Query psy12692
Match_columns 187
No_of_seqs 143 out of 1333
Neff 8.3
Searched_HMMs 46136
Date Fri Aug 16 17:13:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12692.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12692hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07069 NR_LBD_Lrh-1 The ligan 100.0 1.2E-28 2.7E-33 197.9 15.8 151 37-187 39-241 (241)
2 cd06937 NR_LBD_RAR The ligand 100.0 4E-28 8.7E-33 193.9 15.8 143 40-184 40-231 (231)
3 cd07348 NR_LBD_NGFI-B The liga 100.0 3.6E-28 7.7E-33 194.6 15.3 143 40-185 43-235 (238)
4 cd07072 NR_LBD_DHR38_like Liga 100.0 1E-27 2.2E-32 192.1 15.0 144 39-185 43-236 (239)
5 cd07071 NR_LBD_Nurr1 The ligan 100.0 1.5E-27 3.4E-32 191.0 15.1 143 39-184 42-234 (238)
6 cd07070 NR_LBD_SF-1 The ligand 100.0 2E-27 4.4E-32 190.5 15.1 146 40-185 40-237 (237)
7 cd07076 NR_LBD_GR Ligand bindi 99.9 1.7E-26 3.8E-31 185.4 16.8 141 41-183 31-224 (247)
8 cd06944 NR_LBD_Ftz-F1_like The 99.9 1.2E-26 2.6E-31 186.1 15.7 149 37-185 37-237 (237)
9 cd06945 NR_LBD_Nurr1_like The 99.9 1.5E-26 3.2E-31 185.7 15.5 145 38-185 41-236 (239)
10 cd07349 NR_LBD_SHP The ligand 99.9 5.4E-27 1.2E-31 186.2 12.3 146 36-182 17-222 (222)
11 cd06949 NR_LBD_ER Ligand bindi 99.9 8.4E-26 1.8E-30 180.9 16.0 144 40-185 34-235 (235)
12 cd07073 NR_LBD_AR Ligand bindi 99.9 2.7E-25 5.9E-30 178.8 15.8 144 40-185 30-231 (246)
13 cd06935 NR_LBD_TR The ligand b 99.9 1.6E-25 3.5E-30 180.1 14.2 141 39-181 53-243 (243)
14 cd06947 NR_LBD_GR_Like Ligand 99.9 9E-25 2E-29 175.8 16.9 145 41-185 31-231 (246)
15 cd07350 NR_LBD_Dax1 The ligand 99.9 2E-25 4.3E-30 178.2 11.7 143 36-180 17-232 (232)
16 cd06951 NR_LBD_Dax1_like The l 99.9 3.3E-25 7.1E-30 176.1 11.7 145 36-180 17-222 (222)
17 cd07075 NR_LBD_MR Ligand bindi 99.9 1.8E-24 3.9E-29 173.8 14.2 143 40-184 30-226 (248)
18 cd06948 NR_LBD_COUP-TF Ligand 99.9 3.8E-24 8.3E-29 171.5 13.5 148 38-186 30-227 (236)
19 cd06946 NR_LBD_ERR The ligand 99.9 2.1E-23 4.5E-28 165.7 16.8 143 40-184 29-221 (221)
20 cd06941 NR_LBD_DmE78_like The 99.9 2E-23 4.3E-28 162.8 15.2 142 40-183 4-195 (195)
21 cd07068 NR_LBD_ER_like The lig 99.9 5.4E-23 1.2E-27 163.4 17.3 145 38-184 27-221 (221)
22 KOG4218|consensus 99.9 1.6E-22 3.5E-27 164.7 15.3 146 41-186 277-474 (475)
23 cd06940 NR_LBD_REV_ERB The lig 99.9 4.4E-22 9.5E-27 154.6 13.8 129 38-168 12-189 (189)
24 cd06939 NR_LBD_ROR_like The li 99.9 8.2E-22 1.8E-26 158.4 14.9 140 40-182 50-241 (241)
25 cd06938 NR_LBD_EcR The ligand 99.9 1.3E-21 2.8E-26 156.4 15.2 142 39-183 40-230 (231)
26 cd06954 NR_LBD_LXR The ligand 99.9 1.3E-21 2.9E-26 156.8 15.1 141 40-183 45-235 (236)
27 cd06950 NR_LBD_Tlx_PNR_like Th 99.9 7.4E-22 1.6E-26 155.3 12.9 133 36-171 24-206 (206)
28 cd06932 NR_LBD_PPAR The ligand 99.9 3.6E-21 7.9E-26 156.1 14.8 140 41-184 66-258 (259)
29 cd06933 NR_LBD_VDR The ligand 99.9 1.2E-20 2.7E-25 151.3 14.5 142 40-184 39-236 (238)
30 cd06934 NR_LBD_PXR_like The li 99.9 1.8E-20 4E-25 149.3 14.0 137 40-181 37-226 (226)
31 cd06952 NR_LBD_TR2_like The li 99.9 1E-20 2.3E-25 150.3 12.5 147 36-183 19-221 (222)
32 cd06943 NR_LBD_RXR_like The li 99.8 9.6E-20 2.1E-24 143.2 12.5 127 39-167 31-207 (207)
33 KOG4215|consensus 99.8 7.5E-20 1.6E-24 150.2 11.9 148 36-185 152-352 (432)
34 cd06931 NR_LBD_HNF4_like The l 99.8 7.1E-19 1.5E-23 139.7 14.6 143 36-181 30-222 (222)
35 cd06936 NR_LBD_Fxr The ligand 99.8 7.5E-20 1.6E-24 145.3 6.3 104 3-180 118-221 (221)
36 cd07074 NR_LBD_PR Ligand bindi 99.8 2E-18 4.4E-23 138.8 12.8 122 40-163 30-159 (248)
37 cd06929 NR_LBD_F1 Ligand-bindi 99.7 2.9E-17 6.4E-22 125.4 12.1 121 40-162 4-173 (174)
38 cd06953 NR_LBD_DHR4_like The l 99.7 5.7E-17 1.2E-21 128.2 10.6 125 39-164 28-204 (213)
39 cd06930 NR_LBD_F2 Ligand-bindi 99.7 3.6E-16 7.7E-21 118.2 11.5 116 41-158 2-123 (165)
40 cd06942 NR_LBD_Sex_1_like The 99.7 1.1E-15 2.5E-20 118.8 12.8 122 40-165 4-177 (191)
41 KOG4217|consensus 99.6 1.3E-14 2.9E-19 122.8 12.5 137 45-184 415-601 (605)
42 PF00104 Hormone_recep: Ligand 99.4 2.1E-11 4.6E-16 94.1 12.8 129 39-168 18-202 (203)
43 cd06936 NR_LBD_Fxr The ligand 99.3 8E-12 1.7E-16 99.3 10.4 111 39-158 37-155 (221)
44 cd07074 NR_LBD_PR Ligand bindi 99.3 6.2E-12 1.4E-16 101.3 9.1 57 5-61 117-174 (248)
45 cd06937 NR_LBD_RAR The ligand 99.3 4.7E-12 1E-16 101.3 4.8 80 4-92 124-203 (231)
46 cd06951 NR_LBD_Dax1_like The l 99.2 6.4E-12 1.4E-16 100.0 4.7 78 4-91 120-197 (222)
47 cd06940 NR_LBD_REV_ERB The lig 99.2 9.1E-12 2E-16 96.8 4.9 63 3-65 97-159 (189)
48 cd07350 NR_LBD_Dax1 The ligand 99.2 1.3E-11 2.9E-16 98.7 5.9 79 4-91 129-207 (232)
49 cd07069 NR_LBD_Lrh-1 The ligan 99.2 1.4E-11 3E-16 99.2 5.9 79 4-91 131-209 (241)
50 cd07349 NR_LBD_SHP The ligand 99.2 8.7E-12 1.9E-16 99.1 4.7 80 4-92 117-196 (222)
51 cd06932 NR_LBD_PPAR The ligand 99.2 1.5E-11 3.3E-16 99.9 5.6 62 4-65 150-211 (259)
52 cd06935 NR_LBD_TR The ligand b 99.2 1.4E-11 3E-16 99.3 5.0 80 3-91 137-216 (243)
53 cd06934 NR_LBD_PXR_like The li 99.2 1.8E-11 4E-16 97.6 4.7 61 4-64 121-181 (226)
54 cd06933 NR_LBD_VDR The ligand 99.2 1.8E-11 3.8E-16 98.4 4.3 61 4-64 125-185 (238)
55 cd06157 NR_LBD The ligand bind 99.2 3.3E-10 7.3E-15 84.7 10.6 111 42-154 2-120 (168)
56 cd07076 NR_LBD_GR Ligand bindi 99.2 3.1E-11 6.6E-16 97.3 5.0 61 4-64 116-177 (247)
57 cd07070 NR_LBD_SF-1 The ligand 99.2 4.5E-11 9.8E-16 96.0 5.9 79 5-92 130-208 (237)
58 cd06950 NR_LBD_Tlx_PNR_like Th 99.2 3.5E-11 7.6E-16 94.7 4.9 78 4-90 112-189 (206)
59 cd06953 NR_LBD_DHR4_like The l 99.1 6.1E-11 1.3E-15 93.8 5.0 79 4-91 117-195 (213)
60 cd06939 NR_LBD_ROR_like The li 99.1 6E-11 1.3E-15 95.5 4.8 60 3-62 132-191 (241)
61 cd06944 NR_LBD_Ftz-F1_like The 99.1 6.5E-11 1.4E-15 95.1 4.7 62 4-65 129-190 (237)
62 cd06941 NR_LBD_DmE78_like The 99.1 1.2E-10 2.6E-15 90.8 5.9 62 4-65 88-149 (195)
63 cd06954 NR_LBD_LXR The ligand 99.1 1.6E-10 3.6E-15 92.6 6.4 62 4-65 130-191 (236)
64 cd06949 NR_LBD_ER Ligand bindi 99.1 1.5E-10 3.2E-15 92.9 5.6 59 4-62 119-182 (235)
65 cd07075 NR_LBD_MR Ligand bindi 99.1 1.2E-10 2.7E-15 93.8 4.8 61 4-64 116-177 (248)
66 cd07073 NR_LBD_AR Ligand bindi 99.1 1.2E-10 2.5E-15 94.0 4.5 58 5-62 117-175 (246)
67 cd06947 NR_LBD_GR_Like Ligand 99.1 1.2E-10 2.6E-15 94.0 4.5 61 4-64 116-177 (246)
68 cd07348 NR_LBD_NGFI-B The liga 99.1 2.5E-10 5.5E-15 91.6 5.7 79 3-91 125-205 (238)
69 cd06945 NR_LBD_Nurr1_like The 99.0 3.4E-10 7.4E-15 91.0 5.6 61 3-63 125-185 (239)
70 cd06943 NR_LBD_RXR_like The li 99.0 3.2E-10 7E-15 89.1 4.6 59 6-64 119-177 (207)
71 cd07071 NR_LBD_Nurr1 The ligan 99.0 1.9E-10 4.2E-15 92.3 3.4 59 3-62 125-183 (238)
72 cd06929 NR_LBD_F1 Ligand-bindi 99.0 1.2E-09 2.5E-14 83.3 7.1 61 4-64 88-148 (174)
73 cd06948 NR_LBD_COUP-TF Ligand 99.0 5.2E-10 1.1E-14 89.8 4.4 59 6-64 120-178 (236)
74 cd06942 NR_LBD_Sex_1_like The 99.0 1.8E-09 3.9E-14 83.9 7.2 61 4-64 87-149 (191)
75 cd07068 NR_LBD_ER_like The lig 99.0 7.2E-10 1.6E-14 88.1 4.6 60 4-63 113-172 (221)
76 cd06946 NR_LBD_ERR The ligand 98.9 9.5E-10 2.1E-14 87.3 4.6 60 4-63 113-172 (221)
77 cd07072 NR_LBD_DHR38_like Liga 98.9 1E-09 2.3E-14 88.1 4.5 59 3-62 126-184 (239)
78 smart00430 HOLI Ligand binding 98.9 1.8E-08 3.9E-13 74.9 10.4 106 49-158 3-118 (163)
79 cd06952 NR_LBD_TR2_like The li 98.9 2.4E-09 5.2E-14 85.1 6.0 60 6-65 117-176 (222)
80 cd06930 NR_LBD_F2 Ligand-bindi 98.9 2.9E-09 6.3E-14 80.2 5.7 61 4-64 87-147 (165)
81 smart00430 HOLI Ligand binding 98.8 3.4E-09 7.3E-14 78.8 4.7 59 5-63 83-143 (163)
82 cd06938 NR_LBD_EcR The ligand 98.7 2E-08 4.3E-13 80.4 4.4 60 4-64 125-184 (231)
83 cd06931 NR_LBD_HNF4_like The l 98.7 2.8E-08 6.1E-13 78.9 4.6 59 6-64 120-178 (222)
84 KOG4215|consensus 98.6 6.4E-08 1.4E-12 80.5 4.1 54 8-61 245-300 (432)
85 KOG4216|consensus 98.5 4.7E-07 1E-11 75.9 8.4 110 3-186 366-478 (479)
86 cd06157 NR_LBD The ligand bind 98.3 8.5E-07 1.9E-11 66.1 4.4 59 5-63 89-148 (168)
87 PF00104 Hormone_recep: Ligand 97.9 7.9E-06 1.7E-10 62.8 3.3 54 5-58 108-163 (203)
88 KOG4216|consensus 97.3 0.00026 5.6E-09 59.8 3.6 114 48-164 292-410 (479)
89 KOG4218|consensus 96.6 0.0015 3.3E-08 54.5 2.5 57 8-64 369-425 (475)
90 KOG4217|consensus 96.0 0.005 1.1E-07 53.4 2.8 55 4-59 493-547 (605)
91 KOG4846|consensus 29.7 1.3E+02 0.0029 26.4 5.2 26 113-138 439-464 (538)
92 cd03746 SOCS_WSB1_SWIP1 SOCS ( 27.7 82 0.0018 17.9 2.6 36 149-184 3-38 (40)
93 cd03745 SOCS_WSB2_SWIP2 SOCS ( 22.8 1E+02 0.0022 17.4 2.3 35 149-183 3-37 (39)
94 PF11315 Med30: Mediator compl 22.0 3.4E+02 0.0075 20.2 5.8 41 115-155 11-60 (150)
No 1
>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.96 E-value=1.2e-28 Score=197.87 Aligned_cols=151 Identities=34% Similarity=0.549 Sum_probs=137.4
Q ss_pred CCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhh--
Q psy12692 37 ILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSL-- 112 (187)
Q Consensus 37 l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-- 112 (187)
....+.+++++++.++.+++|+ +|.|.+++.+||++||++||.|++++++++++.++...+.+++++|..++....
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 4556899999999999999999 999999999999999999999999999999999875567888999987776542
Q ss_pred -hhcChHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHH
Q psy12692 113 -GLLGVPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGK 144 (187)
Q Consensus 113 -~~~~~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~ 144 (187)
...++.++++.+++++.+|++|++|. +.||++
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 23456678889999999999999999 899999
Q ss_pred HHHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcCCC
Q psy12692 145 LMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAKRK 187 (187)
Q Consensus 145 Lll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~~~ 187 (187)
||+++|++|+++.+++|++||+++.|.+|+++|+.||+.++++
T Consensus 199 LLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Eml~~~~~ 241 (241)
T cd07069 199 LLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKRA 241 (241)
T ss_pred HHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHHHhcccC
Confidence 9999999999999999999999999999999999999999985
No 2
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=99.96 E-value=4e-28 Score=193.89 Aligned_cols=143 Identities=19% Similarity=0.335 Sum_probs=136.0
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
..+++++.++.++.+++|+ +|+|.+++.+||++|||+||.|++++++++|+.+. .+++.|++|..+++......|+
T Consensus 40 ~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~--~~~l~~~~~~~~~~~~~~~~~~ 117 (231)
T cd06937 40 WDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPE--QDTMTFSDGLTLNRTQMHNAGF 117 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC--CCeEEecCCceecHHHHhhcCh
Confidence 4678999999999999999 99999999999999999999999999999999885 6889999999999988888899
Q ss_pred HHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHhCh
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSILP 150 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~lp 150 (187)
+++.+.+.+++.+|++|++|. +.||++||+++|
T Consensus 118 ~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~Lp 197 (231)
T cd06937 118 GPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKIT 197 (231)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhH
Confidence 999999999999999999999 899999999999
Q ss_pred hhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhc
Q psy12692 151 ELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHA 184 (187)
Q Consensus 151 ~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~ 184 (187)
++|+++.+++|+++++|+.|.+|+++|+.||+++
T Consensus 198 ~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~ 231 (231)
T cd06937 198 DLRSISAKGAERVITLKMEIPGPMPPLISEMLEN 231 (231)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhcC
Confidence 9999999999999999999999999999999963
No 3
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=99.96 E-value=3.6e-28 Score=194.64 Aligned_cols=143 Identities=13% Similarity=0.245 Sum_probs=134.7
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
.++++++..+.+..+++|| +|+|.+++.+||++|||+||.|++++++|+|+.+. ++++.|++|..+++.+ ...|+
T Consensus 43 ~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~--~~~l~f~~~~~~~r~~-~~~~~ 119 (238)
T cd07348 43 IQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPE--EGKLIFCNGVVLHRTQ-CVRGF 119 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCC--CCeEEeeCCeeecHHH-HHhhH
Confidence 5789999999999999999 99999999999999999999999999999999986 6889999999998876 46788
Q ss_pred HHHHHHHHHHHHHHhccCCCc------------------------------------------------cchHHHHHHhC
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN------------------------------------------------CDKFGKLMSIL 149 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~------------------------------------------------~~r~~~Lll~l 149 (187)
+++++.+++++.+|++|++|. +.||+|||+++
T Consensus 120 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl~L 199 (238)
T cd07348 120 GDWIDSILEFSQSLHRMNLDVSAFSCLAALVIITDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKL 199 (238)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHHHH
Confidence 899999999999999999998 67899999999
Q ss_pred hhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcC
Q psy12692 150 PELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185 (187)
Q Consensus 150 p~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~ 185 (187)
|++|+++.+++|++|++|+.|.+|+++|+.||+++.
T Consensus 200 p~LRsl~~~~~e~lf~~kl~~~~~~~pLl~e~~~~~ 235 (238)
T cd07348 200 PELRTLCTQGLQRIFYLKLEDLVPPPPIVDKIFMDT 235 (238)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHhcc
Confidence 999999999999999999999999999999999763
No 4
>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=99.95 E-value=1e-27 Score=192.11 Aligned_cols=144 Identities=16% Similarity=0.237 Sum_probs=133.3
Q ss_pred CHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcC
Q psy12692 39 NRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLG 116 (187)
Q Consensus 39 ~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (187)
..++++++..+.+..+++|+ +|+|.+++.+||++|||++|.|++++++++|+.+. ++++.|++|..+++.+.. .+
T Consensus 43 ~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~--~~~l~~~~g~~~~~~~~~-~~ 119 (239)
T cd07072 43 KVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPE--DTKLTFCNGVVLHKQQCQ-RS 119 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCC--CCeEEeeCCeeecHHHHH-hh
Confidence 35668899999999999999 99999999999999999999999999999999986 688999999998887643 37
Q ss_pred hHHHHHHHHHHHHHHhccCCCc------------------------------------------------cchHHHHHHh
Q psy12692 117 VPTLRDRFTQVTHKLSELKFPN------------------------------------------------CDKFGKLMSI 148 (187)
Q Consensus 117 ~~~~~~~l~~~~~~l~~L~ld~------------------------------------------------~~r~~~Lll~ 148 (187)
++++++.+++++.+|++|++|. +.||+|||++
T Consensus 120 ~~~~~~~i~ef~~~l~~L~ld~~E~a~LkAivLf~dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kLLl~ 199 (239)
T cd07072 120 FGDWLHAILEFSKSLHAMDIDISAFACLCALTLITERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGK 199 (239)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHH
Confidence 8888999999999999999998 5789999999
Q ss_pred ChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcC
Q psy12692 149 LPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185 (187)
Q Consensus 149 lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~ 185 (187)
+|++|+++.+++|++|++|+.|.+|+++|+.||+.+.
T Consensus 200 Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em~~~~ 236 (239)
T cd07072 200 LPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMFVAS 236 (239)
T ss_pred hHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHHHhcc
Confidence 9999999999999999999999999999999999864
No 5
>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=99.95 E-value=1.5e-27 Score=191.02 Aligned_cols=143 Identities=14% Similarity=0.248 Sum_probs=134.0
Q ss_pred CHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcC
Q psy12692 39 NRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLG 116 (187)
Q Consensus 39 ~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (187)
..++++++..+.++.+++|+ +|+|.+++.+||++|||++|.|++++++++|+.+. ++++.|++|..+++.+ ...|
T Consensus 42 ~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~--~~~l~~~~g~~~~~~~-~~~~ 118 (238)
T cd07071 42 HIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPV--EGKLIFCNGVVLHRLQ-CVRG 118 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCC--CCceEeeCCceechhh-hhhc
Confidence 35789999999999999999 99999999999999999999999999999999886 6889999999988766 4668
Q ss_pred hHHHHHHHHHHHHHHhccCCCc------------------------------------------------cchHHHHHHh
Q psy12692 117 VPTLRDRFTQVTHKLSELKFPN------------------------------------------------CDKFGKLMSI 148 (187)
Q Consensus 117 ~~~~~~~l~~~~~~l~~L~ld~------------------------------------------------~~r~~~Lll~ 148 (187)
++++++.+.+++.+|++|++|. +.||+|||++
T Consensus 119 ~~~~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl~ 198 (238)
T cd07071 119 FGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVTERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGK 198 (238)
T ss_pred HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHH
Confidence 8899999999999999999998 6789999999
Q ss_pred ChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhc
Q psy12692 149 LPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHA 184 (187)
Q Consensus 149 lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~ 184 (187)
+|++|+++++++|+++++++.|.+|+++|+.||+.+
T Consensus 199 Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~~~ 234 (238)
T cd07071 199 LPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFLD 234 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHh
Confidence 999999999999999999999999999999999975
No 6
>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=99.95 E-value=2e-27 Score=190.51 Aligned_cols=146 Identities=30% Similarity=0.500 Sum_probs=132.4
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhh-hcC
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLG-LLG 116 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 116 (187)
.+.+++++++.++..++|+ .|.|.+++.+||++||+++|.|+++++.|+|+.+....+.+.+.+|..+..+... ..|
T Consensus 40 ~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~~ 119 (237)
T cd07070 40 FGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAAQAG 119 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHHHHHh
Confidence 4789999999999999999 9999999999999999999999999999999998766788999999888766532 333
Q ss_pred h--HHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHH
Q psy12692 117 V--PTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMS 147 (187)
Q Consensus 117 ~--~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll 147 (187)
. ..++..+++++.+|++|++|+ +.||++||+
T Consensus 120 ~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~kLLl 199 (237)
T cd07070 120 SLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLL 199 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHH
Confidence 2 355566799999999999998 899999999
Q ss_pred hChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcC
Q psy12692 148 ILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185 (187)
Q Consensus 148 ~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~ 185 (187)
++|++|+++.+++|+++++++.|.+|+++|+.||+.++
T Consensus 200 ~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~eml~~~ 237 (237)
T cd07070 200 RLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAK 237 (237)
T ss_pred HhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999875
No 7
>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=99.95 E-value=1.7e-26 Score=185.36 Aligned_cols=141 Identities=16% Similarity=0.195 Sum_probs=130.0
Q ss_pred HHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcChH
Q psy12692 41 THVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVP 118 (187)
Q Consensus 41 ~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (187)
+.+++++++.+..+++|| +|+|.+++.+||++||++||.|+++++++||+++......+.|++|..++++.....++.
T Consensus 31 ~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~~ 110 (247)
T cd07076 31 STLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMTLPCMY 110 (247)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHHhhhhHH
Confidence 668999999999999999 999999999999999999999999999999999864334578999999998888888888
Q ss_pred HHHHHHHHHHHHHhccCCCc---------------------------------------------------cchHHHHHH
Q psy12692 119 TLRDRFTQVTHKLSELKFPN---------------------------------------------------CDKFGKLMS 147 (187)
Q Consensus 119 ~~~~~l~~~~~~l~~L~ld~---------------------------------------------------~~r~~~Lll 147 (187)
+++..+++++.+|++|++|. +.||++|++
T Consensus 111 ~~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~RF~kLLl 190 (247)
T cd07076 111 DQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTK 190 (247)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhHHHHHHH
Confidence 88889999999999999998 239999999
Q ss_pred hChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHh
Q psy12692 148 ILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLH 183 (187)
Q Consensus 148 ~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~ 183 (187)
+||.+|+++.+.+| ||++++|+.|+..++.||+.
T Consensus 191 lLp~Lr~i~~~~~e--f~~~~~~~~~~~~~~~~ml~ 224 (247)
T cd07076 191 LLDSMHEVVENLLN--FCFQTFLDKTMSIEFPEMLA 224 (247)
T ss_pred HHHHHHHHHHHHHH--HHHHHhcccchhhhhHHHHH
Confidence 99999999999999 88999999999999999985
No 8
>cd06944 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors. The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not
Probab=99.95 E-value=1.2e-26 Score=186.09 Aligned_cols=149 Identities=41% Similarity=0.668 Sum_probs=136.4
Q ss_pred CCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhh
Q psy12692 37 ILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGL 114 (187)
Q Consensus 37 l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (187)
....+.+++++++.+..+++|+ .|.|.+++.+||++||+++|.|+++++.++|++++...+.+.+.+|..++.+....
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 4456889999999999999999 89999999999999999999999999999999987556889999998887776432
Q ss_pred ---cChHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHH
Q psy12692 115 ---LGVPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGK 144 (187)
Q Consensus 115 ---~~~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~ 144 (187)
.++.++++.+++++.+|++|++|+ +.||++
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 345678889999999999999998 899999
Q ss_pred HHHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcC
Q psy12692 145 LMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185 (187)
Q Consensus 145 Lll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~ 185 (187)
|++++|++|++|.+++|++|++++.|.+|+++|+.||++++
T Consensus 197 LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~eml~~~ 237 (237)
T cd06944 197 LLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHAK 237 (237)
T ss_pred HHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHHHcCC
Confidence 99999999999999999999999999999999999999875
No 9
>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as
Probab=99.95 E-value=1.5e-26 Score=185.72 Aligned_cols=145 Identities=16% Similarity=0.254 Sum_probs=134.2
Q ss_pred CCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhc
Q psy12692 38 LNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLL 115 (187)
Q Consensus 38 ~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (187)
....+++++..+.+..+++|+ +|+|.+++.+||++||+++|.|++++++|+|+.+. .+.+.|++|..+++.+ ...
T Consensus 41 ~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~--~~~l~~~~~~~~~~~~-~~~ 117 (239)
T cd06945 41 QQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPV--DGKLVFCNGLVLHRLQ-CVR 117 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC--CCceEeeCCceecHHH-HHH
Confidence 345778999999999999999 99999999999999999999999999999999986 6889999999988876 355
Q ss_pred ChHHHHHHHHHHHHHHhccCCCc-------------------------------------------------cchHHHHH
Q psy12692 116 GVPTLRDRFTQVTHKLSELKFPN-------------------------------------------------CDKFGKLM 146 (187)
Q Consensus 116 ~~~~~~~~l~~~~~~l~~L~ld~-------------------------------------------------~~r~~~Ll 146 (187)
|++++++.+++++.+|++|++|+ +.||+|||
T Consensus 118 ~~~~~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLL 197 (239)
T cd06945 118 GFGEWLDSILAFSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLL 197 (239)
T ss_pred hHHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHH
Confidence 78889999999999999999998 47999999
Q ss_pred HhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcC
Q psy12692 147 SILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185 (187)
Q Consensus 147 l~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~ 185 (187)
+++|++|+++.+++|++++++++|.+|+++|+.||+...
T Consensus 198 l~Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~~~~ 236 (239)
T cd06945 198 LKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRFLDT 236 (239)
T ss_pred HHhHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHHHhc
Confidence 999999999999999999999999999999999999764
No 10
>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=99.95 E-value=5.4e-27 Score=186.18 Aligned_cols=146 Identities=18% Similarity=0.235 Sum_probs=121.0
Q ss_pred CCCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCc--------EEeeCCc
Q psy12692 36 GILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDE--------TTLHNGQ 105 (187)
Q Consensus 36 ~l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~--------~~~~~~~ 105 (187)
.+...+.+++++++.++..++|+ +|+|.++|.+||++|||++|.|+|++++|||+++++.... +.+ +|.
T Consensus 17 ~~~~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~-~~~ 95 (222)
T cd07349 17 CLCTPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILL-EGQ 95 (222)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHh-ccc
Confidence 46788999999999999999999 9999999999999999999999999999999988742210 112 222
Q ss_pred ccchhh--hhhcC-hHHHHHHHHHHHHHHhccCCCc--------------------------------------------
Q psy12692 106 KFDLLS--LGLLG-VPTLRDRFTQVTHKLSELKFPN-------------------------------------------- 138 (187)
Q Consensus 106 ~~~~~~--~~~~~-~~~~~~~l~~~~~~l~~L~ld~-------------------------------------------- 138 (187)
...... ....+ ....++.+++++.+|++|++|.
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~ 175 (222)
T cd07349 96 SSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLH 175 (222)
T ss_pred ccccccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHC
Confidence 221111 11112 2245567899999999999998
Q ss_pred ---cchHHHHHHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHH
Q psy12692 139 ---CDKFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEML 182 (187)
Q Consensus 139 ---~~r~~~Lll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml 182 (187)
+.||+||++++|++|+++.+++|++||++++|.+||++++.||+
T Consensus 176 p~~~~r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~i~~Ll~eml 222 (222)
T cd07349 176 PQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML 222 (222)
T ss_pred CCcccHHHHHHHHhHHHhcCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence 89999999999999999999999999999999999999999996
No 11
>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=99.94 E-value=8.4e-26 Score=180.94 Aligned_cols=144 Identities=22% Similarity=0.449 Sum_probs=133.4
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhh-hcC
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLG-LLG 116 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 116 (187)
...+++++++.++.+++|+ .|+|.+++.+||++|||++|.|+++++.++|+.+. ++.+.+++|..++.+... ..+
T Consensus 34 ~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~--~~~~~~~~~~~~~~~~~~~~~~ 111 (235)
T cd06949 34 MMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEH--PGKLLFAPDLLLDRNQGSCVEG 111 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCC--CCeEEeeCCceecHHHhhhccc
Confidence 3668999999999999999 99999999999999999999999999999999986 678899999888877654 667
Q ss_pred hHHHHHHHHHHHHHHhccCCCc-------------------------------------------------------cch
Q psy12692 117 VPTLRDRFTQVTHKLSELKFPN-------------------------------------------------------CDK 141 (187)
Q Consensus 117 ~~~~~~~l~~~~~~l~~L~ld~-------------------------------------------------------~~r 141 (187)
+.++.+.+++++.+|++|++|+ +.|
T Consensus 112 ~~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~~~~R 191 (235)
T cd06949 112 MVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQQSRR 191 (235)
T ss_pred HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccH
Confidence 8888899999999999999998 569
Q ss_pred HHHHHHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcC
Q psy12692 142 FGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185 (187)
Q Consensus 142 ~~~Lll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~ 185 (187)
|++||+++|++|+++++++|+++++++.|.+|+++|+.||+++.
T Consensus 192 f~~LLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~~ 235 (235)
T cd06949 192 LAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235 (235)
T ss_pred HHHHHHhchHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999863
No 12
>cd07073 NR_LBD_AR Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator. The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell funct
Probab=99.93 E-value=2.7e-25 Score=178.80 Aligned_cols=144 Identities=15% Similarity=0.242 Sum_probs=129.1
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
.+++++++++.++.+++|+ +|+|.+++.+||++||++||.|++++++|||+++....+.+.+++|..++.......++
T Consensus 30 ~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~~~~~~~ 109 (246)
T cd07073 30 LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRM 109 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhhhccccH
Confidence 4569999999999999999 99999999999999999999999999999999986445678999998888777667777
Q ss_pred HHHHHHHHHHHHHHhccCCCc---------------------------------------------------cchHHHHH
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN---------------------------------------------------CDKFGKLM 146 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~---------------------------------------------------~~r~~~Ll 146 (187)
.+.+..+++++.+|++|++|. +.||++||
T Consensus 110 ~~~~~~l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~Rf~kLL 189 (246)
T cd07073 110 YSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLT 189 (246)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHHHHHH
Confidence 788888899999999999998 46999999
Q ss_pred HhChhhHhhhHHHHHHHHHHhhcCCC-----ChhhHHHHHHhcC
Q psy12692 147 SILPELHEIASRGEEHLYHKHCNGGA-----PTQTLLMEMLHAK 185 (187)
Q Consensus 147 l~lp~lr~ls~~~~e~l~~~~~~g~~-----~~~~ll~eml~~~ 185 (187)
+++|++|+++++. .+++.+++|.. ++++++.||+..+
T Consensus 190 l~Lp~LRsi~~~~--~~~~~~l~~~~~~~~~~~~pll~ei~~~~ 231 (246)
T cd07073 190 KLLDSVQPIAREL--HQFTFDLLIKSHMVSVDFPEMMAEIISVQ 231 (246)
T ss_pred HHHHHHHHHHHHH--HHHHHHHhCccccCccCccHHHHHHHHhc
Confidence 9999999999998 77888888775 6899999999854
No 13
>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=99.93 E-value=1.6e-25 Score=180.15 Aligned_cols=141 Identities=15% Similarity=0.219 Sum_probs=133.3
Q ss_pred CHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcC
Q psy12692 39 NRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLG 116 (187)
Q Consensus 39 ~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (187)
-..+++++.++.+..+++|| +|+|.+++.+||++|||+||.|++++++|+++.+. .+.+.+++|..++++.....|
T Consensus 53 ~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 130 (243)
T cd06935 53 AFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPE--SETLTLSGEMAVTREQLKNGG 130 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcC--CCeEEeeCCeEeeHHHHHhcC
Confidence 35788999999999999999 99999999999999999999999999999998775 678999999999999888899
Q ss_pred hHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHhC
Q psy12692 117 VPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSIL 149 (187)
Q Consensus 117 ~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~l 149 (187)
++++++.+.+++.+|++|++|+ +.||+|||+++
T Consensus 131 ~~~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~L 210 (243)
T cd06935 131 LGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKV 210 (243)
T ss_pred hHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHH
Confidence 9999999999999999999999 78999999999
Q ss_pred hhhHhhhHHHHHHHHHHhhcCCCCh-hhHHHHH
Q psy12692 150 PELHEIASRGEEHLYHKHCNGGAPT-QTLLMEM 181 (187)
Q Consensus 150 p~lr~ls~~~~e~l~~~~~~g~~~~-~~ll~em 181 (187)
|++|+++.+++|++++.|+.|+.|+ ++|+.||
T Consensus 211 ~~LR~i~~~~~e~l~~~k~~~~~~~~~~L~~Em 243 (243)
T cd06935 211 TDLRMIGACHASRFLHMKVECPTELFPPLFLEV 243 (243)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCChhhhcC
Confidence 9999999999999999999999996 9999987
No 14
>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=99.93 E-value=9e-25 Score=175.78 Aligned_cols=145 Identities=14% Similarity=0.263 Sum_probs=131.2
Q ss_pred HHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcChH
Q psy12692 41 THVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVP 118 (187)
Q Consensus 41 ~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (187)
+++++++++.++.+++|+ +|+|.+++.+||++|||+||.|++++++|||+++......+.|++|..++++..+..+++
T Consensus 31 ~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 110 (246)
T cd06947 31 SSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQSAMY 110 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHHhhhccHH
Confidence 479999999999999999 999999999999999999999999999999999875444578889999888887788888
Q ss_pred HHHHHHHHHHHHHhccCCCc---------------------------------------------------cchHHHHHH
Q psy12692 119 TLRDRFTQVTHKLSELKFPN---------------------------------------------------CDKFGKLMS 147 (187)
Q Consensus 119 ~~~~~l~~~~~~l~~L~ld~---------------------------------------------------~~r~~~Lll 147 (187)
+++..+++++.+|++|++|. +.||++|++
T Consensus 111 ~~~~~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~Rf~kLLl 190 (246)
T cd06947 111 SLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQRFYQLTK 190 (246)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHH
Confidence 88888999999999999998 689999999
Q ss_pred hChhhHhhhHHHHHHHHHHhh---cCCCChhhHHHHHHhcC
Q psy12692 148 ILPELHEIASRGEEHLYHKHC---NGGAPTQTLLMEMLHAK 185 (187)
Q Consensus 148 ~lp~lr~ls~~~~e~l~~~~~---~g~~~~~~ll~eml~~~ 185 (187)
++|.+|+++.+++|+++.+.. .+.|++++|+.||+.+.
T Consensus 191 lLp~Lr~i~~~~~e~~~~~~~~~~~~~v~~~~ll~ei~~~~ 231 (246)
T cd06947 191 LLDSMHDLVKNLLQFCFYTFIQSHALSVEFPEMLVEIISDQ 231 (246)
T ss_pred hhhhHHHHHHHHHHHHHHHHhhcCCCccccHHHHHHHHHcc
Confidence 999999999999999998744 34589999999999864
No 15
>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.
Probab=99.93 E-value=2e-25 Score=178.23 Aligned_cols=143 Identities=16% Similarity=0.210 Sum_probs=117.2
Q ss_pred CCCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCc--------
Q psy12692 36 GILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQ-------- 105 (187)
Q Consensus 36 ~l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~-------- 105 (187)
.+...+++|+++++.++..++|+ +|.|.+++.+||++||++||.|+|++++|||+++.. ....+.++.
T Consensus 17 ~l~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~--~~~~~~~~~~~~~l~~~ 94 (232)
T cd07350 17 TLKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFE--TVETSEPSMLQRILTTR 94 (232)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCc--cccccchhHHHHHHhcc
Confidence 57888999999999999999999 999999999999999999999999999999998863 221122111
Q ss_pred -cc------------chhhhhhcCh---HHHHHHHHHHHHHHhccCCCc-------------------------------
Q psy12692 106 -KF------------DLLSLGLLGV---PTLRDRFTQVTHKLSELKFPN------------------------------- 138 (187)
Q Consensus 106 -~~------------~~~~~~~~~~---~~~~~~l~~~~~~l~~L~ld~------------------------------- 138 (187)
.. ........+. ...+..+++++.+|++|++|.
T Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~ 174 (232)
T cd07350 95 PPPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWE 174 (232)
T ss_pred cccccccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHH
Confidence 00 0000011111 134577999999999999998
Q ss_pred ----------------cchHHHHHHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHH
Q psy12692 139 ----------------CDKFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLME 180 (187)
Q Consensus 139 ----------------~~r~~~Lll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~e 180 (187)
+.||+|||+++|++|+++.+.+|++||++++|.+||++++.|
T Consensus 175 ~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll~E 232 (232)
T cd07350 175 AQQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDMLLE 232 (232)
T ss_pred HHHHHHHHHHhhCCChhhHHHHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHhcC
Confidence 679999999999999999999999999999999999999865
No 16
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=99.93 E-value=3.3e-25 Score=176.09 Aligned_cols=145 Identities=16% Similarity=0.198 Sum_probs=119.8
Q ss_pred CCCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCC--------cEEeeCCc
Q psy12692 36 GILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPD--------ETTLHNGQ 105 (187)
Q Consensus 36 ~l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~--------~~~~~~~~ 105 (187)
.+...+.+++++++.++.+++|+ +|+|.+++.+||++|||++|.|+|++++|+++.++.... ......+.
T Consensus 17 ~~~~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~ 96 (222)
T cd06951 17 QLCAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEM 96 (222)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhcccc
Confidence 67889999999999999999999 999999999999999999999999999999998873210 11223333
Q ss_pred ccchhhh----hhcC-hHHHHHHHHHHHHHHhccCCCc------------------------------------------
Q psy12692 106 KFDLLSL----GLLG-VPTLRDRFTQVTHKLSELKFPN------------------------------------------ 138 (187)
Q Consensus 106 ~~~~~~~----~~~~-~~~~~~~l~~~~~~l~~L~ld~------------------------------------------ 138 (187)
....... ...+ ....++.+++++.+|++|++|.
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl~~~~Ve~lQe~~~~aL~~yi~~~ 176 (222)
T cd06951 97 HWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLLCPHYIEALQKEAQQALNEHTMMT 176 (222)
T ss_pred ccccccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCccCHHHHHHHHHHHHHHHHHHHHhh
Confidence 3222111 0111 1235678999999999999998
Q ss_pred ----cchHHHHHHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHH
Q psy12692 139 ----CDKFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLME 180 (187)
Q Consensus 139 ----~~r~~~Lll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~e 180 (187)
+.||+|||+++|++|+++.+++|++||++++|.+|+++++.|
T Consensus 177 ~p~~~~Rf~kLLl~Lp~LRsl~~~~~e~lff~~~~g~~~i~~ll~~ 222 (222)
T cd06951 177 RPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLLQ 222 (222)
T ss_pred CCCcccHHHHHHHHhHHhhcCCHHHHHHHhCccccCCCcHHHHhcC
Confidence 789999999999999999999999999999999999999864
No 17
>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=99.92 E-value=1.8e-24 Score=173.79 Aligned_cols=143 Identities=13% Similarity=0.191 Sum_probs=128.6
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
.+++++++++.++.+++|| +|+|.+++.+||++||++||.|+++++++||+.+....+.+.|++|..+++++....|+
T Consensus 30 ~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~ 109 (248)
T cd07075 30 LSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMHQSAM 109 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHHhhccH
Confidence 4889999999999999999 99999999999999999999999999999999987544568899999999888778888
Q ss_pred HHHHHHHHHHHHHHhccCCCc---------------------------------------------------cchHHHHH
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN---------------------------------------------------CDKFGKLM 146 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~---------------------------------------------------~~r~~~Ll 146 (187)
+++++.+++++.+|++|++|. +.||++|+
T Consensus 110 ~~~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~~RF~~LL 189 (248)
T cd07075 110 YELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSWQRFYQLT 189 (248)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccchhHHHHHH
Confidence 898899999999999999999 48999999
Q ss_pred HhChhhHhhhHHHHHHHHHHhh-cCCCChhhHHHHHHhc
Q psy12692 147 SILPELHEIASRGEEHLYHKHC-NGGAPTQTLLMEMLHA 184 (187)
Q Consensus 147 l~lp~lr~ls~~~~e~l~~~~~-~g~~~~~~ll~eml~~ 184 (187)
+++|.+|+++++++|++||.-. .+.+|+ .+.||+..
T Consensus 190 llLp~Lr~i~~k~iE~lff~~~~~~~~~~--~~~~~~~~ 226 (248)
T cd07075 190 KLLDSMHDLVSDLLEFCFYTFRESQALKV--EFPAMLVE 226 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccccceee--ehHHHHHH
Confidence 9999999999999999988544 477776 67777754
No 18
>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=99.92 E-value=3.8e-24 Score=171.50 Aligned_cols=148 Identities=25% Similarity=0.374 Sum_probs=126.7
Q ss_pred CCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhh-hh
Q psy12692 38 LNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSL-GL 114 (187)
Q Consensus 38 ~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 114 (187)
...+++++.+++.+...++|+ .|.|.+++.+||++|||++|.|+++++.|+|+++.. .+.+.+.+|..+..... ..
T Consensus 30 ~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~-~~~~~~~~g~~~~~~~~~~~ 108 (236)
T cd06948 30 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLH-VAPLLAAAGLHASPMSADRV 108 (236)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHccccc-chhhhhccccccCccchhhH
Confidence 345889999999999999999 999999999999999999999999999999999863 34455666776553322 11
Q ss_pred cChHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHH
Q psy12692 115 LGVPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMS 147 (187)
Q Consensus 115 ~~~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll 147 (187)
..+.+.+..+++++.+|++|++|. +.||++|++
T Consensus 109 ~~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl 188 (236)
T cd06948 109 VAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLL 188 (236)
T ss_pred hHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHH
Confidence 122344456789999999999998 799999999
Q ss_pred hChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcCC
Q psy12692 148 ILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAKR 186 (187)
Q Consensus 148 ~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~~ 186 (187)
++|++|+++.+++|+++++++.|.+|+++++.||+.++-
T Consensus 189 ~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~~~ 227 (236)
T cd06948 189 RLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGS 227 (236)
T ss_pred HHHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhCCC
Confidence 999999999999999999999999999999999998763
No 19
>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=99.91 E-value=2.1e-23 Score=165.72 Aligned_cols=143 Identities=22% Similarity=0.387 Sum_probs=132.8
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
...++++.++.+..+++|+ .|.|..++.+||+.|||++|.|+++++.|+|+.+. .+.+.+++|...++......++
T Consensus 29 ~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~--~~~~~~~~~~~~~~~~~~~~~~ 106 (221)
T cd06946 29 LTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPF--NGELVFAEDFILDEELAREAGL 106 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCC--CCceeecCCeEEcHHHHhhcCH
Confidence 4678999999999999999 89999999999999999999999999999999986 4678888887777777777788
Q ss_pred HHHHHHHHHHHHHHhccCCCc------------------------------------------------cchHHHHHHhC
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN------------------------------------------------CDKFGKLMSIL 149 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~------------------------------------------------~~r~~~Lll~l 149 (187)
.++.+.+.+++.+|++|++|+ +.||++|++.+
T Consensus 107 ~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~LL~~l 186 (221)
T cd06946 107 LELYSACLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTL 186 (221)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHhhc
Confidence 888888999999999999998 78999999999
Q ss_pred hhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhc
Q psy12692 150 PELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHA 184 (187)
Q Consensus 150 p~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~ 184 (187)
|.+|+++.+++|++++.++.|.+|+++|+.||+++
T Consensus 187 ~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~ 221 (221)
T cd06946 187 PLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLEA 221 (221)
T ss_pred hhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHhcC
Confidence 99999999999999999999999999999999975
No 20
>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=99.91 E-value=2e-23 Score=162.83 Aligned_cols=142 Identities=14% Similarity=0.255 Sum_probs=127.3
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
..++.++.++.++.+++|| +|+|.+++.+||++|||++|.|++++++++++.+. ++++.+++|..++.++....+.
T Consensus 4 w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 81 (195)
T cd06941 4 WQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSK--SGSITFDDGISISRQQLDIIYD 81 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCC--CCeEEecCCeEeeHHHHHhccc
Confidence 5788999999999999999 99999999999999999999999999999877664 5789999999998877654444
Q ss_pred HHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHhCh
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSILP 150 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~lp 150 (187)
.++.+.+++++.+|++|++|+ +.||++|++++|
T Consensus 82 ~~~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp 161 (195)
T cd06941 82 SDFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIP 161 (195)
T ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhH
Confidence 578889999999999999998 789999999999
Q ss_pred hhHhhhHHHHHHHH-HHhhcCCCChhhHHHHHHh
Q psy12692 151 ELHEIASRGEEHLY-HKHCNGGAPTQTLLMEMLH 183 (187)
Q Consensus 151 ~lr~ls~~~~e~l~-~~~~~g~~~~~~ll~eml~ 183 (187)
++|+++.+++|++. ++...+.+++++|+.||++
T Consensus 162 ~Lr~l~~~~~e~l~~~~~~~~~~~~p~L~~E~~~ 195 (195)
T cd06941 162 ELRSIGAKHQMHLDWYRVNWPLLRLPPLFAEIYD 195 (195)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHhcC
Confidence 99999999999998 5555677899999999974
No 21
>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=99.91 E-value=5.4e-23 Score=163.35 Aligned_cols=145 Identities=23% Similarity=0.473 Sum_probs=134.1
Q ss_pred CCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhc
Q psy12692 38 LNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLL 115 (187)
Q Consensus 38 ~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (187)
.-.+++++.+.+.+...++|+ .|.|..++.+||++|+|++|.|+++++.|+++.+. .+.+.+.+|..++++.....
T Consensus 27 ~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~--~~~~~~~~~~~~~~~~~~~~ 104 (221)
T cd07068 27 SLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPH--PGKLVFAPDLLLDREQARVE 104 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCC--CCeEEeCCCceECHHHHhhc
Confidence 345789999999999999999 89999999999999999999999999999999876 55788888888887776677
Q ss_pred ChHHHHHHHHHHHHHHhccCCCc------------------------------------------------cchHHHHHH
Q psy12692 116 GVPTLRDRFTQVTHKLSELKFPN------------------------------------------------CDKFGKLMS 147 (187)
Q Consensus 116 ~~~~~~~~l~~~~~~l~~L~ld~------------------------------------------------~~r~~~Lll 147 (187)
++.++.+.+.+++.+|++|++|. +.||++|++
T Consensus 105 ~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~LL~ 184 (221)
T cd07068 105 GLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLL 184 (221)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHH
Confidence 88888888999999999999998 799999999
Q ss_pred hChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhc
Q psy12692 148 ILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHA 184 (187)
Q Consensus 148 ~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~ 184 (187)
.+|.+|+++.+++|+++++++.|.+|+++|+.||+++
T Consensus 185 ~l~~Lr~~~~~~~e~l~~~k~~~~~~~~~Ll~e~l~~ 221 (221)
T cd07068 185 LLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLEA 221 (221)
T ss_pred hccHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHhcC
Confidence 9999999999999999999999999999999999975
No 22
>KOG4218|consensus
Probab=99.90 E-value=1.6e-22 Score=164.67 Aligned_cols=146 Identities=31% Similarity=0.488 Sum_probs=137.5
Q ss_pred HHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcC--
Q psy12692 41 THVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLG-- 116 (187)
Q Consensus 41 ~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-- 116 (187)
.-.|+.+++.+..+|.|+ ...|.++.++|||+||++||+|++|+++++|.+++..++++.+++|..++....+..+
T Consensus 277 gl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgkegsi~lvtGqeV~~~~vA~qags 356 (475)
T KOG4218|consen 277 GLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKEGSIKLVTGQEVPVGLVALQAGS 356 (475)
T ss_pred hhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcccceEEecCCcccchhHhhhhhh
Confidence 336899999999999999 6679999999999999999999999999999999999999999999999998877665
Q ss_pred -hHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHh
Q psy12692 117 -VPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSI 148 (187)
Q Consensus 117 -~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~ 148 (187)
+..++..+++++-++++||+|+ ..+|+++++.
T Consensus 357 ~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LFsld~kfLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF~qllL~ 436 (475)
T KOG4218|consen 357 LLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALFSLDMKFLENFELVRRLQEDSNAALLDYTSCCYPNWEQKFPQLLLV 436 (475)
T ss_pred HHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHHH
Confidence 6788999999999999999998 5899999999
Q ss_pred ChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcCC
Q psy12692 149 LPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAKR 186 (187)
Q Consensus 149 lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~~ 186 (187)
|+++|+++.++.|+++.+++.+++|-++++.||+.+++
T Consensus 437 L~eiRa~smqa~eyly~khl~~~~p~nnllieml~Ak~ 474 (475)
T KOG4218|consen 437 LEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLTAKP 474 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhhccC
Confidence 99999999999999999999999999999999999876
No 23
>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=99.89 E-value=4.4e-22 Score=154.61 Aligned_cols=129 Identities=19% Similarity=0.295 Sum_probs=119.1
Q ss_pred CCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhc
Q psy12692 38 LNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLL 115 (187)
Q Consensus 38 ~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (187)
.-.+++.+..+..++.+++|+ +|+|.+++.+||++|||+||.|++++++++++.+. .+++.+++|..++++.....
T Consensus 12 ~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~--~~~l~~~~~~~~~~~~~~~~ 89 (189)
T cd06940 12 EIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAK--ERSVTFLSGQKYSVDDLHSM 89 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccC--CCeEEecCCcEEcHHHHHHc
Confidence 346778899999999999999 99999999999999999999999999999998765 67889999999998888888
Q ss_pred ChHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHh
Q psy12692 116 GVPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSI 148 (187)
Q Consensus 116 ~~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~ 148 (187)
|++++++.+++++.+|++|++|+ +.||++|+++
T Consensus 90 ~~~~~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL~~ 169 (189)
T cd06940 90 GAGDLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLK 169 (189)
T ss_pred CcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHH
Confidence 88999999999999999999998 7899999999
Q ss_pred ChhhHhhhHHHHHHHHHHhh
Q psy12692 149 LPELHEIASRGEEHLYHKHC 168 (187)
Q Consensus 149 lp~lr~ls~~~~e~l~~~~~ 168 (187)
+|++|+++++++|++++.|.
T Consensus 170 L~~LR~l~~~~~e~l~~~~~ 189 (189)
T cd06940 170 LPDLRTLNNLHSEKLLAFKV 189 (189)
T ss_pred HHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999863
No 24
>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=99.88 E-value=8.2e-22 Score=158.38 Aligned_cols=140 Identities=16% Similarity=0.209 Sum_probs=122.8
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
..+..+.....+..+++|| +|+|.+++.+||++|||+||.|++++++++++.+. .+.+++ +|..++++.....|+
T Consensus 50 ~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~--~~~~~~-~~~~~~~~~~~~~~~ 126 (241)
T cd06939 50 WQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPS--NNTVLF-DGKYAPIDLFKSLGC 126 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCC--CCEEEE-CCccccHHHHHHcCc
Confidence 4556777788899999999 99999999999999999999999999999777653 456666 455567777777888
Q ss_pred HHHHHHHHHHHHHHhccCCCc----------------------------------------------cchHHHHHHhChh
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN----------------------------------------------CDKFGKLMSILPE 151 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~----------------------------------------------~~r~~~Lll~lp~ 151 (187)
++++..+++++.++++|++|+ +.||++||+++|+
T Consensus 127 ~~~~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~rf~kLL~~Lp~ 206 (241)
T cd06939 127 DDLISAVFDFAKSLCELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNHGDDTILTKLLAKMPT 206 (241)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHH
Confidence 899999999999999999998 6899999999999
Q ss_pred hHhhhHHHHHHHHHHhhcCC----CChhhHHHHHH
Q psy12692 152 LHEIASRGEEHLYHKHCNGG----APTQTLLMEML 182 (187)
Q Consensus 152 lr~ls~~~~e~l~~~~~~g~----~~~~~ll~eml 182 (187)
+|+++++++|+++++|...+ .++++|+.||+
T Consensus 207 LR~l~~~~~e~l~~~k~~~p~~~~~~~ppL~~Elf 241 (241)
T cd06939 207 LRALCSLHMEKLQKFKQSYPDIVHLEFPPLYKELF 241 (241)
T ss_pred HHHHHHHHHHHHHHHhccCCCcccCCCCcHHHhhC
Confidence 99999999999999999854 46899999984
No 25
>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=99.88 E-value=1.3e-21 Score=156.45 Aligned_cols=142 Identities=18% Similarity=0.299 Sum_probs=131.3
Q ss_pred CHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcC
Q psy12692 39 NRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLG 116 (187)
Q Consensus 39 ~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (187)
...+++++....++.+++|+ .|.|..++.+||++|||++|.|+++++.++++.+. .+.+.|++|..+++++....|
T Consensus 40 ~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~--~~~~~f~~g~~~~~~~~~~~~ 117 (231)
T cd06938 40 RFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAK--TDSIVFANNQPYTRDSYRKAG 117 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCC--CCeEEeeCCEEecHHHHhhcC
Confidence 34778999999999999999 99999999999999999999999999999987664 688999999999988877788
Q ss_pred hHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHhC
Q psy12692 117 VPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSIL 149 (187)
Q Consensus 117 ~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~l 149 (187)
++++.+.+++++.+|++|++|+ +.||++||+++
T Consensus 118 ~~~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf~d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~~L 197 (231)
T cd06938 118 MGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFSDRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSIL 197 (231)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHHHH
Confidence 8888999999999999999998 67999999999
Q ss_pred hhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHh
Q psy12692 150 PELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLH 183 (187)
Q Consensus 150 p~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~ 183 (187)
|++|++++.++|++++.++. ..++++|+.|+++
T Consensus 198 ~~Lr~l~~~~~e~~~~~k~~-~~~~~pl~~Ei~d 230 (231)
T cd06938 198 TELRTLGNQNSEMCFSLKLK-NRKLPPFLAEIWD 230 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHhC
Confidence 99999999999999999999 6699999999986
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=99.88 E-value=1.3e-21 Score=156.79 Aligned_cols=141 Identities=15% Similarity=0.255 Sum_probs=127.7
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
..++++.....+..+++|+ +|.|..++.+||++|||++|.|++++++++++.+. .+.+.+++|..++++.....|+
T Consensus 45 ~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~--~~~~~~~~g~~~~~~~~~~~~~ 122 (236)
T cd06954 45 FAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPE--SEAITFLKDFPYSRDDFARAGL 122 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCC--CCeEEeeCCccccHHHHHHhcC
Confidence 4678899999999999999 99999999999999999999999999999998764 6888999999888877655554
Q ss_pred -HHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHhC
Q psy12692 118 -PTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSIL 149 (187)
Q Consensus 118 -~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~l 149 (187)
.++.+.+.+++.++++|++|+ +.||+++++++
T Consensus 123 ~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~L 202 (236)
T cd06954 123 QVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKL 202 (236)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence 478899999999999999998 56999999999
Q ss_pred hhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHh
Q psy12692 150 PELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLH 183 (187)
Q Consensus 150 p~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~ 183 (187)
|++|+++++++|++++.++.+ .++++|+.||++
T Consensus 203 ~~Lr~l~~~~~e~l~~~k~~~-~~~~~L~~El~~ 235 (236)
T cd06954 203 VSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWD 235 (236)
T ss_pred HHHHHHHHHHHHHHHHHHhcC-CCCCcHHHHHhc
Confidence 999999999999999999865 699999999986
No 27
>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=99.88 E-value=7.4e-22 Score=155.26 Aligned_cols=133 Identities=22% Similarity=0.312 Sum_probs=112.1
Q ss_pred CCCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEee-CCcccchhhh
Q psy12692 36 GILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLH-NGQKFDLLSL 112 (187)
Q Consensus 36 ~l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 112 (187)
.+.+.+.+|+.+++.++.+++|+ .|.|.+++.+||++|||++|.|++++++++++.+. .+..++. .|...+...
T Consensus 24 ~~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~--~~~~ll~~~~~~~~~~~- 100 (206)
T cd06950 24 YEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPL--DSCPLLAVPGLSPDNTE- 100 (206)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC--CcceeecCCcccccccc-
Confidence 45678999999999999999999 99999999999999999999999999999999886 3444443 343332222
Q ss_pred hhcChHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHH
Q psy12692 113 GLLGVPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKL 145 (187)
Q Consensus 113 ~~~~~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~L 145 (187)
....+.+.+..+++++.+|++|++|. +.||++|
T Consensus 101 ~~~~~~~~~~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf~kL 180 (206)
T cd06950 101 AERTFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKL 180 (206)
T ss_pred hhhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHH
Confidence 11234455677999999999999998 7999999
Q ss_pred HHhChhhHhhhHHHHHHHHHHhhcCC
Q psy12692 146 MSILPELHEIASRGEEHLYHKHCNGG 171 (187)
Q Consensus 146 ll~lp~lr~ls~~~~e~l~~~~~~g~ 171 (187)
++++|++|+++.+++|++||++++|.
T Consensus 181 Ll~Lp~lr~ls~~~~e~l~~~~~~g~ 206 (206)
T cd06950 181 LLLLPSLRFISSSTIEELFFKKTIGN 206 (206)
T ss_pred HHHHHHHHhhhHHHHHHHhccCcCCC
Confidence 99999999999999999999999984
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=99.87 E-value=3.6e-21 Score=156.11 Aligned_cols=140 Identities=14% Similarity=0.215 Sum_probs=118.1
Q ss_pred HHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcc-cchhhhhhcC-
Q psy12692 41 THVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQK-FDLLSLGLLG- 116 (187)
Q Consensus 41 ~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~- 116 (187)
..........+..+++|| +|+|.+++.+||++|||++|.|+++++++++.. .+.+++++|.. ++++.....+
T Consensus 66 ~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~----~~~~~~~~~~~~~~~~~~~~~~~ 141 (259)
T cd06932 66 QRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYN----KDGLLFPEGNGYVTREFLESLRK 141 (259)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcC----CCCeEEeCCCEEeeHHHHHHhcc
Confidence 334455566788999999 999999999999999999999999999997742 35577776644 5666655554
Q ss_pred -hHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHh
Q psy12692 117 -VPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSI 148 (187)
Q Consensus 117 -~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~ 148 (187)
.+++.+.+++++.+|++|++|+ +.||++||++
T Consensus 142 ~~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~kLLl~ 221 (259)
T cd06932 142 PFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQK 221 (259)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHHHHHH
Confidence 4688888999999999999998 8899999999
Q ss_pred ChhhHhhhHHHHHHHHHHh-hcCCCChhhHHHHHHhc
Q psy12692 149 LPELHEIASRGEEHLYHKH-CNGGAPTQTLLMEMLHA 184 (187)
Q Consensus 149 lp~lr~ls~~~~e~l~~~~-~~g~~~~~~ll~eml~~ 184 (187)
+|++|+++.+++|++++.+ ..|.+++++|+.||+..
T Consensus 222 L~~LRsl~~~~~e~l~~~k~~~~~~~~~pLl~Ei~~~ 258 (259)
T cd06932 222 MVDLRQLVTDHVQMVQQIKKTETDASLPPLLQEIYKD 258 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHccCCCCCCCcHHHHHhhc
Confidence 9999999999999999777 56789999999999863
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=99.86 E-value=1.2e-20 Score=151.34 Aligned_cols=142 Identities=14% Similarity=0.240 Sum_probs=115.9
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCC-cEEeeC-Ccccchhhhhhc
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPD-ETTLHN-GQKFDLLSLGLL 115 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~~~ 115 (187)
..+++++..+.+..+++|| +|+|.+++.+||++|||+||.|+++++++++ .+. .+ ...+.+ +..++.......
T Consensus 39 ~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~~~ 115 (238)
T cd06933 39 LPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQS-FSL--DDMSWTCGSPDFKYKVSDVTKA 115 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHh-cCc--CCCeeEecCCceeecHHHHHHc
Confidence 3678999999999999999 9999999999999999999999999998874 433 33 333332 344555555555
Q ss_pred ChH-HHHHHHHHHHHHHhccCCCc-------------------------------------------------cchHHHH
Q psy12692 116 GVP-TLRDRFTQVTHKLSELKFPN-------------------------------------------------CDKFGKL 145 (187)
Q Consensus 116 ~~~-~~~~~l~~~~~~l~~L~ld~-------------------------------------------------~~r~~~L 145 (187)
|.. ++++.+.+++.+|++|++|. +.||+||
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 544 77889999999999999998 3469999
Q ss_pred HHhChhhHhhhHHHHHHHHHHhhcC--CCChhhHHHHHHhc
Q psy12692 146 MSILPELHEIASRGEEHLYHKHCNG--GAPTQTLLMEMLHA 184 (187)
Q Consensus 146 ll~lp~lr~ls~~~~e~l~~~~~~g--~~~~~~ll~eml~~ 184 (187)
|+++|++|+++.++.|.+...++.+ ..++++|+.|+++.
T Consensus 196 Ll~L~~LRsi~~~h~~~~~~~~~~~~~~~~~~pL~~Ei~~~ 236 (238)
T cd06933 196 IQKLADLRSLNEEHSKQYRSLSFQPEHSMKLTPLVLEVFGN 236 (238)
T ss_pred HHHhHHHHhhhHHHHHHHHHHHhccCCCCCCCcHHHHHhcc
Confidence 9999999999999999987766554 34689999999975
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=99.85 E-value=1.8e-20 Score=149.27 Aligned_cols=137 Identities=15% Similarity=0.243 Sum_probs=115.2
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
..+++++..+.++.+++|| +|+|.+++.+||++|||+||.|+++++.++++.+ .....+.+|..+...+....|+
T Consensus 37 ~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~---~~~~~~~~~~~~~~~~~~~~g~ 113 (226)
T cd06934 37 LPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNE---ETGTWECGPLTYCIEDAARAGF 113 (226)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhcc---cCCeEeeCCEeecHHHHHHccc
Confidence 4588999999999999999 9999999999999999999999999999988765 2334556676776666666777
Q ss_pred HH-HHHHHHHHHHHHhccCCCc-----------------------------------------------cch--HHHHHH
Q psy12692 118 PT-LRDRFTQVTHKLSELKFPN-----------------------------------------------CDK--FGKLMS 147 (187)
Q Consensus 118 ~~-~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r--~~~Lll 147 (187)
+. +.+.+++++.+|++|++|+ +.| |++||+
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 74 6688999999999999998 234 999999
Q ss_pred hChhhHhhhHHHHHHHHHHhhcCCCCh-hhHHHHH
Q psy12692 148 ILPELHEIASRGEEHLYHKHCNGGAPT-QTLLMEM 181 (187)
Q Consensus 148 ~lp~lr~ls~~~~e~l~~~~~~g~~~~-~~ll~em 181 (187)
++|++|+++..+++.+.. +.+..|+ ++|+.|+
T Consensus 194 ~L~~LRsl~~~~~~~~~~--~~~~~~~~~pl~~Ei 226 (226)
T cd06934 194 CLTELRTINEEYTKQILH--IQDIQPMATPLMQEI 226 (226)
T ss_pred HhHHHhcchHHHHHHHHH--HhccCCCCCchhhcC
Confidence 999999999999998864 4555675 8999885
No 31
>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=99.85 E-value=1e-20 Score=150.28 Aligned_cols=147 Identities=15% Similarity=0.241 Sum_probs=118.7
Q ss_pred CCCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccc----h
Q psy12692 36 GILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFD----L 109 (187)
Q Consensus 36 ~l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~----~ 109 (187)
...+...+++...+.+...++|+ .|.|..++.+||++||+++|.|++++++++++.+.+. ..+....+..+. .
T Consensus 19 ~~~~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 97 (222)
T cd06952 19 SYLNVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSL-PTILAAIINHLQTSIQQ 97 (222)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCc-hHHhhhhhhhhhhhHhc
Confidence 44567889999999999999999 8999999999999999999999999999988865432 222222111111 1
Q ss_pred hhh---hhcChHHHHHHHHHHHHHHhccCCCc-----------------------------------------------c
Q psy12692 110 LSL---GLLGVPTLRDRFTQVTHKLSELKFPN-----------------------------------------------C 139 (187)
Q Consensus 110 ~~~---~~~~~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~ 139 (187)
+.. +..++.+.+..+++++.+|++|++|. +
T Consensus 98 ~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~ 177 (222)
T cd06952 98 DKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDE 177 (222)
T ss_pred CCCchhhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 111 11223344556789999999999998 8
Q ss_pred chHHHHHHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHh
Q psy12692 140 DKFGKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLH 183 (187)
Q Consensus 140 ~r~~~Lll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~ 183 (187)
.||+++++.||++|+++.+++|++++.+++|.+|+++++..+|-
T Consensus 178 ~R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~~~~ll~~~~~ 221 (222)
T cd06952 178 YRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSVIPYILR 221 (222)
T ss_pred cHHHHHHHHhHHhhhcCHHHHHHHhcccccCCCcHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999874
No 32
>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=99.83 E-value=9.6e-20 Score=143.21 Aligned_cols=127 Identities=25% Similarity=0.449 Sum_probs=115.0
Q ss_pred CHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcC
Q psy12692 39 NRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLG 116 (187)
Q Consensus 39 ~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (187)
..++++++.++.+...++|+ .|.|.+++.+||+.||+++|.|+++++.|+++.+. ++.+.+++|..+.++.....+
T Consensus 31 ~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~--~~~~~~~~~~~~~~~~~~~~~ 108 (207)
T cd06943 31 PVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAV--KDGILLATGLHLHRNSAHQAG 108 (207)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCC--CCeeEecCCceeccchhhhcc
Confidence 45789999999999999999 89999999999999999999999999999999885 577889999888777666667
Q ss_pred hHHHHHH-HHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHh
Q psy12692 117 VPTLRDR-FTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSI 148 (187)
Q Consensus 117 ~~~~~~~-l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~ 148 (187)
...+... +++++.+|++|++|+ +.||++|+++
T Consensus 109 ~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~ 188 (207)
T cd06943 109 VGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLR 188 (207)
T ss_pred chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHH
Confidence 7777665 578999999999998 7899999999
Q ss_pred ChhhHhhhHHHHHHHHHHh
Q psy12692 149 LPELHEIASRGEEHLYHKH 167 (187)
Q Consensus 149 lp~lr~ls~~~~e~l~~~~ 167 (187)
+|++|+++.+++|+++|++
T Consensus 189 L~~lr~l~~~~~e~l~~~~ 207 (207)
T cd06943 189 LPALRSIGLKCLEHLFFFK 207 (207)
T ss_pred HHHHHhHhHHHHHHHhhcC
Confidence 9999999999999999864
No 33
>KOG4215|consensus
Probab=99.82 E-value=7.5e-20 Score=150.19 Aligned_cols=148 Identities=24% Similarity=0.338 Sum_probs=136.7
Q ss_pred CCCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhh
Q psy12692 36 GILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLG 113 (187)
Q Consensus 36 ~l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 113 (187)
...+...|++...+.+..+++|+ ++.|+++|++||++||++.-.++++++.++||+.. .+.+++.++..+.+...+
T Consensus 152 ~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l--~~v~ll~N~~v~~~~~~~ 229 (432)
T KOG4215|consen 152 KIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHL--KDVCLLNNTYVLHRHAPD 229 (432)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhccccc--cceEEecCceeeccCCCC
Confidence 45667789999999999999999 99999999999999999999999999999999985 688888998888888877
Q ss_pred hcChHHHHHH-HHHHHHHHhccCCCc--------------------------------------------------cchH
Q psy12692 114 LLGVPTLRDR-FTQVTHKLSELKFPN--------------------------------------------------CDKF 142 (187)
Q Consensus 114 ~~~~~~~~~~-l~~~~~~l~~L~ld~--------------------------------------------------~~r~ 142 (187)
.+.+.....+ +.|++..||+|++|+ +.||
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 7777777764 699999999999998 8999
Q ss_pred HHHHHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhcC
Q psy12692 143 GKLMSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHAK 185 (187)
Q Consensus 143 ~~Lll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~~ 185 (187)
++||+.+|.|.+++...+|...+.+++|.+.+++++.||+..+
T Consensus 310 g~LLLllPsLqsIt~qliE~iqlaklFGla~vDsll~e~~l~~ 352 (432)
T KOG4215|consen 310 GNLLLLLPSLQSITQQLIEQIQLAKLFGLAKVDSLLQEFLLGG 352 (432)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhcCC
Confidence 9999999999999999999999999999999999999999874
No 34
>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=99.81 E-value=7.1e-19 Score=139.71 Aligned_cols=143 Identities=24% Similarity=0.328 Sum_probs=127.8
Q ss_pred CCCCHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhh
Q psy12692 36 GILNRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLG 113 (187)
Q Consensus 36 ~l~~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 113 (187)
.+.+...+++...+.+...++|+ .|.|..++.+||++|++++|.++++++.|+++.+. .+.+.+++|..++.....
T Consensus 30 ~~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~--~~~l~~~~g~~~~~~~~~ 107 (222)
T cd06931 30 KIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPY--KDILLLGNDLIIPRHCPE 107 (222)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCC--CCeeeeCCCccccccccc
Confidence 45678889999999999999999 89999999999999999999999999999999764 678888999877765433
Q ss_pred hcChHHHHHH-HHHHHHHHhccCCCc-----------------------------------------------cchHHHH
Q psy12692 114 LLGVPTLRDR-FTQVTHKLSELKFPN-----------------------------------------------CDKFGKL 145 (187)
Q Consensus 114 ~~~~~~~~~~-l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~L 145 (187)
.+...++.+ +++++.++++|++|+ +.||++|
T Consensus 108 -~~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~L 186 (222)
T cd06931 108 -PEISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGEL 186 (222)
T ss_pred -chHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHH
Confidence 455555555 578999999999998 8999999
Q ss_pred HHhChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHH
Q psy12692 146 MSILPELHEIASRGEEHLYHKHCNGGAPTQTLLMEM 181 (187)
Q Consensus 146 ll~lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~em 181 (187)
++.+|.+|.++.+.+|++++.++.|.+|+++|+.||
T Consensus 187 L~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e~ 222 (222)
T cd06931 187 LLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222 (222)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhhC
Confidence 999999999999999999999999999999999986
No 35
>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=99.80 E-value=7.5e-20 Score=145.34 Aligned_cols=104 Identities=23% Similarity=0.299 Sum_probs=95.6
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHH
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDML 82 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~ 82 (187)
+++.++.+++++++|.+||+|||||++||||++|+.+...|+++|+++..+|.+|+...+|+
T Consensus 118 ~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~------------------ 179 (221)
T cd06936 118 PMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPE------------------ 179 (221)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCC------------------
Confidence 45677889999999999999999999999999999999999999999999999999777766
Q ss_pred HHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcChHHHHHHHHHHHHHHhccCCCccchHHHHHHhChhhHhhhHHHHHH
Q psy12692 83 VLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVPTLRDRFTQVTHKLSELKFPNCDKFGKLMSILPELHEIASRGEEH 162 (187)
Q Consensus 83 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~~r~~~Lll~lp~lr~ls~~~~e~ 162 (187)
.+.||++||+++|++|+++.+++|+
T Consensus 180 -------------------------------------------------------~p~rf~~LL~~L~~LR~l~~~~~e~ 204 (221)
T cd06936 180 -------------------------------------------------------DPQHFACLLGRLTELRTLNHHHAEM 204 (221)
T ss_pred -------------------------------------------------------chhHHHHHHHHhHHHHHHHHHHHHH
Confidence 3789999999999999999999999
Q ss_pred HHHHhhcCCCChhhHHHH
Q psy12692 163 LYHKHCNGGAPTQTLLME 180 (187)
Q Consensus 163 l~~~~~~g~~~~~~ll~e 180 (187)
++++|... .++++|+.|
T Consensus 205 l~~~k~~~-~~~~pl~~e 221 (221)
T cd06936 205 LMSWKVND-HKFTPLLCE 221 (221)
T ss_pred HHHHHccC-CCCCccccC
Confidence 99999975 488998865
No 36
>cd07074 NR_LBD_PR Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor. The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues
Probab=99.79 E-value=2e-18 Score=138.76 Aligned_cols=122 Identities=15% Similarity=0.247 Sum_probs=107.1
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
.+.+++++++.+..+++|+ .|+|.+++.+||++||+++|.|+++++++||+++...++.+.|++|..++++.....++
T Consensus 30 ~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~~~~~~ 109 (248)
T cd07074 30 LTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSF 109 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhhhhccH
Confidence 4779999999999999999 99999999999999999999999999999999987545567899999988887666677
Q ss_pred HHHHHHHHHHHHHHhccCCCc----cchHHHHHHhCh-hhHhhhHH-HHHHH
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN----CDKFGKLMSILP-ELHEIASR-GEEHL 163 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~----~~r~~~Lll~lp-~lr~ls~~-~~e~l 163 (187)
.+.+..+++++.+|+++++|. |+|+ |+++.| +.++++++ .+|++
T Consensus 110 ~~~~~~m~e~~~~~~~L~ld~~Ey~cLKA--IvLfnp~d~~gL~~q~~Ve~l 159 (248)
T cd07074 110 YSLCLTMWQIPQEFVKLQVSQEEFLCMKA--LLLLNTIPLEGLRSQTQFDEM 159 (248)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHH--HHHCCCCcCCCCCCHHHHHHH
Confidence 787888899999999999999 8988 999999 78888753 44444
No 37
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.74 E-value=2.9e-17 Score=125.43 Aligned_cols=121 Identities=18% Similarity=0.258 Sum_probs=108.6
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcCh
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGV 117 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (187)
..++++..++.++.+++|+ .|.|..++.+||+.|++++|.|++++++++++.+. .+.+.+.+|...+.+.....+.
T Consensus 4 ~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 81 (174)
T cd06929 4 FDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPE--KNSLTFGDGKGNSRDVLLNGGF 81 (174)
T ss_pred HHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhccc--CCeEEecCCceecHHHHHHccc
Confidence 5789999999999999999 99999999999999999999999999999977653 6788899998877777677778
Q ss_pred HHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHHHhCh
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLMSILP 150 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Lll~lp 150 (187)
.++.+.+.+++.+|++|++|. +.||++|++.+|
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 889999999999999999998 778888989999
Q ss_pred hhHhhhHHHHHH
Q psy12692 151 ELHEIASRGEEH 162 (187)
Q Consensus 151 ~lr~ls~~~~e~ 162 (187)
.+|+++..++|.
T Consensus 162 ~lr~l~~~~~e~ 173 (174)
T cd06929 162 ELRTLNELHAEL 173 (174)
T ss_pred HHHHHHHHHHhc
Confidence 999888888774
No 38
>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=99.71 E-value=5.7e-17 Score=128.15 Aligned_cols=125 Identities=16% Similarity=0.200 Sum_probs=98.3
Q ss_pred CHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCC---cEEeeCCcccchhhhh
Q psy12692 39 NRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPD---ETTLHNGQKFDLLSLG 113 (187)
Q Consensus 39 ~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~ 113 (187)
-.+.+++++++.++.+++|+ .|.|.+++.+||++|||++|.|+++++.|+|+.+..... ......|......+ .
T Consensus 28 ~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~~~-~ 106 (213)
T cd06953 28 LFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELER-F 106 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhHHH-H
Confidence 45779999999999999999 999999999999999999999999999999998742110 00111111111111 1
Q ss_pred hcChHHHHHHHHHHHHHHhccCCCc-----------------------------------------------cchHHHHH
Q psy12692 114 LLGVPTLRDRFTQVTHKLSELKFPN-----------------------------------------------CDKFGKLM 146 (187)
Q Consensus 114 ~~~~~~~~~~l~~~~~~l~~L~ld~-----------------------------------------------~~r~~~Ll 146 (187)
..+..++++.+++++.+|++|++|+ +.||++||
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 2234577888999999999999998 78999999
Q ss_pred HhChhhHhhhHHHHHHHH
Q psy12692 147 SILPELHEIASRGEEHLY 164 (187)
Q Consensus 147 l~lp~lr~ls~~~~e~l~ 164 (187)
+++|++|+++.+.+|+-.
T Consensus 187 ~~L~~Lr~l~~~~~e~~~ 204 (213)
T cd06953 187 SCLPEIRAAAGKLLHSKL 204 (213)
T ss_pred HHhHHHHHHHHHHHHHHH
Confidence 999999999998887653
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=99.69 E-value=3.6e-16 Score=118.20 Aligned_cols=116 Identities=24% Similarity=0.392 Sum_probs=101.4
Q ss_pred HHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcChH
Q psy12692 41 THVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVP 118 (187)
Q Consensus 41 ~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (187)
+.++++.++.+...++|+ .|.|..++.+||++|+|++|.+++++..|+++.+....+.+.+++|..++.+.....+..
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 568999999999999999 899999999999999999999999999999999876667888999988887765555667
Q ss_pred HHHHHHHHHHHHHhccCCCc----cchHHHHHHhChhhHhhhHH
Q psy12692 119 TLRDRFTQVTHKLSELKFPN----CDKFGKLMSILPELHEIASR 158 (187)
Q Consensus 119 ~~~~~l~~~~~~l~~L~ld~----~~r~~~Lll~lp~lr~ls~~ 158 (187)
+..+.+.+++.+|++|++|. +.++ |+++-|+.+++++.
T Consensus 82 ~~~~~~~~~~~~l~~L~l~~~E~~lLka--i~l~~p~~~~l~~~ 123 (165)
T cd06930 82 ELVQRLQELLSKLRSLQLDPKEYACLKA--IVLFNPDLPGLKNQ 123 (165)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHH--HHHcCCCCCCCcCH
Confidence 78889999999999999998 5665 88888888777653
No 40
>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.67 E-value=1.1e-15 Score=118.77 Aligned_cols=122 Identities=20% Similarity=0.287 Sum_probs=104.1
Q ss_pred HHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhh-hhcC
Q psy12692 40 RTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSL-GLLG 116 (187)
Q Consensus 40 ~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 116 (187)
+.++++..++.+..+++|+ +|+|.+++.+||++|||++|.|++++++++++.+. ...+.+|..+..+.. ...+
T Consensus 4 w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~----~~~~~~g~~~~~~~~~~~~~ 79 (191)
T cd06942 4 WGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNE----GTVLCDFRPVEFASLLSQLL 79 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcC----CeEEeCCccccHHHHHHhcc
Confidence 5788999999999999999 99999999999999999999999999988766542 455666777665543 2334
Q ss_pred hHHHHHHHHHHHHHHhccCCCc-------------------------------------------------cchHHHHHH
Q psy12692 117 VPTLRDRFTQVTHKLSELKFPN-------------------------------------------------CDKFGKLMS 147 (187)
Q Consensus 117 ~~~~~~~l~~~~~~l~~L~ld~-------------------------------------------------~~r~~~Lll 147 (187)
..++++.+.+++.+|++|++|+ +.||++|++
T Consensus 80 ~~~~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~kLL~ 159 (191)
T cd06942 80 HGKLIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFD 159 (191)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHH
Confidence 5678888999999999999998 678999999
Q ss_pred hChhhHhhhHHHHHHHHH
Q psy12692 148 ILPELHEIASRGEEHLYH 165 (187)
Q Consensus 148 ~lp~lr~ls~~~~e~l~~ 165 (187)
.+|++|+++..+.+.+..
T Consensus 160 ~l~~Lr~~~~~~~~~l~~ 177 (191)
T cd06942 160 ILNRLRNMNKEHQNILAD 177 (191)
T ss_pred HHHHHHHHHHHHHHHHHc
Confidence 999999999999998775
No 41
>KOG4217|consensus
Probab=99.60 E-value=1.3e-14 Score=122.76 Aligned_cols=137 Identities=15% Similarity=0.258 Sum_probs=124.7
Q ss_pred HhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcChHHHHH
Q psy12692 45 EGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVPTLRD 122 (187)
Q Consensus 45 ~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 122 (187)
++-.-.+.++..|+ +|+|.+++.+||-.|+++++.|+|++++|+|+-+. ++.+.|++|..+.+ ..+..|++++++
T Consensus 415 ~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~--e~kliFcsG~vlhr-~qC~rgfgewid 491 (605)
T KOG4217|consen 415 DLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPS--EDKLIFCSGLVLHR-LQCLRGFGEWID 491 (605)
T ss_pred HHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCC--CCeEEEecchhhhH-HHHHHHHHHHHH
Confidence 34444578888999 99999999999999999999999999999999986 89999999999988 457888999999
Q ss_pred HHHHHHHHHhccCCCc------------------------------------------------cchHHHHHHhChhhHh
Q psy12692 123 RFTQVTHKLSELKFPN------------------------------------------------CDKFGKLMSILPELHE 154 (187)
Q Consensus 123 ~l~~~~~~l~~L~ld~------------------------------------------------~~r~~~Lll~lp~lr~ 154 (187)
.+.+|+.-++.+.+|- +.++.++|.++|+||.
T Consensus 492 si~~FS~~l~~l~idi~AfacL~aLa~iTErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr~ 571 (605)
T KOG4217|consen 492 SIREFSRSLHSLNIDISAFACLSALALITERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELRT 571 (605)
T ss_pred HHHHHHHHhhhchhhHHHHHHHHHHHhhhhhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHHH
Confidence 9999999999999997 7789999999999999
Q ss_pred hhHHHHHHHHHHhhcCCCChhhHHHHHHhc
Q psy12692 155 IASRGEEHLYHKHCNGGAPTQTLLMEMLHA 184 (187)
Q Consensus 155 ls~~~~e~l~~~~~~g~~~~~~ll~eml~~ 184 (187)
++..+.++.|..+++..+|++.++..|...
T Consensus 572 l~tqgLqrifyLklEdlvp~p~iidklf~d 601 (605)
T KOG4217|consen 572 LCTQGLQRIFYLKLEDLVPPPAIIDKLFLD 601 (605)
T ss_pred HHHHhhhhhhcccHhhccCchhhhhhhhhc
Confidence 999999999999999999999988877643
No 42
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=99.35 E-value=2.1e-11 Score=94.10 Aligned_cols=129 Identities=19% Similarity=0.398 Sum_probs=108.0
Q ss_pred CHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhc-
Q psy12692 39 NRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLL- 115 (187)
Q Consensus 39 ~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 115 (187)
+.+.+++...+.+..+++|+ .|.|..++.+||..|++++|.+++++..++++.. ...+.+.+.+|..++.......
T Consensus 18 ~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~-~~~~~~~~~~~~~~~~~~~~~~~ 96 (203)
T PF00104_consen 18 TFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQ-CNQDQLMFPNGTFIDKDSFDDFI 96 (203)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEH-TTTTEEEETTTEEEEHHHHHHTS
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcc-ccccccccccccccccccccccc
Confidence 45778899999999999999 8899999999999999999999999999999985 4578889999988877665544
Q ss_pred --ChHHHHHHHHHHHHHHhccCCCc---------------------------------------------------cchH
Q psy12692 116 --GVPTLRDRFTQVTHKLSELKFPN---------------------------------------------------CDKF 142 (187)
Q Consensus 116 --~~~~~~~~l~~~~~~l~~L~ld~---------------------------------------------------~~r~ 142 (187)
...+.++.+.+++.+|+++++|. +.|+
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~~~R~ 176 (203)
T PF00104_consen 97 TGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYYNQSKGPEDYAQRF 176 (203)
T ss_dssp TTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTHTTHH
T ss_pred ccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHHhccCCCccHHHHH
Confidence 45677889999999999999998 5788
Q ss_pred HHHHHhChhhHhhhHHHHHHHHHHhh
Q psy12692 143 GKLMSILPELHEIASRGEEHLYHKHC 168 (187)
Q Consensus 143 ~~Lll~lp~lr~ls~~~~e~l~~~~~ 168 (187)
++|+..+|.++.++....|.+++.++
T Consensus 177 ~~ll~ll~~l~~~~~~~~e~~~~~~l 202 (203)
T PF00104_consen 177 GKLLLLLPSLRKISEKHIENMFLSDL 202 (203)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHhh
Confidence 88888888888888888888776554
No 43
>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=99.35 E-value=8e-12 Score=99.32 Aligned_cols=111 Identities=14% Similarity=0.220 Sum_probs=87.5
Q ss_pred CHHHHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCc-ccchhhhhhc
Q psy12692 39 NRTHVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQ-KFDLLSLGLL 115 (187)
Q Consensus 39 ~~~~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 115 (187)
...++++...+.+..+++|+ .|+|.+++.+||+.|||++|.|+++++.++++... +..|. .+........
T Consensus 37 ~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~~-------~~~~~~~~~~~~~~~~ 109 (221)
T cd06936 37 NFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKK-------LPAGHADLLEERIRSS 109 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhccc-------ccCCCchhhHHHHHhc
Confidence 35678999999999999999 99999999999999999999999999999664311 11222 1222222344
Q ss_pred Ch-HHHHHHHHHHHHHHhccCCCc----cchHHHHHHhChhhHhhhHH
Q psy12692 116 GV-PTLRDRFTQVTHKLSELKFPN----CDKFGKLMSILPELHEIASR 158 (187)
Q Consensus 116 ~~-~~~~~~l~~~~~~l~~L~ld~----~~r~~~Lll~lp~lr~ls~~ 158 (187)
++ .++++.+++++.+|++|++|+ ++++ |+++.||..++++.
T Consensus 110 ~~~~e~~~~i~~~~~kl~~L~l~~~E~~lLka--IvL~npd~~gL~~~ 155 (221)
T cd06936 110 GISDEFITPMFNFYKSMGELKMTQEEYALLTA--ITILFPDRPYLKDK 155 (221)
T ss_pred cchHHHHHHHHHHHHHHHHcCCCHHHHHHHHH--HHHhcCCCcCCCCH
Confidence 44 478889999999999999998 7777 99999999888763
No 44
>cd07074 NR_LBD_PR Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor. The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues
Probab=99.33 E-value=6.2e-12 Score=101.28 Aligned_cols=57 Identities=21% Similarity=0.380 Sum_probs=51.9
Q ss_pred ccccccccccccChhhHHHHHHHHHhCC-CCcCCCCHHHHHHhHHHHHHhHhhhhhhc
Q psy12692 5 YPRQSGELELKFDISDYICVKFLLLLNP-DVRGILNRTHVEEGHEQVQKALLDYCITA 61 (187)
Q Consensus 5 ~~~~~~~~~l~ld~~E~~~Lkai~l~~p-d~~~l~~~~~V~~l~~~~l~~Lv~~~~~~ 61 (187)
+++..+++++++|.+||+|||||+|||| |++|+++...|+++|+++..+|.+|+..+
T Consensus 117 ~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~ 174 (248)
T cd07074 117 WQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLR 174 (248)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 3456789999999999999999999999 89999999999999999999999997433
No 45
>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=99.26 E-value=4.7e-12 Score=101.29 Aligned_cols=80 Identities=19% Similarity=0.199 Sum_probs=66.9
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHHH
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDMLV 83 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~~ 83 (187)
+++++.+++++++|.+||+|||||++|+||++|+.+..+|+++|++++.+|.+|+...+|+.| ..|..++.
T Consensus 124 ~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p---------~rf~kLLl 194 (231)
T cd06937 124 VFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKP---------HMFPKMLM 194 (231)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcc---------cHHHHHHH
Confidence 577889999999999999999999999999999999999999999999999999977777643 23555555
Q ss_pred HHHHHHHhh
Q psy12692 84 LDHMHQRMH 92 (187)
Q Consensus 84 l~~~~~~~~ 92 (187)
.-..-|++.
T Consensus 195 ~Lp~LR~l~ 203 (231)
T cd06937 195 KITDLRSIS 203 (231)
T ss_pred HhHHHHHHH
Confidence 544445443
No 46
>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=99.25 E-value=6.4e-12 Score=99.96 Aligned_cols=78 Identities=17% Similarity=0.153 Sum_probs=64.3
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHHH
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDMLV 83 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~~ 83 (187)
+++++.+++++++|.+||+|||||++||||++|+ +.++|+++|++++.+|.+|+...+|+.+ ..+..++.
T Consensus 120 l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~p~~~---------~Rf~kLLl 189 (222)
T cd06951 120 IQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMTRPLEQ---------LRSARLLL 189 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhhCCCcc---------cHHHHHHH
Confidence 5678889999999999999999999999999999 9999999999999999999977777642 23555555
Q ss_pred HHHHHHHh
Q psy12692 84 LDHMHQRM 91 (187)
Q Consensus 84 l~~~~~~~ 91 (187)
.--.-|++
T Consensus 190 ~Lp~LRsl 197 (222)
T cd06951 190 MLSLLRGI 197 (222)
T ss_pred HhHHhhcC
Confidence 54444443
No 47
>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=99.24 E-value=9.1e-12 Score=96.75 Aligned_cols=63 Identities=17% Similarity=0.161 Sum_probs=58.3
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCc
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQI 65 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l 65 (187)
.+++++.+++++++|.+||+|||||++||||++|+.+..+|+++|++++.+|.+|+...+|+.
T Consensus 97 ~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~ 159 (189)
T cd06940 97 SMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNE 159 (189)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 357788899999999999999999999999999999999999999999999999997777764
No 48
>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=99.23 E-value=1.3e-11 Score=98.65 Aligned_cols=79 Identities=15% Similarity=0.139 Sum_probs=65.4
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHHH
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDMLV 83 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~~ 83 (187)
+++++.+++++++|.+||+|||||+|||||++|+.+.++|+++|++++.+|.+|+...+|+.+ .-+..++.
T Consensus 129 l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~---------~rf~kLLl 199 (232)
T cd07350 129 IKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQ---------ARFAKLNI 199 (232)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHHHHHHHHHHHhhCCChh---------hHHHHHHH
Confidence 457778899999999999999999999999999999999999999999999999977777632 23555555
Q ss_pred HHHHHHHh
Q psy12692 84 LDHMHQRM 91 (187)
Q Consensus 84 l~~~~~~~ 91 (187)
.--.-|++
T Consensus 200 ~Lp~LRsi 207 (232)
T cd07350 200 ALSLLRAI 207 (232)
T ss_pred HhHHHHcc
Confidence 54444544
No 49
>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=99.23 E-value=1.4e-11 Score=99.18 Aligned_cols=79 Identities=32% Similarity=0.495 Sum_probs=66.0
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHHH
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDMLV 83 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~~ 83 (187)
+++++.+++++++|.+||+|||||+|||||++|+.+.++|+++|++++.+|.+|+...+|+. ...+.+++.
T Consensus 131 ~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~---------~~Rf~kLLl 201 (241)
T cd07069 131 AQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQ---------TEKFGQLLL 201 (241)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCc---------hhHHHHHHH
Confidence 45677889999999999999999999999999999999999999999999999997777764 234556665
Q ss_pred HHHHHHHh
Q psy12692 84 LDHMHQRM 91 (187)
Q Consensus 84 l~~~~~~~ 91 (187)
.-..-|++
T Consensus 202 ~Lp~LR~i 209 (241)
T cd07069 202 RLPEIRAI 209 (241)
T ss_pred HhHHHHHh
Confidence 54444444
No 50
>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=99.23 E-value=8.7e-12 Score=99.13 Aligned_cols=80 Identities=23% Similarity=0.259 Sum_probs=65.2
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHHH
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDMLV 83 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~~ 83 (187)
+.+++.+++++++|.+||+|||||++||||++|+.+.++|+++|++++.+|.+|+...+|+.+ ..+..++.
T Consensus 117 l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~~---------~r~~kLLl 187 (222)
T cd07349 117 LQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQ---------GRFARILL 187 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCcc---------cHHHHHHH
Confidence 346677899999999999999999999999999999999999999999999999977777643 23455555
Q ss_pred HHHHHHHhh
Q psy12692 84 LDHMHQRMH 92 (187)
Q Consensus 84 l~~~~~~~~ 92 (187)
.--.-|++.
T Consensus 188 ~Lp~LR~i~ 196 (222)
T cd07349 188 TASTLKSIP 196 (222)
T ss_pred HhHHHhcCC
Confidence 544444443
No 51
>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=99.22 E-value=1.5e-11 Score=99.91 Aligned_cols=62 Identities=24% Similarity=0.241 Sum_probs=58.1
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCc
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQI 65 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l 65 (187)
+|+++.+++++++|++||+|||||++|+||++|+.+..+|+++|++++.+|.+|+...+|+.
T Consensus 150 ~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~ 211 (259)
T cd06932 150 KFEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDS 211 (259)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCc
Confidence 57888999999999999999999999999999999999999999999999999997777764
No 52
>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=99.21 E-value=1.4e-11 Score=99.31 Aligned_cols=80 Identities=14% Similarity=0.211 Sum_probs=67.1
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHH
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDML 82 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~ 82 (187)
.+++++.+++++++|.+||+|||||++|+||++|+.+.+.|+++|++++.+|.+|+..++|+.+ ..|..++
T Consensus 137 ~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~---------~rf~kLL 207 (243)
T cd06935 137 AIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVP---------HFWPKLL 207 (243)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCc---------cHHHHHH
Confidence 4678889999999999999999999999999999999999999999999999999976776642 3466666
Q ss_pred HHHHHHHHh
Q psy12692 83 VLDHMHQRM 91 (187)
Q Consensus 83 ~l~~~~~~~ 91 (187)
..-..-|++
T Consensus 208 ~~L~~LR~i 216 (243)
T cd06935 208 MKVTDLRMI 216 (243)
T ss_pred HHHHHHHHH
Confidence 554444544
No 53
>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=99.19 E-value=1.8e-11 Score=97.56 Aligned_cols=61 Identities=16% Similarity=0.298 Sum_probs=56.7
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++++.+++++++|.+||+|||||++|+||++|+.+...|+++|++++.+|.+|+...+|.
T Consensus 121 ~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~ 181 (226)
T cd06934 121 LLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPG 181 (226)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcChHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 4677888999999999999999999999999999999999999999999999999766764
No 54
>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=99.18 E-value=1.8e-11 Score=98.40 Aligned_cols=61 Identities=18% Similarity=0.297 Sum_probs=56.3
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
++++..+++++++|.+||+|||||++||||++|+.+.+.|+++|++++.+|.+|+...+|.
T Consensus 125 l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~ 185 (238)
T cd06933 125 LVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPP 185 (238)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCCCCcchHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 4567788999999999999999999999999999999999999999999999999766663
No 55
>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=99.17 E-value=3.3e-10 Score=84.70 Aligned_cols=111 Identities=21% Similarity=0.267 Sum_probs=84.9
Q ss_pred HHHHhHHHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCc--ccchhhhhhcCh
Q psy12692 42 HVEEGHEQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQ--KFDLLSLGLLGV 117 (187)
Q Consensus 42 ~V~~l~~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~ 117 (187)
.+++...+.+...++|+ .|.|..++.+||+.|++++|.++++++.++++............++. ..+.+.......
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (168)
T cd06157 2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK 81 (168)
T ss_pred cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence 46778888899999999 89999999999999999999999999999999997544433333332 122233333334
Q ss_pred HHHHHHHHHHHHHHhccCCCc----cchHHHHHHhChhhHh
Q psy12692 118 PTLRDRFTQVTHKLSELKFPN----CDKFGKLMSILPELHE 154 (187)
Q Consensus 118 ~~~~~~l~~~~~~l~~L~ld~----~~r~~~Lll~lp~lr~ 154 (187)
+.+.+.+.+++.+|++|++|+ +.++ ++++-|+..+
T Consensus 82 ~~~~~~~~~~~~~~~~L~l~~~E~~~l~a--i~l~~~~~~~ 120 (168)
T cd06157 82 GELIRLLFEFVNPLRALKLDDEEYALLKA--IVLFSPDRKE 120 (168)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHH--HHHhCCCCCC
Confidence 456677899999999999999 5655 7777788763
No 56
>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=99.17 E-value=3.1e-11 Score=97.28 Aligned_cols=61 Identities=21% Similarity=0.239 Sum_probs=56.4
Q ss_pred cccccccccccccChhhHHHHHHHHHhCC-CCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNP-DVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~p-d~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++++.+++++++|.+||+|||||+|||| |++|+++.+.|+++|++++.+|.+|+..++++
T Consensus 116 l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~ 177 (247)
T cd07076 116 MLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGN 177 (247)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 35677899999999999999999999999 99999999999999999999999999766665
No 57
>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=99.16 E-value=4.5e-11 Score=95.96 Aligned_cols=79 Identities=25% Similarity=0.463 Sum_probs=66.1
Q ss_pred ccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHHHH
Q psy12692 5 YPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDMLVL 84 (187)
Q Consensus 5 ~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~~l 84 (187)
.+++.+++++++|.+||+|||||++||||++|+.+...|+++|+++..+|.+|+...+|..+ ..+.+++..
T Consensus 130 ~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~---------~Rf~kLLl~ 200 (237)
T cd07070 130 QELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCG---------DKFQQLLLR 200 (237)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcc---------hHHHHHHHH
Confidence 35677899999999999999999999999999999999999999999999999977777643 345666665
Q ss_pred HHHHHHhh
Q psy12692 85 DHMHQRMH 92 (187)
Q Consensus 85 ~~~~~~~~ 92 (187)
-..-|++.
T Consensus 201 Lp~LRsis 208 (237)
T cd07070 201 LVEVRALS 208 (237)
T ss_pred hHHHHHhh
Confidence 55555543
No 58
>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=99.16 E-value=3.5e-11 Score=94.65 Aligned_cols=78 Identities=24% Similarity=0.382 Sum_probs=64.3
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHHH
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDMLV 83 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~~ 83 (187)
+.+++.+++++++|.+||+|||||++||||++|+.+.++|+++|++++.+|.+|+...++..+ ..+.+++.
T Consensus 112 i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~---------~Rf~kLLl 182 (206)
T cd06950 112 LQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQP---------ARFGKLLL 182 (206)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc---------cHHHHHHH
Confidence 456777899999999999999999999999999999999999999999999999966666532 34556665
Q ss_pred HHHHHHH
Q psy12692 84 LDHMHQR 90 (187)
Q Consensus 84 l~~~~~~ 90 (187)
.-..-|+
T Consensus 183 ~Lp~lr~ 189 (206)
T cd06950 183 LLPSLRF 189 (206)
T ss_pred HHHHHHh
Confidence 5444444
No 59
>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=99.13 E-value=6.1e-11 Score=93.77 Aligned_cols=79 Identities=23% Similarity=0.341 Sum_probs=64.6
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHHH
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDMLV 83 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~~ 83 (187)
+++++.+++++++|.+||+|||||++||||++|+++.++|+++|+++..+|.+|+...++..| ..+.+++.
T Consensus 117 i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p---------~Rf~~LL~ 187 (213)
T cd06953 117 LTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQP---------NRFSDLLS 187 (213)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc---------hHHHHHHH
Confidence 456677899999999999999999999999999999999999999999999999966666643 33555555
Q ss_pred HHHHHHHh
Q psy12692 84 LDHMHQRM 91 (187)
Q Consensus 84 l~~~~~~~ 91 (187)
.-..-|++
T Consensus 188 ~L~~Lr~l 195 (213)
T cd06953 188 CLPEIRAA 195 (213)
T ss_pred HhHHHHHH
Confidence 54444443
No 60
>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=99.12 E-value=6e-11 Score=95.47 Aligned_cols=60 Identities=18% Similarity=0.224 Sum_probs=56.5
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcC
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAY 62 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f 62 (187)
.+|+++.+++++++|++||+|||||++++||++|+.+...|+++|++++.+|.+|+...+
T Consensus 132 ~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~ 191 (241)
T cd06939 132 AVFDFAKSLCELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNH 191 (241)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 468899999999999999999999999999999999999999999999999999996555
No 61
>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=99.12 E-value=6.5e-11 Score=95.07 Aligned_cols=62 Identities=47% Similarity=0.772 Sum_probs=56.6
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCc
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQI 65 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l 65 (187)
+.+++.+++++++|.+||+|||||++||||++|+++.+.|++.|+++..+|.+|+...+++.
T Consensus 129 i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~ 190 (237)
T cd06944 129 AQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQ 190 (237)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCC
Confidence 34667789999999999999999999999999999999999999999999999997677664
No 62
>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=99.11 E-value=1.2e-10 Score=90.76 Aligned_cols=62 Identities=18% Similarity=0.145 Sum_probs=56.8
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCc
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQI 65 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l 65 (187)
+++++.+++++++|++||+|||||++|+||++|+.+...|+++|++++.+|.+|+...+|+.
T Consensus 88 ~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~ 149 (195)
T cd06941 88 LFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAE 149 (195)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCc
Confidence 45677889999999999999999999999999999999999999999999999997667653
No 63
>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=99.10 E-value=1.6e-10 Score=92.59 Aligned_cols=62 Identities=19% Similarity=0.247 Sum_probs=57.5
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCc
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQI 65 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l 65 (187)
+++++.+++++++|.+||+|||||++||||++|+.+...|+++|+++..+|.+|+...+|+.
T Consensus 130 i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~ 191 (236)
T cd06954 130 IFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSD 191 (236)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 46678899999999999999999999999999999999999999999999999997777763
No 64
>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=99.09 E-value=1.5e-10 Score=92.86 Aligned_cols=59 Identities=25% Similarity=0.434 Sum_probs=54.9
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcC-----CCCHHHHHHhHHHHHHhHhhhhhhcC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRG-----ILNRTHVEEGHEQVQKALLDYCITAY 62 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~-----l~~~~~V~~l~~~~l~~Lv~~~~~~f 62 (187)
+++++.+++++++|.+||+|||||++||||++| +.+.++|+++|++++.+|.+|+..++
T Consensus 119 ~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~ 182 (235)
T cd06949 119 LLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRG 182 (235)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 456788899999999999999999999999999 89999999999999999999997666
No 65
>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=99.08 E-value=1.2e-10 Score=93.82 Aligned_cols=61 Identities=21% Similarity=0.217 Sum_probs=54.6
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCC-CcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPD-VRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd-~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++++.+++++++|.+||+|||||+||||| ++|+++.+.|+++|++++.+|.+|+...+++
T Consensus 116 ~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~ 177 (248)
T cd07075 116 MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKAPNN 177 (248)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 456678899999999999999999999997 7999999999999999999999999644443
No 66
>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=99.07 E-value=1.2e-10 Score=94.04 Aligned_cols=58 Identities=21% Similarity=0.196 Sum_probs=53.1
Q ss_pred ccccccccccccChhhHHHHHHHHHhCC-CCcCCCCHHHHHHhHHHHHHhHhhhhhhcC
Q psy12692 5 YPRQSGELELKFDISDYICVKFLLLLNP-DVRGILNRTHVEEGHEQVQKALLDYCITAY 62 (187)
Q Consensus 5 ~~~~~~~~~l~ld~~E~~~Lkai~l~~p-d~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f 62 (187)
++++.+++++++|.+||+|||||+|||| |++|+.+.++|+++|++++.+|.+|+...+
T Consensus 117 ~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~ 175 (246)
T cd07073 117 RHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKR 175 (246)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4567788999999999999999999999 999999999999999999999999995543
No 67
>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=99.07 E-value=1.2e-10 Score=93.97 Aligned_cols=61 Identities=18% Similarity=0.278 Sum_probs=54.9
Q ss_pred cccccccccccccChhhHHHHHHHHHhCC-CCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNP-DVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~p-d~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++++.+++++++|.+||+|||||++||| |++|+.+.+.|+++|++++.+|.+|+..++++
T Consensus 116 ~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~ 177 (246)
T cd06947 116 MRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKN 177 (246)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 34667789999999999999999999999 79999999999999999999999999655543
No 68
>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=99.06 E-value=2.5e-10 Score=91.65 Aligned_cols=79 Identities=18% Similarity=0.254 Sum_probs=63.3
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhc--CCCcchhHHHHHHHHhhHH
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITA--YPQIQVDDQMKLLQHSWSD 80 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~--f~~l~~~DQ~~LL~~~w~e 80 (187)
.+++++.+++++++|.+||+|||||++| ||++|+.+.+.|+++|++++.+|.+|+..+ +|+.| ..|..
T Consensus 125 ~i~ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p---------~rf~k 194 (238)
T cd07348 125 SILEFSQSLHRMNLDVSAFSCLAALVII-TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRP---------NCLSR 194 (238)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccc---------cHHHH
Confidence 3678889999999999999999999999 799999999999999999999999999543 34432 23555
Q ss_pred HHHHHHHHHHh
Q psy12692 81 MLVLDHMHQRM 91 (187)
Q Consensus 81 l~~l~~~~~~~ 91 (187)
+++.-..-|++
T Consensus 195 LLl~Lp~LRsl 205 (238)
T cd07348 195 LLGKLPELRTL 205 (238)
T ss_pred HHHHHHHHHHH
Confidence 55554444443
No 69
>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=99.03 E-value=3.4e-10 Score=90.98 Aligned_cols=61 Identities=26% Similarity=0.328 Sum_probs=56.9
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCC
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYP 63 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~ 63 (187)
.+++++.+++++++|++||+|||||++++||++|+.+.++|+++|++++.+|.+|+..++|
T Consensus 125 ~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p 185 (239)
T cd06945 125 SILAFSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSNYP 185 (239)
T ss_pred HHHHHHHHHHHHhCChHHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3567788999999999999999999999999999999999999999999999999976776
No 70
>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=99.01 E-value=3.2e-10 Score=89.05 Aligned_cols=59 Identities=32% Similarity=0.578 Sum_probs=54.6
Q ss_pred cccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 6 PRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 6 ~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++.+++++++|.+||+|||||++|+||++|+.+.+.|.+.|+++..+|.+|+...++.
T Consensus 119 ~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~ 177 (207)
T cd06943 119 ELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPE 177 (207)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 56778999999999999999999999999999999999999999999999999666665
No 71
>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=99.01 E-value=1.9e-10 Score=92.32 Aligned_cols=59 Identities=20% Similarity=0.309 Sum_probs=54.3
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcC
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAY 62 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f 62 (187)
.+++++.+++++++|.+||+|||||++| ||++|+.+.++|+++|++++.+|.+|+..++
T Consensus 125 ~i~ef~~~l~~L~ld~~E~alLkAIvLf-~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~ 183 (238)
T cd07071 125 SIVEFSSNLQNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQNKIVNCLKDHVTFNN 183 (238)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4678899999999999999999999999 5999999999999999999999999985443
No 72
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.00 E-value=1.2e-09 Score=83.33 Aligned_cols=61 Identities=23% Similarity=0.375 Sum_probs=56.0
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++++.+++++++|.+||+|||||++||||++|+.+...|.+.|+++..+|.+|+...+++
T Consensus 88 ~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~ 148 (174)
T cd06929 88 LFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPD 148 (174)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 4566788999999999999999999999999999999999999999999999999666664
No 73
>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=98.97 E-value=5.2e-10 Score=89.77 Aligned_cols=59 Identities=29% Similarity=0.508 Sum_probs=54.4
Q ss_pred cccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 6 PRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 6 ~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+.+.+++++++|.+||+|||||++||||++|+.+.++|.++|++++.+|.+|+...++.
T Consensus 120 ~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~ 178 (236)
T cd06948 120 EQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPN 178 (236)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 45678999999999999999999999999999999999999999999999999766664
No 74
>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=98.97 E-value=1.8e-09 Score=83.95 Aligned_cols=61 Identities=11% Similarity=0.002 Sum_probs=56.7
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCC--CcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPD--VRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd--~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
++.++.+++++++|++||+||+||++|+|| ++|+.+...|++.|+++..++.+|+...+++
T Consensus 87 ~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~ 149 (191)
T cd06942 87 MLQFANKILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGED 149 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 456788999999999999999999999999 9999999999999999999999999767766
No 75
>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin
Probab=98.95 E-value=7.2e-10 Score=88.06 Aligned_cols=60 Identities=25% Similarity=0.362 Sum_probs=55.8
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYP 63 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~ 63 (187)
+++++.+++++++|.+||+|||||++||||++|+.+.+.|++.|++++.+|.+|+...++
T Consensus 113 ~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~ 172 (221)
T cd07068 113 LLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHG 172 (221)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 466788999999999999999999999999999999999999999999999999966666
No 76
>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-
Probab=98.93 E-value=9.5e-10 Score=87.34 Aligned_cols=60 Identities=23% Similarity=0.266 Sum_probs=55.5
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYP 63 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~ 63 (187)
+++++.+++++++|.+||+|||||++||||++|+.+...|++.|+++..+|.+|+...++
T Consensus 113 ~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~ 172 (221)
T cd06946 113 CLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHP 172 (221)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 456778899999999999999999999999999999999999999999999999966666
No 77
>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=98.92 E-value=1e-09 Score=88.13 Aligned_cols=59 Identities=19% Similarity=0.252 Sum_probs=53.9
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcC
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAY 62 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f 62 (187)
.+++++.+++++++|.+||+|||||++|+ |++|+.+.++|+++|++++.+|.+|+..++
T Consensus 126 ~i~ef~~~l~~L~ld~~E~a~LkAivLf~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~ 184 (239)
T cd07072 126 AILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNA 184 (239)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 35788899999999999999999999995 999999999999999999999999985443
No 78
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=98.91 E-value=1.8e-08 Score=74.91 Aligned_cols=106 Identities=17% Similarity=0.231 Sum_probs=79.9
Q ss_pred HHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhh-h---hcChHHHHH
Q psy12692 49 QVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSL-G---LLGVPTLRD 122 (187)
Q Consensus 49 ~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---~~~~~~~~~ 122 (187)
+.+...++|+ .|.|..++.+||+.|++++|.+++++..++++.... ....+.+|..+..... . .........
T Consensus 3 ~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (163)
T smart00430 3 RDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMK--KSLLLLPDGTFIDNDKVDLLRKLFSPFLDR 80 (163)
T ss_pred hHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc--CCEEEeCCCcccCcchhHHHHHHHHHHHHH
Confidence 3467788898 799999999999999999999999999999999863 3244444444332221 1 122235556
Q ss_pred HHHHHHHHHhccCCCc----cchHHHHHHhChhhHhhhHH
Q psy12692 123 RFTQVTHKLSELKFPN----CDKFGKLMSILPELHEIASR 158 (187)
Q Consensus 123 ~l~~~~~~l~~L~ld~----~~r~~~Lll~lp~lr~ls~~ 158 (187)
.+.+++.++++|++|. +.++ ++++-|+..+++..
T Consensus 81 ~~~~~~~~l~~L~l~~~E~~~l~a--i~l~~~~~~~l~~~ 118 (163)
T smart00430 81 ILQELVKPLRELKLDDEEYALLKA--ILLFNPAGPGLSEE 118 (163)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHH--HHHcChhhhhhChH
Confidence 7899999999999998 5655 77788888887776
No 79
>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=98.91 E-value=2.4e-09 Score=85.05 Aligned_cols=60 Identities=27% Similarity=0.375 Sum_probs=54.5
Q ss_pred cccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCc
Q psy12692 6 PRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQI 65 (187)
Q Consensus 6 ~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l 65 (187)
+++.+++++++|.+||+|||||++|+||++|+.+.+.|+++|++++.+|.+|+...+|..
T Consensus 117 ~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~ 176 (222)
T cd06952 117 EFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPED 176 (222)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 456789999999999999999999999999999999999999999999999996556553
No 80
>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=98.89 E-value=2.9e-09 Score=80.24 Aligned_cols=61 Identities=38% Similarity=0.610 Sum_probs=54.9
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++.+.+++++++|.+||++||||++|+||.+|+.+...|.+.|+++..+|.+|+...+++
T Consensus 87 ~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~ 147 (165)
T cd06930 87 LQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQ 147 (165)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 3456778999999999999999999999999999999999999999999999999655554
No 81
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=98.85 E-value=3.4e-09 Score=78.84 Aligned_cols=59 Identities=32% Similarity=0.474 Sum_probs=52.3
Q ss_pred ccccccccccccChhhHHHHHHHHHhCCCCcCCCCH--HHHHHhHHHHHHhHhhhhhhcCC
Q psy12692 5 YPRQSGELELKFDISDYICVKFLLLLNPDVRGILNR--THVEEGHEQVQKALLDYCITAYP 63 (187)
Q Consensus 5 ~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~--~~V~~l~~~~l~~Lv~~~~~~f~ 63 (187)
.+.+..+++++++.+||++|+|+++++|+.+++.+. +.+++.++.+..+|.+|+....+
T Consensus 83 ~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~ 143 (163)
T smart00430 83 QELVKPLRELKLDDEEYALLKAILLFNPAGPGLSEEGKEILEKLQEKLANALHDYYLKNYP 143 (163)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHcChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 344667899999999999999999999999999988 88999999999999999865544
No 82
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=98.68 E-value=2e-08 Score=80.36 Aligned_cols=60 Identities=22% Similarity=0.318 Sum_probs=54.0
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++++.+++++++|.+||+|||||++|+ |++|+.+...|+++|+++..+|.+|+...+|.
T Consensus 125 l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~ 184 (231)
T cd06938 125 LFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPP 184 (231)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 4567788999999999999999999998 56899999999999999999999999666654
No 83
>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal lig
Probab=98.65 E-value=2.8e-08 Score=78.87 Aligned_cols=59 Identities=24% Similarity=0.379 Sum_probs=53.4
Q ss_pred cccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 6 PRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 6 ~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+++.+++++++|.+||+|||||++|+|+.+|+++...+.+++++++.+|.+|+...+++
T Consensus 120 ~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~ 178 (222)
T cd06931 120 ELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYD 178 (222)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCc
Confidence 45678999999999999999999999999999999999999999999999998555544
No 84
>KOG4215|consensus
Probab=98.55 E-value=6.4e-08 Score=80.47 Aligned_cols=54 Identities=24% Similarity=0.523 Sum_probs=49.5
Q ss_pred cccccccccChhhHHHHHHHHHhCCCCcCCCCHH--HHHHhHHHHHHhHhhhhhhc
Q psy12692 8 QSGELELKFDISDYICVKFLLLLNPDVRGILNRT--HVEEGHEQVQKALLDYCITA 61 (187)
Q Consensus 8 ~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~--~V~~l~~~~l~~Lv~~~~~~ 61 (187)
+.-++++++|..||+|||||++|+|+++|+.+.+ .|++.+.+++..|.+|+.-.
T Consensus 245 v~Pmr~L~md~~Ey~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~ 300 (432)
T KOG4215|consen 245 VNPMRRLQMDEIEYVCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDR 300 (432)
T ss_pred hhHHHHhccchHHHHHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhc
Confidence 4468999999999999999999999999999988 89999999999999999433
No 85
>KOG4216|consensus
Probab=98.52 E-value=4.7e-07 Score=75.92 Aligned_cols=110 Identities=15% Similarity=0.170 Sum_probs=93.4
Q ss_pred CcccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCCcchhHHHHHHHHhhHHHH
Q psy12692 3 NYYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQIQVDDQMKLLQHSWSDML 82 (187)
Q Consensus 3 ~~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~l~~~DQ~~LL~~~w~el~ 82 (187)
.+|++..++-.|++..+|.+++.|+||.+|+++|+.+..+|++++.+...++.+...+.+..
T Consensus 366 ~vf~~~ksL~~Lq~te~EiAL~~alVL~~~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~~------------------ 427 (479)
T KOG4216|consen 366 RVFEFGKSLCSLQLTEDEIALFSALVLMSADRSGLQEKVKIEKLQQKIQLALQHVLQKNHRE------------------ 427 (479)
T ss_pred HHHhhhHHHHhhccCcHHHHHHHHHHhhCCccccccchHHHHHHHHHHHHHHHHHHHhcCCh------------------
Confidence 36888999999999999999999999999999999999999999999999988776555443
Q ss_pred HHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcChHHHHHHHHHHHHHHhccCCCccchHHHHHHhChhhHhhhHHHHHH
Q psy12692 83 VLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVPTLRDRFTQVTHKLSELKFPNCDKFGKLMSILPELHEIASRGEEH 162 (187)
Q Consensus 83 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~~r~~~Lll~lp~lr~ls~~~~e~ 162 (187)
..-.++|+-..|.+|.++..+.|.
T Consensus 428 --------------------------------------------------------~~~l~kl~~k~~~~r~~~~lH~E~ 451 (479)
T KOG4216|consen 428 --------------------------------------------------------DGILTKLICKVSTLRALCGLHTEK 451 (479)
T ss_pred --------------------------------------------------------hhhHHHhhcccchHHHHHHHHHHH
Confidence 123567889999999999999999
Q ss_pred HHHHhhcCCCCh---hhHHHHHHhcCC
Q psy12692 163 LYHKHCNGGAPT---QTLLMEMLHAKR 186 (187)
Q Consensus 163 l~~~~~~g~~~~---~~ll~eml~~~~ 186 (187)
|.-++...+.-+ ++|.-|++.++.
T Consensus 452 Lq~Fk~~hP~iv~~fP~LYKELFt~d~ 478 (479)
T KOG4216|consen 452 LQAFKASHPDIVRHFPPLYKELFTSDF 478 (479)
T ss_pred HHHHhhcCchHHhhccHHHHHHhcccC
Confidence 999998877544 778888776553
No 86
>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=98.29 E-value=8.5e-07 Score=66.09 Aligned_cols=59 Identities=32% Similarity=0.496 Sum_probs=52.9
Q ss_pred ccccccccccccChhhHHHHHHHHHhCCCCc-CCCCHHHHHHhHHHHHHhHhhhhhhcCC
Q psy12692 5 YPRQSGELELKFDISDYICVKFLLLLNPDVR-GILNRTHVEEGHEQVQKALLDYCITAYP 63 (187)
Q Consensus 5 ~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~-~l~~~~~V~~l~~~~l~~Lv~~~~~~f~ 63 (187)
++++..+.++++|.+||+++|||++++|+.+ +..+...+.+.++++..+|.+|+...++
T Consensus 89 ~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~ 148 (168)
T cd06157 89 FEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLRKNYP 148 (168)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4556789999999999999999999999988 7889999999999999999999965554
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=7.9e-06 Score=62.77 Aligned_cols=54 Identities=30% Similarity=0.419 Sum_probs=48.0
Q ss_pred ccccccccccccChhhHHHHHHHHHhCCCCcCCC-CHHH-HHHhHHHHHHhHhhhh
Q psy12692 5 YPRQSGELELKFDISDYICVKFLLLLNPDVRGIL-NRTH-VEEGHEQVQKALLDYC 58 (187)
Q Consensus 5 ~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~-~~~~-V~~l~~~~l~~Lv~~~ 58 (187)
.+.+..++++++|.+||++++|+++++|+.+++. +... +.+.++++..+|.+|.
T Consensus 108 ~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~ 163 (203)
T PF00104_consen 108 NEVLRPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYY 163 (203)
T ss_dssp HHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHH
Confidence 4456689999999999999999999999999998 7766 8999999999999998
No 88
>KOG4216|consensus
Probab=97.27 E-value=0.00026 Score=59.77 Aligned_cols=114 Identities=14% Similarity=0.204 Sum_probs=84.2
Q ss_pred HHHHHhHhhhh--hhcCCCcchhHHHHHHHHhhHHHHHHHHHHHHhhcCCCCcEEeeCCcccchhhhhhcChHHHHHHHH
Q psy12692 48 EQVQKALLDYC--ITAYPQIQVDDQMKLLQHSWSDMLVLDHMHQRMHNALPDETTLHNGQKFDLLSLGLLGVPTLRDRFT 125 (187)
Q Consensus 48 ~~~l~~Lv~~~--~~~f~~l~~~DQ~~LL~~~w~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 125 (187)
....+.++|++ +++|-+|+++||+.|||++-.|+....++..+-.. ..++.+ .|...........+..+++.+..
T Consensus 292 t~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~--~ntV~~-e~~~~g~~~f~a~~~~elis~vf 368 (479)
T KOG4216|consen 292 TPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVD--NNTVYF-EGKYAGPEVFYALGCEELISRVF 368 (479)
T ss_pred HHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhccc--ccceee-cccccchhheeccChHHHHHHHH
Confidence 34577888999 89999999999999999999999998888877653 334443 44444555556677788999999
Q ss_pred HHHHHHhccCCCccc--hHHHHHHhChhhHhhhH-HHHHHHH
Q psy12692 126 QVTHKLSELKFPNCD--KFGKLMSILPELHEIAS-RGEEHLY 164 (187)
Q Consensus 126 ~~~~~l~~L~ld~~~--r~~~Lll~lp~lr~ls~-~~~e~l~ 164 (187)
++...+..||+..+. -|..+++.-|+=.++-. .-|+.++
T Consensus 369 ~~~ksL~~Lq~te~EiAL~~alVL~~~~r~gl~e~~ki~~lq 410 (479)
T KOG4216|consen 369 EFGKSLCSLQLTEDEIALFSALVLMSADRSGLQEKVKIEKLQ 410 (479)
T ss_pred hhhHHHHhhccCcHHHHHHHHHHhhCCccccccchHHHHHHH
Confidence 999999999999832 24556676666655544 3444443
No 89
>KOG4218|consensus
Probab=96.57 E-value=0.0015 Score=54.50 Aligned_cols=57 Identities=33% Similarity=0.521 Sum_probs=52.4
Q ss_pred cccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhhhcCCC
Q psy12692 8 QSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCITAYPQ 64 (187)
Q Consensus 8 ~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~~~f~~ 64 (187)
+.+++++++|.-||+|||-++||+-|..-+.+...|..+|++...+|.+|..-.+|.
T Consensus 369 V~~Lr~lqfd~~efvclkFl~LFsld~kfLenf~lv~~~qe~~naaLldyt~c~yp~ 425 (475)
T KOG4218|consen 369 VIRLRNLQFDNFEFVCLKFLALFSLDMKFLENFELVRRLQEDSNAALLDYTSCCYPN 425 (475)
T ss_pred HHHHHhcCCccchhhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCcc
Confidence 456899999999999999999999999999999999999999999999998766766
No 90
>KOG4217|consensus
Probab=96.02 E-value=0.005 Score=53.42 Aligned_cols=55 Identities=24% Similarity=0.347 Sum_probs=50.6
Q ss_pred cccccccccccccChhhHHHHHHHHHhCCCCcCCCCHHHHHHhHHHHHHhHhhhhh
Q psy12692 4 YYPRQSGELELKFDISDYICVKFLLLLNPDVRGILNRTHVEEGHEQVQKALLDYCI 59 (187)
Q Consensus 4 ~~~~~~~~~~l~ld~~E~~~Lkai~l~~pd~~~l~~~~~V~~l~~~~l~~Lv~~~~ 59 (187)
|-+|.+.+..+++|..-|+||.|+++.. ++.||.+...|+++|.++.-+|.+++.
T Consensus 493 i~~FS~~l~~l~idi~AfacL~aLa~iT-ErhGL~epkrVeelqnkIi~~LKDHvt 547 (605)
T KOG4217|consen 493 IREFSRSLHSLNIDISAFACLSALALIT-ERHGLKEPKRVEELQNKIINCLKDHVT 547 (605)
T ss_pred HHHHHHHhhhchhhHHHHHHHHHHHhhh-hhhcCCCcchHHHHHHHHHHHHHHHhh
Confidence 4567788899999999999999999988 789999999999999999999999973
No 91
>KOG4846|consensus
Probab=29.69 E-value=1.3e+02 Score=26.41 Aligned_cols=26 Identities=12% Similarity=-0.028 Sum_probs=15.7
Q ss_pred hhcChHHHHHHHHHHHHHHhccCCCc
Q psy12692 113 GLLGVPTLRDRFTQVTHKLSELKFPN 138 (187)
Q Consensus 113 ~~~~~~~~~~~l~~~~~~l~~L~ld~ 138 (187)
...++++.+..+..++.++..|....
T Consensus 439 ~~~~~gd~~~a~~~~~~~ln~L~~~~ 464 (538)
T KOG4846|consen 439 TCRIDGDTYKALMKCIHELNRLNELH 464 (538)
T ss_pred HhhhchHHHHHHHHhhcchhhcCchH
Confidence 33445566666666666666666554
No 92
>cd03746 SOCS_WSB1_SWIP1 SOCS (suppressors of cytokine signaling) box of WSB1/SWiP1-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2) and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh). The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=27.70 E-value=82 Score=17.89 Aligned_cols=36 Identities=14% Similarity=0.205 Sum_probs=27.0
Q ss_pred ChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHhc
Q psy12692 149 LPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLHA 184 (187)
Q Consensus 149 lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~~ 184 (187)
+|.|.+++-..|......+.++..|++.-+.+-|..
T Consensus 3 v~sLQhLCR~~Ir~~~~~~~i~~LpLP~~Lk~YL~y 38 (40)
T cd03746 3 VASLQHLCRMAIRRVMPTQQVKELPIPSKLLEFLTY 38 (40)
T ss_pred CcCHHHHHHHHHHHHccccccccCCCCHHHHHHHhc
Confidence 577778888888777666667778888888877654
No 93
>cd03745 SOCS_WSB2_SWIP2 SOCS (suppressors of cytokine signaling) box of WSB2/SWiP2-like proteins. This family consists of WSB-2 (SOCS-box-containing WD-40 protein) and SWiP-2 (SOCS box and WD-repeats in Protein). No functional information is available for WSB2 or SWiP-2, but limited information is available for the isoforms WSB-1 and SWiP-1. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=22.81 E-value=1e+02 Score=17.44 Aligned_cols=35 Identities=20% Similarity=0.303 Sum_probs=25.0
Q ss_pred ChhhHhhhHHHHHHHHHHhhcCCCChhhHHHHHHh
Q psy12692 149 LPELHEIASRGEEHLYHKHCNGGAPTQTLLMEMLH 183 (187)
Q Consensus 149 lp~lr~ls~~~~e~l~~~~~~g~~~~~~ll~eml~ 183 (187)
+|.|.+++-..|.......-....|++.-+.|-|.
T Consensus 3 v~SLQHLCR~~I~~~~~~~~~~~LPLP~~Lk~yL~ 37 (39)
T cd03745 3 LPSLRHLCRKALRHFLTTYQVLALPIPKKMKEFLT 37 (39)
T ss_pred cccHHHHHHHHHHHhccccccccCCCcHHHHHHHc
Confidence 57888888888877754444556788888777654
No 94
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=22.01 E-value=3.4e+02 Score=20.25 Aligned_cols=41 Identities=22% Similarity=0.301 Sum_probs=28.8
Q ss_pred cChHHHHHHHHHHHHHHhccCCCc---------cchHHHHHHhChhhHhh
Q psy12692 115 LGVPTLRDRFTQVTHKLSELKFPN---------CDKFGKLMSILPELHEI 155 (187)
Q Consensus 115 ~~~~~~~~~l~~~~~~l~~L~ld~---------~~r~~~Lll~lp~lr~l 155 (187)
..+++++++.+++...++..|+.. -.|.+++...+-.++.+
T Consensus 11 EtVQdIvsrt~elF~~lk~~QlPng~t~~~~~aqdr~~kl~e~lr~i~~L 60 (150)
T PF11315_consen 11 ETVQDIVSRTQELFQALKNPQLPNGSTQQQNMAQDRRNKLQEQLRTIKVL 60 (150)
T ss_pred HHHHHHHHHHHHHHHHHhcccCCCCccchhhhhhhHHHHHHHHHHHHHHH
Confidence 345688899999999999999776 45566665555544443
Done!