+++ +++.||++|+.+
T Consensus 82 ~~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~ 161 (168)
T cd06157 82 GELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLL 161 (168)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHhCCccchhHHHHHHHh
Confidence 34457788999999999999999999999999999998 6777999999999999999999999986 899999999999
Q ss_pred hhHhHhh
Q psy6602 244 LPSLRAV 250 (367)
Q Consensus 244 l~~Lr~l 250 (367)
++.++++
T Consensus 162 l~~l~~~ 168 (168)
T cd06157 162 LPSLRKL 168 (168)
T ss_pred chhcccC
Confidence 9999863
No 41
>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=99.93 E-value=5.4e-25 Score=195.01 Aligned_cols=181 Identities=33% Similarity=0.490 Sum_probs=149.4
Q ss_pred hhccCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccc-cCCC--
Q psy6602 83 QILMSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKAR-ERLP-- 159 (367)
Q Consensus 83 ~~~~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~-~~~~-- 159 (367)
.+..+++++++++.+.+..+|+|||.+|+|..|+.+||++|+|++|+++++|..++++.......+...++.. ....
T Consensus 14 ~~~~~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~ 93 (203)
T PF00104_consen 14 LRPATFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDSFD 93 (203)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHHHH
T ss_pred CcHhhHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcccccccccccccccccccccc
Confidence 4455688999999999999999999999999999999999999999999999999999833344444444332 2111
Q ss_pred -CCccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCC-Ch-hHHHHHHHHHHHHHHHHH-HhhCC-Ccc
Q psy6602 160 -PDDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLV-DA-QPVEMLQDQAQCILGDYV-RGRYS-RQP 234 (367)
Q Consensus 160 -~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~-~~-~~v~~~q~~~~~~L~~y~-~~~~~-~~~ 234 (367)
.......+.++.+.+++.+|+++++|++||++|+|+++|+|+.++++ +. ..++++|+++.++|+.|+ ...++ +.+
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~~ 173 (203)
T PF00104_consen 94 DFITGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYYNQSKGPEDYA 173 (203)
T ss_dssp HTSTTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTHT
T ss_pred cccccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHHhccCCCccHH
Confidence 01123456678899999999999999999999999999999999998 54 459999999999999999 66665 458
Q ss_pred hHHHHHHHhhhHhHhhhhhHHHHHHhhhc
Q psy6602 235 TRFGRLLLMLPSLRAVRQSTIERLFFKET 263 (367)
Q Consensus 235 ~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~ 263 (367)
.||++|+.+++.++.+.....|.+++..+
T Consensus 174 ~R~~~ll~ll~~l~~~~~~~~e~~~~~~l 202 (203)
T PF00104_consen 174 QRFGKLLLLLPSLRKISEKHIENMFLSDL 202 (203)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHhh
Confidence 99999999999999999999999877654
No 42
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=99.92 E-value=1.1e-24 Score=186.18 Aligned_cols=154 Identities=33% Similarity=0.514 Sum_probs=134.9
Q ss_pred HHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCc----cchHHHHHH
Q psy6602 96 ARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDD----VRVNNEIKL 171 (367)
Q Consensus 96 ~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~----~~~~~~~~~ 171 (367)
.+.+..+|+|||++|+|++|+.+||+.|+|++|++++++..++++.......++.+++.+....... .......+.
T Consensus 2 ~~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (163)
T smart00430 2 ERDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRI 81 (163)
T ss_pred hhHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999999999999999998877777787877655433221 112334477
Q ss_pred HHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCCh--hHHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHhhhHhH
Q psy6602 172 IQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDA--QPVEMLQDQAQCILGDYVRGRYS-RQPTRFGRLLLMLPSLR 248 (367)
Q Consensus 172 ~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~--~~v~~~q~~~~~~L~~y~~~~~~-~~~~Rf~~LL~~l~~Lr 248 (367)
+.+++.+|++|++|++||++|+|+++|+|+.+|+.+. ..++++|+.+.++|+.|+..+++ +.+.||++|+.+++.++
T Consensus 82 ~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~i~ 161 (163)
T smart00430 82 LQELVKPLRELKLDDEEYALLKAILLFNPAGPGLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGRFGELLLILNAIQ 161 (163)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHHHHhh
Confidence 8899999999999999999999999999999999986 89999999999999999999887 67899999999999987
Q ss_pred h
Q psy6602 249 A 249 (367)
Q Consensus 249 ~ 249 (367)
.
T Consensus 162 ~ 162 (163)
T smart00430 162 K 162 (163)
T ss_pred c
Confidence 5
No 43
>KOG4218|consensus
Probab=99.92 E-value=1.3e-24 Score=196.43 Aligned_cols=196 Identities=26% Similarity=0.327 Sum_probs=162.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCC--CceEecCC-ccccCC--CC
Q psy6602 86 MSAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWD--LSLLINCE-KARERL--PP 160 (367)
Q Consensus 86 ~~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~--~~~l~~~~-~~~~~~--~~ 160 (367)
.++--.|.++++.++.+|+|||+--.|.+|+.+||++||++||.|+.+++..|+.+..+ +++.+.++ .+.-.. ..
T Consensus 274 ~~fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgkegsi~lvtGqeV~~~~vA~q 353 (475)
T KOG4218|consen 274 EKFGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKEGSIKLVTGQEVPVGLVALQ 353 (475)
T ss_pred hhhhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcccceEEecCCcccchhHhhh
Confidence 34445799999999999999999999999999999999999999999999999988543 33333332 221111 11
Q ss_pred CccchHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHH
Q psy6602 161 DDVRVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRL 240 (367)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~L 240 (367)
........+...++++.+++.|++|+.||+|||-|+||+-|..
T Consensus 354 ags~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LFsld~k------------------------------------- 396 (475)
T KOG4218|consen 354 AGSLLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALFSLDMK------------------------------------- 396 (475)
T ss_pred hhhHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHHhhhHH-------------------------------------
Confidence 1111334456778999999999999999999999999995531
Q ss_pred HHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChH
Q psy6602 241 LLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRF 320 (367)
Q Consensus 241 L~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~ 320 (367)
.|++-..|+++|+++..||-+|...+||+....|
T Consensus 397 ----------------------------------------------fLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF 430 (475)
T KOG4218|consen 397 ----------------------------------------------FLENFELVRRLQEDSNAALLDYTSCCYPNWEQKF 430 (475)
T ss_pred ----------------------------------------------HHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHH
Confidence 1122336889999999999999999999999999
Q ss_pred HHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602 321 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK 364 (367)
Q Consensus 321 ~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~ 364 (367)
+++|++|+++|+++.+..|+++.+++.|++|-++|+.|||.++.
T Consensus 431 ~qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~Ak~ 474 (475)
T KOG4218|consen 431 PQLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLTAKP 474 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhhccC
Confidence 99999999999999999999999999999999999999999985
No 44
>KOG4217|consensus
Probab=99.88 E-value=3e-22 Score=187.87 Aligned_cols=190 Identities=27% Similarity=0.382 Sum_probs=173.5
Q ss_pred CHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchH
Q psy6602 87 SAEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVN 166 (367)
Q Consensus 87 ~~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 166 (367)
.+..++++..-.+-.+-.||.+||||.+|..+||-.||.++++|+|+|+.|||+.+.++..+|+++.+..+.+... +++
T Consensus 409 ~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~e~kliFcsG~vlhr~qC~r-gfg 487 (605)
T KOG4217|consen 409 HVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPSEDKLIFCSGLVLHRLQCLR-GFG 487 (605)
T ss_pred HHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEecchhhhHHHHHH-HHH
Confidence 3677899999999999999999999999999999999999999999999999999988888898888877754333 477
Q ss_pred HHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHhh
Q psy6602 167 NEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQPTRFGRLLLML 244 (367)
Q Consensus 167 ~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~--~~~~~Rf~~LL~~l 244 (367)
+.++.+.+|...+..|.+|-.-|+||.|+.+.. ++-||.+...||++|++++.+|.+|+.... ...+.++.+++..+
T Consensus 488 ewidsi~~FS~~l~~l~idi~AfacL~aLa~iT-ErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgkl 566 (605)
T KOG4217|consen 488 EWIDSIREFSRSLHSLNIDISAFACLSALALIT-ERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKL 566 (605)
T ss_pred HHHHHHHHHHHHhhhchhhHHHHHHHHHHHhhh-hhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhh
Confidence 889999999999999999999999999999987 889999999999999999999999997554 46788999999999
Q ss_pred hHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHc
Q psy6602 245 PSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 278 (367)
Q Consensus 245 ~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~ 278 (367)
++||.+..+....+|+.+....++.+.++..||.
T Consensus 567 peLr~l~tqgLqrifyLklEdlvp~p~iidklf~ 600 (605)
T KOG4217|consen 567 PELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL 600 (605)
T ss_pred HHHHHHHHHhhhhhhcccHhhccCchhhhhhhhh
Confidence 9999999999999999999988888888887775
No 45
>KOG4216|consensus
Probab=99.85 E-value=3.1e-21 Score=177.39 Aligned_cols=189 Identities=17% Similarity=0.188 Sum_probs=160.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchHH
Q psy6602 88 AEKCQETTARLLFMAVRWVRCLAPFQTLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNN 167 (367)
Q Consensus 88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 167 (367)
|+.+..-....|+.+|||||.|+||.+|+++|||+|||.+.+|+.+.++++.++..++.+.+..+..- .......+..+
T Consensus 284 We~cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~ntV~~e~~~~g-~~~f~a~~~~e 362 (479)
T KOG4216|consen 284 WELCAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNNTVYFEGKYAG-PEVFYALGCEE 362 (479)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhcccccceeecccccc-hhheeccChHH
Confidence 45566666778999999999999999999999999999999999999999988876666665554432 22223344677
Q ss_pred HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHh
Q psy6602 168 EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSL 247 (367)
Q Consensus 168 ~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~L 247 (367)
++..++++...+..|++++.|.|++.|++|.+||++|+.+..+|++++++...++++.+.+++.. ..-..+|+...+.+
T Consensus 363 lis~vf~~~ksL~~Lq~te~EiAL~~alVL~~~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~~-~~~l~kl~~k~~~~ 441 (479)
T KOG4216|consen 363 LISRVFEFGKSLCSLQLTEDEIALFSALVLMSADRSGLQEKVKIEKLQQKIQLALQHVLQKNHRE-DGILTKLICKVSTL 441 (479)
T ss_pred HHHHHHhhhHHHHhhccCcHHHHHHHHHHhhCCccccccchHHHHHHHHHHHHHHHHHHHhcCCh-hhhHHHhhcccchH
Confidence 88999999999999999999999999999999999999999999999999999999999988632 23689999999999
Q ss_pred HhhhhhHHHHHHhhhccCCchh---HhHHHHHHc
Q psy6602 248 RAVRQSTIERLFFKETIGDIPI---QRLLGDMYT 278 (367)
Q Consensus 248 r~l~~~~~e~l~~~~~~~~~~~---~~Ll~eml~ 278 (367)
|.+...+.|.+..++..+...+ ++|..|+|.
T Consensus 442 r~~~~lH~E~Lq~Fk~~hP~iv~~fP~LYKELFt 475 (479)
T KOG4216|consen 442 RALCGLHTEKLQAFKASHPDIVRHFPPLYKELFT 475 (479)
T ss_pred HHHHHHHHHHHHHHhhcCchHHhhccHHHHHHhc
Confidence 9999999999998888766554 556666654
No 46
>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.77 E-value=9.4e-19 Score=159.27 Aligned_cols=111 Identities=31% Similarity=0.448 Sum_probs=103.2
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR 319 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r 319 (367)
+..+...+|.+..+..|+++++...- .+||++|+.+..+|+++|++++.||++|+..+||+++.|
T Consensus 131 ~~e~~~~lr~L~ld~~E~a~LKaivL---------------fnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~R 195 (241)
T cd07069 131 AQELVAKLRSLQFDQREFVCLKFLVL---------------FSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEK 195 (241)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhH
Confidence 34567789999999999999998863 348999999999999999999999999999999999999
Q ss_pred HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcccc
Q psy6602 320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKS 365 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~~ 365 (367)
|+|||++||+||+++..++|++||++++|.+|+++|+.||+++|+.
T Consensus 196 f~kLLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Eml~~~~~ 241 (241)
T cd07069 196 FGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKRA 241 (241)
T ss_pred HHHHHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHHHhcccC
Confidence 9999999999999999999999999999999999999999999863
No 47
>cd07349 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.
Probab=99.77 E-value=1e-18 Score=156.93 Aligned_cols=107 Identities=34% Similarity=0.466 Sum_probs=99.3
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 318 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~ 318 (367)
.+......++.+..+..|+.+++.+.- .+||++|+++..+|+++|++++.||++|+..+||+++.
T Consensus 116 ~l~e~~~~l~~L~ld~~Eya~LkaivL---------------f~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~~~ 180 (222)
T cd07349 116 WLQCCLNKFWSLDLSPKEYAYLKGTIL---------------FNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQG 180 (222)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCccc
Confidence 344577789999999999999997753 24799999999999999999999999999999999999
Q ss_pred hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHH
Q psy6602 319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 360 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml 360 (367)
||+|||++||+||+++.+++|++||++++|++||++|+.|||
T Consensus 181 r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~i~~Ll~eml 222 (222)
T cd07349 181 RFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML 222 (222)
T ss_pred HHHHHHHHhHHHhcCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence 999999999999999999999999999999999999999996
No 48
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=99.75 E-value=1.3e-17 Score=151.07 Aligned_cols=109 Identities=19% Similarity=0.237 Sum_probs=99.4
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP 317 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~ 317 (367)
..+......++.+..+..|+.+++...- .+||++|+++..+|+++|+++..||++|+..+||++|
T Consensus 122 ~~~~~~~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p 186 (231)
T cd06937 122 DLVFTFANQLLPLEMDDTEIGLLSAICL---------------ICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKP 186 (231)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcc
Confidence 3345566678888889999988887753 2489999999999999999999999999999999999
Q ss_pred ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602 318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 361 (367)
Q Consensus 318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~ 361 (367)
.||+|||++||+||+++.+++|++|+.|++|.+|+++|+.|||+
T Consensus 187 ~rf~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~ 230 (231)
T cd06937 187 HMFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEMLE 230 (231)
T ss_pred cHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhc
Confidence 99999999999999999999999999999999999999999996
No 49
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.75 E-value=4.1e-18 Score=154.91 Aligned_cols=107 Identities=26% Similarity=0.284 Sum_probs=100.1
Q ss_pred HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG 321 (367)
Q Consensus 242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~ 321 (367)
.+...++.+..+..|+++++...- .+||++|+.+...|+.+|+++..||.+|+..+||+.+.||+
T Consensus 131 e~~~kl~~L~ld~~Ey~~LkaIiL---------------fnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~ 195 (237)
T cd07070 131 ELVLQLHALQLDRQEFVCLKFLIL---------------FSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQ 195 (237)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHh---------------cCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHH
Confidence 466678899999999999988753 24899999999999999999999999999999999999999
Q ss_pred HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602 322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 363 (367)
Q Consensus 322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~ 363 (367)
+||++||+||+++.+++|++||.+++|.+|+++|+.||+++|
T Consensus 196 kLLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~eml~~~ 237 (237)
T cd07070 196 QLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAK 237 (237)
T ss_pred HHHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHHHhcCC
Confidence 999999999999999999999999999999999999999875
No 50
>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=99.72 E-value=9.8e-17 Score=145.41 Aligned_cols=108 Identities=21% Similarity=0.322 Sum_probs=95.9
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh--CCCC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSRQ 316 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~--~p~~ 316 (367)
.+......++.+..+..|+.+++.+.- | +|++||++..+||++|+++..||++|+..+ +|++
T Consensus 125 ~i~ef~~~l~~L~ld~~E~a~LkAIvL-----------f-----~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~ 188 (238)
T cd07348 125 SILEFSQSLHRMNLDVSAFSCLAALVI-----------I-----TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQR 188 (238)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHH-----------c-----CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCcc
Confidence 344566677888888888888876642 1 499999999999999999999999999985 4999
Q ss_pred cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602 317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 362 (367)
Q Consensus 317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~ 362 (367)
+.||+|||++||+||+++.+++|++|+.|++|.+|+++|+.|||..
T Consensus 189 p~rf~kLLl~Lp~LRsl~~~~~e~lf~~kl~~~~~~~pLl~e~~~~ 234 (238)
T cd07348 189 PNCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIVDKIFMD 234 (238)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999964
No 51
>cd06944 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors. The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not
Probab=99.72 E-value=2.6e-17 Score=149.79 Aligned_cols=109 Identities=31% Similarity=0.450 Sum_probs=101.4
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR 319 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r 319 (367)
+..+...++.+..+..|+++++..+- .+||++|+++...|+++|+++..||.+|+..+||+.+.|
T Consensus 129 i~~~~~~l~~L~ld~~E~~lLkaIiL---------------~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~R 193 (237)
T cd06944 129 AQELVNKLRELQFDRQEFVCLKFLIL---------------FNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDK 193 (237)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccH
Confidence 44567788999999999999998763 347899999999999999999999999999999999999
Q ss_pred HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602 320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 363 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~ 363 (367)
|++||++||+||+++.+++|++||++++|.+|+++|+.||+++|
T Consensus 194 f~~LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~eml~~~ 237 (237)
T cd06944 194 FGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHAK 237 (237)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999876
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=99.72 E-value=2.9e-17 Score=149.13 Aligned_cols=113 Identities=24% Similarity=0.278 Sum_probs=102.6
Q ss_pred HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCC-----CCCCchhhhhHHHHHHHHHHHHH
Q psy6602 236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPG-----LVDAQPVEMLQDQAQCILGDYVR 310 (367)
Q Consensus 236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~g-----l~~~~~ve~lq~~~~~aL~~~~~ 310 (367)
.+..+......++++..+..|+++++.+.- .+||++| +++..+|+++|+++..||.+|+.
T Consensus 115 ~~~~~~~~~~~l~~L~ld~~EyalLKAIvL---------------fnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~ 179 (235)
T cd06949 115 IFDMLLATASRFRELQLQREEYVCLKAIIL---------------LNSSVYTFLLESLESRRQVQRLLDKITDALVHACS 179 (235)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHH---------------cCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHH
Confidence 344566677788999999999999988753 2478999 99999999999999999999999
Q ss_pred hhC---CCCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602 311 GRY---SRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 363 (367)
Q Consensus 311 ~~~---p~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~ 363 (367)
++| |+++.||++||++||+||+++++++|+||++|++|.+|+++|+.|||+++
T Consensus 180 ~~~~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~~ 235 (235)
T cd06949 180 KRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235 (235)
T ss_pred hcCCCCCCcccHHHHHHHhchHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhcCC
Confidence 999 99999999999999999999999999999999999999999999999863
No 53
>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.
Probab=99.71 E-value=1.6e-17 Score=150.07 Aligned_cols=106 Identities=29% Similarity=0.367 Sum_probs=97.7
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP 317 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~ 317 (367)
..+......++.+..+..|+++++.+.- .+||++|+++..+|+++|++++.||.+|+..+||+++
T Consensus 127 ~~l~e~~~~l~~L~ld~~E~a~LkAivL---------------f~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~ 191 (232)
T cd07350 127 RAIKAFLAKCWSLDISTKEYAYLKGTVL---------------FNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQ 191 (232)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCcccCCCHHHHHHHHHHHHHHHHHHHHhhCCChh
Confidence 3455677789999999999999998752 2479999999999999999999999999999999999
Q ss_pred ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHH
Q psy6602 318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 358 (367)
Q Consensus 318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~e 358 (367)
.||+|||++||+||+++.+++|++||++++|.++|++|+.|
T Consensus 192 ~rf~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll~E 232 (232)
T cd07350 192 ARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDMLLE 232 (232)
T ss_pred hHHHHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHhcC
Confidence 99999999999999999999999999999999999999975
No 54
>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=99.69 E-value=6.1e-17 Score=147.29 Aligned_cols=110 Identities=26% Similarity=0.405 Sum_probs=98.2
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC--CC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS--RQ 316 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p--~~ 316 (367)
.++.....++++.....|+++++...- .++|++||++..+|+++|+++..||++|+..+|| ++
T Consensus 125 ~i~~f~~~l~~L~ld~~E~~~LkaivL---------------~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~ 189 (239)
T cd06945 125 SILAFSSSLQSLLLDDISAFCCLALLL---------------LITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDK 189 (239)
T ss_pred HHHHHHHHHHHHhCChHHHHHHHHHHH---------------hCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCccc
Confidence 344555677778888888888876642 2479999999999999999999999999999999 99
Q ss_pred cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhcc
Q psy6602 317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 363 (367)
Q Consensus 317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~ 363 (367)
+.||+|||++||+||+++.+++|++||.|++|.+|+++|+.|||...
T Consensus 190 ~~rf~kLLl~Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~~~~ 236 (239)
T cd06945 190 PNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRFLDT 236 (239)
T ss_pred ccHHHHHHHHhHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999754
No 55
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=99.69 E-value=4.5e-17 Score=146.57 Aligned_cols=104 Identities=25% Similarity=0.329 Sum_probs=95.6
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 318 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~ 318 (367)
.+..+...++.+..+..|+++++.+.- .+||++|+ +..+|+++|++++.||++|+..+||+++.
T Consensus 119 ~l~e~~~~l~~L~ld~~Eya~LkAivL---------------fnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~ 182 (222)
T cd06951 119 DIQQFLMKCWSLDLDCKEYAYLKGAVL---------------FTPVPPLL-CPHYIEALQKEAQQALNEHTMMTRPLEQL 182 (222)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhhCCCccc
Confidence 345677788999999999999988753 34899999 99999999999999999999999999999
Q ss_pred hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHH
Q psy6602 319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 358 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~e 358 (367)
||+|||++||+||+++.+++|++||.+++|.+||++++.|
T Consensus 183 Rf~kLLl~Lp~LRsl~~~~~e~lff~~~~g~~~i~~ll~~ 222 (222)
T cd06951 183 RSARLLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLLQ 222 (222)
T ss_pred HHHHHHHHhHHhhcCCHHHHHHHhCccccCCCcHHHHhcC
Confidence 9999999999999999999999999999999999999864
No 56
>cd07071 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.68 E-value=1.6e-16 Score=144.17 Aligned_cols=109 Identities=19% Similarity=0.252 Sum_probs=96.8
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh--CCC
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR--YSR 315 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~--~p~ 315 (367)
..+......++.+..+..|+.+++.+.- | +|++||++..+|+++|++++.||++|+..+ +|+
T Consensus 124 ~~i~ef~~~l~~L~ld~~E~alLkAIvL-----------f-----~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~ 187 (238)
T cd07071 124 DSIVEFSSNLQNMNIDISAFSCIAALAM-----------V-----TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLN 187 (238)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHH-----------c-----CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence 3345667788888999999998876642 1 389999999999999999999999999977 468
Q ss_pred CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602 316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 362 (367)
Q Consensus 316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~ 362 (367)
++.||+|||++||+||+++.+++|++|+.+++|.+|+++|+.||+..
T Consensus 188 ~~~rf~kLLl~Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~~~ 234 (238)
T cd07071 188 RPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFLD 234 (238)
T ss_pred cccHHHHHHHHhHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999854
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=99.68 E-value=4e-15 Score=134.96 Aligned_cols=107 Identities=26% Similarity=0.329 Sum_probs=93.9
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhC--CCCc
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRY--SRQP 317 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~--p~~~ 317 (367)
+......++.+..+..|+.+++.+.- | +|++|+++..+|+++|+++..||++|+..++ |+++
T Consensus 127 i~ef~~~l~~L~ld~~E~a~LkAivL-----------f-----~dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~ 190 (239)
T cd07072 127 ILEFSKSLHAMDIDISAFACLCALTL-----------I-----TERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKP 190 (239)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH-----------h-----CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccc
Confidence 34555667778888888888876641 1 3899999999999999999999999999765 4789
Q ss_pred ChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602 318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 362 (367)
Q Consensus 318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~ 362 (367)
.||+|||++||+||+++.+++|++||.|++|.+|+++|+.||+.+
T Consensus 191 ~rf~kLLl~Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em~~~ 235 (239)
T cd07072 191 HYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMFVA 235 (239)
T ss_pred cHHHHHHHHhHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHHHhc
Confidence 999999999999999999999999999999999999999999974
No 58
>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=99.65 E-value=1.8e-15 Score=139.20 Aligned_cols=107 Identities=22% Similarity=0.322 Sum_probs=95.4
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR 319 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r 319 (367)
+......++.+..+..|+.+++...- .+||++||++..+|+++|+++..||+.|+..+||+++.|
T Consensus 150 ~~e~~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~r 214 (259)
T cd06932 150 KFEFAEKFNALELTDSELALFCAVII---------------LSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQL 214 (259)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccH
Confidence 44566777888888888888877652 248999999999999999999999999999999999999
Q ss_pred HHHHHhhchhhhhhchhhHHHHHHhh-hcCCCChHHHHHHHHh
Q psy6602 320 FGRLLLMLPSLRAVRQSTIERLFFKE-TIGDIPIQRLLGDMYT 361 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~-~~g~~~i~~ll~eml~ 361 (367)
|+|||++||+||+++.+++|.+++.+ ..|.+++++|+.|||+
T Consensus 215 f~kLLl~L~~LRsl~~~~~e~l~~~k~~~~~~~~~pLl~Ei~~ 257 (259)
T cd06932 215 FAKLLQKMVDLRQLVTDHVQMVQQIKKTETDASLPPLLQEIYK 257 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCcHHHHHhh
Confidence 99999999999999999999999766 5678999999999996
No 59
>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=99.64 E-value=5.7e-16 Score=140.94 Aligned_cols=108 Identities=41% Similarity=0.655 Sum_probs=99.7
Q ss_pred HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG 321 (367)
Q Consensus 242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~ 321 (367)
.++..++.+..+..|+++++.++- .+||++|+.+..+|+++|+++..||.+|+..+||+.+.||+
T Consensus 120 ~l~~~l~~L~ld~~E~~lLkaiiL---------------~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~ 184 (236)
T cd06948 120 EQVEKLKALHVDSAEFSCLKAIVL---------------FTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFG 184 (236)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHH---------------cCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHH
Confidence 355678999999999999987752 24789999999999999999999999999999999999999
Q ss_pred HHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602 322 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK 364 (367)
Q Consensus 322 ~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~ 364 (367)
+||++||+||+++..++|++||.+++|.+++++|+.||+.++.
T Consensus 185 ~LLl~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~~~ 227 (236)
T cd06948 185 KLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGS 227 (236)
T ss_pred HHHHHHHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhCCC
Confidence 9999999999999999999999999999999999999998763
No 60
>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=99.63 E-value=2.9e-15 Score=136.74 Aligned_cols=106 Identities=19% Similarity=0.267 Sum_probs=94.9
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 318 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~ 318 (367)
.+......++.+..+..|+++++...- .+||++||++..+|+++|+.+..||++|+..+||+.+.
T Consensus 137 ~i~~f~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~ 201 (243)
T cd06935 137 AIFDLGVSLSSFNLDDTEVALLQAVLL---------------MSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPH 201 (243)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCcc
Confidence 344466667778888888888877642 25899999999999999999999999999999999999
Q ss_pred hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCCh-HHHHHHH
Q psy6602 319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI-QRLLGDM 359 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i-~~ll~em 359 (367)
||+|||++||+||+++.+++|++++.|+.|..++ ++|+.||
T Consensus 202 rf~kLL~~L~~LR~i~~~~~e~l~~~k~~~~~~~~~~L~~Em 243 (243)
T cd06935 202 FWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEV 243 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChhhhcC
Confidence 9999999999999999999999999999999996 9999997
No 61
>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=99.59 E-value=1.7e-14 Score=127.57 Aligned_cols=109 Identities=21% Similarity=0.282 Sum_probs=95.9
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP 317 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~ 317 (367)
..+......++.+..+..|+.+++...- .+||++|+++..+|+++|+.+..||++|+..+||+.+
T Consensus 86 ~~~~~~~~~l~~L~ld~~E~allkAi~L---------------f~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~ 150 (195)
T cd06941 86 KALFEFSDSFNSLGLSDTEVALFCAVVL---------------LSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEA 150 (195)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcc
Confidence 3445566678888888888888876642 2479999999999999999999999999999999999
Q ss_pred ChHHHHHhhchhhhhhchhhHHHHH-HhhhcCCCChHHHHHHHHh
Q psy6602 318 TRFGRLLLMLPSLRAVRQSTIERLF-FKETIGDIPIQRLLGDMYT 361 (367)
Q Consensus 318 ~r~~~lLl~Lp~lr~i~~~~~e~l~-~~~~~g~~~i~~ll~eml~ 361 (367)
.||++||++||+||+++..+.++++ |+...+.+++++|+.|||+
T Consensus 151 ~rf~~Ll~~Lp~Lr~l~~~~~e~l~~~~~~~~~~~~p~L~~E~~~ 195 (195)
T cd06941 151 QLFASLLMKIPELRSIGAKHQMHLDWYRVNWPLLRLPPLFAEIYD 195 (195)
T ss_pred cHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHhcC
Confidence 9999999999999999999999998 6777788999999999985
No 62
>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=99.59 E-value=5.8e-15 Score=133.11 Aligned_cols=110 Identities=26% Similarity=0.387 Sum_probs=100.1
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC-CC
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQ 316 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p-~~ 316 (367)
..+...+..++++..+..|+++++...- .+||++|+++...|+++|+++..||.+|+..+|| +.
T Consensus 111 ~~~~~~~~~l~~L~ld~~E~~lLkaIil---------------~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~ 175 (221)
T cd07068 111 DMLLQLVRRFRELGLQREEYVCLKAIIL---------------ANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQ 175 (221)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 3445567789999999999999887652 2489999999999999999999999999999999 99
Q ss_pred cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602 317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 362 (367)
Q Consensus 317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~ 362 (367)
+.||++||++||+||+++..++|++++.+++|.+|+++|+.|||++
T Consensus 176 ~~Rf~~LL~~l~~Lr~~~~~~~e~l~~~k~~~~~~~~~Ll~e~l~~ 221 (221)
T cd07068 176 PRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLEA 221 (221)
T ss_pred ccHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999975
No 63
>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=99.57 E-value=1.1e-14 Score=131.38 Aligned_cols=110 Identities=25% Similarity=0.381 Sum_probs=99.7
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCC-CC
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYS-RQ 316 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p-~~ 316 (367)
..+..+...++.+..+..|+++++..+- .+||+.|+++...|+++|+.+..||.+|+..+|| +.
T Consensus 111 ~~~~~~~~~l~~L~l~~~E~~lLkai~L---------------~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~ 175 (221)
T cd06946 111 SACLQLVRRLQRLRLEKEEYVLLKALAL---------------ANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEA 175 (221)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 3345567788999999999999887752 3478899999999999999999999999999999 78
Q ss_pred cChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhc
Q psy6602 317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTM 362 (367)
Q Consensus 317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~ 362 (367)
|.||++||+++|+||+++.++++++++.+++|.+|+++|+.|||++
T Consensus 176 p~Rf~~LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~ 221 (221)
T cd06946 176 PRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLEA 221 (221)
T ss_pred hhHHHHHHhhchhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999974
No 64
>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=99.56 E-value=3.3e-14 Score=129.46 Aligned_cols=106 Identities=22% Similarity=0.281 Sum_probs=91.8
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 318 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~ 318 (367)
.+......++.+..+..|+.+++...- .+||++||++..+|+++|+++..||++|+..+| +++.
T Consensus 132 ~~~~f~~~l~~L~ld~~E~all~AivL---------------~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~ 195 (241)
T cd06939 132 AVFDFAKSLCELKLTEDEIALFSALVL---------------ISADRPGLQEKRKVEKLQQKIELALRHVLQKNH-GDDT 195 (241)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHH---------------hcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCcc
Confidence 344556667777778888887776642 248999999999999999999999999999999 8999
Q ss_pred hHHHHHhhchhhhhhchhhHHHHHHhhhcCC----CChHHHHHHHH
Q psy6602 319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGD----IPIQRLLGDMY 360 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~----~~i~~ll~eml 360 (367)
||+|||++||+||+++..++|+|++.|+..+ .++++|+.|||
T Consensus 196 rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~p~~~~~~~ppL~~Elf 241 (241)
T cd06939 196 ILTKLLAKMPTLRALCSLHMEKLQKFKQSYPDIVHLEFPPLYKELF 241 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcccCCCCcHHHhhC
Confidence 9999999999999999999999999999843 47899999986
No 65
>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=99.56 E-value=1.3e-14 Score=131.66 Aligned_cols=105 Identities=21% Similarity=0.215 Sum_probs=93.6
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 318 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~ 318 (367)
+..+...++.+..+..|+++++.+.- .++ |++||++...|+++|+++..||++|+.++||+.+.
T Consensus 116 l~e~~~~~r~L~ld~~EfacLKAIvL---------------fnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~ 180 (247)
T cd07076 116 MLYVSSELHRLQVSYEEYLCMKTLLL---------------LSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQ 180 (247)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh---------------CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcch
Confidence 44566778889999999999988763 125 89999999999999999999999999999987655
Q ss_pred ---hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602 319 ---RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 361 (367)
Q Consensus 319 ---r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~ 361 (367)
||+|||++||+||+|+.+..| ||++++|+.|+..++.|||.
T Consensus 181 ~~~RF~kLLllLp~Lr~i~~~~~e--f~~~~~~~~~~~~~~~~ml~ 224 (247)
T cd07076 181 NWQRFYQLTKLLDSMHEVVENLLN--FCFQTFLDKTMSIEFPEMLA 224 (247)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHH--HHHHHhcccchhhhhHHHHH
Confidence 999999999999999999999 99999999999999988874
No 66
>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=99.55 E-value=1.4e-14 Score=130.82 Aligned_cols=108 Identities=30% Similarity=0.457 Sum_probs=98.6
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 318 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~ 318 (367)
.+..+...++.+..+..|+++.+.+.- .++|++|+++...|+++|+++..||.+|+..+||+++.
T Consensus 114 ~l~~~~~~l~~L~ld~~E~~~LkaiiL---------------f~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~ 178 (222)
T cd06952 114 KLQEFVNSMQKLDVDDHEYAYLKAIVL---------------FSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEY 178 (222)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCccc
Confidence 344567788899999999999987752 23789999999999999999999999999999999999
Q ss_pred hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602 319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 361 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~ 361 (367)
||++||++||+||+++.+++|++||.+++|.+++++++..+|.
T Consensus 179 R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~~~~ll~~~~~ 221 (222)
T cd06952 179 RLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSVIPYILR 221 (222)
T ss_pred HHHHHHHHhHHhhhcCHHHHHHHhcccccCCCcHHHHHHHHHh
Confidence 9999999999999999999999999999999999999998874
No 67
>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=99.55 E-value=1.4e-14 Score=132.01 Aligned_cols=107 Identities=13% Similarity=0.147 Sum_probs=92.5
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhC---CC
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SR 315 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~---p~ 315 (367)
+..+...++.+..+..|+++++.+.- .++ |++||+++.+|+++|++++.||.+|+.+++ |+
T Consensus 116 l~~~~~~l~~L~ld~~EyacLKAIiL---------------fnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~ 180 (246)
T cd07073 116 MRHLSQEFGWLQITPQEFLCMKALLL---------------FSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTS 180 (246)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcc
Confidence 44557778889999999999988753 225 789999999999999999999999998875 36
Q ss_pred CcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCC-----ChHHHHHHHHhcc
Q psy6602 316 QPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDI-----PIQRLLGDMYTME 363 (367)
Q Consensus 316 ~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~-----~i~~ll~eml~~~ 363 (367)
++.||+|||++||+||+|+.++ .+||.+++|.. ++++||.|||..+
T Consensus 181 ~~~Rf~kLLl~Lp~LRsi~~~~--~~~~~~l~~~~~~~~~~~~pll~ei~~~~ 231 (246)
T cd07073 181 CSRRFYQLTKLLDSVQPIAREL--HQFTFDLLIKSHMVSVDFPEMMAEIISVQ 231 (246)
T ss_pred cchHHHHHHHHHHHHHHHHHHH--HHHHHHHhCccccCccCccHHHHHHHHhc
Confidence 6899999999999999999998 77888888875 7999999999854
No 68
>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=99.53 E-value=3.1e-14 Score=129.71 Aligned_cols=106 Identities=22% Similarity=0.285 Sum_probs=96.8
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR 319 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r 319 (367)
+......++.+..+..|+++++..+- .+||++||.+...|+.+|+.+..||.+|+..+||+++.|
T Consensus 130 i~~~~~~l~~L~ld~~E~~lL~aivL---------------f~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~r 194 (236)
T cd06954 130 IFEFSKSMRELQLDDAEYALLIAINI---------------FSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLM 194 (236)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh---------------ccCCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccH
Confidence 44566788999999999999887753 348999999999999999999999999999999999999
Q ss_pred HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602 320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 361 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~ 361 (367)
|++||++||+||+++..++|++|+.++.+ .++++|+.|||+
T Consensus 195 f~klL~~L~~Lr~l~~~~~e~l~~~k~~~-~~~~~L~~El~~ 235 (236)
T cd06954 195 FPRMLMKLVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWD 235 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCcHHHHHhc
Confidence 99999999999999999999999999976 699999999996
No 69
>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=99.52 E-value=5e-14 Score=128.35 Aligned_cols=107 Identities=14% Similarity=0.129 Sum_probs=93.3
Q ss_pred HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhCC---CCc
Q psy6602 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRYS---RQP 317 (367)
Q Consensus 242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p---~~~ 317 (367)
.+...++.+..+..|+++++.++- .++ |++|+++...|+++|++++.||++|+.++|| +.+
T Consensus 118 e~~~~l~~L~ld~~E~acLKAIvL---------------fn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~ 182 (246)
T cd06947 118 QISQEFVRLQVTYEEFLCMKVLLL---------------LSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSW 182 (246)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHH---------------cCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccc
Confidence 456778889999999999887752 124 6899999999999999999999999998874 558
Q ss_pred ChHHHHHhhchhhhhhchhhHHHHHHhhhcC---CCChHHHHHHHHhcc
Q psy6602 318 TRFGRLLLMLPSLRAVRQSTIERLFFKETIG---DIPIQRLLGDMYTME 363 (367)
Q Consensus 318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g---~~~i~~ll~eml~~~ 363 (367)
.||+|||++||+||+++.+++|++|++.... .|++++|+.|||+++
T Consensus 183 ~Rf~kLLllLp~Lr~i~~~~~e~~~~~~~~~~~~~v~~~~ll~ei~~~~ 231 (246)
T cd06947 183 QRFYQLTKLLDSMHDLVKNLLQFCFYTFIQSHALSVEFPEMLVEIISDQ 231 (246)
T ss_pred hHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcCCCccccHHHHHHHHHcc
Confidence 9999999999999999999999999885544 489999999999966
No 70
>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=99.52 E-value=4e-14 Score=128.81 Aligned_cols=109 Identities=17% Similarity=0.242 Sum_probs=92.9
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC--C
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR--Q 316 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~--~ 316 (367)
.+......++.+..+..|+++++...- .+||++||++...|+++|+++..||++|+..+||. .
T Consensus 124 ~l~~~~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~ 188 (238)
T cd06933 124 PLVKFQVGLKKLNLHEEEHVLLMAICI---------------LSPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGS 188 (238)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHH---------------HCCCCCCCcchHHHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence 344555678889999999999887752 24799999999999999999999999999999984 4
Q ss_pred cChHHHHHhhchhhhhhchhhHHHHHHhhhcC--CCChHHHHHHHHhc
Q psy6602 317 PTRFGRLLLMLPSLRAVRQSTIERLFFKETIG--DIPIQRLLGDMYTM 362 (367)
Q Consensus 317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g--~~~i~~ll~eml~~ 362 (367)
+.||+|||++||+||+|+.+|.+.++..++.+ +.++++|+.|||+.
T Consensus 189 ~~~f~kLLl~L~~LRsi~~~h~~~~~~~~~~~~~~~~~~pL~~Ei~~~ 236 (238)
T cd06933 189 RLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMKLTPLVLEVFGN 236 (238)
T ss_pred hhHHHHHHHHhHHHHhhhHHHHHHHHHHHhccCCCCCCCcHHHHHhcc
Confidence 56799999999999999999999987766655 44699999999975
No 71
>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge
Probab=99.48 E-value=9.8e-14 Score=123.69 Aligned_cols=95 Identities=49% Similarity=0.696 Sum_probs=86.7
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR 319 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r 319 (367)
+...+..++.+..+..|+++++...- .+||++|+++...|+++|+++..||.+|+..+||+++.|
T Consensus 112 i~~~~~~~~~L~ld~~EyalLKai~L---------------~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~R 176 (206)
T cd06950 112 LQETLSRFRQLRVDATEFACLKAIVL---------------FKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPAR 176 (206)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccH
Confidence 44566678999999999999987752 247999999999999999999999999999999999999
Q ss_pred HHHHHhhchhhhhhchhhHHHHHHhhhcCC
Q psy6602 320 FGRLLLMLPSLRAVRQSTIERLFFKETIGD 349 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~ 349 (367)
|++||++||+||+++++++|++||.+++|.
T Consensus 177 f~kLLl~Lp~lr~ls~~~~e~l~~~~~~g~ 206 (206)
T cd06950 177 FGKLLLLLPSLRFISSSTIEELFFKKTIGN 206 (206)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHhccCcCCC
Confidence 999999999999999999999999999985
No 72
>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=99.46 E-value=4.6e-13 Score=120.60 Aligned_cols=103 Identities=20% Similarity=0.221 Sum_probs=91.1
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR 319 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r 319 (367)
+..+...++.+..+..|+++++..+- .+||++||.+...|+.+|+.+..||.+|+..+||++|.|
T Consensus 119 i~~~~~kl~~L~l~~~E~~lLkaIvL---------------~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~r 183 (221)
T cd06936 119 MFNFYKSMGELKMTQEEYALLTAITI---------------LFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQH 183 (221)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH---------------hcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhH
Confidence 33455667888888888888877652 248999999999999999999999999999999999999
Q ss_pred HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHH
Q psy6602 320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGD 358 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~e 358 (367)
|++||++||+||+++..++|+|++.|+.. .++++|+.|
T Consensus 184 f~~LL~~L~~LR~l~~~~~e~l~~~k~~~-~~~~pl~~e 221 (221)
T cd06936 184 FACLLGRLTELRTLNHHHAEMLMSWKVND-HKFTPLLCE 221 (221)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHccC-CCCCccccC
Confidence 99999999999999999999999999975 589999875
No 73
>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=99.46 E-value=1.1e-12 Score=119.16 Aligned_cols=105 Identities=21% Similarity=0.347 Sum_probs=92.3
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC-CcC
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR-QPT 318 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~-~~~ 318 (367)
+......++.+..+..|+++++...- + +|++||.+...|+++|+.+..||..|+..+||. .+.
T Consensus 125 l~~~~~~l~~L~ld~~E~~lL~AI~L-----------f-----~d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~ 188 (231)
T cd06938 125 LFRFCRAMCSMKVDNAEYALLTAIVI-----------F-----SDRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRV 188 (231)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH-----------c-----cCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccc
Confidence 44456677888888888888766541 1 268899999999999999999999999999998 899
Q ss_pred hHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHh
Q psy6602 319 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYT 361 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~ 361 (367)
||++||++|++||+++..+.|.+|+.+++ .+++++|+.|+|+
T Consensus 189 rf~kLL~~L~~Lr~l~~~~~e~~~~~k~~-~~~~~pl~~Ei~d 230 (231)
T cd06938 189 IFAKLLSILTELRTLGNQNSEMCFSLKLK-NRKLPPFLAEIWD 230 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHhC
Confidence 99999999999999999999999999999 6799999999996
No 74
>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=99.45 E-value=9.4e-13 Score=115.74 Aligned_cols=95 Identities=24% Similarity=0.327 Sum_probs=84.3
Q ss_pred HHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCC
Q psy6602 237 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQ 316 (367)
Q Consensus 237 f~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~ 316 (367)
...+......++++..+..|+.+++.+.- .+||++|+++..+|+++|+.+..||++|+..+||++
T Consensus 95 ~~~~~~~~~~l~~L~ld~~E~a~LkAivL---------------f~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~ 159 (189)
T cd06940 95 LNSMFDFSEKLNSLQLSDEEMGLFTAVVL---------------VSADRSGLENVNLVEALQETLIRALRTLIAKNHPNE 159 (189)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHH---------------hCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 34455667778888888889888887752 247999999999999999999999999999999999
Q ss_pred cChHHHHHhhchhhhhhchhhHHHHHHhhh
Q psy6602 317 PTRFGRLLLMLPSLRAVRQSTIERLFFKET 346 (367)
Q Consensus 317 ~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~ 346 (367)
+.||+|||++||+||++++.++|++||.|+
T Consensus 160 ~~rf~kLL~~L~~LR~l~~~~~e~l~~~~~ 189 (189)
T cd06940 160 PSIFTKLLLKLPDLRTLNNLHSEKLLAFKV 189 (189)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999863
No 75
>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=99.41 E-value=4.1e-13 Score=121.30 Aligned_cols=103 Identities=18% Similarity=0.343 Sum_probs=88.0
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcCh
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTR 319 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r 319 (367)
+......++.+..+..|+.+++...- .+||++||++...|+++|+++..||++|+..+||..+.|
T Consensus 121 ~~~~~~~l~~L~ld~~E~alLkAivL---------------f~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r 185 (226)
T cd06934 121 LLRFHYTLRKLQLQEEEYVLMQAMSL---------------FSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKR 185 (226)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCcCCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcc
Confidence 44556678888999999999887752 248999999999999999999999999999999876555
Q ss_pred --HHHHHhhchhhhhhchhhHHHHHHhhhcCCCCh-HHHHHHH
Q psy6602 320 --FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPI-QRLLGDM 359 (367)
Q Consensus 320 --~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i-~~ll~em 359 (367)
|+|||++||+||+++..+.+.++ +++|..|+ ++|+.|+
T Consensus 186 ~~f~kLLl~L~~LRsl~~~~~~~~~--~~~~~~~~~~pl~~Ei 226 (226)
T cd06934 186 FLYPKILACLTELRTINEEYTKQIL--HIQDIQPMATPLMQEI 226 (226)
T ss_pred cHHHHHHHHhHHHhcchHHHHHHHH--HHhccCCCCCchhhcC
Confidence 99999999999999999999885 45566675 9999885
No 76
>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=4.5e-12 Score=115.29 Aligned_cols=104 Identities=15% Similarity=0.091 Sum_probs=87.2
Q ss_pred HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCC-CCCCCCCchhhhhHHHHHHHHHHHHHhhCC---CCc
Q psy6602 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYE-TPGLVDAQPVEMLQDQAQCILGDYVRGRYS---RQP 317 (367)
Q Consensus 242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d-~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p---~~~ 317 (367)
.....++.+..+..|+++++...- .++| ++||++...|+++|+++..||++|+.++++ +.+
T Consensus 118 e~~~~l~~L~Ld~~E~acLKAIvL---------------fn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~ 182 (248)
T cd07075 118 QISLQFVRLQLTFEEYTIMKVLLL---------------LSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSW 182 (248)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccch
Confidence 345677888888999998887752 1354 799999999999999999999999997765 456
Q ss_pred ChHHHHHhhchhhhhhchhhHHHHHHhhhc-CCCChHHHHHHHHhc
Q psy6602 318 TRFGRLLLMLPSLRAVRQSTIERLFFKETI-GDIPIQRLLGDMYTM 362 (367)
Q Consensus 318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~-g~~~i~~ll~eml~~ 362 (367)
.||++||++||.||+++.+++|++||.-.. +.+++ .+.||+..
T Consensus 183 ~RF~~LLllLp~Lr~i~~k~iE~lff~~~~~~~~~~--~~~~~~~~ 226 (248)
T cd07075 183 QRFYQLTKLLDSMHDLVSDLLEFCFYTFRESQALKV--EFPAMLVE 226 (248)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHccccceee--ehHHHHHH
Confidence 999999999999999999999999987666 67777 77787764
No 77
>KOG4215|consensus
Probab=99.28 E-value=9.6e-12 Score=114.58 Aligned_cols=107 Identities=25% Similarity=0.418 Sum_probs=97.7
Q ss_pred hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCc--hhhhhHHHHHHHHHHHHHhhCCCC-cCh
Q psy6602 243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQ--PVEMLQDQAQCILGDYVRGRYSRQ-PTR 319 (367)
Q Consensus 243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~--~ve~lq~~~~~aL~~~~~~~~p~~-~~r 319 (367)
++.-+|.+..+..||++.+.+.- .+|+..|+.+.. .|+.++.+++.+|++||..+.|.+ ++|
T Consensus 244 lv~Pmr~L~md~~Ey~cLKAi~F---------------fdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R 308 (432)
T KOG4215|consen 244 LVNPMRRLQMDEIEYVCLKAIAF---------------FDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGR 308 (432)
T ss_pred HhhHHHHhccchHHHHHHHHHHh---------------cCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccc
Confidence 55678999999999999998742 248999999999 799999999999999999999755 689
Q ss_pred HHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHHhccc
Q psy6602 320 FGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEK 364 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml~~~~ 364 (367)
|++||++||+|.+|+...+|...+.+++|-+.|++|+.||+..+.
T Consensus 309 ~g~LLLllPsLqsIt~qliE~iqlaklFGla~vDsll~e~~l~~~ 353 (432)
T KOG4215|consen 309 FGNLLLLLPSLQSITQQLIEQIQLAKLFGLAKVDSLLQEFLLGGE 353 (432)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhcCCC
Confidence 999999999999999999999999999999999999999998753
No 78
>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=99.28 E-value=9.7e-12 Score=111.04 Aligned_cols=89 Identities=30% Similarity=0.484 Sum_probs=81.6
Q ss_pred HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHH
Q psy6602 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG 321 (367)
Q Consensus 242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~ 321 (367)
.+...++.+..+..|+++++.++- .+||++|+.+...|+++|+++..||.+|+..+||+.+.||+
T Consensus 119 ~~~~~l~~L~ld~~E~~lLkaI~L---------------~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~ 183 (207)
T cd06943 119 ELVVKMRDLKMDRTELGCLRAIIL---------------FNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFA 183 (207)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHh---------------cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHH
Confidence 466789999999999999987753 23789999999999999999999999999999999999999
Q ss_pred HHHhhchhhhhhchhhHHHHHHhh
Q psy6602 322 RLLLMLPSLRAVRQSTIERLFFKE 345 (367)
Q Consensus 322 ~lLl~Lp~lr~i~~~~~e~l~~~~ 345 (367)
+||++||+||+++.+++|+|||.+
T Consensus 184 ~LLl~L~~lr~l~~~~~e~l~~~~ 207 (207)
T cd06943 184 KLLLRLPALRSIGLKCLEHLFFFK 207 (207)
T ss_pred HHHHHHHHHHhHhHHHHHHHhhcC
Confidence 999999999999999999999875
No 79
>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=99.28 E-value=9.1e-12 Score=112.45 Aligned_cols=102 Identities=31% Similarity=0.461 Sum_probs=93.3
Q ss_pred hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHHH
Q psy6602 243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGR 322 (367)
Q Consensus 243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~~ 322 (367)
++..++.+..+..|+++.+.+.- .+|+++|+.+...|+.+|+++..||.+|+..++|+.+.||++
T Consensus 121 ~~~~l~~L~l~~~E~~lLkaiil---------------~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~ 185 (222)
T cd06931 121 LVLPLRDLNIDDNEYACLKAIVF---------------FDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGE 185 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHH---------------cCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHH
Confidence 55678888888889888877652 237899999999999999999999999999999999999999
Q ss_pred HHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHH
Q psy6602 323 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDM 359 (367)
Q Consensus 323 lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~em 359 (367)
||+++|+||.++..+.|++++.+++|.+|+++|+.||
T Consensus 186 LL~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e~ 222 (222)
T cd06931 186 LLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhhC
Confidence 9999999999999999999999999999999999987
No 80
>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=99.15 E-value=1e-10 Score=104.81 Aligned_cols=94 Identities=30% Similarity=0.442 Sum_probs=81.1
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP 317 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~ 317 (367)
..+..++..++.+..+..|+++.+..+- .+||++|+.+..+|+++|+.+..||.+|+..+||+.|
T Consensus 115 ~~i~~l~~~l~~L~ld~eEy~lLkAIvL---------------fnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p 179 (213)
T cd06953 115 ERLTYLLAKFRQLKVSNEEYVCLKVINF---------------LNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQP 179 (213)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 3345677788889999999999887752 3478999999999999999999999999999999999
Q ss_pred ChHHHHHhhchhhhhhchhhHHH-HHHhhh
Q psy6602 318 TRFGRLLLMLPSLRAVRQSTIER-LFFKET 346 (367)
Q Consensus 318 ~r~~~lLl~Lp~lr~i~~~~~e~-l~~~~~ 346 (367)
.||++||++||+||+++.+.+|. +++.|.
T Consensus 180 ~Rf~~LL~~L~~Lr~l~~~~~e~~~~~~~~ 209 (213)
T cd06953 180 NRFSDLLSCLPEIRAAAGKLLHSKLFYLPL 209 (213)
T ss_pred hHHHHHHHHhHHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999999854 455553
No 81
>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=98.92 E-value=2.2e-09 Score=93.03 Aligned_cols=90 Identities=23% Similarity=0.301 Sum_probs=79.4
Q ss_pred HHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCC
Q psy6602 236 RFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSR 315 (367)
Q Consensus 236 Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~ 315 (367)
-+..+......++++..+..|+++++...- .+||++|+.+...|+..|+++..||.+|+..+||+
T Consensus 84 ~~~~~~~~~~~l~~L~l~~~E~~llkai~l---------------~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~ 148 (174)
T cd06929 84 FIEPLFEFAEKMNKLQLDDNEYALLTAIVL---------------FSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPD 148 (174)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 344555677889999999999998887652 24788999999999999999999999999999999
Q ss_pred CcChHHHHHhhchhhhhhchhhHHH
Q psy6602 316 QPTRFGRLLLMLPSLRAVRQSTIER 340 (367)
Q Consensus 316 ~~~r~~~lLl~Lp~lr~i~~~~~e~ 340 (367)
.+.||++||+++|+||.++..+.|.
T Consensus 149 ~~~Rf~~Ll~~l~~lr~l~~~~~e~ 173 (174)
T cd06929 149 APQMFAKLLKKLTELRTLNELHAEL 173 (174)
T ss_pred ChhHHHHHHHHhHHHHHHHHHHHhc
Confidence 9999999999999999999999875
No 82
>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=98.92 E-value=1e-08 Score=90.33 Aligned_cols=89 Identities=11% Similarity=0.039 Sum_probs=78.8
Q ss_pred HHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCC--CCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCc
Q psy6602 240 LLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYE--TPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQP 317 (367)
Q Consensus 240 LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d--~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~ 317 (367)
+......++.+..+..|+++++...- .+|| ++|+.+...|+.+|+.+..+|.+|+..+||+.+
T Consensus 87 ~~~~~~~l~~L~l~~~E~~lL~Aivl---------------~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~ 151 (191)
T cd06942 87 MLQFANKILTLNLTNAELALLCAAEL---------------LQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTE 151 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH---------------hCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChH
Confidence 44566778888888888888877652 2478 999999999999999999999999999999999
Q ss_pred ChHHHHHhhchhhhhhchhhHHHHHH
Q psy6602 318 TRFGRLLLMLPSLRAVRQSTIERLFF 343 (367)
Q Consensus 318 ~r~~~lLl~Lp~lr~i~~~~~e~l~~ 343 (367)
.||+|||+++++||+++..+.+.+..
T Consensus 152 ~rf~kLL~~l~~Lr~~~~~~~~~l~~ 177 (191)
T cd06942 152 QRLQKLFDILNRLRNMNKEHQNILAD 177 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999999999997775
No 83
>KOG4217|consensus
Probab=98.67 E-value=2.9e-07 Score=87.81 Aligned_cols=123 Identities=24% Similarity=0.338 Sum_probs=96.9
Q ss_pred HHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHh-HHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhh--CC
Q psy6602 238 GRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQR-LLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGR--YS 314 (367)
Q Consensus 238 ~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~-Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~--~p 314 (367)
|.++.++.-+|.++.+.....-|....+...++- -+..+--....+||-||+++..||+||.++..+|++|+... .+
T Consensus 474 G~vlhr~qC~rgfgewidsi~~FS~~l~~l~idi~AfacL~aLa~iTErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~ 553 (605)
T KOG4217|consen 474 GLVLHRLQCLRGFGEWIDSIREFSRSLHSLNIDISAFACLSALALITERHGLKEPKRVEELQNKIINCLKDHVTGSAGKL 553 (605)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHhhhchhhHHHHHHHHHHHhhhhhhcCCCcchHHHHHHHHHHHHHHHhhhccccc
Confidence 6677777778888755555555655555544441 12222223446899999999999999999999999999544 46
Q ss_pred CCcChHHHHHhhchhhhhhchhhHHHHHHhhhcCCCChHHHHHHHH
Q psy6602 315 RQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMY 360 (367)
Q Consensus 315 ~~~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~g~~~i~~ll~eml 360 (367)
..+.++.|+|.+||+||.++..+....|+.|+...||++.++..|+
T Consensus 554 ~k~~~lSrllgklpeLr~l~tqgLqrifyLklEdlvp~p~iidklf 599 (605)
T KOG4217|consen 554 AKPVYLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLF 599 (605)
T ss_pred ccchHHHHHhhhhHHHHHHHHHhhhhhhcccHhhccCchhhhhhhh
Confidence 7889999999999999999999999999999999999988887765
No 84
>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=98.57 E-value=1.5e-07 Score=80.63 Aligned_cols=80 Identities=41% Similarity=0.645 Sum_probs=69.7
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 318 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~ 318 (367)
.+..+...++.+..+..|+++++...- .+||++|+.+...|+..|+.+..||..|+..+||+.+.
T Consensus 86 ~~~~~~~~l~~L~l~~~E~~lLkai~l---------------~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~ 150 (165)
T cd06930 86 RLQELLSKLRSLQLDPKEYACLKAIVL---------------FNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPA 150 (165)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHH---------------cCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchh
Confidence 334466778889999999998887752 23788999999999999999999999999999999999
Q ss_pred hHHHHHhhchhhhhh
Q psy6602 319 RFGRLLLMLPSLRAV 333 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i 333 (367)
||++||+.||+||++
T Consensus 151 R~~~ll~~l~~lr~~ 165 (165)
T cd06930 151 RFAKLLLRLPELRSI 165 (165)
T ss_pred HHHHHHHHhHhhccC
Confidence 999999999999975
No 85
>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=98.28 E-value=5e-06 Score=75.82 Aligned_cols=105 Identities=10% Similarity=0.056 Sum_probs=80.1
Q ss_pred hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCC-CCCCCCCCchhhhhHHHHHHHHHHHHHhhC---CCCcC
Q psy6602 243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSY-ETPGLVDAQPVEMLQDQAQCILGDYVRGRY---SRQPT 318 (367)
Q Consensus 243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~-d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~---p~~~~ 318 (367)
....++.+..+..|+++++.+.- .++ |++||++...|+++|+++..||.+|+..++ ++.|+
T Consensus 119 ~~~~~~~L~ld~~Ey~cLKAIvL---------------fnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~ 183 (248)
T cd07074 119 IPQEFVKLQVSQEEFLCMKALLL---------------LNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQ 183 (248)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHH---------------CCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcH
Confidence 56788889999999999998753 235 789999999999999999999999987775 35789
Q ss_pred hHHHHHhhchhhhhhchhhHHHHHHhhhc---CCCChHHHHHHHHhc
Q psy6602 319 RFGRLLLMLPSLRAVRQSTIERLFFKETI---GDIPIQRLLGDMYTM 362 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~---g~~~i~~ll~eml~~ 362 (367)
||++|++.++.|+.+-...-...|..... -.|..+..+.|+.-.
T Consensus 184 RF~~Ll~ll~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (248)
T cd07074 184 RFYQLTKLMDNMHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAA 230 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeecHHHHHHHHHh
Confidence 99999999999995444444433322221 256667777777653
No 86
>KOG4216|consensus
Probab=98.02 E-value=4.1e-05 Score=71.84 Aligned_cols=196 Identities=15% Similarity=0.087 Sum_probs=119.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCccccCCCCCccchHHHHHHHHHHHHHH------------Hh
Q psy6602 114 TLSKRDQLLLLQESWKELFLLHLAQWSIPWDLSLLINCEKARERLPPDDVRVNNEIKLIQEILARF------------RQ 181 (367)
Q Consensus 114 ~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l------------~~ 181 (367)
+...-+-+.-+++...|.||..+|.... ..+..+.+|++.+ .-
T Consensus 265 ~~~~~e~I~~yq~k~~e~mWe~cA~~lt-------------------------~~IQ~vVEFAK~I~GFM~L~Q~dQI~L 319 (479)
T KOG4216|consen 265 QTFDQEEIENYQNKGREEMWELCAIKLT-------------------------PAIQYVVEFAKRIDGFMELCQNDQIVL 319 (479)
T ss_pred ccCCHHHHHHHHhhhHHHHHHHHHHHHH-------------------------HHHHHHHHHHHhhhHhhccCccceEEe
Confidence 3344556666777777777777775432 3344555555544 23
Q ss_pred cCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhh
Q psy6602 182 LSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFK 261 (367)
Q Consensus 182 L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~ 261 (367)
|+-...|.++..+-.+++.|....---.+.--..--|...+ ..-...+.....+|..+...-.|...+.
T Consensus 320 LKaGsfEv~lvrm~r~~~v~~ntV~~e~~~~g~~~f~a~~~-----------~elis~vf~~~ksL~~Lq~te~EiAL~~ 388 (479)
T KOG4216|consen 320 LKAGSFEVVLVRMCRAFDVDNNTVYFEGKYAGPEVFYALGC-----------EELISRVFEFGKSLCSLQLTEDEIALFS 388 (479)
T ss_pred eecCceeeeHHHHHHhhcccccceeecccccchhheeccCh-----------HHHHHHHHhhhHHHHhhccCcHHHHHHH
Confidence 44555666666666666665422211111100001011111 1112222333344444444444544444
Q ss_pred hccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcChHHHHHhhchhhhhhchhhHHHH
Q psy6602 262 ETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERL 341 (367)
Q Consensus 262 ~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~r~~~lLl~Lp~lr~i~~~~~e~l 341 (367)
.++. .+++|+||.+..+|++||..+..|++.++.++|. +.+-++||+-+.|.||+++..|.|.|
T Consensus 389 alVL---------------~~~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~-~~~~l~kl~~k~~~~r~~~~lH~E~L 452 (479)
T KOG4216|consen 389 ALVL---------------MSADRSGLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKVSTLRALCGLHTEKL 452 (479)
T ss_pred HHHh---------------hCCccccccchHHHHHHHHHHHHHHHHHHHhcCC-hhhhHHHhhcccchHHHHHHHHHHHH
Confidence 3321 2578999999999999999999999999999985 34489999999999999999999999
Q ss_pred HHhhhcCCCCh---HHHHHHHHh
Q psy6602 342 FFKETIGDIPI---QRLLGDMYT 361 (367)
Q Consensus 342 ~~~~~~g~~~i---~~ll~eml~ 361 (367)
..++..-+.-+ ++|--|++.
T Consensus 453 q~Fk~~hP~iv~~fP~LYKELFt 475 (479)
T KOG4216|consen 453 QAFKASHPDIVRHFPPLYKELFT 475 (479)
T ss_pred HHHhhcCchHHhhccHHHHHHhc
Confidence 98888765444 344444443
No 87
>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=97.93 E-value=3e-05 Score=68.12 Aligned_cols=94 Identities=30% Similarity=0.484 Sum_probs=76.2
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCC-CCch-hhhhHHHHHHHHHHHH-HhhCCC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLV-DAQP-VEMLQDQAQCILGDYV-RGRYSR 315 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~-~~~~-ve~lq~~~~~aL~~~~-~~~~p~ 315 (367)
.+...+..++.+..+..|+++++...- -+++.+++. +... ++++|+.+..+|..|+ ...++.
T Consensus 106 ~~~~~~~~~~~l~l~~~E~~~l~~l~l---------------~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~ 170 (203)
T PF00104_consen 106 YMNEVLRPFRRLKLDEEEFALLKALIL---------------FNPDYPGLSEETREIVEELRDRIIQALHSYYNQSKGPE 170 (203)
T ss_dssp HHHHHHHHHHHTT-BHHHHHHHHHHHH---------------SSTTSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHhh---------------hcccccccccchhHHHHHHHHHHHHHHHHHHhccCCCc
Confidence 445566678888888888888876641 235777877 5555 9999999999999999 878887
Q ss_pred C-cChHHHHHhhchhhhhhchhhHHHHHHhhhc
Q psy6602 316 Q-PTRFGRLLLMLPSLRAVRQSTIERLFFKETI 347 (367)
Q Consensus 316 ~-~~r~~~lLl~Lp~lr~i~~~~~e~l~~~~~~ 347 (367)
+ +.||++|++.+|.++.++..+.|+.++..++
T Consensus 171 ~~~~R~~~ll~ll~~l~~~~~~~~e~~~~~~lf 203 (203)
T PF00104_consen 171 DYAQRFGKLLLLLPSLRKISEKHIENMFLSDLF 203 (203)
T ss_dssp THTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhhC
Confidence 7 7999999999999999999999998887653
No 88
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=97.70 E-value=6.2e-05 Score=63.57 Aligned_cols=76 Identities=29% Similarity=0.489 Sum_probs=63.6
Q ss_pred hhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCC--chhhhhHHHHHHHHHHHHHhhCC-CCcCh
Q psy6602 243 MLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDA--QPVEMLQDQAQCILGDYVRGRYS-RQPTR 319 (367)
Q Consensus 243 ~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~--~~ve~lq~~~~~aL~~~~~~~~p-~~~~r 319 (367)
....++.+.....|+++++...- .+++++++.+. ..++++|+.+..+|..|+..++| +.+.|
T Consensus 85 ~~~~l~~L~l~~~E~~~l~ai~l---------------~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R 149 (163)
T smart00430 85 LVKPLRELKLDDEEYALLKAILL---------------FNPAGPGLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGR 149 (163)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHH---------------cChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhH
Confidence 45567888888899888876642 12567888888 78999999999999999999998 56899
Q ss_pred HHHHHhhchhhhhh
Q psy6602 320 FGRLLLMLPSLRAV 333 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i 333 (367)
|++|++++|++|.+
T Consensus 150 ~~~ll~~l~~i~~~ 163 (163)
T smart00430 150 FGELLLILNAIQKI 163 (163)
T ss_pred HHHHHHHHHHhhcC
Confidence 99999999999863
No 89
>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=97.61 E-value=0.00013 Score=62.00 Aligned_cols=77 Identities=36% Similarity=0.568 Sum_probs=63.9
Q ss_pred HhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCC-CCCCCchhhhhHHHHHHHHHHHHHhhCC-CCcCh
Q psy6602 242 LMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETP-GLVDAQPVEMLQDQAQCILGDYVRGRYS-RQPTR 319 (367)
Q Consensus 242 ~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~-gl~~~~~ve~lq~~~~~aL~~~~~~~~p-~~~~r 319 (367)
.++..++.+..+..|+++.+...- | +++.+ +..+...+++.|+.+..+|..|+..+++ +.+.|
T Consensus 90 ~~~~~~~~L~l~~~E~~~l~ai~l-----------~----~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R 154 (168)
T cd06157 90 EFVNPLRALKLDDEEYALLKAIVL-----------F----SPDRKESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSR 154 (168)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHH-----------h----CCCCCCCccCHHHHHHHHHHHHHHHHHHHHHhCCccchhH
Confidence 355677788888888888877642 1 24444 7889999999999999999999999997 88999
Q ss_pred HHHHHhhchhhhhh
Q psy6602 320 FGRLLLMLPSLRAV 333 (367)
Q Consensus 320 ~~~lLl~Lp~lr~i 333 (367)
|++|+++++++|.+
T Consensus 155 ~~~ll~~l~~l~~~ 168 (168)
T cd06157 155 FAKLLLLLPSLRKL 168 (168)
T ss_pred HHHHHHhchhcccC
Confidence 99999999999864
No 90
>KOG4846|consensus
Probab=96.85 E-value=0.0036 Score=59.59 Aligned_cols=158 Identities=9% Similarity=0.016 Sum_probs=113.4
Q ss_pred hHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCC------CCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHH
Q psy6602 165 VNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPG------LVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFG 238 (367)
Q Consensus 165 ~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~------L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~ 238 (367)
+....+.+..|.+....+...+...+++..+.++.+.... .....+..++...+..-+.++...+. .+ .-+.
T Consensus 371 ~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f~~~~Q~~~mfl~~~~~~~Q~~~~~~-~g-d~~~ 448 (538)
T KOG4846|consen 371 YGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNFKSQLQLLEMFLFYKKVLFQKMTCRI-DG-DTYK 448 (538)
T ss_pred hhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-ch-HHHH
Confidence 3455688899999999999999999999888888874321 11233444455556666665555542 22 5577
Q ss_pred HHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHcccCCCCCCCCCCCchhhhhHHHHHHHHHHHHHhhCCCCcC
Q psy6602 239 RLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTMEKSYETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPT 318 (367)
Q Consensus 239 ~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~s~d~~gl~~~~~ve~lq~~~~~aL~~~~~~~~p~~~~ 318 (367)
.++.++-.+..++..+.+.+-.. .+.++.+.+....||.|||....++ ..-.+.|-...
T Consensus 449 a~~~~~~~ln~L~~~~~~~~~~l-------------------~s~~s~~~e~~~sVe~lqe~~lr~~--~~~~n~pl~~s 507 (538)
T KOG4846|consen 449 ALMKCIHELNRLNELHKQQLNIL-------------------RSNLSFLNEPPLSVEMLQESTLRLP--VNHNNQPLNQS 507 (538)
T ss_pred HHHHhhcchhhcCchHHHHHHHH-------------------HHhhhhhccCCchHHHHHhhhhhcc--ccccCCccccc
Confidence 77777777777777766653332 2345677888889999999998888 44455677788
Q ss_pred hHHHHHhhchhhhhhchhhHHHHHHhh
Q psy6602 319 RFGRLLLMLPSLRAVRQSTIERLFFKE 345 (367)
Q Consensus 319 r~~~lLl~Lp~lr~i~~~~~e~l~~~~ 345 (367)
++.+.++.++++|++.+.+.+.+...+
T Consensus 508 ~~~~~~~~~~d~~sl~~lhs~kv~~~~ 534 (538)
T KOG4846|consen 508 LPHVRHQVKRDVQSLENLHSMKVHPVP 534 (538)
T ss_pred CcchhhccCCcCCcccchhcccccccc
Confidence 999999999999999998888776544
No 91
>KOG4218|consensus
Probab=95.96 E-value=0.021 Score=53.16 Aligned_cols=72 Identities=31% Similarity=0.401 Sum_probs=65.7
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhhhHhHhhhhhHHHHHHhhhccCCchhHhHHHHHHccc
Q psy6602 209 QPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLMLPSLRAVRQSTIERLFFKETIGDIPIQRLLGDMYTME 280 (367)
Q Consensus 209 ~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~ 280 (367)
..|+.+|+....+|-+|-...||+....|+++++.|.++|.++....|+++.+.+-...+-..++.+|+...
T Consensus 402 ~lv~~~qe~~naaLldyt~c~yp~~~~kF~qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~Ak 473 (475)
T KOG4218|consen 402 ELVRRLQEDSNAALLDYTSCCYPNWEQKFPQLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLTAK 473 (475)
T ss_pred HHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhhcc
Confidence 468899999999999999999999999999999999999999999999999999888877778888887643
No 92
>KOG4846|consensus
Probab=94.84 E-value=0.0064 Score=57.93 Aligned_cols=163 Identities=7% Similarity=-0.078 Sum_probs=111.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHhhccCCC---ceEecCCccccCCCCCcc
Q psy6602 88 AEKCQETTARLLFMAVRWVRCLAPFQTLS-KRDQLLLLQESWKELFLLHLAQWSIPWDL---SLLINCEKARERLPPDDV 163 (367)
Q Consensus 88 ~~~l~e~~~~~l~~~V~waK~lp~F~~L~-~~DQ~~LLk~~~~el~lL~~a~~~~~~~~---~~l~~~~~~~~~~~~~~~ 163 (367)
|+++.-+....+-.+++||+.+++|..++ ..++..+|+.+-++...-..+-....... ..++.......... +.
T Consensus 364 ~~~~~ll~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f~~~~Q~~~mfl~~~~~~~Q~~~--~~ 441 (538)
T KOG4846|consen 364 FKSLQLLYGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNFKSQLQLLEMFLFYKKVLFQKMT--CR 441 (538)
T ss_pred cchhhhhhhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hh
Confidence 66777788888889999999999999999 89999999998888776655532221000 00000001111111 11
Q ss_pred chHHHHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHh
Q psy6602 164 RVNNEIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVDAQPVEMLQDQAQCILGDYVRGRYSRQPTRFGRLLLM 243 (367)
Q Consensus 164 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~~~~v~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~ 243 (367)
++++....+..++.++..|.....|. +.++-+-+..+......|+.+|+....++- ...+.|-...++......
T Consensus 442 ~~gd~~~a~~~~~~~ln~L~~~~~~~----~~~l~s~~s~~~e~~~sVe~lqe~~lr~~~--~~~n~pl~~s~~~~~~~~ 515 (538)
T KOG4846|consen 442 IDGDTYKALMKCIHELNRLNELHKQQ----LNILRSNLSFLNEPPLSVEMLQESTLRLPV--NHNNQPLNQSLPHVRHQV 515 (538)
T ss_pred hchHHHHHHHHhhcchhhcCchHHHH----HHHHHHhhhhhccCCchHHHHHhhhhhccc--cccCCcccccCcchhhcc
Confidence 24567788889999999999988886 556666677777778999999999888772 222234455677777778
Q ss_pred hhHhHhhhhhHHHHH
Q psy6602 244 LPSLRAVRQSTIERL 258 (367)
Q Consensus 244 l~~Lr~l~~~~~e~l 258 (367)
.+.++++...+.+.+
T Consensus 516 ~~d~~sl~~lhs~kv 530 (538)
T KOG4846|consen 516 KRDVQSLENLHSMKV 530 (538)
T ss_pred CCcCCcccchhcccc
Confidence 888887776666544
No 93
>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=35.86 E-value=32 Score=25.35 Aligned_cols=23 Identities=17% Similarity=0.127 Sum_probs=17.9
Q ss_pred HHhhcCCCCCCCCHHHHHHHHHH
Q psy6602 104 RWVRCLAPFQTLSKRDQLLLLQE 126 (367)
Q Consensus 104 ~waK~lp~F~~L~~~DQ~~LLk~ 126 (367)
.=+..|+||..|..+||..+.+.
T Consensus 58 ~~~~~i~G~~~L~~~Dq~~i~~~ 80 (82)
T PF00645_consen 58 GDIEEIKGFDELKPEDQEKIRKL 80 (82)
T ss_dssp SCGGGCETCCCS-HHHHHHHHHH
T ss_pred CCHHHCCChHHCCHHHHHHHHHH
Confidence 34677999999999999988653
No 94
>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=35.69 E-value=40 Score=25.62 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=19.3
Q ss_pred hhcCCCCCCCCHHHHHHHHHHH
Q psy6602 106 VRCLAPFQTLSKRDQLLLLQES 127 (367)
Q Consensus 106 aK~lp~F~~L~~~DQ~~LLk~~ 127 (367)
++.+|+|..|+..-|..|+-++
T Consensus 31 t~~vPgF~~ls~sKqRRLi~~A 52 (92)
T PF10330_consen 31 TTSVPGFSDLSPSKQRRLIMAA 52 (92)
T ss_pred hccCCCcccCCHHHHHHHHHHH
Confidence 5889999999999999997654
No 95
>PF04048 Sec8_exocyst: Sec8 exocyst complex component specific domain; InterPro: IPR007191 Sec8 is a component of the exocyst complex involved in the docking of exocystic vesicles with a fusion site on the plasma membrane. The exocyst complex is composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84.; GO: 0006904 vesicle docking involved in exocytosis, 0015031 protein transport, 0000145 exocyst
Probab=24.27 E-value=1.8e+02 Score=24.03 Aligned_cols=90 Identities=16% Similarity=0.123 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHhcCCCcchhhhhHHHHhcCCCCCCCCC-hhHHHHHHHHHHHHHHHHHHhhCC---CcchHHHHHHHh
Q psy6602 168 EIKLIQEILARFRQLSPDGSECGCMKAVILFTPETPGLVD-AQPVEMLQDQAQCILGDYVRGRYS---RQPTRFGRLLLM 243 (367)
Q Consensus 168 ~~~~~~~~~~~l~~L~ld~~E~alLkai~L~~pd~~~L~~-~~~v~~~q~~~~~~L~~y~~~~~~---~~~~Rf~~LL~~ 243 (367)
.++.+..-+..+..=+....| -|+-+++....|+.. ...++++.+.+-.+|...+..+|. ..-..|..++..
T Consensus 5 ~l~~I~~~W~~~~~~~~~pv~----~al~~ld~ss~g~~~~~~~f~~~~~~~~~~L~~vV~eh~q~Fn~sI~sy~~i~~~ 80 (142)
T PF04048_consen 5 VLNEIKDEWPFMLTDDFNPVE----LALSLLDDSSVGRAHRYQEFEELKKRIEKALQEVVNEHYQGFNSSIGSYSQILSS 80 (142)
T ss_pred HHHHHHHHHHHHhcCCCcHHH----HHHHhcCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555533333333 356677765556655 788999999999999999999874 344578888887
Q ss_pred hhHhHhhhhhHHHHHHhh
Q psy6602 244 LPSLRAVRQSTIERLFFK 261 (367)
Q Consensus 244 l~~Lr~l~~~~~e~l~~~ 261 (367)
+..-+.-.....+.+-..
T Consensus 81 i~~sq~~i~~lK~~L~~a 98 (142)
T PF04048_consen 81 ISESQERIRELKESLQEA 98 (142)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 777766655555555433
Done!