Query psy3092
Match_columns 347
No_of_seqs 290 out of 1423
Neff 9.3
Searched_HMMs 46136
Date Sat Aug 17 01:26:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3092.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3092hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 100.0 3.6E-70 7.9E-75 474.6 20.8 289 55-346 19-323 (432)
2 KOG4217|consensus 100.0 1.1E-52 2.5E-57 375.4 22.4 288 55-346 269-573 (605)
3 KOG4216|consensus 100.0 8E-50 1.7E-54 349.7 9.5 286 57-346 48-445 (479)
4 KOG4218|consensus 100.0 7.5E-47 1.6E-51 326.0 17.7 292 55-346 15-444 (475)
5 KOG4846|consensus 100.0 6.6E-37 1.4E-41 270.4 8.1 82 55-136 132-214 (538)
6 cd06943 NR_LBD_RXR_like The li 100.0 1E-32 2.2E-37 237.9 20.3 168 180-347 30-197 (207)
7 cd07076 NR_LBD_GR Ligand bindi 100.0 2.4E-32 5.1E-37 237.7 19.7 168 178-346 26-199 (247)
8 cd06949 NR_LBD_ER Ligand bindi 100.0 1.5E-31 3.2E-36 233.7 19.1 170 177-347 29-207 (235)
9 cd06937 NR_LBD_RAR The ligand 100.0 1E-31 2.2E-36 234.1 17.9 166 180-346 38-203 (231)
10 cd07160 NR_DBD_LXR DNA-binding 100.0 1.4E-33 2.9E-38 210.0 5.2 82 55-136 18-99 (101)
11 cd06956 NR_DBD_RXR DNA-binding 100.0 1.4E-33 3E-38 201.1 4.3 76 57-132 2-77 (77)
12 cd06944 NR_LBD_Ftz-F1_like The 100.0 1.9E-31 4.1E-36 233.7 18.4 166 180-346 38-208 (237)
13 cd06935 NR_LBD_TR The ligand b 100.0 1.4E-31 2.9E-36 235.1 17.1 167 179-346 51-217 (243)
14 cd06940 NR_LBD_REV_ERB The lig 100.0 2.7E-31 5.8E-36 224.7 17.3 166 180-346 12-177 (189)
15 cd06961 NR_DBD_TR DNA-binding 100.0 2.1E-33 4.5E-38 203.7 3.5 81 58-138 2-82 (85)
16 cd06947 NR_LBD_GR_Like Ligand 100.0 4.9E-31 1.1E-35 230.7 19.0 167 179-346 27-199 (246)
17 cd07075 NR_LBD_MR Ligand bindi 100.0 7.4E-31 1.6E-35 228.5 19.9 167 179-346 27-199 (248)
18 cd06964 NR_DBD_RAR DNA-binding 100.0 1.3E-33 2.8E-38 204.5 2.0 79 56-134 5-83 (85)
19 cd07170 NR_DBD_ERR DNA-binding 100.0 3E-33 6.5E-38 206.8 3.7 81 56-136 5-85 (97)
20 cd07171 NR_DBD_ER DNA-binding 100.0 7.9E-33 1.7E-37 198.8 5.5 78 56-133 4-81 (82)
21 cd07161 NR_DBD_EcR DNA-binding 100.0 6E-33 1.3E-37 203.3 4.2 83 56-138 2-84 (91)
22 cd07070 NR_LBD_SF-1 The ligand 100.0 7.8E-31 1.7E-35 229.4 17.9 167 180-347 38-209 (237)
23 cd06950 NR_LBD_Tlx_PNR_like Th 100.0 1.2E-30 2.7E-35 223.8 18.7 168 179-347 25-192 (206)
24 cd07073 NR_LBD_AR Ligand bindi 100.0 1.6E-30 3.5E-35 227.4 19.4 167 179-346 27-199 (246)
25 cd06931 NR_LBD_HNF4_like The l 100.0 2.5E-30 5.4E-35 225.4 20.5 167 179-346 31-197 (222)
26 cd07155 NR_DBD_ER_like DNA-bin 100.0 6.7E-33 1.4E-37 196.8 3.5 75 58-132 1-75 (75)
27 cd07348 NR_LBD_NGFI-B The liga 100.0 8.7E-31 1.9E-35 228.0 17.3 164 180-346 41-206 (238)
28 cd07168 NR_DBD_DHR4_like DNA-b 100.0 1.3E-32 2.8E-37 201.6 4.3 80 56-135 7-86 (90)
29 cd06962 NR_DBD_FXR DNA-binding 100.0 6E-33 1.3E-37 200.3 2.3 80 56-135 2-81 (84)
30 cd07068 NR_LBD_ER_like The lig 100.0 3.1E-30 6.8E-35 224.1 19.5 167 179-346 26-193 (221)
31 cd06967 NR_DBD_TR2_like DNA-bi 100.0 5.6E-33 1.2E-37 202.1 1.8 80 56-135 4-83 (87)
32 cd06970 NR_DBD_PNR DNA-binding 100.0 5.2E-33 1.1E-37 203.7 1.5 79 57-135 8-87 (92)
33 cd06929 NR_LBD_F1 Ligand-bindi 100.0 2E-30 4.3E-35 217.9 17.1 165 181-346 3-167 (174)
34 cd07164 NR_DBD_PNR_like_1 DNA- 100.0 1.6E-32 3.5E-37 196.3 3.6 77 58-134 1-77 (78)
35 cd06930 NR_LBD_F2 Ligand-bindi 100.0 3.2E-30 7E-35 214.8 18.1 162 183-345 2-165 (165)
36 cd06946 NR_LBD_ERR The ligand 100.0 3.9E-30 8.4E-35 223.7 19.2 167 179-346 26-193 (221)
37 cd07069 NR_LBD_Lrh-1 The ligan 100.0 3.1E-30 6.8E-35 225.8 18.5 166 180-346 40-210 (241)
38 cd06957 NR_DBD_PNR_like_2 DNA- 100.0 3.8E-33 8.3E-38 201.1 0.1 79 58-136 1-80 (82)
39 cd07071 NR_LBD_Nurr1 The ligan 100.0 3E-30 6.5E-35 224.9 18.0 164 180-346 41-206 (238)
40 cd07163 NR_DBD_TLX DNA-binding 100.0 8.3E-33 1.8E-37 203.4 1.5 80 56-135 7-88 (92)
41 cd06954 NR_LBD_LXR The ligand 100.0 2.6E-30 5.6E-35 227.1 17.3 167 180-346 43-209 (236)
42 cd07165 NR_DBD_DmE78_like DNA- 100.0 1.9E-32 4.2E-37 197.2 3.1 79 58-136 1-79 (81)
43 cd07166 NR_DBD_REV_ERB DNA-bin 100.0 9.7E-33 2.1E-37 201.8 1.6 82 56-137 4-86 (89)
44 cd07167 NR_DBD_Lrh-1_like The 100.0 2.8E-32 6E-37 200.1 3.9 78 58-135 1-78 (93)
45 cd07169 NR_DBD_GCNF_like DNA-b 100.0 2.8E-32 6.1E-37 199.5 3.6 80 55-134 6-85 (90)
46 cd06941 NR_LBD_DmE78_like The 100.0 4.1E-30 8.9E-35 219.4 17.5 164 182-346 4-167 (195)
47 cd06966 NR_DBD_CAR DNA-binding 100.0 1.5E-32 3.2E-37 202.7 2.0 82 57-138 2-83 (94)
48 cd06951 NR_LBD_Dax1_like The l 100.0 4.3E-30 9.3E-35 222.4 17.1 167 180-347 19-199 (222)
49 cd06945 NR_LBD_Nurr1_like The 100.0 5.1E-30 1.1E-34 224.4 17.7 165 180-346 41-207 (239)
50 cd06960 NR_DBD_HNF4A DNA-bindi 100.0 2.1E-32 4.6E-37 195.1 2.0 76 58-133 1-76 (76)
51 cd06959 NR_DBD_EcR_like The DN 100.0 5.9E-32 1.3E-36 190.9 4.1 73 57-129 1-73 (73)
52 cd07074 NR_LBD_PR Ligand bindi 100.0 1.6E-29 3.5E-34 219.9 20.2 167 178-345 26-198 (248)
53 cd06958 NR_DBD_COUP_TF DNA-bin 100.0 5.5E-32 1.2E-36 191.0 3.8 72 58-129 1-72 (73)
54 cd06969 NR_DBD_NGFI-B DNA-bind 100.0 2E-32 4.3E-37 194.1 1.5 74 57-130 2-75 (75)
55 cd07156 NR_DBD_VDR_like The DN 100.0 6.6E-32 1.4E-36 190.1 3.9 71 58-128 1-71 (72)
56 cd06955 NR_DBD_VDR DNA-binding 100.0 4E-32 8.6E-37 204.0 3.0 76 56-131 7-82 (107)
57 cd07162 NR_DBD_PXR DNA-binding 100.0 8.2E-32 1.8E-36 196.5 4.1 80 57-136 1-80 (87)
58 cd07173 NR_DBD_AR DNA-binding 100.0 1.5E-31 3.2E-36 191.9 5.4 76 56-131 4-79 (82)
59 cd06948 NR_LBD_COUP-TF Ligand 100.0 1.4E-29 3E-34 221.9 18.9 166 180-347 30-198 (236)
60 cd07179 2DBD_NR_DBD2 The secon 100.0 1E-31 2.2E-36 190.0 4.2 73 58-130 1-73 (74)
61 cd06968 NR_DBD_ROR DNA-binding 100.0 5.3E-32 1.1E-36 199.9 2.7 83 56-138 6-88 (95)
62 cd07349 NR_LBD_SHP The ligand 100.0 1E-29 2.2E-34 219.4 17.2 168 180-347 19-197 (222)
63 cd06963 NR_DBD_GR_like The DNA 100.0 1.4E-31 3.1E-36 188.5 4.4 72 58-129 1-72 (73)
64 cd07072 NR_LBD_DHR38_like Liga 100.0 2.4E-29 5.3E-34 219.1 19.3 166 178-346 40-207 (239)
65 cd07172 NR_DBD_GR_PR DNA-bindi 100.0 1.5E-31 3.3E-36 190.5 4.2 74 56-129 3-76 (78)
66 cd07158 NR_DBD_Ppar_like The D 100.0 1.6E-31 3.5E-36 189.0 3.9 72 58-129 1-73 (73)
67 cd06934 NR_LBD_PXR_like The li 100.0 1.8E-29 4E-34 219.2 17.6 166 180-346 35-202 (226)
68 cd07154 NR_DBD_PNR_like The DN 100.0 6E-32 1.3E-36 191.0 1.4 72 58-129 1-73 (73)
69 cd07350 NR_LBD_Dax1 The ligand 100.0 2.2E-29 4.8E-34 218.6 17.7 167 180-346 19-208 (232)
70 cd06916 NR_DBD_like DNA-bindin 100.0 7.4E-32 1.6E-36 190.0 1.2 72 58-129 1-72 (72)
71 cd06939 NR_LBD_ROR_like The li 100.0 3.7E-29 8E-34 219.0 17.4 164 180-346 48-211 (241)
72 cd06953 NR_LBD_DHR4_like The l 100.0 2.8E-29 6.2E-34 216.4 16.5 167 178-346 25-196 (213)
73 cd07157 2DBD_NR_DBD1 The first 100.0 1.2E-31 2.6E-36 194.7 1.3 78 57-134 2-81 (86)
74 cd06965 NR_DBD_Ppar DNA-bindin 100.0 1.6E-31 3.5E-36 193.4 1.8 78 58-137 2-80 (84)
75 cd06933 NR_LBD_VDR The ligand 100.0 1E-28 2.2E-33 216.2 18.4 166 180-346 37-206 (238)
76 cd06936 NR_LBD_Fxr The ligand 100.0 9.9E-29 2.2E-33 214.0 17.0 162 179-346 35-198 (221)
77 cd06938 NR_LBD_EcR The ligand 100.0 1.2E-28 2.5E-33 215.5 17.0 165 180-346 39-204 (231)
78 cd06932 NR_LBD_PPAR The ligand 100.0 2.7E-28 5.8E-33 215.7 17.7 163 181-346 64-229 (259)
79 smart00399 ZnF_C4 c4 zinc fing 100.0 3.5E-30 7.5E-35 181.0 3.1 69 58-126 2-70 (70)
80 cd06942 NR_LBD_Sex_1_like The 100.0 5.9E-28 1.3E-32 205.2 17.4 163 181-346 3-168 (191)
81 cd06952 NR_LBD_TR2_like The li 100.0 7.4E-28 1.6E-32 209.6 16.3 167 180-346 21-194 (222)
82 PF00105 zf-C4: Zinc finger, C 100.0 3.6E-29 7.8E-34 176.4 4.5 69 57-125 2-70 (70)
83 cd06157 NR_LBD The ligand bind 99.9 4.7E-26 1E-30 189.7 17.2 162 184-345 2-168 (168)
84 smart00430 HOLI Ligand binding 99.9 8.2E-26 1.8E-30 187.3 15.1 156 190-345 2-163 (163)
85 PF00104 Hormone_recep: Ligand 99.9 7.4E-25 1.6E-29 188.3 17.0 169 177-346 14-190 (203)
86 KOG3277|consensus 82.2 0.91 2E-05 36.2 1.8 26 56-81 80-113 (165)
87 PF12760 Zn_Tnp_IS1595: Transp 80.7 0.93 2E-05 28.5 1.2 40 76-116 4-46 (46)
88 PF01412 ArfGap: Putative GTPa 80.4 1.1 2.5E-05 34.5 1.9 31 55-85 13-46 (116)
89 PF03107 C1_2: C1 domain; Int 74.7 1.6 3.5E-05 24.6 0.9 21 57-79 2-22 (30)
90 PLN02638 cellulose synthase A 69.8 2.6 5.6E-05 44.4 1.7 48 56-119 18-73 (1079)
91 PF09289 FOLN: Follistatin/Ost 68.5 1.5 3.3E-05 22.8 -0.1 20 91-110 3-22 (22)
92 PLN02189 cellulose synthase 66.8 2.4 5.2E-05 44.5 0.8 48 56-119 35-90 (1040)
93 KOG4399|consensus 66.4 3.2 6.9E-05 36.2 1.3 41 56-102 262-302 (325)
94 PLN02400 cellulose synthase 65.7 3 6.5E-05 44.0 1.2 48 56-119 37-92 (1085)
95 PHA03124 dUTPase; Provisional 62.5 3.9 8.5E-05 37.8 1.2 16 71-86 189-204 (418)
96 PTZ00218 40S ribosomal protein 61.0 3.9 8.4E-05 26.6 0.7 23 56-78 17-40 (54)
97 PLN02915 cellulose synthase A 58.1 5.5 0.00012 42.0 1.6 48 56-119 16-71 (1044)
98 smart00105 ArfGap Putative GTP 57.7 8.2 0.00018 29.4 2.1 31 55-85 3-36 (112)
99 PLN02436 cellulose synthase A 57.6 5.6 0.00012 42.0 1.5 48 56-119 37-92 (1094)
100 PF09788 Tmemb_55A: Transmembr 56.3 32 0.0007 30.2 5.7 24 56-79 66-92 (256)
101 TIGR00269 conserved hypothetic 56.2 6.8 0.00015 29.5 1.4 19 56-79 81-99 (104)
102 PF00357 Integrin_alpha: Integ 48.2 6 0.00013 18.5 0.0 7 80-86 3-9 (15)
103 PF07649 C1_3: C1-like domain; 46.6 8.7 0.00019 21.5 0.5 20 57-79 2-22 (30)
104 smart00249 PHD PHD zinc finger 45.0 14 0.00031 22.3 1.4 27 58-86 2-28 (47)
105 PF12238 MSA-2c: Merozoite sur 40.9 1E+02 0.0022 26.3 6.3 10 65-74 194-203 (205)
106 COG3677 Transposase and inacti 39.5 6.7 0.00014 30.9 -0.9 40 66-117 24-63 (129)
107 smart00274 FOLN Follistatin-N- 39.4 15 0.00032 20.0 0.7 20 91-110 4-23 (26)
108 PF10764 Gin: Inhibitor of sig 38.1 17 0.00036 22.9 0.9 23 57-79 1-25 (46)
109 PRK00420 hypothetical protein; 37.6 17 0.00036 27.8 1.0 25 56-80 24-48 (112)
110 PRK05766 rps14P 30S ribosomal 37.5 28 0.00061 22.5 1.9 23 56-78 15-38 (52)
111 PF10080 DUF2318: Predicted me 36.9 13 0.00029 27.8 0.4 26 57-82 37-62 (102)
112 PF13901 DUF4206: Domain of un 36.2 19 0.00041 30.7 1.2 32 56-87 153-187 (202)
113 PRK01343 zinc-binding protein; 35.3 34 0.00073 22.6 2.0 23 56-79 10-32 (57)
114 PF04444 Dioxygenase_N: Catech 35.0 87 0.0019 21.9 4.2 32 260-291 5-36 (74)
115 COG1997 RPL43A Ribosomal prote 34.5 13 0.00027 26.8 -0.1 27 55-81 35-62 (89)
116 smart00401 ZnF_GATA zinc finge 34.0 38 0.00083 21.8 2.1 30 56-85 4-38 (52)
117 PRK08359 transcription factor; 33.0 25 0.00054 29.2 1.4 29 56-84 7-42 (176)
118 KOG3362|consensus 32.0 23 0.00049 28.1 0.9 18 56-79 119-136 (156)
119 cd00729 rubredoxin_SM Rubredox 31.8 16 0.00036 21.2 0.1 12 56-67 19-30 (34)
120 PF01286 XPA_N: XPA protein N- 31.0 28 0.00061 20.3 1.0 23 57-79 5-31 (34)
121 PF10013 DUF2256: Uncharacteri 30.1 28 0.00062 21.3 0.9 9 56-64 9-17 (42)
122 PF03811 Zn_Tnp_IS1: InsA N-te 30.0 17 0.00036 21.6 -0.1 10 105-114 27-36 (36)
123 COG5347 GTPase-activating prot 29.8 26 0.00056 32.2 1.1 31 55-85 20-53 (319)
124 PF03802 CitX: Apo-citrate lya 28.5 22 0.00047 29.4 0.4 13 54-66 131-143 (170)
125 KOG4327|consensus 28.3 83 0.0018 26.5 3.6 6 66-71 200-205 (218)
126 PF03002 Somatostatin: Somatos 28.3 12 0.00026 18.2 -0.7 9 77-85 6-14 (18)
127 TIGR03124 ctirate_citX holo-AC 27.9 21 0.00046 29.3 0.2 12 55-66 130-141 (165)
128 PF04438 zf-HIT: HIT zinc fing 27.9 19 0.00042 20.3 -0.1 18 56-79 3-20 (30)
129 PLN03114 ADP-ribosylation fact 27.3 36 0.00079 31.5 1.5 31 55-85 22-55 (395)
130 PRK06424 transcription factor; 26.7 29 0.00064 27.8 0.8 23 58-81 3-32 (144)
131 PF02318 FYVE_2: FYVE-type zin 26.5 46 0.001 25.5 1.9 47 56-117 55-104 (118)
132 PF12156 ATPase-cat_bd: Putati 26.2 55 0.0012 23.7 2.1 32 58-89 3-43 (88)
133 PRK00418 DNA gyrase inhibitor; 26.0 50 0.0011 22.2 1.7 25 56-80 7-34 (62)
134 KOG3506|consensus 25.9 32 0.00068 22.4 0.6 23 56-78 19-42 (56)
135 COG4338 Uncharacterized protei 25.9 26 0.00056 22.1 0.2 11 55-65 12-22 (54)
136 PF14446 Prok-RING_1: Prokaryo 25.6 29 0.00064 22.6 0.5 32 54-86 4-35 (54)
137 PRK01392 citX 2'-(5''-triphosp 25.4 25 0.00054 29.4 0.2 12 55-66 139-150 (180)
138 PF00628 PHD: PHD-finger; Int 25.4 14 0.0003 23.4 -1.1 26 58-85 2-27 (51)
139 KOG4323|consensus 24.9 39 0.00085 32.5 1.4 58 55-117 168-225 (464)
140 PF00645 zf-PARP: Poly(ADP-rib 24.1 71 0.0015 22.5 2.3 20 201-220 61-80 (82)
141 PF01780 Ribosomal_L37ae: Ribo 23.6 25 0.00054 25.7 -0.2 24 56-79 36-60 (90)
142 TIGR03655 anti_R_Lar restricti 23.5 31 0.00067 22.3 0.3 14 57-70 3-16 (53)
143 PF00320 GATA: GATA zinc finge 23.4 56 0.0012 19.1 1.4 16 70-85 17-33 (36)
144 KOG0703|consensus 22.6 28 0.0006 31.3 -0.1 31 55-85 25-58 (287)
145 smart00154 ZnF_AN1 AN1-like Zi 22.6 28 0.00061 20.9 -0.0 20 58-80 1-20 (39)
146 PTZ00255 60S ribosomal protein 22.1 43 0.00093 24.4 0.8 24 56-79 37-61 (90)
147 PF14445 Prok-RING_2: Prokaryo 21.7 15 0.00033 23.4 -1.3 9 56-64 23-31 (57)
148 PF01753 zf-MYND: MYND finger; 21.6 18 0.00039 21.3 -1.1 16 58-79 1-16 (37)
149 PF11494 Ta0938: Ta0938; Inte 21.4 23 0.0005 26.0 -0.7 31 56-86 15-51 (105)
150 PF14569 zf-UDP: Zinc-binding 21.3 45 0.00097 23.5 0.7 9 56-64 10-18 (80)
151 TIGR00270 conserved hypothetic 20.7 48 0.001 26.9 0.9 26 58-84 3-35 (154)
152 KOG4443|consensus 20.5 22 0.00048 35.4 -1.2 33 56-88 19-51 (694)
No 1
>KOG4215|consensus
Probab=100.00 E-value=3.6e-70 Score=474.63 Aligned_cols=289 Identities=41% Similarity=0.776 Sum_probs=247.1
Q ss_pred CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
...|.||||+|+|+||||.+|.||||||||+|+++..|.|+.+.+|.|||+.|+.||+|||+||+.+||++++||.+||+
T Consensus 19 ~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDr 98 (432)
T KOG4215|consen 19 AEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDR 98 (432)
T ss_pred cchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhccccc
Confidence 35799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccccccccCCCCCCCCCcHHHHHHHHHhccCCCC------CCcc-c------cchhHHHhhhhHHHHHHHHHHHHHHh
Q psy3092 135 TKERDSNEVESTSGTLIEMPVERILEAEQRVDMKQE------PADQ-D------IVNEQQATNICKATDKQLFQLVDWAK 201 (347)
Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~------~~~~-~------~~~~~~~~~~~~~~~~~l~~~~~w~k 201 (347)
+..+.+.... +...+..++.++.++..+..... +... + .-......++++....++..+|||||
T Consensus 99 Ig~Rr~~~~~---~n~~~~~id~L~~aE~~~~q~~~srs~~~~~~~~d~r~~~~n~~~at~~Dv~eSm~qqLlllVEWAK 175 (432)
T KOG4215|consen 99 IGSRRPSYEA---GNENSPSIDALVQAEALVRQLRSSRSGGVPGIDGDIRQGPPNKKIATENDVCESMKQQLLLLVEWAK 175 (432)
T ss_pred ccccCCCCCC---CCCCchhHHHHHhHHHHHhhhhccccccCcCcchhhhcCccccccccHHHHHHHHHHHHHHHHHHHH
Confidence 8775432211 11233345666666654432211 1000 0 11224567889999999999999999
Q ss_pred hCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCCCH
Q psy3092 202 HIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKMDK 281 (347)
Q Consensus 202 ~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l~~ 281 (347)
.+|.|.+|+.+||+.|||+...+.+++..++|++..++..++.+...+..+..+......+..|+++|++.||++|++|+
T Consensus 176 ~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~Pmr~L~md~ 255 (432)
T KOG4215|consen 176 YIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLNNTYVLHRHAPDLPEISRVAPRIIDELVNPMRRLQMDE 255 (432)
T ss_pred hccchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEecCceeeccCCCChHHHHHHHHHHHHHHhhHHHHhccch
Confidence 99999999999999999999999999999999999989888888887777666555566788899999999999999999
Q ss_pred hHHHHHHHHHhhcCCCCCCCCH--HHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHhhhhhhhccC
Q psy3092 282 TELGCLRTIILFNPDVRGLKSQ--QVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLLRLPSLRSIE 346 (347)
Q Consensus 282 ~E~~lL~ai~l~~p~~~~l~~~--~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~ll~~lr~i~ 346 (347)
.||++||||+||+|+..||++. ..|+++|++++..|+.|+..+.+ +.+.|||+||++||+|++|+
T Consensus 256 ~Ey~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~g~LLLllPsLqsIt 323 (432)
T KOG4215|consen 256 IEYVCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRFGNLLLLLPSLQSIT 323 (432)
T ss_pred HHHHHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccchhhHHHHHHHHHHHH
Confidence 9999999999999999999984 48999999999999999998875 78999999999999999874
No 2
>KOG4217|consensus
Probab=100.00 E-value=1.1e-52 Score=375.37 Aligned_cols=288 Identities=33% Similarity=0.646 Sum_probs=229.2
Q ss_pred CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
...|.||||.|.--||||.||+||||||+|+|+|+.+|.|-.+++|.|||..|++||+||||||++|||-+|.|+.+--+
T Consensus 269 e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLk 348 (605)
T KOG4217|consen 269 EGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLK 348 (605)
T ss_pred cceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheeccccc
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999875322
Q ss_pred hhc-cccccccCCCCCCCCCcHHHHHHHHHhccCCCCC--C------------ccccchhHHHhhhhHHHHHHHHHHHHH
Q psy3092 135 TKE-RDSNEVESTSGTLIEMPVERILEAEQRVDMKQEP--A------------DQDIVNEQQATNICKATDKQLFQLVDW 199 (347)
Q Consensus 135 ~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~--~------------~~~~~~~~~~~~~~~~~~~~l~~~~~w 199 (347)
.++ +-..+..+........|+. ++.+..+......+ . .........+..+.+...-.+-.+-.|
T Consensus 349 GRRGRLpSKpKs~q~sppSpPi~-LltalvrAh~Dstp~~~~ldys~~q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~ 427 (605)
T KOG4217|consen 349 GRRGRLPSKPKSRQPSPPSPPIS-LLTALVRAHVDSTPSTMTLDYSRFQELVPHFSGTDALHVQQFYDLLTGSLEVIRKW 427 (605)
T ss_pred cccCCCCCCCCCCCCCCCCCchH-HHHHHHHHhhcCCCCcchhhHHHhccccccccccHHHHHHHHHHHhhhhHHHHHHH
Confidence 111 1111111111122222332 22222211110110 0 001122344566667677777788899
Q ss_pred HhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHHhhHHHHHHHHHhcCC
Q psy3092 200 AKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFDRVLTELVSKMREMKM 279 (347)
Q Consensus 200 ~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~~l~~~l~~L~l 279 (347)
|..+|+|.+|+.+||.+||.+.+.+++++++|||+...++.++|.+|..+.+-... .++++++|.++ ++...+..|.+
T Consensus 428 aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~e~kliFcsG~vlhr~qC~-rgfgewidsi~-~FS~~l~~l~i 505 (605)
T KOG4217|consen 428 AEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPSEDKLIFCSGLVLHRLQCL-RGFGEWIDSIR-EFSRSLHSLNI 505 (605)
T ss_pred HHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEecchhhhHHHHH-HHHHHHHHHHH-HHHHHhhhchh
Confidence 99999999999999999999999999999999999999999999999999885543 45777777765 89999999999
Q ss_pred CHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc--CCCCchHHHHHHhhhhhhhccC
Q psy3092 280 DKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN--HSEEPGRFAKLLLRLPSLRSIE 346 (347)
Q Consensus 280 ~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~--~~~~~~Rf~~LL~ll~~lr~i~ 346 (347)
|..-|++|.|+.+.. ++.||.+...||++|++|.++|.+|+..+ ....+.++.++|-.|++||+|+
T Consensus 506 di~AfacL~aLa~iT-ErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr~l~ 573 (605)
T KOG4217|consen 506 DISAFACLSALALIT-ERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELRTLC 573 (605)
T ss_pred hHHHHHHHHHHHhhh-hhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHHHHH
Confidence 999999999999874 78999999999999999999999999654 3467899999999999999875
No 3
>KOG4216|consensus
Probab=100.00 E-value=8e-50 Score=349.71 Aligned_cols=286 Identities=31% Similarity=0.588 Sum_probs=211.1
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK 136 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~ 136 (347)
+|.||||+++|.||||+||+||||||||+-+.+..|.|.+.++|.||...|++||+||+|||+++||.+++|.+.|..+|
T Consensus 48 PCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKK 127 (479)
T KOG4216|consen 48 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK 127 (479)
T ss_pred eeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHh
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999886554
Q ss_pred ccccc---------------ccc--------CCCC-------------------------C--------CCCC-------
Q psy3092 137 ERDSN---------------EVE--------STSG-------------------------T--------LIEM------- 153 (347)
Q Consensus 137 ~~~~~---------------~~~--------~~~~-------------------------~--------~~~~------- 153 (347)
.++.. +.+ ++++ . .++.
T Consensus 128 QRdsl~aEVq~h~~q~q~q~~a~~~~~~y~~s~p~~~~~l~~~~s~y~~g~~p~~~k~~~s~Ys~~~q~tPdq~~~d~~g 207 (479)
T KOG4216|consen 128 QRDSLYAEVQKHRMQQQQQDEAEPLTPTYDISPPNGLTELHDDLSNYSDGHSPEGSKADSSFYSLDIQPTPDQSGLDING 207 (479)
T ss_pred hHHHHHHHHHHHHHHHHhhhhcCCcccccccCCCCCccccccCcccccCCcCCCCCCCCCCcceeccccCCCccccccCC
Confidence 33210 000 0000 0 0000
Q ss_pred --------------------------c---HH----HHHHHHHhc----------cCCCCCCcccc--chhHH----Hhh
Q psy3092 154 --------------------------P---VE----RILEAEQRV----------DMKQEPADQDI--VNEQQ----ATN 184 (347)
Q Consensus 154 --------------------------~---~~----~l~~~~~~~----------~~~~~~~~~~~--~~~~~----~~~ 184 (347)
+ ++ ++.++.... .+.... .+.+ ....+ |+.
T Consensus 208 ~~~d~t~~~~~~~~~s~~~~~~~p~~~~~e~d~laq~i~ksh~etq~~~e~lh~~~~~~~~-~e~I~~yq~k~~e~mWe~ 286 (479)
T KOG4216|consen 208 PICDSTPGSGYFPYCSFTNGETSPTVSMAELDHLAQNIIKSHLETQYLLEELHQITWQTFD-QEEIENYQNKGREEMWEL 286 (479)
T ss_pred CcccCCCCCCcccccccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-HHHHHHHHhhhHHHHHHH
Confidence 0 00 111111000 000000 0000 00001 112
Q ss_pred hhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchhhHH
Q psy3092 185 ICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGGIFD 264 (347)
Q Consensus 185 ~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~ 264 (347)
........+..+|||||.+++|.+|+++||+.|||.+.+++.+..++.. ++..+..++..|.+....-+...+..++..
T Consensus 287 cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~-~~v~~ntV~~e~~~~g~~~f~a~~~~elis 365 (479)
T KOG4216|consen 287 CAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRA-FDVDNNTVYFEGKYAGPEVFYALGCEELIS 365 (479)
T ss_pred HHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHh-hcccccceeecccccchhheeccChHHHHH
Confidence 2222344677889999999999999999999999999999888877643 455555666666666655555555556667
Q ss_pred hhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhhhhc
Q psy3092 265 RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPSLRS 344 (347)
Q Consensus 265 ~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~lr~ 344 (347)
+++ ++...+..|++++.|++|+.|++|.++++.||.+..+|+++++++..+|++.+..+|... .-+.+|+-.+|.||.
T Consensus 366 ~vf-~~~ksL~~Lq~te~EiAL~~alVL~~~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~~~-~~l~kl~~k~~~~r~ 443 (479)
T KOG4216|consen 366 RVF-EFGKSLCSLQLTEDEIALFSALVLMSADRSGLQEKVKIEKLQQKIQLALQHVLQKNHRED-GILTKLICKVSTLRA 443 (479)
T ss_pred HHH-hhhHHHHhhccCcHHHHHHHHHHhhCCccccccchHHHHHHHHHHHHHHHHHHHhcCChh-hhHHHhhcccchHHH
Confidence 766 788999999999999999999999999999999999999999999999999998876533 478899999999987
Q ss_pred cC
Q psy3092 345 IE 346 (347)
Q Consensus 345 i~ 346 (347)
++
T Consensus 444 ~~ 445 (479)
T KOG4216|consen 444 LC 445 (479)
T ss_pred HH
Confidence 64
No 4
>KOG4218|consensus
Probab=100.00 E-value=7.5e-47 Score=325.99 Aligned_cols=292 Identities=35% Similarity=0.620 Sum_probs=219.1
Q ss_pred CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
.+.|.||||+.+|||||-.+|+.|||||+|+|+.++.|.|..+.+|.||+..|.+|.+||||||+.|||+-++|+-+|.+
T Consensus 15 ~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMR 94 (475)
T KOG4218|consen 15 GELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMR 94 (475)
T ss_pred ccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhc
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999988764
Q ss_pred hhcc--------c-------------------------cccccC-C--CCCC------------------CCCc--H---
Q psy3092 135 TKER--------D-------------------------SNEVES-T--SGTL------------------IEMP--V--- 155 (347)
Q Consensus 135 ~~~~--------~-------------------------~~~~~~-~--~~~~------------------~~~~--~--- 155 (347)
.... + ....++ + ++.. ++.+ +
T Consensus 95 GGRNKFGpmYKrDRAlkqQkkAqirAng~KlE~~~~~~~~~~psp~~~ss~~q~lh~~~~kgL~~~~aa~pp~~~~l~~f 174 (475)
T KOG4218|consen 95 GGRNKFGPMYKRDRALKQQKKAQIRANGIKLEYIKTEYDAHLPSPTLSSSTNQQLHVSDFKGLAVLLAATPPDPLQLNEF 174 (475)
T ss_pred ccccccCchhhhhHHHHHHHHHHhhhcceeeeccccccCCCCCCCcccccccccccCCCcccchhhhccCCCCCcccccc
Confidence 2110 0 000000 0 0000 0000 0
Q ss_pred --------------------------HHHHHHHHhc---cCCC--------------CCC--------------------
Q psy3092 156 --------------------------ERILEAEQRV---DMKQ--------------EPA-------------------- 172 (347)
Q Consensus 156 --------------------------~~l~~~~~~~---~~~~--------------~~~-------------------- 172 (347)
.+.+..+... ...+ .+.
T Consensus 175 ~~~p~~ms~p~~HgsL~gY~tY~~fp~raikseyP~py~Sspqs~~~ygym~~~ss~sP~lP~lil~llk~epdE~qv~a 254 (475)
T KOG4218|consen 175 KQEPFDMSEPFIHGSLHGYPTYTSFPTRAIKSEYPMPYVSSPQSLVTYGYMTEASSTSPILPLLILPLLKTEPDEMQVTA 254 (475)
T ss_pred cCCCccccCccCCCcccCCcccCCCcchhhhhcCCCCcCCCCcccccccccCccccCCCCccccchhhhccCChhhhhcc
Confidence 0000000000 0000 000
Q ss_pred ------------ccccchhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--C
Q psy3092 173 ------------DQDIVNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--K 238 (347)
Q Consensus 173 ------------~~~~~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~ 238 (347)
......+..+.-.+++.+..+..+++||+.--.|.+|+.+||++||+++|.++++++..|+.... .
T Consensus 255 ~i~a~lq~~~ts~s~~~kp~~fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgke 334 (475)
T KOG4218|consen 255 PIDAQLQRIFTSVSGTSKPEKFGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKE 334 (475)
T ss_pred hhHHHHhhhhhcccCCCchhhhhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcc
Confidence 00001112334457788889999999999999999999999999999999999999998887644 3
Q ss_pred CceEecCCccccccchhhcC--chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHH
Q psy3092 239 DGILLAPGVTVYRSSAHEAG--VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTS 316 (347)
Q Consensus 239 ~~~~~~~g~~i~~~~~~~~~--~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~ 316 (347)
..+.+.+|..+.-.-..... ...-+-....++|.+++.|++|..||++|+-|+||+-|...|...+.|+.+++....+
T Consensus 335 gsi~lvtGqeV~~~~vA~qags~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LFsld~kfLenf~lv~~~qe~~naa 414 (475)
T KOG4218|consen 335 GSIKLVTGQEVPVGLVALQAGSLLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALFSLDMKFLENFELVRRLQEDSNAA 414 (475)
T ss_pred cceEEecCCcccchhHhhhhhhHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence 45667788776654332211 1112223346899999999999999999999999999998888899999999999999
Q ss_pred HHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092 317 LEEYTRVNHSEEPGRFAKLLLRLPSLRSIE 346 (347)
Q Consensus 317 L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~ 346 (347)
|.+|....+++....|+++++.|+.||.++
T Consensus 415 Lldyt~c~yp~~~~kF~qllL~L~eiRa~s 444 (475)
T KOG4218|consen 415 LLDYTSCCYPNWEQKFPQLLLVLEEIRATS 444 (475)
T ss_pred HHHhhccCCccHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999875
No 5
>KOG4846|consensus
Probab=100.00 E-value=6.6e-37 Score=270.38 Aligned_cols=82 Identities=50% Similarity=1.160 Sum_probs=77.3
Q ss_pred CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcc-cccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092 55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ 133 (347)
Q Consensus 55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~-~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~ 133 (347)
.-.|+||||.|+|+||||.+|+||||||||+|+.+..| .|-+..+|.|.++.|++||+|||+||+++||.+++|++.+.
T Consensus 132 ~~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m 211 (538)
T KOG4846|consen 132 ISLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQM 211 (538)
T ss_pred eEeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhccc
Confidence 45799999999999999999999999999999999999 79999999999999999999999999999999999998766
Q ss_pred hhh
Q psy3092 134 RTK 136 (347)
Q Consensus 134 ~~~ 136 (347)
+.+
T Consensus 212 ~~r 214 (538)
T KOG4846|consen 212 KFR 214 (538)
T ss_pred ccc
Confidence 543
No 6
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=100.00 E-value=1e-32 Score=237.91 Aligned_cols=168 Identities=75% Similarity=1.222 Sum_probs=156.9
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
...+.++++....+..+|+|+|++|+|..|+.+||+.|+|++|.+++++..+++++...+++++.+|..+.++.....++
T Consensus 30 ~~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~ 109 (207)
T cd06943 30 DPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQAGV 109 (207)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCceeccchhhhccc
Confidence 34678999999999999999999999999999999999999999999999999999888999999998887776655666
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL 339 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll 339 (347)
..++++++.+++.+|++|++|++||++|+||+|||||.+|+++...|+++|+++.++|++|+..++++++.||++||++|
T Consensus 110 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L 189 (207)
T cd06943 110 GAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRL 189 (207)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHH
Confidence 77788888899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccCC
Q psy3092 340 PSLRSIEV 347 (347)
Q Consensus 340 ~~lr~i~~ 347 (347)
|+||+|+.
T Consensus 190 ~~lr~l~~ 197 (207)
T cd06943 190 PALRSIGL 197 (207)
T ss_pred HHHHhHhH
Confidence 99999873
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=100.00 E-value=2.4e-32 Score=237.75 Aligned_cols=168 Identities=23% Similarity=0.371 Sum_probs=148.4
Q ss_pred hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc--eEecCCccccccchh
Q psy3092 178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG--ILLAPGVTVYRSSAH 255 (347)
Q Consensus 178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~--~~~~~g~~i~~~~~~ 255 (347)
...-.+.+++..+++++.+|+|||++|+|.+|+.+||+.|||++|.++++++.+||+++..+. +++++|..+.++...
T Consensus 26 ~~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~~ 105 (247)
T cd07076 26 TWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMT 105 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHHh
Confidence 345578899999999999999999999999999999999999999999999999999887654 577888888776654
Q ss_pred hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCch---H
Q psy3092 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPG---R 331 (347)
Q Consensus 256 ~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~---R 331 (347)
..+...+. +.+.+++.+|++|++|.+||+|||||+|||| |.+|+++...|+++|+++..+|.+|+..++++.+. |
T Consensus 106 ~~~~~~~~-~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~R 184 (247)
T cd07076 106 LPCMYDQC-KHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQR 184 (247)
T ss_pred hhhHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhH
Confidence 44443333 3466899999999999999999999999999 99999999999999999999999999988876554 9
Q ss_pred HHHHHhhhhhhhccC
Q psy3092 332 FAKLLLRLPSLRSIE 346 (347)
Q Consensus 332 f~~LL~ll~~lr~i~ 346 (347)
||+||++||+||+|+
T Consensus 185 F~kLLllLp~Lr~i~ 199 (247)
T cd07076 185 FYQLTKLLDSMHEVV 199 (247)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999999986
No 8
>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal doma
Probab=100.00 E-value=1.5e-31 Score=233.65 Aligned_cols=170 Identities=32% Similarity=0.550 Sum_probs=152.1
Q ss_pred chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchh-
Q psy3092 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH- 255 (347)
Q Consensus 177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~- 255 (347)
.....+..++++.++.++.+|+|||++|+|.+|+.+||+.|+|++|.++++++.++++....+.+.+.+|..+..+...
T Consensus 29 ~~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~~~~~~~~~~~~~~~ 108 (235)
T cd06949 29 TEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQGSC 108 (235)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCceecHHHhhh
Confidence 3455688899999999999999999999999999999999999999999999999999888888888888877766543
Q ss_pred hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCC-----CCCHHHHHHHHHHHHHHHHHHHHhcC---CC
Q psy3092 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRG-----LKSQQVVEMLREKVYTSLEEYTRVNH---SE 327 (347)
Q Consensus 256 ~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~-----l~~~~~i~~~r~~~~~~L~~y~~~~~---~~ 327 (347)
..++..+++.+. +++.+|++|++|++||++||||+|||||++| +++...|+++|+++..+|++|+..++ ++
T Consensus 109 ~~~~~~~~~~~~-~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~ 187 (235)
T cd06949 109 VEGMVEIFDMLL-ATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQ 187 (235)
T ss_pred cccHHHHHHHHH-HHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence 334455555544 8999999999999999999999999999999 88899999999999999999999888 88
Q ss_pred CchHHHHHHhhhhhhhccCC
Q psy3092 328 EPGRFAKLLLRLPSLRSIEV 347 (347)
Q Consensus 328 ~~~Rf~~LL~ll~~lr~i~~ 347 (347)
++.||++||++||.||+|++
T Consensus 188 ~~~Rf~~LLl~Lp~LR~l~~ 207 (235)
T cd06949 188 QSRRLAQLLLILSHIRHVSN 207 (235)
T ss_pred cccHHHHHHHhchHHHHhhH
Confidence 99999999999999999863
No 9
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=100.00 E-value=1e-31 Score=234.13 Aligned_cols=166 Identities=31% Similarity=0.540 Sum_probs=154.7
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..+++.....++.+|+|||.+|+|.+|+.+||+.|||++|.+++++..++++....+.+.+.+|..+.++.....++
T Consensus 38 ~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 117 (231)
T cd06937 38 GLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGF 117 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhhcCh
Confidence 45778899999999999999999999999999999999999999999999999998888888898998888777766677
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL 339 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll 339 (347)
+.++++++ +++.+|++|++|++||+||+||+||+||++|+.+...|+++|+++..+|++|+..++|+.+.||++||++|
T Consensus 118 ~~~~~~~~-~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~L 196 (231)
T cd06937 118 GPLTDLVF-TFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKI 196 (231)
T ss_pred HHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHh
Confidence 77777766 79999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccC
Q psy3092 340 PSLRSIE 346 (347)
Q Consensus 340 ~~lr~i~ 346 (347)
|+||+|+
T Consensus 197 p~LR~l~ 203 (231)
T cd06937 197 TDLRSIS 203 (231)
T ss_pred HHHHHHH
Confidence 9999986
No 10
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=100.00 E-value=1.4e-33 Score=209.97 Aligned_cols=82 Identities=49% Similarity=1.031 Sum_probs=77.7
Q ss_pred CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
...|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.|+...|..||+|||+||+++||++++||.+|+.
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~ 97 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI 97 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence 35699999999999999999999999999999999999999999999999999999999999999999999999999886
Q ss_pred hh
Q psy3092 135 TK 136 (347)
Q Consensus 135 ~~ 136 (347)
..
T Consensus 98 ~~ 99 (101)
T cd07160 98 RL 99 (101)
T ss_pred hh
Confidence 54
No 11
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=99.98 E-value=1.4e-33 Score=201.11 Aligned_cols=76 Identities=87% Similarity=1.653 Sum_probs=73.3
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHH
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER 132 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r 132 (347)
+|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..||+|||+||+++||++++||.+|
T Consensus 2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 5999999999999999999999999999999999999999999999999999999999999999999999999865
No 12
>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=99.98 E-value=1.9e-31 Score=233.66 Aligned_cols=166 Identities=40% Similarity=0.730 Sum_probs=150.2
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCC--CceEecCCccccccchhh-
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK--DGILLAPGVTVYRSSAHE- 256 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~--~~~~~~~g~~i~~~~~~~- 256 (347)
..+..++++.+..++.+|+|||++|+|..|+.+||+.|+|++|.+++++..+|+++..+ +.+.+++|..++++....
T Consensus 38 ~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~ 117 (237)
T cd06944 38 DTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLASQ 117 (237)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhhh
Confidence 45788999999999999999999999999999999999999999999999999998764 678889998887765432
Q ss_pred c--CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092 257 A--GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK 334 (347)
Q Consensus 257 ~--~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~ 334 (347)
. +...+.++ +.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++.++|++|+..++++++.||++
T Consensus 118 ~~~~~~~~~~~-i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~ 196 (237)
T cd06944 118 AGLGLSSLVDR-AQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQ 196 (237)
T ss_pred ccccHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHH
Confidence 2 23445555 56899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhhhhccC
Q psy3092 335 LLLRLPSLRSIE 346 (347)
Q Consensus 335 LL~ll~~lr~i~ 346 (347)
||++||+||+|+
T Consensus 197 LL~~Lp~Lr~is 208 (237)
T cd06944 197 LLLRLPEIRAIS 208 (237)
T ss_pred HHHHhHHHHHHH
Confidence 999999999987
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=99.98 E-value=1.4e-31 Score=235.07 Aligned_cols=167 Identities=26% Similarity=0.449 Sum_probs=155.4
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~ 258 (347)
...+..+++.....+..+|+|||++|+|..|+.+||+.|||++|.++++++.++++....+.+.+++|..+.++.....+
T Consensus 51 ~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 (243)
T cd06935 51 LEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKNGG 130 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCeEeeHHHHHhcC
Confidence 44578889999999999999999999999999999999999999999999999998777888999999888877777777
Q ss_pred chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338 (347)
Q Consensus 259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l 338 (347)
++.+.+.++ +++.+|++|++|++||++|+||+||+||++|+++...|+++|+.+..+|++|+..++++.+.||++||++
T Consensus 131 ~~~~~~~i~-~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~ 209 (243)
T cd06935 131 LGVVSDAIF-DLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMK 209 (243)
T ss_pred hHHHHHHHH-HHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHH
Confidence 777777655 8999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccC
Q psy3092 339 LPSLRSIE 346 (347)
Q Consensus 339 l~~lr~i~ 346 (347)
||.||+|+
T Consensus 210 L~~LR~i~ 217 (243)
T cd06935 210 VTDLRMIG 217 (243)
T ss_pred HHHHHHHH
Confidence 99999986
No 14
>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=99.98 E-value=2.7e-31 Score=224.70 Aligned_cols=166 Identities=28% Similarity=0.503 Sum_probs=152.7
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..+.+.....+..+|+|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+.+.+|..+.++.....++
T Consensus 12 ~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 91 (189)
T cd06940 12 EIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLHSMGA 91 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCcEEcHHHHHHcCc
Confidence 45778888889999999999999999999999999999999999999999999877777778888998887776666667
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL 339 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll 339 (347)
+.+.+.++ +++.+|++|++|++||++|+||+|||||++|+.+...|+++|+++..+|++|+..++|+.+.||++||++|
T Consensus 92 ~~~~~~~~-~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL~~L 170 (189)
T cd06940 92 GDLLNSMF-DFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKL 170 (189)
T ss_pred HHHHHHHH-HHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHH
Confidence 77777765 89999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccC
Q psy3092 340 PSLRSIE 346 (347)
Q Consensus 340 ~~lr~i~ 346 (347)
|+||+|+
T Consensus 171 ~~LR~l~ 177 (189)
T cd06940 171 PDLRTLN 177 (189)
T ss_pred HHHHHHH
Confidence 9999986
No 15
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=99.97 E-value=2.1e-33 Score=203.70 Aligned_cols=81 Identities=52% Similarity=1.164 Sum_probs=77.5
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhhc
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTKE 137 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~~ 137 (347)
|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+|++..+
T Consensus 2 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~ 81 (85)
T cd06961 2 CVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAK 81 (85)
T ss_pred CceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988654
Q ss_pred c
Q psy3092 138 R 138 (347)
Q Consensus 138 ~ 138 (347)
+
T Consensus 82 ~ 82 (85)
T cd06961 82 R 82 (85)
T ss_pred c
Confidence 3
No 16
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=99.97 E-value=4.9e-31 Score=230.67 Aligned_cols=167 Identities=21% Similarity=0.407 Sum_probs=145.8
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc--eEecCCccccccchhh
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG--ILLAPGVTVYRSSAHE 256 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~--~~~~~g~~i~~~~~~~ 256 (347)
...+..++++.+++++.+|+|||++|+|.+|+.+||+.|||++|.++++++.+|+++...+. +.+.+|..+.++....
T Consensus 27 ~~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~ 106 (246)
T cd06947 27 ARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQ 106 (246)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHHhhh
Confidence 45578999999999999999999999999999999999999999999999999998876543 5667777776665544
Q ss_pred cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC---CCchHH
Q psy3092 257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNHS---EEPGRF 332 (347)
Q Consensus 257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~---~~~~Rf 332 (347)
.+...+.. .+.+++.+|++|++|++||+||+||+|||| +++|+++...|+++|+++..+|.+|+..+++ +.+.||
T Consensus 107 ~~~~~~~~-~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~Rf 185 (246)
T cd06947 107 SAMYSLCL-GMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQRF 185 (246)
T ss_pred ccHHHHHH-HHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHH
Confidence 45554333 345899999999999999999999999999 7999999999999999999999999987764 558999
Q ss_pred HHHHhhhhhhhccC
Q psy3092 333 AKLLLRLPSLRSIE 346 (347)
Q Consensus 333 ~~LL~ll~~lr~i~ 346 (347)
|+||++||.||+|+
T Consensus 186 ~kLLllLp~Lr~i~ 199 (246)
T cd06947 186 YQLTKLLDSMHDLV 199 (246)
T ss_pred HHHHHhhhhHHHHH
Confidence 99999999999986
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=99.97 E-value=7.4e-31 Score=228.52 Aligned_cols=167 Identities=24% Similarity=0.399 Sum_probs=147.4
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc--eEecCCccccccchhh
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG--ILLAPGVTVYRSSAHE 256 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~--~~~~~g~~i~~~~~~~ 256 (347)
...+..+++..+++++.+|+|||++|+|.+|+.+||+.|||++|.+++++..+||+++..+. +.+.+|..+..+....
T Consensus 27 ~~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~~~ 106 (248)
T cd07075 27 ENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMHQ 106 (248)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHHhh
Confidence 34578999999999999999999999999999999999999999999999999999887543 7778888877776655
Q ss_pred cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCC-CCCCCCHHHHHHHHHHHHHHHHHHHHhcCC---CCchHH
Q psy3092 257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD-VRGLKSQQVVEMLREKVYTSLEEYTRVNHS---EEPGRF 332 (347)
Q Consensus 257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~-~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~---~~~~Rf 332 (347)
.+..++ .+.+.+++.+|++|++|++||+||+||+||||| ++||++...|+++|+++..+|++|+..+++ +.+.||
T Consensus 107 ~~~~~~-~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~~RF 185 (248)
T cd07075 107 SAMYEL-CQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSWQRF 185 (248)
T ss_pred ccHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccchhHH
Confidence 555553 344668999999999999999999999999996 799999999999999999999999996655 356999
Q ss_pred HHHHhhhhhhhccC
Q psy3092 333 AKLLLRLPSLRSIE 346 (347)
Q Consensus 333 ~~LL~ll~~lr~i~ 346 (347)
|+|+++||.||+|+
T Consensus 186 ~~LLllLp~Lr~i~ 199 (248)
T cd07075 186 YQLTKLLDSMHDLV 199 (248)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999986
No 18
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=99.97 E-value=1.3e-33 Score=204.51 Aligned_cols=79 Identities=53% Similarity=1.244 Sum_probs=75.9
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
.+|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.+++..|..||+|||+||+++||++++||.+|++
T Consensus 5 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~ 83 (85)
T cd06964 5 KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK 83 (85)
T ss_pred CCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence 4699999999999999999999999999999988999999999999999999999999999999999999999999876
No 19
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=99.97 E-value=3e-33 Score=206.82 Aligned_cols=81 Identities=52% Similarity=1.073 Sum_probs=76.7
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT 135 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~ 135 (347)
..|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.+++..|..||+|||+||+++||++++||.+|+..
T Consensus 5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~ 84 (97)
T cd07170 5 RLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRG 84 (97)
T ss_pred CCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCC
Confidence 45999999999999999999999999999999999999999999999999999999999999999999999999988764
Q ss_pred h
Q psy3092 136 K 136 (347)
Q Consensus 136 ~ 136 (347)
.
T Consensus 85 ~ 85 (97)
T cd07170 85 G 85 (97)
T ss_pred C
Confidence 3
No 20
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=99.97 E-value=7.9e-33 Score=198.78 Aligned_cols=78 Identities=49% Similarity=1.112 Sum_probs=74.4
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ 133 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~ 133 (347)
..|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..||+|||+||+++||++++|+.+|.
T Consensus 4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~ 81 (82)
T cd07171 4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERR 81 (82)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhhc
Confidence 459999999999999999999999999999998999999999999999999999999999999999999999998763
No 21
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=99.97 E-value=6e-33 Score=203.25 Aligned_cols=83 Identities=52% Similarity=1.066 Sum_probs=77.6
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT 135 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~ 135 (347)
+.|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+++-.
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~ 81 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCA 81 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhh
Confidence 35999999999999999999999999999999999999999999999999999999999999999999999999997765
Q ss_pred hcc
Q psy3092 136 KER 138 (347)
Q Consensus 136 ~~~ 138 (347)
.++
T Consensus 82 ~~~ 84 (91)
T cd07161 82 IKR 84 (91)
T ss_pred HHH
Confidence 443
No 22
>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=99.97 E-value=7.8e-31 Score=229.41 Aligned_cols=167 Identities=31% Similarity=0.526 Sum_probs=146.9
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchhh-
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAHE- 256 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~~- 256 (347)
..+..++++.+..++.+|+|+|++|+|..|+.+||+.|||++|.+++++..+|+++.. .+.+.+++|..++.+....
T Consensus 38 ~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~ 117 (237)
T cd07070 38 APFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAAQ 117 (237)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHHHH
Confidence 4578899999999999999999999999999999999999999999999999998754 4678888998887665422
Q ss_pred cCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092 257 AGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK 334 (347)
Q Consensus 257 ~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~ 334 (347)
.+. .... ..+.+++.+|++|++|.+||++|+||+|||||.+|+++...|+++|+++..+|.+|+..++|+.+.||++
T Consensus 118 ~~~~~~~~~-~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~k 196 (237)
T cd07070 118 AGSLLHSLV-LRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQ 196 (237)
T ss_pred HhHHHHHHH-HHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHH
Confidence 221 1122 2246899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhhhhccCC
Q psy3092 335 LLLRLPSLRSIEV 347 (347)
Q Consensus 335 LL~ll~~lr~i~~ 347 (347)
||++||+||+|+.
T Consensus 197 LLl~Lp~LRsis~ 209 (237)
T cd07070 197 LLLRLVEVRALSM 209 (237)
T ss_pred HHHHhHHHHHhhH
Confidence 9999999999873
No 23
>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=99.97 E-value=1.2e-30 Score=223.83 Aligned_cols=168 Identities=37% Similarity=0.638 Sum_probs=143.1
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~ 258 (347)
....+.+++++.+.++.+|+|+|++|+|..|+.+||+.|+|++|.+++++..++++...++..++.++............
T Consensus 25 ~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~~~~~~~~ 104 (206)
T cd06950 25 EVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERT 104 (206)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCcccccccchhhH
Confidence 35678999999999999999999999999999999999999999999999999998877665555543332222211111
Q ss_pred chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338 (347)
Q Consensus 259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l 338 (347)
+.... +.+.+++.+|++|++|++||++||||+|||||++|+++...|+++|+++..+|++|+..++++++.||++||++
T Consensus 105 ~~~~~-~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf~kLLl~ 183 (206)
T cd06950 105 FLSEV-RALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLL 183 (206)
T ss_pred HHHHH-HHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHH
Confidence 11222 44678999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCC
Q psy3092 339 LPSLRSIEV 347 (347)
Q Consensus 339 l~~lr~i~~ 347 (347)
||+||+++.
T Consensus 184 Lp~lr~ls~ 192 (206)
T cd06950 184 LPSLRFISS 192 (206)
T ss_pred HHHHHhhhH
Confidence 999999873
No 24
>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=99.97 E-value=1.6e-30 Score=227.40 Aligned_cols=167 Identities=23% Similarity=0.427 Sum_probs=144.7
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC-C-CceEecCCccccccchhh
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV-K-DGILLAPGVTVYRSSAHE 256 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~-~-~~~~~~~g~~i~~~~~~~ 256 (347)
....+.++++.+++++.+|+|||++|+|.+|+.+||+.|||++|.++++++.+|+++.. + +.+.+.+|..+.......
T Consensus 27 ~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~~~~ 106 (246)
T cd07073 27 AALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK 106 (246)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhhhcc
Confidence 34577899999999999999999999999999999999999999999999999999876 3 347888887766554433
Q ss_pred cCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC---CCchHH
Q psy3092 257 AGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVNHS---EEPGRF 332 (347)
Q Consensus 257 ~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~---~~~~Rf 332 (347)
.+......+ +.+++.+|++|++|.+||+|||||+|||| +.+|+++...|+++|+++..+|.+|+..+++ +.+.||
T Consensus 107 ~~~~~~~~~-l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~Rf 185 (246)
T cd07073 107 SRMYSQCVR-MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRF 185 (246)
T ss_pred ccHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHH
Confidence 333344333 34899999999999999999999999999 8999999999999999999999999987642 568999
Q ss_pred HHHHhhhhhhhccC
Q psy3092 333 AKLLLRLPSLRSIE 346 (347)
Q Consensus 333 ~~LL~ll~~lr~i~ 346 (347)
++||++||+||+|+
T Consensus 186 ~kLLl~Lp~LRsi~ 199 (246)
T cd07073 186 YQLTKLLDSVQPIA 199 (246)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999986
No 25
>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=99.97 E-value=2.5e-30 Score=225.37 Aligned_cols=167 Identities=39% Similarity=0.690 Sum_probs=152.0
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~ 258 (347)
..+..+++..|..+++.+++|+|+||+|+.|+.+||+.|+|++|.+++++..+++++..++.+++++|..++.+... .+
T Consensus 31 ~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~l~~~~g~~~~~~~~~-~~ 109 (222)
T cd06931 31 IASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHCPE-PE 109 (222)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCCeeeeCCCccccccccc-ch
Confidence 35678999999999999999999999999999999999999999999999999999888888999999877665433 34
Q ss_pred chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhh
Q psy3092 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLR 338 (347)
Q Consensus 259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~l 338 (347)
+..+..+++.+++.+|++|++|++||++|+||++|+|+.+|+++...++++|+++.++|.+|+..++++++.||++||++
T Consensus 110 ~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL~~ 189 (222)
T cd06931 110 ISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLL 189 (222)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHH
Confidence 45566777788999999999999999999999999999999999999999999999999999988888999999999999
Q ss_pred hhhhhccC
Q psy3092 339 LPSLRSIE 346 (347)
Q Consensus 339 l~~lr~i~ 346 (347)
+|.||+++
T Consensus 190 l~~lr~~~ 197 (222)
T cd06931 190 LPTLQSIT 197 (222)
T ss_pred HHHHHHHH
Confidence 99999875
No 26
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=99.97 E-value=6.7e-33 Score=196.76 Aligned_cols=75 Identities=55% Similarity=1.140 Sum_probs=72.5
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEER 132 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r 132 (347)
|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.+++..|..||+|||+||+++||++++||.+|
T Consensus 1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 899999999999999999999999999999889999999999999999999999999999999999999999865
No 27
>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=99.97 E-value=8.7e-31 Score=228.00 Aligned_cols=164 Identities=27% Similarity=0.504 Sum_probs=150.4
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..+++.....+..+++|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+++.+|..+.+... ..++
T Consensus 41 ~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~~-~~~~ 119 (238)
T cd07348 41 SDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQC-VRGF 119 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHHH-HhhH
Confidence 457888999999999999999999999999999999999999999999999999998888899999988876653 4566
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc--CCCCchHHHHHHh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVN--HSEEPGRFAKLLL 337 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~--~~~~~~Rf~~LL~ 337 (347)
+++.+.++ +++.+|++|++|.+||+||+||+|| ||++||++...|+++|+++..+|++|+..+ +++.+.||++||+
T Consensus 120 ~~~~~~i~-ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl 197 (238)
T cd07348 120 GDWIDSIL-EFSQSLHRMNLDVSAFSCLAALVII-TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLG 197 (238)
T ss_pred HHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHc-CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHH
Confidence 77777755 8999999999999999999999999 799999999999999999999999999875 4789999999999
Q ss_pred hhhhhhccC
Q psy3092 338 RLPSLRSIE 346 (347)
Q Consensus 338 ll~~lr~i~ 346 (347)
+||+||+|+
T Consensus 198 ~Lp~LRsl~ 206 (238)
T cd07348 198 KLPELRTLC 206 (238)
T ss_pred HHHHHHHHH
Confidence 999999986
No 28
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=99.97 E-value=1.3e-32 Score=201.58 Aligned_cols=80 Identities=56% Similarity=1.145 Sum_probs=76.6
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT 135 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~ 135 (347)
..|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|++.
T Consensus 7 ~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~ 86 (90)
T cd07168 7 KLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPG 86 (90)
T ss_pred CCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCC
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999998864
No 29
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=99.97 E-value=6e-33 Score=200.35 Aligned_cols=80 Identities=49% Similarity=1.053 Sum_probs=75.7
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT 135 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~ 135 (347)
..|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.++...|..||+|||+||+++||++++|+.+++..
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~ 81 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCK 81 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHHh
Confidence 35999999999999999999999999999999999999999999999999999999999999999999999999887653
No 30
>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin
Probab=99.97 E-value=3.1e-30 Score=224.15 Aligned_cols=167 Identities=35% Similarity=0.649 Sum_probs=150.6
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~ 258 (347)
...+..++++..+.++.+++|+|.+|+|..|+.+||+.|+|++|.+++++..|++++..++.+.+++|..+.++.....+
T Consensus 26 ~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~ 105 (221)
T cd07068 26 VSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARVEG 105 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCCeEEeCCCceECHHHHhhcc
Confidence 45688999999999999999999999999999999999999999999999999999888887888888766655444445
Q ss_pred chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHh
Q psy3092 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLL 337 (347)
Q Consensus 259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~ 337 (347)
...+.+. +.+++.+|++|++|++||++|+||++||||++|+.+...|+++|+++.++|++|+..+++ +++.||++||+
T Consensus 106 ~~~~~~~-~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~LL~ 184 (221)
T cd07068 106 LLEIFDM-LLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLL 184 (221)
T ss_pred HHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHH
Confidence 5555554 468999999999999999999999999999999999999999999999999999999999 99999999999
Q ss_pred hhhhhhccC
Q psy3092 338 RLPSLRSIE 346 (347)
Q Consensus 338 ll~~lr~i~ 346 (347)
+++.||+++
T Consensus 185 ~l~~Lr~~~ 193 (221)
T cd07068 185 LLPHLRQAS 193 (221)
T ss_pred hccHHHHHH
Confidence 999999875
No 31
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=99.97 E-value=5.6e-33 Score=202.14 Aligned_cols=80 Identities=64% Similarity=1.349 Sum_probs=76.6
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT 135 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~ 135 (347)
..|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.+++..|..|++|||+||+++||++++||.+|++.
T Consensus 4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~ 83 (87)
T cd06967 4 ELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPI 83 (87)
T ss_pred CCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCC
Confidence 45999999999999999999999999999999999999999999999999999999999999999999999999998864
No 32
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=99.97 E-value=5.2e-33 Score=203.74 Aligned_cols=79 Identities=58% Similarity=1.262 Sum_probs=75.4
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCC-CCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREG-RNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT 135 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~-~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~ 135 (347)
.|.|||++++|+||||.+|+|||+||||++.++..|.|..+ ++|.++...|..||+|||+||+++||++++||.+|++.
T Consensus 8 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~ 87 (92)
T cd06970 8 LCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR 87 (92)
T ss_pred CCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCcc
Confidence 49999999999999999999999999999999999999985 89999999999999999999999999999999998854
No 33
>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=99.97 E-value=2e-30 Score=217.88 Aligned_cols=165 Identities=31% Similarity=0.540 Sum_probs=148.9
Q ss_pred HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCch
Q psy3092 181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVG 260 (347)
Q Consensus 181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~ 260 (347)
.+..+++..+..+..+++|+|++|+|..|+.+||+.|+|++|.+++++..++++....+.+.+++|.....+.....+..
T Consensus 3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (174)
T cd06929 3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSRDVLLNGGFG 82 (174)
T ss_pred HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcccCCeEEecCCceecHHHHHHcccH
Confidence 36788899999999999999999999999999999999999999999999997777677888889887655544444555
Q ss_pred hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhh
Q psy3092 261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP 340 (347)
Q Consensus 261 ~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~ 340 (347)
.+.+++. +++.+|++|++|++||++|+||+||+|+.+|+++...+++.|+++..+|++|+..++++++.||++||++++
T Consensus 83 ~~~~~~~-~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~Ll~~l~ 161 (174)
T cd06929 83 EFIEPLF-EFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLT 161 (174)
T ss_pred HHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHhH
Confidence 6666655 699999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccC
Q psy3092 341 SLRSIE 346 (347)
Q Consensus 341 ~lr~i~ 346 (347)
.||.++
T Consensus 162 ~lr~l~ 167 (174)
T cd06929 162 ELRTLN 167 (174)
T ss_pred HHHHHH
Confidence 999876
No 34
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=99.97 E-value=1.6e-32 Score=196.35 Aligned_cols=77 Identities=58% Similarity=1.316 Sum_probs=74.5
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+|++
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 77 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP 77 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence 89999999999999999999999999999988999999999999999999999999999999999999999998874
No 35
>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=99.97 E-value=3.2e-30 Score=214.76 Aligned_cols=162 Identities=44% Similarity=0.812 Sum_probs=144.1
Q ss_pred hhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchhhcCch
Q psy3092 183 TNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAHEAGVG 260 (347)
Q Consensus 183 ~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~~~~~~ 260 (347)
+.++++..+.++.+++|+|.+|+|..|+.+||+.|+|++|.+++++..|++++.. .+.+.+++|..+..+.....+..
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 4678888999999999999999999999999999999999999999999999876 45677888887776654433334
Q ss_pred hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhh
Q psy3092 261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLP 340 (347)
Q Consensus 261 ~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~ 340 (347)
.+.+ .+.+++.+|++|++|++||++|+||++|+|+++|+++...+++.|+++.++|++|+..++++++.||++||+++|
T Consensus 82 ~~~~-~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~ll~~l~ 160 (165)
T cd06930 82 ELVQ-RLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLP 160 (165)
T ss_pred HHHH-HHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhH
Confidence 4444 456899999999999999999999999999999999999999999999999999999888899999999999999
Q ss_pred hhhcc
Q psy3092 341 SLRSI 345 (347)
Q Consensus 341 ~lr~i 345 (347)
.||+|
T Consensus 161 ~lr~~ 165 (165)
T cd06930 161 ELRSI 165 (165)
T ss_pred hhccC
Confidence 99986
No 36
>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-
Probab=99.97 E-value=3.9e-30 Score=223.71 Aligned_cols=167 Identities=30% Similarity=0.555 Sum_probs=148.5
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcC
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAG 258 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~ 258 (347)
...+..++++..+.++.+++|+|++|+|..|+.+||+.|||++|.+++++..+++++..++.+++.+|....+......+
T Consensus 26 ~~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~ 105 (221)
T cd06946 26 IKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEELAREAG 105 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCceeecCCeEEcHHHHhhcC
Confidence 35578899999999999999999999999999999999999999999999999999988888888777655544443344
Q ss_pred chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHh
Q psy3092 259 VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLL 337 (347)
Q Consensus 259 ~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~ 337 (347)
...+. +.+.+++.+|++|++|++||++|+||+||||+..++++.+.|+++|+++.++|.+||..+++ +++.||++||+
T Consensus 106 ~~~~~-~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~LL~ 184 (221)
T cd06946 106 LLELY-SACLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLL 184 (221)
T ss_pred HHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHh
Confidence 44444 34568999999999999999999999999999999999999999999999999999998888 89999999999
Q ss_pred hhhhhhccC
Q psy3092 338 RLPSLRSIE 346 (347)
Q Consensus 338 ll~~lr~i~ 346 (347)
++|.||+++
T Consensus 185 ~l~~Lr~~~ 193 (221)
T cd06946 185 TLPLLRQTD 193 (221)
T ss_pred hchhHHHHH
Confidence 999999875
No 37
>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=99.97 E-value=3.1e-30 Score=225.79 Aligned_cols=166 Identities=35% Similarity=0.610 Sum_probs=145.2
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccC--CCceEecCCccccccchh--
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISV--KDGILLAPGVTVYRSSAH-- 255 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~--~~~~~~~~g~~i~~~~~~-- 255 (347)
..+..++++.+..++.+|+|||++|+|.+|+.+||+.|||++|.++++++.++++... .+.+.+.+|..++.....
T Consensus 40 ~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~~ 119 (241)
T cd07069 40 STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQ 119 (241)
T ss_pred chHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhhh
Confidence 4578899999999999999999999999999999999999999999999999998754 355777788765543211
Q ss_pred -hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHH
Q psy3092 256 -EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAK 334 (347)
Q Consensus 256 -~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~ 334 (347)
..++..+. +.+.+++.+|++|++|.+||++||||+|||||++|+++...|+++|+++..+|++|+..++|+.+.||++
T Consensus 120 ~~~~~~~~~-~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~k 198 (241)
T cd07069 120 AGATLNNLM-SHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQ 198 (241)
T ss_pred hhhHHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHH
Confidence 11233333 4467999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhhhhccC
Q psy3092 335 LLLRLPSLRSIE 346 (347)
Q Consensus 335 LL~ll~~lr~i~ 346 (347)
||++||+||+|+
T Consensus 199 LLl~Lp~LR~is 210 (241)
T cd07069 199 LLLRLPEIRAIS 210 (241)
T ss_pred HHHHhHHHHHhh
Confidence 999999999986
No 38
>cd06957 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members
Probab=99.97 E-value=3.8e-33 Score=201.11 Aligned_cols=79 Identities=57% Similarity=1.229 Sum_probs=74.9
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCccccc-CCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACR-EGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK 136 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~-~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~ 136 (347)
|.|||++++|+||||.+|+|||+||||++.++..|.|. .+++|.++...|..||+|||+||+++||++++||.+|++.+
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~ 80 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK 80 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCC
Confidence 89999999999999999999999999999999999999 56899999999999999999999999999999999887654
No 39
>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=99.97 E-value=3e-30 Score=224.87 Aligned_cols=164 Identities=28% Similarity=0.508 Sum_probs=149.4
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+++.+|..+.+... ..++
T Consensus 41 ~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~~-~~~~ 119 (238)
T cd07071 41 QHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC-VRGF 119 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhhh-hhcH
Confidence 457788899999999999999999999999999999999999999999999999988888899999988776553 3566
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC--CCCchHHHHHHh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH--SEEPGRFAKLLL 337 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~--~~~~~Rf~~LL~ 337 (347)
+.+++.+ .+++.+|++|++|++||+||+||+|| +|++|+.+...|+++|+++..+|++|+..++ ++.+.||++||+
T Consensus 120 ~~~~~~i-~ef~~~l~~L~ld~~E~alLkAIvLf-~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl 197 (238)
T cd07071 120 GEWIDSI-VEFSSNLQNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLG 197 (238)
T ss_pred HHHHHHH-HHHHHHHHhcCCCHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHH
Confidence 7777776 48999999999999999999999999 5999999999999999999999999998764 589999999999
Q ss_pred hhhhhhccC
Q psy3092 338 RLPSLRSIE 346 (347)
Q Consensus 338 ll~~lr~i~ 346 (347)
+||+||+|+
T Consensus 198 ~Lp~LRsl~ 206 (238)
T cd07071 198 KLPELRTLC 206 (238)
T ss_pred HhHHHHHHH
Confidence 999999986
No 40
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=8.3e-33 Score=203.43 Aligned_cols=80 Identities=50% Similarity=1.198 Sum_probs=75.5
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccC--CCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACRE--GRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ 133 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~--~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~ 133 (347)
..|.|||++++|+||||.+|+|||+||||++..+..|.|.. +++|.+++..|..||+|||+||+++||++++||.+|+
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~ 86 (92)
T cd07163 7 IPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERG 86 (92)
T ss_pred CCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccC
Confidence 45999999999999999999999999999999999999997 4799999999999999999999999999999999888
Q ss_pred hh
Q psy3092 134 RT 135 (347)
Q Consensus 134 ~~ 135 (347)
+.
T Consensus 87 p~ 88 (92)
T cd07163 87 PR 88 (92)
T ss_pred cC
Confidence 64
No 41
>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee
Probab=99.97 E-value=2.6e-30 Score=227.05 Aligned_cols=167 Identities=26% Similarity=0.407 Sum_probs=149.6
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..++++....+..+|+|||.+|+|..|+.+||+.|||++|.+++++..++++....+.+.+++|..+.++.....+.
T Consensus 43 ~~~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 122 (236)
T cd06954 43 QRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFARAGL 122 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCccccHHHHHHhcC
Confidence 45677788888899999999999999999999999999999999999999999987778888999998877766543443
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL 339 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll 339 (347)
...+.+.+.+++.+|++|++|++||++|+||+|||||++|+++...|+++|+++..+|++|+..++|+.+.||++||++|
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 33333445589999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccC
Q psy3092 340 PSLRSIE 346 (347)
Q Consensus 340 ~~lr~i~ 346 (347)
++||+|+
T Consensus 203 ~~Lr~l~ 209 (236)
T cd06954 203 VSLRTLS 209 (236)
T ss_pred HHHHHHH
Confidence 9999986
No 42
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=99.97 E-value=1.9e-32 Score=197.20 Aligned_cols=79 Identities=52% Similarity=1.170 Sum_probs=75.9
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK 136 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~ 136 (347)
|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.+++..|..|++|||+||+++||++++||.+|++.+
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~ 79 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR 79 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence 8999999999999999999999999999998999999999999999999999999999999999999999999988754
No 43
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=99.97 E-value=9.7e-33 Score=201.78 Aligned_cols=82 Identities=52% Similarity=1.171 Sum_probs=77.0
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcc-cccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~-~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
.+|.|||++++|+||||.+|+||++||||++..+..| .|..+++|.+++..|..|++|||+||+++||++++||.+|++
T Consensus 4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~ 83 (89)
T cd07166 4 VLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIP 83 (89)
T ss_pred CCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCCC
Confidence 4699999999999999999999999999999988999 599999999999999999999999999999999999999887
Q ss_pred hhc
Q psy3092 135 TKE 137 (347)
Q Consensus 135 ~~~ 137 (347)
.++
T Consensus 84 ~~~ 86 (89)
T cd07166 84 KRE 86 (89)
T ss_pred Ccc
Confidence 543
No 44
>cd07167 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regu
Probab=99.97 E-value=2.8e-32 Score=200.06 Aligned_cols=78 Identities=60% Similarity=1.255 Sum_probs=75.1
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT 135 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~ 135 (347)
|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|.+.
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~ 78 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRG 78 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999988753
No 45
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=2.8e-32 Score=199.53 Aligned_cols=80 Identities=55% Similarity=1.220 Sum_probs=76.2
Q ss_pred CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
...|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|.+
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 85 (90)
T cd07169 6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP 85 (90)
T ss_pred CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccCC
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999998764
No 46
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=99.97 E-value=4.1e-30 Score=219.35 Aligned_cols=164 Identities=27% Similarity=0.447 Sum_probs=145.6
Q ss_pred HhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCchh
Q psy3092 182 ATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGVGG 261 (347)
Q Consensus 182 ~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~~~ 261 (347)
+..+.+..+..+..+|+|||++|+|+.|+.+||+.|+|++|.+++++..++++....+.+.+.+|..+..+.........
T Consensus 4 w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (195)
T cd06941 4 WQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDSD 83 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCeEEecCCeEeeHHHHHhccchH
Confidence 56778888999999999999999999999999999999999999999999877666678888898887765543222223
Q ss_pred hHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhhhh
Q psy3092 262 IFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRLPS 341 (347)
Q Consensus 262 ~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll~~ 341 (347)
+.+ .+.+++.+|++|++|++||++|+||+||+||++|+++...|+++|+++..+|++|+..++++.+.||++||++||+
T Consensus 84 ~~~-~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~ 162 (195)
T cd06941 84 FVK-ALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPE 162 (195)
T ss_pred HHH-HHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHH
Confidence 444 4568999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccC
Q psy3092 342 LRSIE 346 (347)
Q Consensus 342 lr~i~ 346 (347)
||+|+
T Consensus 163 Lr~l~ 167 (195)
T cd06941 163 LRSIG 167 (195)
T ss_pred HHHHH
Confidence 99886
No 47
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=99.97 E-value=1.5e-32 Score=202.67 Aligned_cols=82 Identities=37% Similarity=0.891 Sum_probs=77.8
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK 136 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~ 136 (347)
.|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|+...
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~ 81 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSE 81 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhH
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999988765
Q ss_pred cc
Q psy3092 137 ER 138 (347)
Q Consensus 137 ~~ 138 (347)
++
T Consensus 82 ~r 83 (94)
T cd06966 82 KR 83 (94)
T ss_pred HH
Confidence 44
No 48
>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=99.97 E-value=4.3e-30 Score=222.35 Aligned_cols=167 Identities=24% Similarity=0.356 Sum_probs=139.3
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce----------EecCCccc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI----------LLAPGVTV 249 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~----------~~~~g~~i 249 (347)
.+...+++...+.++.+|+|||++|+|..|+.+||+.|||++|.++++++.++++...++.. +..++...
T Consensus 19 ~~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~ 98 (222)
T cd06951 19 CAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMHW 98 (222)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhcccccc
Confidence 45788999999999999999999999999999999999999999999999999987665432 22222222
Q ss_pred cccch--hhcCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Q psy3092 250 YRSSA--HEAGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNH 325 (347)
Q Consensus 250 ~~~~~--~~~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~ 325 (347)
..... ...+. ...+.+.+.+++.+|++|++|++||++|+||+|||||++|+ +...|+++|+++..+|++|+..++
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~ 177 (222)
T cd06951 99 GGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMTR 177 (222)
T ss_pred ccccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhhC
Confidence 21110 00111 11233557799999999999999999999999999999999 999999999999999999999999
Q ss_pred CCCchHHHHHHhhhhhhhccCC
Q psy3092 326 SEEPGRFAKLLLRLPSLRSIEV 347 (347)
Q Consensus 326 ~~~~~Rf~~LL~ll~~lr~i~~ 347 (347)
++.+.||++||++||+||+|++
T Consensus 178 p~~~~Rf~kLLl~Lp~LRsl~~ 199 (222)
T cd06951 178 PLEQLRSARLLLMLSLLRGIKT 199 (222)
T ss_pred CCcccHHHHHHHHhHHhhcCCH
Confidence 9999999999999999999973
No 49
>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=99.97 E-value=5.1e-30 Score=224.35 Aligned_cols=165 Identities=29% Similarity=0.502 Sum_probs=152.0
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..+++.....+..+++|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+++++|..+.++.. ..++
T Consensus 41 ~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~~-~~~~ 119 (239)
T cd06945 41 QQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQC-VRGF 119 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHHH-HHhH
Confidence 457888899999999999999999999999999999999999999999999999988888889999988777653 3456
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHHHh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKLLL 337 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~LL~ 337 (347)
+.+++.++ +++.+|++|++|++||++|+||+||+||++|+++...|+++|+++..+|++|+..+++ +.+.||++||+
T Consensus 120 ~~~~~~i~-~f~~~l~~L~ld~~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl 198 (239)
T cd06945 120 GEWLDSIL-AFSSSLQSLLLDDISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLL 198 (239)
T ss_pred HHHHHHHH-HHHHHHHHHhCChHHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHH
Confidence 66777755 7999999999999999999999999999999999999999999999999999999998 89999999999
Q ss_pred hhhhhhccC
Q psy3092 338 RLPSLRSIE 346 (347)
Q Consensus 338 ll~~lr~i~ 346 (347)
+||+||+|+
T Consensus 199 ~Lp~LR~ls 207 (239)
T cd06945 199 KLPELRTLS 207 (239)
T ss_pred HhHHHHHHH
Confidence 999999986
No 50
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=99.97 E-value=2.1e-32 Score=195.11 Aligned_cols=76 Identities=64% Similarity=1.406 Sum_probs=73.4
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHh
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQ 133 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~ 133 (347)
|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+||
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 8999999999999999999999999999998889999999999999999999999999999999999999998775
No 51
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=99.97 E-value=5.9e-32 Score=190.88 Aligned_cols=73 Identities=52% Similarity=1.116 Sum_probs=69.9
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ 129 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq 129 (347)
+|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..||+|||+||+++||+++.|+
T Consensus 1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (73)
T cd06959 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73 (73)
T ss_pred CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence 4999999999999999999999999999999899999999999999999999999999999999999998763
No 52
>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=99.97 E-value=1.6e-29 Score=219.91 Aligned_cols=167 Identities=19% Similarity=0.419 Sum_probs=141.1
Q ss_pred hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCC-C-ceEecCCccccccchh
Q psy3092 178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVK-D-GILLAPGVTVYRSSAH 255 (347)
Q Consensus 178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~-~-~~~~~~g~~i~~~~~~ 255 (347)
.......+++..+++++.+|+|||++|+|.+|+.+||+.|+|++|.+++++..+|+++... + .+.+.+|..+.++...
T Consensus 26 ~~~~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~~ 105 (248)
T cd07074 26 PSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMK 105 (248)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhhh
Confidence 3345788899999999999999999999999999999999999999999999999998764 3 3556677777766543
Q ss_pred hcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHhc-C--CCCchH
Q psy3092 256 EAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNP-DVRGLKSQQVVEMLREKVYTSLEEYTRVN-H--SEEPGR 331 (347)
Q Consensus 256 ~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p-~~~~l~~~~~i~~~r~~~~~~L~~y~~~~-~--~~~~~R 331 (347)
..++.... ..+.+++.+|++|++|.+||+|||||+|||| +.+||+++..|+++|++|.++|.+|+..+ + .+++.|
T Consensus 106 ~~~~~~~~-~~m~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~R 184 (248)
T cd07074 106 ESSFYSLC-LTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQR 184 (248)
T ss_pred hccHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcHH
Confidence 33333322 2345789999999999999999999999999 79999999999999999999999996554 3 378999
Q ss_pred HHHHHhhhhhhhcc
Q psy3092 332 FAKLLLRLPSLRSI 345 (347)
Q Consensus 332 f~~LL~ll~~lr~i 345 (347)
|++|+++++.|+++
T Consensus 185 F~~Ll~ll~~l~~~ 198 (248)
T cd07074 185 FYQLTKLMDNMHDL 198 (248)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999853
No 53
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=99.97 E-value=5.5e-32 Score=191.00 Aligned_cols=72 Identities=65% Similarity=1.438 Sum_probs=70.1
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ 129 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq 129 (347)
|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..|++|||+||+++||++++||
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (73)
T cd06958 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 899999999999999999999999999999999999999999999999999999999999999999999987
No 54
>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B. DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcrip
Probab=99.97 E-value=2e-32 Score=194.12 Aligned_cols=74 Identities=62% Similarity=1.334 Sum_probs=71.2
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHH
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQE 130 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~ 130 (347)
+|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..||+|||+||+++||++++||+
T Consensus 2 ~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~ 75 (75)
T cd06969 2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75 (75)
T ss_pred CCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence 49999999999999999999999999999998899999999999999999999999999999999999999873
No 55
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=99.97 E-value=6.6e-32 Score=190.09 Aligned_cols=71 Identities=46% Similarity=1.161 Sum_probs=69.0
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAV 128 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~v 128 (347)
|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..||+|||+||+++||++++|
T Consensus 1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (72)
T cd07156 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence 89999999999999999999999999999988999999999999999999999999999999999999987
No 56
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=99.97 E-value=4e-32 Score=204.00 Aligned_cols=76 Identities=39% Similarity=1.053 Sum_probs=71.6
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHH
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEE 131 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~ 131 (347)
..|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++|+.+
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 82 (107)
T cd06955 7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82 (107)
T ss_pred CCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence 5699999999999999999999999999999999999999999999999999999999999999999998766654
No 57
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=99.97 E-value=8.2e-32 Score=196.46 Aligned_cols=80 Identities=43% Similarity=1.058 Sum_probs=74.7
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK 136 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~ 136 (347)
+|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+++-.+
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~~~ 80 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEAVEK 80 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHHHHH
Confidence 39999999999999999999999999999999999999999999999999999999999999999999999988755433
No 58
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=99.97 E-value=1.5e-31 Score=191.94 Aligned_cols=76 Identities=43% Similarity=0.912 Sum_probs=71.3
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHH
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEE 131 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~ 131 (347)
..|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..|..||+|||+||+++||+++....+
T Consensus 4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~ 79 (82)
T cd07173 4 KTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK 79 (82)
T ss_pred CCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence 4599999999999999999999999999999999999999999999999999999999999999999998766543
No 59
>cd06948 NR_LBD_COUP-TF Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family. The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone
Probab=99.97 E-value=1.4e-29 Score=221.90 Aligned_cols=166 Identities=39% Similarity=0.699 Sum_probs=143.8
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc-eEecCCccccccchhhcC
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG-ILLAPGVTVYRSSAHEAG 258 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~-~~~~~g~~i~~~~~~~~~ 258 (347)
...+.++++..+.++.+|+|+|.+|+|.+|+.+||+.|||++|.+++++..++++...... +++++|..+...... .
T Consensus 30 ~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~~--~ 107 (236)
T cd06948 30 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSAD--R 107 (236)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccchh--h
Confidence 4578999999999999999999999999999999999999999999999999998776544 455667665443321 1
Q ss_pred chhhHH--hhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHH
Q psy3092 259 VGGIFD--RVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL 336 (347)
Q Consensus 259 ~~~~~~--~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL 336 (347)
...+.+ +.+.+++.+|++|++|++||++|+||+|||||.+|+++.+.|+++|+++..+|++|+..++++++.||++||
T Consensus 108 ~~~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL 187 (236)
T cd06948 108 VVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLL 187 (236)
T ss_pred HhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHH
Confidence 222222 345689999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhccCC
Q psy3092 337 LRLPSLRSIEV 347 (347)
Q Consensus 337 ~ll~~lr~i~~ 347 (347)
++||.||+|+.
T Consensus 188 l~Lp~Lr~is~ 198 (236)
T cd06948 188 LRLPSLRTVSS 198 (236)
T ss_pred HHHHHHHhccH
Confidence 99999999873
No 60
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=99.97 E-value=1e-31 Score=190.00 Aligned_cols=73 Identities=45% Similarity=1.095 Sum_probs=70.3
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQE 130 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~ 130 (347)
|.|||++++|+||||.+|+|||+||||++.++..|.|..+++|.+++..|..|++|||+||+++||++++|+.
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 73 (74)
T cd07179 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73 (74)
T ss_pred CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999864
No 61
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=99.97 E-value=5.3e-32 Score=199.89 Aligned_cols=83 Identities=55% Similarity=1.175 Sum_probs=77.7
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhh
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRT 135 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~ 135 (347)
..|.|||++++|+||||.+|+||++||||++.++..|.|..+++|.++...|..|++|||+||+++||++++||.+|.+.
T Consensus 6 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~ 85 (95)
T cd06968 6 IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSK 85 (95)
T ss_pred cCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCCh
Confidence 45999999999999999999999999999999999999999999999999999999999999999999999999987765
Q ss_pred hcc
Q psy3092 136 KER 138 (347)
Q Consensus 136 ~~~ 138 (347)
+.+
T Consensus 86 ~~~ 88 (95)
T cd06968 86 KQR 88 (95)
T ss_pred hhh
Confidence 543
No 62
>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=99.97 E-value=1e-29 Score=219.42 Aligned_cols=168 Identities=26% Similarity=0.435 Sum_probs=138.4
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce---------EecCCcccc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI---------LLAPGVTVY 250 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~---------~~~~g~~i~ 250 (347)
..++.+++...+.++.+|+|+|++|+|..|+.+||+.|||++|.++++++.++++....... ++..|....
T Consensus 19 ~~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~~~~~~ 98 (222)
T cd07349 19 CTPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQSSS 98 (222)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhcccccc
Confidence 34778899999999999999999999999999999999999999999999999986654321 112222111
Q ss_pred ccc-h-hhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3092 251 RSS-A-HEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEE 328 (347)
Q Consensus 251 ~~~-~-~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~ 328 (347)
... . ...+......+.+.+++.+|++|++|.+||++|+||+|||||++|+++...|+.+|+++..+|++|+..++++.
T Consensus 99 ~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~ 178 (222)
T cd07349 99 GGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQD 178 (222)
T ss_pred cccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCc
Confidence 111 0 01111111224467899999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHhhhhhhhccCC
Q psy3092 329 PGRFAKLLLRLPSLRSIEV 347 (347)
Q Consensus 329 ~~Rf~~LL~ll~~lr~i~~ 347 (347)
+.||++||++||.||+|+.
T Consensus 179 ~~r~~kLLl~Lp~LR~i~~ 197 (222)
T cd07349 179 QGRFARILLTASTLKSIPP 197 (222)
T ss_pred ccHHHHHHHHhHHHhcCCH
Confidence 9999999999999999873
No 63
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=99.97 E-value=1.4e-31 Score=188.53 Aligned_cols=72 Identities=49% Similarity=1.001 Sum_probs=69.3
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ 129 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq 129 (347)
|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.|++..|..||+|||+||+++||+++++.
T Consensus 1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 899999999999999999999999999999999999999999999999999999999999999999998763
No 64
>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=99.97 E-value=2.4e-29 Score=219.06 Aligned_cols=166 Identities=25% Similarity=0.436 Sum_probs=148.6
Q ss_pred hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhc
Q psy3092 178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEA 257 (347)
Q Consensus 178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~ 257 (347)
....+..+++.....+..+++|||++|+|.+|+.+||+.|||++|.++++++.++++....+.+.+.+|..+.+.....
T Consensus 40 ~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~~g~~~~~~~~~~- 118 (239)
T cd07072 40 EAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQR- 118 (239)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEeeCCeeecHHHHHh-
Confidence 3456788888899999999999999999999999999999999999999999999998888888899998877765433
Q ss_pred CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHH
Q psy3092 258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKL 335 (347)
Q Consensus 258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~L 335 (347)
+++.+.+. +.+++.+|++|++|++||+||+||+||+ |++|+.+...|+++|+++..+|++|+..+++ +.+.||++|
T Consensus 119 ~~~~~~~~-i~ef~~~l~~L~ld~~E~a~LkAivLf~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kL 196 (239)
T cd07072 119 SFGDWLHA-ILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRL 196 (239)
T ss_pred hHHHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHH
Confidence 56665554 4599999999999999999999999995 9999999999999999999999999987544 678999999
Q ss_pred HhhhhhhhccC
Q psy3092 336 LLRLPSLRSIE 346 (347)
Q Consensus 336 L~ll~~lr~i~ 346 (347)
|++||.||+|+
T Consensus 197 Ll~Lp~LRsl~ 207 (239)
T cd07072 197 LGKLPELRSLS 207 (239)
T ss_pred HHHhHHHHhhH
Confidence 99999999986
No 65
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=99.97 E-value=1.5e-31 Score=190.47 Aligned_cols=74 Identities=47% Similarity=0.994 Sum_probs=70.2
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ 129 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq 129 (347)
..|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.++...|..||+|||+||+++||+..++.
T Consensus 3 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 3 KICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence 35999999999999999999999999999999999999999999999999999999999999999999987763
No 66
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=1.6e-31 Score=189.03 Aligned_cols=72 Identities=61% Similarity=1.406 Sum_probs=69.5
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcc-cccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSY-ACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ 129 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~-~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq 129 (347)
|.|||++++|+||||.+|+||++||||++..+..| .|..+++|.+++..|..|++|||+||+++||++++|+
T Consensus 1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 73 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence 89999999999999999999999999999999999 8999999999999999999999999999999999874
No 67
>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of
Probab=99.97 E-value=1.8e-29 Score=219.19 Aligned_cols=166 Identities=23% Similarity=0.361 Sum_probs=141.4
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|.+++++.+++++....+ .++.+|..+...+....++
T Consensus 35 ~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~ 113 (226)
T cd06934 35 SLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETG-TWECGPLTYCIEDAARAGF 113 (226)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhcccCC-eEeeCCEeecHHHHHHccc
Confidence 346677888888999999999999999999999999999999999999998877655444 4455555544444444555
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCc--hHHHHHHh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEP--GRFAKLLL 337 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~--~Rf~~LL~ 337 (347)
...+.+.+.+++.+|++|++|++||+||+||+||+||++||++...|+++|+++..+|++|+..+++..+ .||++||+
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 5555556678999999999999999999999999999999999999999999999999999998887544 45999999
Q ss_pred hhhhhhccC
Q psy3092 338 RLPSLRSIE 346 (347)
Q Consensus 338 ll~~lr~i~ 346 (347)
+||+||+|+
T Consensus 194 ~L~~LRsl~ 202 (226)
T cd06934 194 CLTELRTIN 202 (226)
T ss_pred HhHHHhcch
Confidence 999999997
No 68
>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear
Probab=99.97 E-value=6e-32 Score=191.02 Aligned_cols=72 Identities=57% Similarity=1.359 Sum_probs=69.4
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCccccc-CCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACR-EGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ 129 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~-~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq 129 (347)
|.|||++++|+||||.+|+|||+||||++..+..|.|. .+++|.++...|..||+|||+||+++||++++||
T Consensus 1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 89999999999999999999999999999999999999 6789999999999999999999999999999886
No 69
>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=99.97 E-value=2.2e-29 Score=218.55 Aligned_cols=167 Identities=27% Similarity=0.454 Sum_probs=138.5
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEe---------cCCcccc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILL---------APGVTVY 250 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~---------~~g~~i~ 250 (347)
..++.+++...+.++.+|+|||++|+|.+|+.+||+.|||++|.++++++.++++++.+....+ .++....
T Consensus 19 ~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~~~~ 98 (232)
T cd07350 19 KSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPPPT 98 (232)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhcccccc
Confidence 4578889999999999999999999999999999999999999999999999998776543222 1111110
Q ss_pred ccc------------hhhcCc--hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHH
Q psy3092 251 RSS------------AHEAGV--GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTS 316 (347)
Q Consensus 251 ~~~------------~~~~~~--~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~ 316 (347)
... ....+. .....+.+.+++.+|++|+||++||++|+||+|||||++|+++...|+++|+++..+
T Consensus 99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~a 178 (232)
T cd07350 99 SGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQA 178 (232)
T ss_pred cccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHHHHH
Confidence 000 000011 111224577999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCchHHHHHHhhhhhhhccC
Q psy3092 317 LEEYTRVNHSEEPGRFAKLLLRLPSLRSIE 346 (347)
Q Consensus 317 L~~y~~~~~~~~~~Rf~~LL~ll~~lr~i~ 346 (347)
|++|+..++++.+.||++||++||.||+|+
T Consensus 179 L~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~ 208 (232)
T cd07350 179 LNEHVRMIHRGDQARFAKLNIALSLLRAIN 208 (232)
T ss_pred HHHHHHhhCCChhhHHHHHHHHhHHHHccC
Confidence 999999999999999999999999999986
No 70
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or hetero
Probab=99.97 E-value=7.4e-32 Score=190.02 Aligned_cols=72 Identities=65% Similarity=1.429 Sum_probs=69.8
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchhHHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQ 129 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq 129 (347)
|.|||++++|+||||.+|+|||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||
T Consensus 1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999886
No 71
>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=99.96 E-value=3.7e-29 Score=219.02 Aligned_cols=164 Identities=24% Similarity=0.385 Sum_probs=142.6
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..+.+.....+..+|+|||++|+|.+|+.+||+.|||++|.+++++.+++++.. .+..++.+|....++.....+.
T Consensus 48 ~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 126 (241)
T cd06939 48 EMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNP-SNNTVLFDGKYAPIDLFKSLGC 126 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCC-CCCEEEECCccccHHHHHHcCc
Confidence 457777788888999999999999999999999999999999999999999965544 4444555666555555455566
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHhhh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLLRL 339 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ll 339 (347)
+++.+.+ .+++.+|++|++|++||++|+||+||+||++||.+...|+++|+++..+|+.|+..++ +.+.||++||++|
T Consensus 127 ~~~~~~~-~~f~~~l~~L~ld~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~kLL~~L 204 (241)
T cd06939 127 DDLISAV-FDFAKSLCELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTKLLAKM 204 (241)
T ss_pred HHHHHHH-HHHHHHHHhcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHHHHHHH
Confidence 6666554 4899999999999999999999999999999999999999999999999999999888 8899999999999
Q ss_pred hhhhccC
Q psy3092 340 PSLRSIE 346 (347)
Q Consensus 340 ~~lr~i~ 346 (347)
|.||+|+
T Consensus 205 p~LR~l~ 211 (241)
T cd06939 205 PTLRALC 211 (241)
T ss_pred HHHHHHH
Confidence 9999986
No 72
>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=99.96 E-value=2.8e-29 Score=216.35 Aligned_cols=167 Identities=28% Similarity=0.511 Sum_probs=139.3
Q ss_pred hhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce-----EecCCcccccc
Q psy3092 178 NEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI-----LLAPGVTVYRS 252 (347)
Q Consensus 178 ~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~-----~~~~g~~i~~~ 252 (347)
....+..+++..++.++.+|+|+|.+|+|.+|+.+||+.|||++|.+++++..+++++...... ..+.|......
T Consensus 25 ~~~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~~ 104 (213)
T cd06953 25 QAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELE 104 (213)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhHH
Confidence 3456788999999999999999999999999999999999999999999999999987643211 11111111000
Q ss_pred chhhcCchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHH
Q psy3092 253 SAHEAGVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRF 332 (347)
Q Consensus 253 ~~~~~~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf 332 (347)
.. .....++.+++ .+++.+|++|++|++||++|+||+|||||++|+++.+.|+++|+++.++|++|+..++++++.||
T Consensus 105 ~~-~~~~~~~~~~i-~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf 182 (213)
T cd06953 105 RF-GDEGGEVVERL-TYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRF 182 (213)
T ss_pred HH-HhhHHHHHHHH-HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHH
Confidence 00 11234556664 58999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhhhhhccC
Q psy3092 333 AKLLLRLPSLRSIE 346 (347)
Q Consensus 333 ~~LL~ll~~lr~i~ 346 (347)
++||+++|.||+|+
T Consensus 183 ~~LL~~L~~Lr~l~ 196 (213)
T cd06953 183 SDLLSCLPEIRAAA 196 (213)
T ss_pred HHHHHHhHHHHHHH
Confidence 99999999999986
No 73
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=99.96 E-value=1.2e-31 Score=194.71 Aligned_cols=78 Identities=45% Similarity=0.955 Sum_probs=72.7
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCC--cccccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhh
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDL--SYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQR 134 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~--~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~ 134 (347)
.|.|||++++|+||||.+|+|||+||||++..+. .|.|..+++|.++...|..||+|||+||+++||+++.++.+|+.
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~ 81 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS 81 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence 4999999999999999999999999999987654 89999999999999999999999999999999999999887664
No 74
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=99.96 E-value=1.6e-31 Score=193.36 Aligned_cols=78 Identities=58% Similarity=1.209 Sum_probs=72.6
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCccc-ccCCCCcccccccccCchhhhhHHHHhcCcchhHHHHHHhhhh
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYA-CREGRNCIIDKRQRNRCQYCRYQKCLNMGMKREAVQEERQRTK 136 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~-C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~ 136 (347)
|.|||++++|+||||.+|+||++||||++..+..|. |..+ |.+++..|..|++|||+||+++||++++||.+|++..
T Consensus 2 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~ 79 (84)
T cd06965 2 CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRV 79 (84)
T ss_pred CcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCch
Confidence 999999999999999999999999999999888995 9754 9999999999999999999999999999999888644
Q ss_pred c
Q psy3092 137 E 137 (347)
Q Consensus 137 ~ 137 (347)
+
T Consensus 80 ~ 80 (84)
T cd06965 80 E 80 (84)
T ss_pred h
Confidence 3
No 75
>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=99.96 E-value=1e-28 Score=216.24 Aligned_cols=166 Identities=21% Similarity=0.359 Sum_probs=136.8
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCc-eEecCC-ccccccchhhc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDG-ILLAPG-VTVYRSSAHEA 257 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~-~~~~~g-~~i~~~~~~~~ 257 (347)
.-+..+++.....+..+|+|||++|+|.+|+.+||+.|||++|.++++++.++. +...+. +.+.++ ..+..+.....
T Consensus 37 ~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (238)
T cd06933 37 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQS-FSLDDMSWTCGSPDFKYKVSDVTKA 115 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHh-cCcCCCeeEecCCceeecHHHHHHc
Confidence 345677888889999999999999999999999999999999999999998764 444443 443332 22333333333
Q ss_pred CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCC--CCchHHHHH
Q psy3092 258 GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHS--EEPGRFAKL 335 (347)
Q Consensus 258 ~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~--~~~~Rf~~L 335 (347)
+....+.+.+.++..+|++|++|++||+||+||+|||||++|+.+...|+++|+++..+|.+|+..+++ +.+.||++|
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 333233345668999999999999999999999999999999999999999999999999999998877 456789999
Q ss_pred HhhhhhhhccC
Q psy3092 336 LLRLPSLRSIE 346 (347)
Q Consensus 336 L~ll~~lr~i~ 346 (347)
|++||+||+|+
T Consensus 196 Ll~L~~LRsi~ 206 (238)
T cd06933 196 IQKLADLRSLN 206 (238)
T ss_pred HHHhHHHHhhh
Confidence 99999999987
No 76
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=99.96 E-value=9.9e-29 Score=214.03 Aligned_cols=162 Identities=28% Similarity=0.431 Sum_probs=137.3
Q ss_pred hHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccc-cchhhc
Q psy3092 179 EQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYR-SSAHEA 257 (347)
Q Consensus 179 ~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~-~~~~~~ 257 (347)
+..+..+++|....++.+|+|+|++|+|..|+.+||+.|||++|.+++++..++++ ..+ ++.|..+.. +.....
T Consensus 35 ~~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~-~~~----~~~~~~~~~~~~~~~~ 109 (221)
T cd06936 35 EENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIY-NKK----LPAGHADLLEERIRSS 109 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHh-ccc----ccCCCchhhHHHHHhc
Confidence 45688899999999999999999999999999999999999999999999988543 211 344442222 222222
Q ss_pred Cc-hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHH
Q psy3092 258 GV-GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLL 336 (347)
Q Consensus 258 ~~-~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL 336 (347)
+. ..+.+.+. +++.+|++|++|++||+||+||+|||||++||++...|+.+|+++.++|++|+..++++.+.||++||
T Consensus 110 ~~~~e~~~~i~-~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~LL 188 (221)
T cd06936 110 GISDEFITPMF-NFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLL 188 (221)
T ss_pred cchHHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHH
Confidence 32 24555554 79999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhccC
Q psy3092 337 LRLPSLRSIE 346 (347)
Q Consensus 337 ~ll~~lr~i~ 346 (347)
++||.||+|+
T Consensus 189 ~~L~~LR~l~ 198 (221)
T cd06936 189 GRLTELRTLN 198 (221)
T ss_pred HHhHHHHHHH
Confidence 9999999986
No 77
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=99.96 E-value=1.2e-28 Score=215.46 Aligned_cols=165 Identities=30% Similarity=0.413 Sum_probs=147.5
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchhhcCc
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAHEAGV 259 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~~~~~ 259 (347)
..+..++++....+..+|+|+|++|+|..|+.+||+.|+|++|.+++++..++++....+.+.+++|..+.++.....+.
T Consensus 39 ~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~~~~~~f~~g~~~~~~~~~~~~~ 118 (231)
T cd06938 39 MRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYRKAGM 118 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEeeCCEEecHHHHhhcCH
Confidence 45778888888999999999999999999999999999999999999999999877777888999998877766555555
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCC-CchHHHHHHhh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSE-EPGRFAKLLLR 338 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~-~~~Rf~~LL~l 338 (347)
+.+.+. +.+++.+|++|++|++||++|+||+||+ +++|+++...|+++|+++..+|+.|+..+++. ++.||++||++
T Consensus 119 ~~~~~~-l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~~ 196 (231)
T cd06938 119 GDSAED-LFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSI 196 (231)
T ss_pred HHHHHH-HHHHHHHHHHcCCCHHHHHHHHHHHHcc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHHH
Confidence 555554 4479999999999999999999999997 67899999999999999999999999999886 89999999999
Q ss_pred hhhhhccC
Q psy3092 339 LPSLRSIE 346 (347)
Q Consensus 339 l~~lr~i~ 346 (347)
|+.||+|+
T Consensus 197 L~~Lr~l~ 204 (231)
T cd06938 197 LTELRTLG 204 (231)
T ss_pred HHHHHHHH
Confidence 99999986
No 78
>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, P
Probab=99.96 E-value=2.7e-28 Score=215.69 Aligned_cols=163 Identities=29% Similarity=0.458 Sum_probs=139.0
Q ss_pred HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCc-cccccchhhcC-
Q psy3092 181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGV-TVYRSSAHEAG- 258 (347)
Q Consensus 181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~-~i~~~~~~~~~- 258 (347)
-+..+.......+..+++|||++|+|.+|+.+||+.|||++|.+++++.++.+. ..++.++++|. ++.++.....+
T Consensus 64 ~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~--~~~~~~~~~~~~~~~~~~~~~~~~ 141 (259)
T cd06932 64 LFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLY--NKDGLLFPEGNGYVTREFLESLRK 141 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhc--CCCCeEEeCCCEEeeHHHHHHhcc
Confidence 345555566678999999999999999999999999999999999999888653 34567777653 34444433332
Q ss_pred -chhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q psy3092 259 -VGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLL 337 (347)
Q Consensus 259 -~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ 337 (347)
...+++.++ +++.+|++|+||++||+||+||+||+||++||.+...|+++|+++..+|+.|+..++|+.+.||++||+
T Consensus 142 ~~~~~~~~~~-e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~kLLl 220 (259)
T cd06932 142 PFCDIMEPKF-EFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQ 220 (259)
T ss_pred cHHHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHHHHH
Confidence 245566654 899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhccC
Q psy3092 338 RLPSLRSIE 346 (347)
Q Consensus 338 ll~~lr~i~ 346 (347)
+||.||+|+
T Consensus 221 ~L~~LRsl~ 229 (259)
T cd06932 221 KMVDLRQLV 229 (259)
T ss_pred HHHHHHHHH
Confidence 999999986
No 79
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.96 E-value=3.5e-30 Score=180.98 Aligned_cols=69 Identities=54% Similarity=1.141 Sum_probs=66.7
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcchh
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKRE 126 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~ 126 (347)
|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..|..|++|||+||+++||+++
T Consensus 2 C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 2 CCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 999999999999999999999999999999888999999999999999999999999999999999874
No 80
>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=99.96 E-value=5.9e-28 Score=205.15 Aligned_cols=163 Identities=20% Similarity=0.272 Sum_probs=143.4
Q ss_pred HHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecCCccccccchh-hcCc
Q psy3092 181 QATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAPGVTVYRSSAH-EAGV 259 (347)
Q Consensus 181 ~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~g~~i~~~~~~-~~~~ 259 (347)
.+..+.+.....+..+|+|+|++|+|..|+.+||+.|+|++|.+++++..++ ++... ..++++|..+.++... ....
T Consensus 3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~-~~~~~-~~~~~~g~~~~~~~~~~~~~~ 80 (191)
T cd06942 3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSR-DYNNE-GTVLCDFRPVEFASLLSQLLH 80 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHH-HhCcC-CeEEeCCccccHHHHHHhcch
Confidence 4677888889999999999999999999999999999999999999998775 44444 6788888888765432 2233
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCC--CCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPD--VRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRFAKLLL 337 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~--~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf~~LL~ 337 (347)
..+.+++ .+++.+|++|++|++||++|+||+||+|| ++++++...++++|+.+..+|.+|+..++++.+.||++||+
T Consensus 81 ~~~~~~~-~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~kLL~ 159 (191)
T cd06942 81 GKLIDEM-LQFANKILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFD 159 (191)
T ss_pred HHHHHHH-HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHH
Confidence 4566664 58999999999999999999999999999 99999999999999999999999999999988899999999
Q ss_pred hhhhhhccC
Q psy3092 338 RLPSLRSIE 346 (347)
Q Consensus 338 ll~~lr~i~ 346 (347)
+++.||+++
T Consensus 160 ~l~~Lr~~~ 168 (191)
T cd06942 160 ILNRLRNMN 168 (191)
T ss_pred HHHHHHHHH
Confidence 999999875
No 81
>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=99.96 E-value=7.4e-28 Score=209.64 Aligned_cols=167 Identities=32% Similarity=0.553 Sum_probs=136.8
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceEecC-Cccc----cccch
Q psy3092 180 QQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGILLAP-GVTV----YRSSA 254 (347)
Q Consensus 180 ~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~-g~~i----~~~~~ 254 (347)
.....+++.+.+++..+++|+|++|+|..|+.+||+.|+|++|.+++++..++++.......+++. +... ..+..
T Consensus 21 ~~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (222)
T cd06952 21 LNVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQDKL 100 (222)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhhhHhcCCC
Confidence 347788999999999999999999999999999999999999999999988877654443333322 1111 11111
Q ss_pred hhcCchhhHHhh--HHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCchHH
Q psy3092 255 HEAGVGGIFDRV--LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQQVVEMLREKVYTSLEEYTRVNHSEEPGRF 332 (347)
Q Consensus 255 ~~~~~~~~~~~~--~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~~~i~~~r~~~~~~L~~y~~~~~~~~~~Rf 332 (347)
.......+++.+ +.+++.+|++|++|++||++|+||+||+||++|+++.+.|+++|+++.++|.+|+..++++.+.||
T Consensus 101 ~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~R~ 180 (222)
T cd06952 101 SADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRL 180 (222)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHH
Confidence 111222333322 458999999999999999999999999999999999999999999999999999998889999999
Q ss_pred HHHHhhhhhhhccC
Q psy3092 333 AKLLLRLPSLRSIE 346 (347)
Q Consensus 333 ~~LL~ll~~lr~i~ 346 (347)
++||++||.||+++
T Consensus 181 ~klLl~Lp~Lr~~~ 194 (222)
T cd06952 181 SKLLLRLPPLRSLS 194 (222)
T ss_pred HHHHHHhHHhhhcC
Confidence 99999999999986
No 82
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=99.95 E-value=3.6e-29 Score=176.39 Aligned_cols=69 Identities=55% Similarity=1.222 Sum_probs=62.6
Q ss_pred cCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHHHHhcCcch
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQKCLNMGMKR 125 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~ 125 (347)
.|.|||++++|+||||.+|++|++||||++.++..|.|..+++|.+++..+..|++|||+||+++||++
T Consensus 2 ~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 2 KCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred CCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence 599999999999999999999999999999999999999999999999999999999999999999974
No 83
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.94 E-value=4.7e-26 Score=189.71 Aligned_cols=162 Identities=39% Similarity=0.682 Sum_probs=137.6
Q ss_pred hhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCceE-ecCCcccc--ccchhhcCch
Q psy3092 184 NICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGIL-LAPGVTVY--RSSAHEAGVG 260 (347)
Q Consensus 184 ~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~-~~~g~~i~--~~~~~~~~~~ 260 (347)
.++.++..++..+++|++++|+|+.|+.+||+.|+|++|.+++++..++++........ .+++.... ........+.
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (168)
T cd06157 2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK 81 (168)
T ss_pred cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence 46788999999999999999999999999999999999999999999999887765443 34443321 1111122334
Q ss_pred hhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCC-CCCCHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHhh
Q psy3092 261 GIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVR-GLKSQQVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLLR 338 (347)
Q Consensus 261 ~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~-~l~~~~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~l 338 (347)
..+.+.+.+++.+|.+|++|++||++|+||++|+|+.+ +..+.+.+++.|+++..+|+.|+..+++ +++.||++||++
T Consensus 82 ~~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~ 161 (168)
T cd06157 82 GELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLL 161 (168)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHhCCccchhHHHHHHHh
Confidence 56777888999999999999999999999999999998 5667999999999999999999998887 899999999999
Q ss_pred hhhhhcc
Q psy3092 339 LPSLRSI 345 (347)
Q Consensus 339 l~~lr~i 345 (347)
+++||++
T Consensus 162 l~~l~~~ 168 (168)
T cd06157 162 LPSLRKL 168 (168)
T ss_pred chhcccC
Confidence 9999975
No 84
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=99.94 E-value=8.2e-26 Score=187.32 Aligned_cols=156 Identities=36% Similarity=0.630 Sum_probs=134.7
Q ss_pred HHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccccCCCce-EecCCccccccchh--hcCchhhHHhh
Q psy3092 190 DKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSISVKDGI-LLAPGVTVYRSSAH--EAGVGGIFDRV 266 (347)
Q Consensus 190 ~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~~~~~~~-~~~~g~~i~~~~~~--~~~~~~~~~~~ 266 (347)
...+..+++|++++|+|+.|+.+||..|+|++|.+++++..++++....... ..++|..+..+... ...+...+.+.
T Consensus 2 ~~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (163)
T smart00430 2 ERDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRI 81 (163)
T ss_pred hhHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHH
Confidence 4678899999999999999999999999999999999999999988776644 44555555544322 13344566778
Q ss_pred HHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCCCH--HHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHhhhhhhh
Q psy3092 267 LTELVSKMREMKMDKTELGCLRTIILFNPDVRGLKSQ--QVVEMLREKVYTSLEEYTRVNHS-EEPGRFAKLLLRLPSLR 343 (347)
Q Consensus 267 ~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~~~--~~i~~~r~~~~~~L~~y~~~~~~-~~~~Rf~~LL~ll~~lr 343 (347)
+.+++.+|++|++|++||++|+||++|+|+..++++. +.++++|+.+.++|+.|+..+.+ +++.||++||+++++|+
T Consensus 82 ~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~i~ 161 (163)
T smart00430 82 LQELVKPLRELKLDDEEYALLKAILLFNPAGPGLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGRFGELLLILNAIQ 161 (163)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHHHHhh
Confidence 8899999999999999999999999999999999885 89999999999999999998877 78999999999999998
Q ss_pred cc
Q psy3092 344 SI 345 (347)
Q Consensus 344 ~i 345 (347)
++
T Consensus 162 ~~ 163 (163)
T smart00430 162 KI 163 (163)
T ss_pred cC
Confidence 74
No 85
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=99.93 E-value=7.4e-25 Score=188.27 Aligned_cols=169 Identities=33% Similarity=0.629 Sum_probs=144.2
Q ss_pred chhHHHhhhhHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccc-cCCCceEecCCccccccchh
Q psy3092 177 VNEQQATNICKATDKQLFQLVDWAKHIPHFTTLPLEDQVLLLRAGWNELLIASFSHRSI-SVKDGILLAPGVTVYRSSAH 255 (347)
Q Consensus 177 ~~~~~~~~~~~~~~~~l~~~~~w~k~~p~F~~L~~~dq~~Llk~~~~~~~~l~~a~~s~-~~~~~~~~~~g~~i~~~~~~ 255 (347)
.....++.+++++...+..+++|++.||+|..|+.+||+.|+|++|.+++++..++++. ...+.+.+++|..++.....
T Consensus 14 ~~~~~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~ 93 (203)
T PF00104_consen 14 LRPATFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDSFD 93 (203)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHHHH
T ss_pred CcHhhHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcccccccccccccccccccccc
Confidence 45567899999999999999999999999999999999999999999999999999988 56678899999988766554
Q ss_pred hc---CchhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHHhhcCCCCCCC-C-HHHHHHHHHHHHHHHHHHH-HhcCC-CC
Q psy3092 256 EA---GVGGIFDRVLTELVSKMREMKMDKTELGCLRTIILFNPDVRGLK-S-QQVVEMLREKVYTSLEEYT-RVNHS-EE 328 (347)
Q Consensus 256 ~~---~~~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~l~~p~~~~l~-~-~~~i~~~r~~~~~~L~~y~-~~~~~-~~ 328 (347)
.. ...+.+ +.+.+++.+|.++++|++||++|+|+++|+|+.++++ + .+.++++|+++..+|++|+ ...++ ++
T Consensus 94 ~~~~~~~~~~~-~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~ 172 (203)
T PF00104_consen 94 DFITGIFSEFI-QYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYYNQSKGPEDY 172 (203)
T ss_dssp HTSTTTHHHHH-HHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTH
T ss_pred cccccccccch-hHHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHHhccCCCccH
Confidence 33 122333 3556889999999999999999999999999999998 5 4559999999999999999 65555 66
Q ss_pred chHHHHHHhhhhhhhccC
Q psy3092 329 PGRFAKLLLRLPSLRSIE 346 (347)
Q Consensus 329 ~~Rf~~LL~ll~~lr~i~ 346 (347)
+.||++||++++.|+.++
T Consensus 173 ~~R~~~ll~ll~~l~~~~ 190 (203)
T PF00104_consen 173 AQRFGKLLLLLPSLRKIS 190 (203)
T ss_dssp TTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 899999999999999864
No 86
>KOG3277|consensus
Probab=82.23 E-value=0.91 Score=36.21 Aligned_cols=26 Identities=35% Similarity=0.865 Sum_probs=19.5
Q ss_pred CcCcccCCCC------CCccccc--ccchhhHHH
Q psy3092 56 HLCSICGDRA------SGKHYGV--YSCEGCKGF 81 (347)
Q Consensus 56 ~~C~VCg~~a------~g~HyGv--~sC~~Ck~F 81 (347)
-.|.||+.+. ..||=|+ ++|.||+.+
T Consensus 80 yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~ 113 (165)
T KOG3277|consen 80 YTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNH 113 (165)
T ss_pred EEeeccCCccccccChhhhhCceEEEECCCCccc
Confidence 3699999865 3467786 479999865
No 87
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=80.70 E-value=0.93 Score=28.53 Aligned_cols=40 Identities=30% Similarity=0.735 Sum_probs=26.5
Q ss_pred hhhHHHHHhhhcCCCcccccC-C--CCcccccccccCchhhhhH
Q psy3092 76 EGCKGFFKRTVRKDLSYACRE-G--RNCIIDKRQRNRCQYCRYQ 116 (347)
Q Consensus 76 ~~Ck~FFRR~v~~~~~~~C~~-~--~~C~~~~~~r~~Cr~CR~~ 116 (347)
++|..||+..-..+- +.|.. + .-..+...+++.|+.||.|
T Consensus 4 ~~c~~~l~~~RW~~g-~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 4 EACREYLEEIRWPDG-FVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred HHHHHHHHHhcCCCC-CCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 468888888765555 45653 2 2334455688999999864
No 88
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=80.45 E-value=1.1 Score=34.45 Aligned_cols=31 Identities=26% Similarity=0.808 Sum_probs=21.5
Q ss_pred CCcCcccCCCCCC---cccccccchhhHHHHHhh
Q psy3092 55 KHLCSICGDRASG---KHYGVYSCEGCKGFFKRT 85 (347)
Q Consensus 55 ~~~C~VCg~~a~g---~HyGv~sC~~Ck~FFRR~ 85 (347)
++.|.-||.+... ..||+..|..|++.-|-.
T Consensus 13 N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~l 46 (116)
T PF01412_consen 13 NKVCADCGAPNPTWASLNYGIFLCLECAGIHRSL 46 (116)
T ss_dssp CTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHH
T ss_pred cCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHh
Confidence 4679999977643 589999999999996653
No 89
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=74.71 E-value=1.6 Score=24.61 Aligned_cols=21 Identities=29% Similarity=0.879 Sum_probs=17.6
Q ss_pred cCcccCCCCCCcccccccchhhH
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCK 79 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck 79 (347)
.|.||+....|+. ++.|..|-
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 3999999999987 77888775
No 90
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=69.77 E-value=2.6 Score=44.43 Aligned_cols=48 Identities=31% Similarity=0.892 Sum_probs=32.1
Q ss_pred CcCcccCCC----CCCcccccccchhhHHHHHhhhcCCCcccccCCCCcc--cccccccCchhh--hhHHHH
Q psy3092 56 HLCSICGDR----ASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCI--IDKRQRNRCQYC--RYQKCL 119 (347)
Q Consensus 56 ~~C~VCg~~----a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~--~~~~~r~~Cr~C--R~~KCl 119 (347)
+.|+||||. +.|--| ++|+.|+ .-.|+ .|. ..+++...|..| ||+++.
T Consensus 18 qiCqICGD~vg~~~~Ge~F--VAC~eC~-----------FPVCr---pCYEYEr~eG~q~CPqCktrYkr~k 73 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPF--VACDVCA-----------FPVCR---PCYEYERKDGNQSCPQCKTKYKRHK 73 (1079)
T ss_pred ceeeecccccCcCCCCCEE--EEeccCC-----------Ccccc---chhhhhhhcCCccCCccCCchhhhc
Confidence 579999985 677777 7888885 12453 242 234556677777 777766
No 91
>PF09289 FOLN: Follistatin/Osteonectin-like EGF domain; InterPro: IPR015369 This domain is predominantly found in osteonectin and follistatin. They adopt an EGF-like structure [, ]. Follistatin is involved in diverse activities from embryonic development to cell secretion. ; GO: 0005515 protein binding; PDB: 1LR7_A 1LR8_A 1LR9_A 2ARP_F 3B4V_H 2KCX_A 3SEK_C 2P6A_D 3HH2_C 2B0U_D ....
Probab=68.53 E-value=1.5 Score=22.79 Aligned_cols=20 Identities=25% Similarity=0.994 Sum_probs=14.2
Q ss_pred cccccCCCCcccccccccCc
Q psy3092 91 SYACREGRNCIIDKRQRNRC 110 (347)
Q Consensus 91 ~~~C~~~~~C~~~~~~r~~C 110 (347)
.+.|+.++.|.+++.++-.|
T Consensus 3 n~~Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 3 NFHCKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp T---BTTEEEEEETTTCEEE
T ss_pred CcccCCCCEeeeCCCCCcCC
Confidence 46799999999998887665
No 92
>PLN02189 cellulose synthase
Probab=66.82 E-value=2.4 Score=44.51 Aligned_cols=48 Identities=31% Similarity=0.897 Sum_probs=33.0
Q ss_pred CcCcccCCC----CCCcccccccchhhHHHHHhhhcCCCcccccCCCCcc--cccccccCchhh--hhHHHH
Q psy3092 56 HLCSICGDR----ASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCI--IDKRQRNRCQYC--RYQKCL 119 (347)
Q Consensus 56 ~~C~VCg~~----a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~--~~~~~r~~Cr~C--R~~KCl 119 (347)
..|+||||. +.|--| ++|..|. .-.|+ .|. ..+++...|..| ||+++.
T Consensus 35 ~~C~iCgd~vg~~~~g~~f--vaC~~C~-----------fpvCr---~Cyeyer~eg~q~CpqCkt~Y~r~k 90 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLF--VACNECG-----------FPVCR---PCYEYERREGTQNCPQCKTRYKRLK 90 (1040)
T ss_pred ccccccccccCcCCCCCEE--EeeccCC-----------Ccccc---chhhhhhhcCCccCcccCCchhhcc
Confidence 479999997 788777 7888884 12453 232 235566678778 788766
No 93
>KOG4399|consensus
Probab=66.39 E-value=3.2 Score=36.15 Aligned_cols=41 Identities=22% Similarity=0.353 Sum_probs=23.7
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCccc
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCII 102 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~ 102 (347)
+-|.|||.-.+.. .+|..|+|- |.+...+.-+|+....|..
T Consensus 262 ~~C~iC~~~~~~R----~~C~~~kA~--~~~~Q~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 262 HGCFICGELDHKR----STCPNIKAV--RKQKQRKSNKMKMETTKGQ 302 (325)
T ss_pred cceeecccccccc----ccCccHHHH--HHHHhcccchhhhhhhhhh
Confidence 4477777665544 577777763 4444444445655555544
No 94
>PLN02400 cellulose synthase
Probab=65.72 E-value=3 Score=44.02 Aligned_cols=48 Identities=33% Similarity=0.892 Sum_probs=32.0
Q ss_pred CcCcccCCC----CCCcccccccchhhHHHHHhhhcCCCcccccCCCCcc--cccccccCchhh--hhHHHH
Q psy3092 56 HLCSICGDR----ASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCI--IDKRQRNRCQYC--RYQKCL 119 (347)
Q Consensus 56 ~~C~VCg~~----a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~--~~~~~r~~Cr~C--R~~KCl 119 (347)
..|+||||. +.|--| ++|+.|+ ...|+ .|. ..+++...|..| ||+++.
T Consensus 37 qiCqICGD~VG~t~dGe~F--VAC~eCa-----------FPVCR---pCYEYERkeGnq~CPQCkTrYkR~K 92 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVF--VACNECA-----------FPVCR---PCYEYERKDGTQCCPQCKTRYRRHK 92 (1085)
T ss_pred ceeeecccccCcCCCCCEE--EEEccCC-----------Ccccc---chhheecccCCccCcccCCcccccc
Confidence 579999985 677777 7888885 12453 243 234566678888 677664
No 95
>PHA03124 dUTPase; Provisional
Probab=62.52 E-value=3.9 Score=37.76 Aligned_cols=16 Identities=44% Similarity=1.238 Sum_probs=13.1
Q ss_pred ccccchhhHHHHHhhh
Q psy3092 71 GVYSCEGCKGFFKRTV 86 (347)
Q Consensus 71 Gv~sC~~Ck~FFRR~v 86 (347)
|-+-|-|||+||||..
T Consensus 189 ~~~~~~~~~~~~~~~~ 204 (418)
T PHA03124 189 GNFGCMGCKAFYRRLF 204 (418)
T ss_pred ccccccchHHHHHHHH
Confidence 3445999999999985
No 96
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=60.97 E-value=3.9 Score=26.60 Aligned_cols=23 Identities=30% Similarity=0.931 Sum_probs=19.0
Q ss_pred CcCcccCCCC-CCcccccccchhh
Q psy3092 56 HLCSICGDRA-SGKHYGVYSCEGC 78 (347)
Q Consensus 56 ~~C~VCg~~a-~g~HyGv~sC~~C 78 (347)
+.|.|||.+. --..||..-|+-|
T Consensus 17 r~C~vCg~~~gliRkygL~~CRqC 40 (54)
T PTZ00218 17 RQCRVCSNRHGLIRKYGLNVCRQC 40 (54)
T ss_pred CeeecCCCcchhhhhcCcchhhHH
Confidence 5699999874 3368999999999
No 97
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=58.13 E-value=5.5 Score=41.97 Aligned_cols=48 Identities=27% Similarity=0.809 Sum_probs=32.6
Q ss_pred CcCcccCCC----CCCcccccccchhhHHHHHhhhcCCCcccccCCCCcc--cccccccCchhh--hhHHHH
Q psy3092 56 HLCSICGDR----ASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCI--IDKRQRNRCQYC--RYQKCL 119 (347)
Q Consensus 56 ~~C~VCg~~----a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~--~~~~~r~~Cr~C--R~~KCl 119 (347)
+.|+||||. +.|--| ++|+.|+ .-.|+ .|. ..++++..|..| ||++|.
T Consensus 16 ~~c~iCGd~vg~~~~Ge~F--VAC~eC~-----------fpvCr---~cyeye~~~g~~~cp~c~t~y~~~~ 71 (1044)
T PLN02915 16 KTCRVCGDEVGVKEDGQPF--VACHVCG-----------FPVCK---PCYEYERSEGNQCCPQCNTRYKRHK 71 (1044)
T ss_pred chhhccccccCcCCCCCEE--EEeccCC-----------Ccccc---chhhhhhhcCCccCCccCCchhhhc
Confidence 579999985 677767 7888885 12453 232 234566778778 788876
No 98
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=57.73 E-value=8.2 Score=29.44 Aligned_cols=31 Identities=26% Similarity=0.671 Sum_probs=25.2
Q ss_pred CCcCcccCCCCC---CcccccccchhhHHHHHhh
Q psy3092 55 KHLCSICGDRAS---GKHYGVYSCEGCKGFFKRT 85 (347)
Q Consensus 55 ~~~C~VCg~~a~---g~HyGv~sC~~Ck~FFRR~ 85 (347)
+..|.=||.+.- ...||+..|..|++.-|..
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~l 36 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSL 36 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHHhc
Confidence 356999997653 3699999999999998864
No 99
>PLN02436 cellulose synthase A
Probab=57.60 E-value=5.6 Score=41.98 Aligned_cols=48 Identities=31% Similarity=0.890 Sum_probs=31.6
Q ss_pred CcCcccCCC----CCCcccccccchhhHHHHHhhhcCCCcccccCCCCcc--cccccccCchhh--hhHHHH
Q psy3092 56 HLCSICGDR----ASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCI--IDKRQRNRCQYC--RYQKCL 119 (347)
Q Consensus 56 ~~C~VCg~~----a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~--~~~~~r~~Cr~C--R~~KCl 119 (347)
..|+||||. +.|--| ++|+.|. .-.|+ .|. ..++++..|..| ||+++.
T Consensus 37 ~iCqICGD~Vg~t~dGe~F--VACn~C~-----------fpvCr---~Cyeyer~eg~~~Cpqckt~Y~r~k 92 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPF--VACNECA-----------FPVCR---PCYEYERREGNQACPQCKTRYKRIK 92 (1094)
T ss_pred ccccccccccCcCCCCCEE--EeeccCC-----------Ccccc---chhhhhhhcCCccCcccCCchhhcc
Confidence 579999985 577666 7888884 12453 232 235566677777 777766
No 100
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=56.26 E-value=32 Score=30.16 Aligned_cols=24 Identities=25% Similarity=0.609 Sum_probs=19.4
Q ss_pred CcCcccCCC---CCCcccccccchhhH
Q psy3092 56 HLCSICGDR---ASGKHYGVYSCEGCK 79 (347)
Q Consensus 56 ~~C~VCg~~---a~g~HyGv~sC~~Ck 79 (347)
..|+||+.. ....|--|+-|..|.
T Consensus 66 v~CrVCq~~I~i~gk~~QhVVkC~~Cn 92 (256)
T PF09788_consen 66 VTCRVCQSLIDIEGKMHQHVVKCSVCN 92 (256)
T ss_pred EEeecCCceecccCccceeeEECCCCC
Confidence 479999954 455788999999994
No 101
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=56.18 E-value=6.8 Score=29.46 Aligned_cols=19 Identities=42% Similarity=1.153 Sum_probs=16.1
Q ss_pred CcCcccCCCCCCcccccccchhhH
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCK 79 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck 79 (347)
..|.+||.+++|- .|..|+
T Consensus 81 ~~C~~CG~pss~~-----iC~~C~ 99 (104)
T TIGR00269 81 RRCERCGEPTSGR-----ICKACK 99 (104)
T ss_pred CcCCcCcCcCCcc-----ccHhhh
Confidence 5699999999864 899996
No 102
>PF00357 Integrin_alpha: Integrin alpha cytoplasmic region; InterPro: IPR018184 Some alpha subunits are cleaved post- translationally to produce a heavy and a light chain linked by a disulphide bond [, ]. Integrin alpha chains share a conserved sequence which is found at the beginning of the cytoplasmic domain, just after the end of the transmembrane region. Within the N-terminal domain of alpha subunits, seven sequence repeats, each of approximately 60 amino acids, have been found []. It has been predicted that these repeats assume the beta-propeller fold. The domains contain seven four-stranded beta-sheets arranged in a torus around a pseudosymmetry axis []. Integrin ligands and a putative Mg2+ ion are predicted to bind to the upper face of the propeller, in a manner analogous to the way in which the trimeric G-protein beta subunit (G beta) (which also has a beta-propeller fold) binds the G protein alpha subunit []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences []. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first ten residues of the alpha-subunit cytoplasmic domain appear to form an alpha helix that is terminated by a proline residue. The remainder of the domain is highly acidic in nature and this loops back to contact the membrane-proximal lysine anchor residue. This entry represents the conserved site of the C-terminal integrin alpha chain. ; PDB: 2LKJ_A 2LKE_A 2K8O_A 1DPK_A 2K9J_A 1DPQ_A 1S4W_A 1M8O_A 2K1A_A 2KNC_A ....
Probab=48.18 E-value=6 Score=18.52 Aligned_cols=7 Identities=71% Similarity=1.260 Sum_probs=5.4
Q ss_pred HHHHhhh
Q psy3092 80 GFFKRTV 86 (347)
Q Consensus 80 ~FFRR~v 86 (347)
|||+|.-
T Consensus 3 GFFKR~~ 9 (15)
T PF00357_consen 3 GFFKRQR 9 (15)
T ss_dssp CHHHHHH
T ss_pred ccccccC
Confidence 6999974
No 103
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=46.63 E-value=8.7 Score=21.51 Aligned_cols=20 Identities=35% Similarity=0.998 Sum_probs=7.8
Q ss_pred cCcccCCCCCC-cccccccchhhH
Q psy3092 57 LCSICGDRASG-KHYGVYSCEGCK 79 (347)
Q Consensus 57 ~C~VCg~~a~g-~HyGv~sC~~Ck 79 (347)
.|.+|+.+..+ ..| .|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y---~C~~Cd 22 (30)
T PF07649_consen 2 RCDACGKPIDGGWFY---RCSECD 22 (30)
T ss_dssp --TTTS----S--EE---E-TTT-
T ss_pred cCCcCCCcCCCCceE---ECccCC
Confidence 49999999888 555 455554
No 104
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF12238 MSA-2c: Merozoite surface antigen 2c; InterPro: IPR021060 This family of proteins are restricted to the apicomplexan Babesia bovis. Proteins in this entry are typically between 263 and 318 amino acids in length and plasma membrane glycoproteins. These antigens present on the merozoite surface (MSA) and are involved in the parasite invasion of the bovine erythrocyte. MSA-2c has been suggested as a possible antigen for a vaccine candidate [].
Probab=40.92 E-value=1e+02 Score=26.26 Aligned_cols=10 Identities=20% Similarity=0.315 Sum_probs=8.3
Q ss_pred CCCccccccc
Q psy3092 65 ASGKHYGVYS 74 (347)
Q Consensus 65 a~g~HyGv~s 74 (347)
.+.+-||.+|
T Consensus 194 gsSFTfGGLT 203 (205)
T PF12238_consen 194 GSSFTFGGLT 203 (205)
T ss_pred CCceecCCcc
Confidence 7889999875
No 106
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.53 E-value=6.7 Score=30.85 Aligned_cols=40 Identities=18% Similarity=0.223 Sum_probs=25.0
Q ss_pred CCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHH
Q psy3092 66 SGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117 (347)
Q Consensus 66 ~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~K 117 (347)
.+.+.+-..|..|+.|. +...+. +.+ ..+|+.|+.|+..-
T Consensus 24 ~~~~~~~~~cP~C~s~~-~~k~g~--~~~---------~~qRyrC~~C~~tf 63 (129)
T COG3677 24 IRMQITKVNCPRCKSSN-VVKIGG--IRR---------GHQRYKCKSCGSTF 63 (129)
T ss_pred HhhhcccCcCCCCCccc-eeeECC--ccc---------cccccccCCcCcce
Confidence 45677778888998887 321111 111 15688888887665
No 107
>smart00274 FOLN Follistatin-N-terminal domain-like. Follistatin-N-terminal domain-like, EGF-like. Region distinct from the kazal-like sequence
Probab=39.37 E-value=15 Score=20.02 Aligned_cols=20 Identities=35% Similarity=0.886 Sum_probs=16.2
Q ss_pred cccccCCCCcccccccccCc
Q psy3092 91 SYACREGRNCIIDKRQRNRC 110 (347)
Q Consensus 91 ~~~C~~~~~C~~~~~~r~~C 110 (347)
.+.|..+..|.+++.++-+|
T Consensus 4 ~v~C~~G~~C~~d~~g~p~C 23 (26)
T smart00274 4 NVQCPFGKVCVVDKGGNARC 23 (26)
T ss_pred CEECCCCCEEEeCCCCCEEE
Confidence 35799999999988777776
No 108
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=38.07 E-value=17 Score=22.90 Aligned_cols=23 Identities=39% Similarity=1.060 Sum_probs=18.6
Q ss_pred cCcccCCCC-CCc-ccccccchhhH
Q psy3092 57 LCSICGDRA-SGK-HYGVYSCEGCK 79 (347)
Q Consensus 57 ~C~VCg~~a-~g~-HyGv~sC~~Ck 79 (347)
.|.|||++. .|. =||..-|..|-
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE 25 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCE 25 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHH
Confidence 399999764 585 48999999996
No 109
>PRK00420 hypothetical protein; Validated
Probab=37.59 E-value=17 Score=27.77 Aligned_cols=25 Identities=20% Similarity=0.329 Sum_probs=20.2
Q ss_pred CcCcccCCCCCCcccccccchhhHH
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKG 80 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~ 80 (347)
..|.|||.+-.+.+=|..-|-.|..
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCC
Confidence 4599999998887778888888853
No 110
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=37.47 E-value=28 Score=22.52 Aligned_cols=23 Identities=35% Similarity=0.990 Sum_probs=18.6
Q ss_pred CcCcccCCCC-CCcccccccchhh
Q psy3092 56 HLCSICGDRA-SGKHYGVYSCEGC 78 (347)
Q Consensus 56 ~~C~VCg~~a-~g~HyGv~sC~~C 78 (347)
..|.|||.+- --..||..-|+-|
T Consensus 15 nrC~~~Gr~rgvirkf~l~lcR~~ 38 (52)
T PRK05766 15 RECQRCGRKQGLIRKYGLYLCRQC 38 (52)
T ss_pred ceeecCCCCceeHHhhCCcccHHH
Confidence 4699999864 3368999999988
No 111
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=36.89 E-value=13 Score=27.81 Aligned_cols=26 Identities=27% Similarity=0.625 Sum_probs=20.4
Q ss_pred cCcccCCCCCCcccccccchhhHHHH
Q psy3092 57 LCSICGDRASGKHYGVYSCEGCKGFF 82 (347)
Q Consensus 57 ~C~VCg~~a~g~HyGv~sC~~Ck~FF 82 (347)
.|.||++......=+.+.|..|..=|
T Consensus 37 aCeiC~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 37 ACEICGPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred eccccCCCceEEECCEEEEecCCCEE
Confidence 49999887766677888999997533
No 112
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=36.23 E-value=19 Score=30.72 Aligned_cols=32 Identities=22% Similarity=0.546 Sum_probs=24.5
Q ss_pred CcCcccCCCCCC--ccc-ccccchhhHHHHHhhhc
Q psy3092 56 HLCSICGDRASG--KHY-GVYSCEGCKGFFKRTVR 87 (347)
Q Consensus 56 ~~C~VCg~~a~g--~Hy-Gv~sC~~Ck~FFRR~v~ 87 (347)
..|.+|.+..-= +.. ++..|..|++.|.|...
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~ 187 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCF 187 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchhhc
Confidence 469999976544 455 67889999999998743
No 113
>PRK01343 zinc-binding protein; Provisional
Probab=35.26 E-value=34 Score=22.62 Aligned_cols=23 Identities=22% Similarity=0.599 Sum_probs=15.0
Q ss_pred CcCcccCCCCCCcccccccchhhH
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCK 79 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck 79 (347)
..|.+||.+... .|--++...|+
T Consensus 10 ~~CP~C~k~~~~-~~rPFCS~RC~ 32 (57)
T PRK01343 10 RPCPECGKPSTR-EAYPFCSERCR 32 (57)
T ss_pred CcCCCCCCcCcC-CCCcccCHHHh
Confidence 469999998653 34455555554
No 114
>PF04444 Dioxygenase_N: Catechol dioxygenase N terminus; InterPro: IPR007535 This domain is the N-terminal region of catechol, chlorocatechol or hydroxyquinol 1,2-dioxygenase proteins. This region is always found adjacent to the dioxygenase domain (IPR000627 from INTERPRO). Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes (IPR000486 from INTERPRO) use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) []. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) (1.13.11.1 from EC); protocatechuate 3,4-dioxygenase (3,4-PCD) (1.13.11.3 from EC); and chlorocatechol 1,2-dioxygenase (1.13.11.1 from EC) [].; GO: 0005506 iron ion binding, 0018576 catechol 1,2-dioxygenase activity, 0009712 catechol-containing compound metabolic process, 0055114 oxidation-reduction process; PDB: 3O6R_B 1S9A_A 3O6J_A 3O5U_B 3O32_B 3HHY_A 3HHX_A 3HJS_A 3HJQ_A 3HKP_A ....
Probab=35.00 E-value=87 Score=21.92 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=23.0
Q ss_pred hhhHHhhHHHHHHHHHhcCCCHhHHHHHHHHH
Q psy3092 260 GGIFDRVLTELVSKMREMKMDKTELGCLRTII 291 (347)
Q Consensus 260 ~~~~~~~~~~l~~~l~~L~l~~~E~~lL~ai~ 291 (347)
..++.+++..+..-+++.++|.+||......+
T Consensus 5 ~~i~~~lv~~lh~~i~e~~lT~~E~~~av~~L 36 (74)
T PF04444_consen 5 KEIMARLVRHLHDFIREVDLTEDEWWAAVDFL 36 (74)
T ss_dssp HHHHHHHHHHHHHHHHHCT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 35666777888889999999999998655444
No 115
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=34.52 E-value=13 Score=26.82 Aligned_cols=27 Identities=30% Similarity=0.833 Sum_probs=20.6
Q ss_pred CCcCcccCCCCCC-cccccccchhhHHH
Q psy3092 55 KHLCSICGDRASG-KHYGVYSCEGCKGF 81 (347)
Q Consensus 55 ~~~C~VCg~~a~g-~HyGv~sC~~Ck~F 81 (347)
.+.|..||.++.- .-.|+-.|+.|..-
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAK 62 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCe
Confidence 3569999998644 47788999999643
No 116
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=34.02 E-value=38 Score=21.81 Aligned_cols=30 Identities=27% Similarity=0.636 Sum_probs=21.5
Q ss_pred CcCcccCCCCCCc----cccc-ccchhhHHHHHhh
Q psy3092 56 HLCSICGDRASGK----HYGV-YSCEGCKGFFKRT 85 (347)
Q Consensus 56 ~~C~VCg~~a~g~----HyGv-~sC~~Ck~FFRR~ 85 (347)
..|..|+...+-. -.|. .-|++|-.||++-
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~ 38 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKH 38 (52)
T ss_pred CCcCCCCCCCCCccccCCCCCCcEeecccHHHHHc
Confidence 4599999655432 3443 7799999999874
No 117
>PRK08359 transcription factor; Validated
Probab=33.01 E-value=25 Score=29.24 Aligned_cols=29 Identities=28% Similarity=0.738 Sum_probs=21.9
Q ss_pred CcCcccCCCCCCccccc-------ccchhhHHHHHh
Q psy3092 56 HLCSICGDRASGKHYGV-------YSCEGCKGFFKR 84 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv-------~sC~~Ck~FFRR 84 (347)
..|-+||.+-.|.-|-| ..|+.|+.=|.+
T Consensus 7 ~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~G~ 42 (176)
T PRK08359 7 RYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKYGR 42 (176)
T ss_pred ceeecCCCccCCCCeEEEEcCeEEehHHHHHHHhCC
Confidence 45999999998885443 579999955554
No 118
>KOG3362|consensus
Probab=32.00 E-value=23 Score=28.11 Aligned_cols=18 Identities=39% Similarity=1.108 Sum_probs=13.1
Q ss_pred CcCcccCCCCCCcccccccchhhH
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCK 79 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck 79 (347)
..|.|||- .+.++|-.|-
T Consensus 119 ~fCaVCG~------~S~ysC~~CG 136 (156)
T KOG3362|consen 119 KFCAVCGY------DSKYSCVNCG 136 (156)
T ss_pred hhhhhcCC------CchhHHHhcC
Confidence 56999993 4666777773
No 119
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.81 E-value=16 Score=21.21 Aligned_cols=12 Identities=33% Similarity=0.828 Sum_probs=8.8
Q ss_pred CcCcccCCCCCC
Q psy3092 56 HLCSICGDRASG 67 (347)
Q Consensus 56 ~~C~VCg~~a~g 67 (347)
..|.|||.++..
T Consensus 19 ~~CP~Cg~~~~~ 30 (34)
T cd00729 19 EKCPICGAPKEK 30 (34)
T ss_pred CcCcCCCCchHH
Confidence 469999987643
No 120
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=31.03 E-value=28 Score=20.35 Aligned_cols=23 Identities=22% Similarity=0.700 Sum_probs=12.0
Q ss_pred cCcccCCCC----CCcccccccchhhH
Q psy3092 57 LCSICGDRA----SGKHYGVYSCEGCK 79 (347)
Q Consensus 57 ~C~VCg~~a----~g~HyGv~sC~~Ck 79 (347)
.|.-||++= --.||+...|..|+
T Consensus 5 ~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp E-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred hHhHhCCHHHHHHHHHhCCcccccccc
Confidence 599999752 33699999999995
No 121
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.06 E-value=28 Score=21.32 Aligned_cols=9 Identities=33% Similarity=1.305 Sum_probs=7.8
Q ss_pred CcCcccCCC
Q psy3092 56 HLCSICGDR 64 (347)
Q Consensus 56 ~~C~VCg~~ 64 (347)
++|.|||.+
T Consensus 9 K~C~~C~rp 17 (42)
T PF10013_consen 9 KICPVCGRP 17 (42)
T ss_pred CcCcccCCc
Confidence 679999987
No 122
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=29.97 E-value=17 Score=21.57 Aligned_cols=10 Identities=60% Similarity=1.255 Sum_probs=6.6
Q ss_pred ccccCchhhh
Q psy3092 105 RQRNRCQYCR 114 (347)
Q Consensus 105 ~~r~~Cr~CR 114 (347)
.+|++|+.||
T Consensus 27 ~qryrC~~C~ 36 (36)
T PF03811_consen 27 HQRYRCKDCR 36 (36)
T ss_pred CEeEecCcCC
Confidence 4567777775
No 123
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=29.83 E-value=26 Score=32.17 Aligned_cols=31 Identities=26% Similarity=0.715 Sum_probs=26.3
Q ss_pred CCcCcccCCCC---CCcccccccchhhHHHHHhh
Q psy3092 55 KHLCSICGDRA---SGKHYGVYSCEGCKGFFKRT 85 (347)
Q Consensus 55 ~~~C~VCg~~a---~g~HyGv~sC~~Ck~FFRR~ 85 (347)
...|.=||.+. ....|||+-|--|+|--|-.
T Consensus 20 Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsL 53 (319)
T COG5347 20 NKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSL 53 (319)
T ss_pred cCccccCCCCCCceEecccCeEEEeecchhhhcc
Confidence 46799999886 45799999999999987754
No 124
>PF03802 CitX: Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; InterPro: IPR005551 Members of this protein family are annotated as CitX, containing the CitX domain, the domain is also found in the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25 from EC), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems.; GO: 0051191 prosthetic group biosynthetic process
Probab=28.51 E-value=22 Score=29.42 Aligned_cols=13 Identities=38% Similarity=0.795 Sum_probs=10.6
Q ss_pred CCCcCcccCCCCC
Q psy3092 54 SKHLCSICGDRAS 66 (347)
Q Consensus 54 ~~~~C~VCg~~a~ 66 (347)
+++.|.||+++|.
T Consensus 131 ~~R~CliC~~~Ak 143 (170)
T PF03802_consen 131 PPRRCLICGRPAK 143 (170)
T ss_pred CCCcccCCChhHH
Confidence 3478999999974
No 125
>KOG4327|consensus
Probab=28.28 E-value=83 Score=26.48 Aligned_cols=6 Identities=67% Similarity=0.966 Sum_probs=2.8
Q ss_pred CCcccc
Q psy3092 66 SGKHYG 71 (347)
Q Consensus 66 ~g~HyG 71 (347)
+|||=|
T Consensus 200 SGYhTG 205 (218)
T KOG4327|consen 200 SGYHTG 205 (218)
T ss_pred hhhhHH
Confidence 455544
No 126
>PF03002 Somatostatin: Somatostatin/Cortistatin family; InterPro: IPR018142 Somatostatin inhibits the release of the pituitary growth hormone, somatotropin and inhibits the release of glucagon and insulin from the pancreas of fasted animals. Cortistatin is a cortical neuropeptide with neuronal depressant and sleep-modulating properties [].; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=28.25 E-value=12 Score=18.23 Aligned_cols=9 Identities=67% Similarity=1.383 Sum_probs=6.8
Q ss_pred hhHHHHHhh
Q psy3092 77 GCKGFFKRT 85 (347)
Q Consensus 77 ~Ck~FFRR~ 85 (347)
+|+-||..+
T Consensus 6 ~CknffWK~ 14 (18)
T PF03002_consen 6 GCKNFFWKT 14 (18)
T ss_pred cccceeecc
Confidence 688888754
No 127
>TIGR03124 ctirate_citX holo-ACP synthase CitX. Members of this protein family are the CitX protein, or CitX domain of the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems.
Probab=27.95 E-value=21 Score=29.31 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=10.2
Q ss_pred CCcCcccCCCCC
Q psy3092 55 KHLCSICGDRAS 66 (347)
Q Consensus 55 ~~~C~VCg~~a~ 66 (347)
++.|.|||++|.
T Consensus 130 ~R~CliC~~~Ak 141 (165)
T TIGR03124 130 PRKCLLCEEDAK 141 (165)
T ss_pred CCeeecCCchHH
Confidence 478999999984
No 128
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=27.87 E-value=19 Score=20.30 Aligned_cols=18 Identities=44% Similarity=1.209 Sum_probs=10.4
Q ss_pred CcCcccCCCCCCcccccccchhhH
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCK 79 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck 79 (347)
..|.|||. .+-++|.+|.
T Consensus 3 ~~C~vC~~------~~kY~Cp~C~ 20 (30)
T PF04438_consen 3 KLCSVCGN------PAKYRCPRCG 20 (30)
T ss_dssp EEETSSSS------EESEE-TTT-
T ss_pred CCCccCcC------CCEEECCCcC
Confidence 46899987 2344666664
No 129
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=27.31 E-value=36 Score=31.50 Aligned_cols=31 Identities=19% Similarity=0.702 Sum_probs=25.5
Q ss_pred CCcCcccCCCC---CCcccccccchhhHHHHHhh
Q psy3092 55 KHLCSICGDRA---SGKHYGVYSCEGCKGFFKRT 85 (347)
Q Consensus 55 ~~~C~VCg~~a---~g~HyGv~sC~~Ck~FFRR~ 85 (347)
++.|.=||.+. ....||+..|-.|.+.-|..
T Consensus 22 Nk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsL 55 (395)
T PLN03114 22 NKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 55 (395)
T ss_pred CCcCccCCCCCCCceeeccceeehhhhhHhhccC
Confidence 46799999654 45799999999999998764
No 130
>PRK06424 transcription factor; Provisional
Probab=26.70 E-value=29 Score=27.80 Aligned_cols=23 Identities=30% Similarity=0.956 Sum_probs=16.7
Q ss_pred CcccCCCCCCccccc-------ccchhhHHH
Q psy3092 58 CSICGDRASGKHYGV-------YSCEGCKGF 81 (347)
Q Consensus 58 C~VCg~~a~g~HyGv-------~sC~~Ck~F 81 (347)
|-+||....+.| -| ..|..|+-|
T Consensus 3 CE~CG~~~~~~~-~v~ieg~~l~vC~~Ca~~ 32 (144)
T PRK06424 3 CEMCGKKVPQTT-KVMIDGAILNVCDDCAKF 32 (144)
T ss_pred ccccCcccCCce-EEEEcCeeeehhHHHHHc
Confidence 999999988874 32 247777765
No 131
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=26.55 E-value=46 Score=25.54 Aligned_cols=47 Identities=28% Similarity=0.658 Sum_probs=28.6
Q ss_pred CcCcccCCCCCCcccc-cccchhhHHHHHhhhcCCCcccccCCCCcccc--cccccCchhhhhHH
Q psy3092 56 HLCSICGDRASGKHYG-VYSCEGCKGFFKRTVRKDLSYACREGRNCIID--KRQRNRCQYCRYQK 117 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyG-v~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~--~~~r~~Cr~CR~~K 117 (347)
+.|..|+.+ .|+=+| ...|..|+ ...|. .|.+. +..-+.|..|+-++
T Consensus 55 ~~C~~C~~~-fg~l~~~~~~C~~C~-----------~~VC~---~C~~~~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 55 RHCARCGKP-FGFLFNRGRVCVDCK-----------HRVCK---KCGVYSKKEPIWLCKVCQKQR 104 (118)
T ss_dssp SB-TTTS-B-CSCTSTTCEEETTTT-----------EEEET---TSEEETSSSCCEEEHHHHHHH
T ss_pred cchhhhCCc-ccccCCCCCcCCcCC-----------ccccC---ccCCcCCCCCCEEChhhHHHH
Confidence 469999986 333332 26788885 24563 36654 34568999998776
No 132
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=26.22 E-value=55 Score=23.71 Aligned_cols=32 Identities=25% Similarity=0.745 Sum_probs=20.9
Q ss_pred CcccCCCCC-Cccc-----c---cccchhhHHHHHhhhcCC
Q psy3092 58 CSICGDRAS-GKHY-----G---VYSCEGCKGFFKRTVRKD 89 (347)
Q Consensus 58 C~VCg~~a~-g~Hy-----G---v~sC~~Ck~FFRR~v~~~ 89 (347)
|--||.+.. +.++ | ..+|.||++-+.=.+..+
T Consensus 3 C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i~~~g 43 (88)
T PF12156_consen 3 CYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLIHENG 43 (88)
T ss_pred CCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHHHHcc
Confidence 888888763 3222 3 679999998877443333
No 133
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=26.03 E-value=50 Score=22.24 Aligned_cols=25 Identities=16% Similarity=0.470 Sum_probs=19.0
Q ss_pred CcCcccCCCC---CCcccccccchhhHH
Q psy3092 56 HLCSICGDRA---SGKHYGVYSCEGCKG 80 (347)
Q Consensus 56 ~~C~VCg~~a---~g~HyGv~sC~~Ck~ 80 (347)
..|.+||.+. ....|.-.+.+.|+.
T Consensus 7 v~CP~C~k~~~w~~~~~~rPFCS~RCk~ 34 (62)
T PRK00418 7 VNCPTCGKPVEWGEISPFRPFCSKRCQL 34 (62)
T ss_pred ccCCCCCCcccccCCCCcCCcccHHHHh
Confidence 4599999985 356777788888864
No 134
>KOG3506|consensus
Probab=25.89 E-value=32 Score=22.39 Aligned_cols=23 Identities=30% Similarity=0.960 Sum_probs=18.5
Q ss_pred CcCcccCCCCC-Ccccccccchhh
Q psy3092 56 HLCSICGDRAS-GKHYGVYSCEGC 78 (347)
Q Consensus 56 ~~C~VCg~~a~-g~HyGv~sC~~C 78 (347)
+.|.||+..-. -.-||-..|+-|
T Consensus 19 rsC~vCsn~~gLIrKYGL~vcr~c 42 (56)
T KOG3506|consen 19 RSCRVCSNRHGLIRKYGLNVCRQC 42 (56)
T ss_pred cceeeeccchhHHHHhhhHHhHHH
Confidence 56999997643 368999999988
No 135
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.88 E-value=26 Score=22.09 Aligned_cols=11 Identities=18% Similarity=0.785 Sum_probs=8.9
Q ss_pred CCcCcccCCCC
Q psy3092 55 KHLCSICGDRA 65 (347)
Q Consensus 55 ~~~C~VCg~~a 65 (347)
.++|.||+.|-
T Consensus 12 ~KICpvCqRPF 22 (54)
T COG4338 12 DKICPVCQRPF 22 (54)
T ss_pred hhhhhhhcCch
Confidence 47899999873
No 136
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.57 E-value=29 Score=22.62 Aligned_cols=32 Identities=19% Similarity=0.571 Sum_probs=23.2
Q ss_pred CCCcCcccCCCCCCcccccccchhhHHHHHhhh
Q psy3092 54 SKHLCSICGDRASGKHYGVYSCEGCKGFFKRTV 86 (347)
Q Consensus 54 ~~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v 86 (347)
....|.+||++-.-- =-++.|..|.+=+.|.-
T Consensus 4 ~~~~C~~Cg~~~~~~-dDiVvCp~CgapyHR~C 35 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDG-DDIVVCPECGAPYHRDC 35 (54)
T ss_pred cCccChhhCCcccCC-CCEEECCCCCCcccHHH
Confidence 345799999875211 14678999999888874
No 137
>PRK01392 citX 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase; Reviewed
Probab=25.39 E-value=25 Score=29.36 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=10.2
Q ss_pred CCcCcccCCCCC
Q psy3092 55 KHLCSICGDRAS 66 (347)
Q Consensus 55 ~~~C~VCg~~a~ 66 (347)
++.|.|||++|.
T Consensus 139 ~R~CliC~~~Ak 150 (180)
T PRK01392 139 PRRCLLCGQDAK 150 (180)
T ss_pred CCeeecCCchHH
Confidence 478999999984
No 138
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=25.39 E-value=14 Score=23.36 Aligned_cols=26 Identities=23% Similarity=0.910 Sum_probs=18.3
Q ss_pred CcccCCCCCCcccccccchhhHHHHHhh
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKGFFKRT 85 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~FFRR~ 85 (347)
|.|||. .+.--..+.|..|...|...
T Consensus 2 C~vC~~--~~~~~~~i~C~~C~~~~H~~ 27 (51)
T PF00628_consen 2 CPVCGQ--SDDDGDMIQCDSCNRWYHQE 27 (51)
T ss_dssp BTTTTS--SCTTSSEEEBSTTSCEEETT
T ss_pred CcCCCC--cCCCCCeEEcCCCChhhCcc
Confidence 889998 34445678899997655543
No 139
>KOG4323|consensus
Probab=24.89 E-value=39 Score=32.53 Aligned_cols=58 Identities=17% Similarity=0.392 Sum_probs=39.2
Q ss_pred CCcCcccCCCCCCcccccccchhhHHHHHhhhcCCCcccccCCCCcccccccccCchhhhhHH
Q psy3092 55 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLSYACREGRNCIIDKRQRNRCQYCRYQK 117 (347)
Q Consensus 55 ~~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~~~~~~C~~~~~C~~~~~~r~~Cr~CR~~K 117 (347)
...|.||+.-..|.-+-.+-|.+|..-|.+...+-..-. .=.-|...-|.|--|+..+
T Consensus 168 n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~-----~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKD-----ELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred cceeeeeecCCcCccceeeeecccccHHHHHhccCCCCH-----hhccCccceEeehhhccch
Confidence 456999997777766699999999999999843322110 0011234457899898766
No 140
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=24.07 E-value=71 Score=22.50 Aligned_cols=20 Identities=30% Similarity=0.346 Sum_probs=15.9
Q ss_pred hhCCCCCCCCHHHHHHHHHH
Q psy3092 201 KHIPHFTTLPLEDQVLLLRA 220 (347)
Q Consensus 201 k~~p~F~~L~~~dq~~Llk~ 220 (347)
..|++|..|..+||..|.+.
T Consensus 61 ~~i~G~~~L~~~Dq~~i~~~ 80 (82)
T PF00645_consen 61 EEIKGFDELKPEDQEKIRKL 80 (82)
T ss_dssp GGCETCCCS-HHHHHHHHHH
T ss_pred HHCCChHHCCHHHHHHHHHH
Confidence 46999999999999887653
No 141
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=23.64 E-value=25 Score=25.65 Aligned_cols=24 Identities=25% Similarity=0.810 Sum_probs=18.8
Q ss_pred CcCcccCCCCCC-cccccccchhhH
Q psy3092 56 HLCSICGDRASG-KHYGVYSCEGCK 79 (347)
Q Consensus 56 ~~C~VCg~~a~g-~HyGv~sC~~Ck 79 (347)
..|..||..+-. .--|+-.|..|.
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~ 60 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCG 60 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTT
T ss_pred CcCCCCCCceeEEeeeEEeecCCCC
Confidence 469999988754 477888898885
No 142
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=23.52 E-value=31 Score=22.26 Aligned_cols=14 Identities=21% Similarity=0.468 Sum_probs=10.5
Q ss_pred cCcccCCCCCCccc
Q psy3092 57 LCSICGDRASGKHY 70 (347)
Q Consensus 57 ~C~VCg~~a~g~Hy 70 (347)
.|.-||..+..+++
T Consensus 3 PCPfCGg~~~~~~~ 16 (53)
T TIGR03655 3 PCPFCGGADVYLRR 16 (53)
T ss_pred CCCCCCCcceeeEe
Confidence 49999988775653
No 143
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=23.41 E-value=56 Score=19.14 Aligned_cols=16 Identities=25% Similarity=0.671 Sum_probs=12.3
Q ss_pred cccc-cchhhHHHHHhh
Q psy3092 70 YGVY-SCEGCKGFFKRT 85 (347)
Q Consensus 70 yGv~-sC~~Ck~FFRR~ 85 (347)
.|.. -|++|-.+||+.
T Consensus 17 ~g~~~LCn~Cg~~~kk~ 33 (36)
T PF00320_consen 17 NGNRTLCNACGLYYKKY 33 (36)
T ss_dssp TSEE-EEHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 4555 799999998874
No 144
>KOG0703|consensus
Probab=22.59 E-value=28 Score=31.27 Aligned_cols=31 Identities=26% Similarity=0.785 Sum_probs=25.5
Q ss_pred CCcCcccCCCC---CCcccccccchhhHHHHHhh
Q psy3092 55 KHLCSICGDRA---SGKHYGVYSCEGCKGFFKRT 85 (347)
Q Consensus 55 ~~~C~VCg~~a---~g~HyGv~sC~~Ck~FFRR~ 85 (347)
++.|.-||.+. ....+||.-|-.|+|.-|-.
T Consensus 25 N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~l 58 (287)
T KOG0703|consen 25 NKVCADCGAKGPRWASWNLGVFICLRCAGIHRSL 58 (287)
T ss_pred cCcccccCCCCCCeEEeecCeEEEeecccccccc
Confidence 46799999764 45799999999999987764
No 145
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=22.56 E-value=28 Score=20.95 Aligned_cols=20 Identities=20% Similarity=0.757 Sum_probs=9.1
Q ss_pred CcccCCCCCCcccccccchhhHH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCKG 80 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck~ 80 (347)
|.+|+....-. ...|+.|+.
T Consensus 1 C~~C~~~~~l~---~f~C~~C~~ 20 (39)
T smart00154 1 CHFCRKKVGLT---GFKCRHCGN 20 (39)
T ss_pred CcccCCccccc---CeECCccCC
Confidence 44555443222 345666653
No 146
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=22.11 E-value=43 Score=24.42 Aligned_cols=24 Identities=38% Similarity=1.101 Sum_probs=18.4
Q ss_pred CcCcccCCCCCC-cccccccchhhH
Q psy3092 56 HLCSICGDRASG-KHYGVYSCEGCK 79 (347)
Q Consensus 56 ~~C~VCg~~a~g-~HyGv~sC~~Ck 79 (347)
..|..||..+-. .--|+-.|+.|.
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~ 61 (90)
T PTZ00255 37 YFCPFCGKHAVKRQAVGIWRCKGCK 61 (90)
T ss_pred ccCCCCCCCceeeeeeEEEEcCCCC
Confidence 469999977654 455889999985
No 147
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=21.68 E-value=15 Score=23.36 Aligned_cols=9 Identities=33% Similarity=1.055 Sum_probs=7.1
Q ss_pred CcCcccCCC
Q psy3092 56 HLCSICGDR 64 (347)
Q Consensus 56 ~~C~VCg~~ 64 (347)
+.|.+||.=
T Consensus 23 RQCvlCGRW 31 (57)
T PF14445_consen 23 RQCVLCGRW 31 (57)
T ss_pred HHHhhhchh
Confidence 679999864
No 148
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=21.60 E-value=18 Score=21.29 Aligned_cols=16 Identities=44% Similarity=1.263 Sum_probs=8.3
Q ss_pred CcccCCCCCCcccccccchhhH
Q psy3092 58 CSICGDRASGKHYGVYSCEGCK 79 (347)
Q Consensus 58 C~VCg~~a~g~HyGv~sC~~Ck 79 (347)
|.+|+.++ ...|.+|+
T Consensus 1 C~~C~~~~------~~~C~~C~ 16 (37)
T PF01753_consen 1 CAVCGKPA------LKRCSRCK 16 (37)
T ss_dssp -TTTSSCS------SEEETTTS
T ss_pred CcCCCCCc------CCcCCCCC
Confidence 55666632 22677773
No 149
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=21.38 E-value=23 Score=25.96 Aligned_cols=31 Identities=26% Similarity=0.628 Sum_probs=12.7
Q ss_pred CcCcccCCCCCCccccc------ccchhhHHHHHhhh
Q psy3092 56 HLCSICGDRASGKHYGV------YSCEGCKGFFKRTV 86 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv------~sC~~Ck~FFRR~v 86 (347)
.-|.+||.+=.+++=-+ .+|.-|+.=|++.+
T Consensus 15 ~~CalCG~tWg~~y~Ev~G~rLfFCCd~ca~EF~nmi 51 (105)
T PF11494_consen 15 MGCALCGATWGDYYEEVDGERLFFCCDDCAKEFKNMI 51 (105)
T ss_dssp GS-SS---S---SS-B-TT--BSSS--SSSS-TTS-T
T ss_pred ccccccCCcHHHHHHhhcCCEEEEEcHHHHHHHHHHH
Confidence 35999999877776543 46888887777764
No 150
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=21.29 E-value=45 Score=23.50 Aligned_cols=9 Identities=56% Similarity=1.560 Sum_probs=4.2
Q ss_pred CcCcccCCC
Q psy3092 56 HLCSICGDR 64 (347)
Q Consensus 56 ~~C~VCg~~ 64 (347)
.+|+||||.
T Consensus 10 qiCqiCGD~ 18 (80)
T PF14569_consen 10 QICQICGDD 18 (80)
T ss_dssp -B-SSS--B
T ss_pred cccccccCc
Confidence 579999985
No 151
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.70 E-value=48 Score=26.94 Aligned_cols=26 Identities=35% Similarity=0.974 Sum_probs=19.2
Q ss_pred CcccCCCCCCcccc-------cccchhhHHHHHh
Q psy3092 58 CSICGDRASGKHYG-------VYSCEGCKGFFKR 84 (347)
Q Consensus 58 C~VCg~~a~g~HyG-------v~sC~~Ck~FFRR 84 (347)
|-+||.+-.|.-|- ...|..|+ =|.+
T Consensus 3 CEiCG~~i~~~~~~v~iega~l~vC~~C~-k~G~ 35 (154)
T TIGR00270 3 CEICGRKIKGKGFKIVIEGSEMTVCGECR-KFGK 35 (154)
T ss_pred cccCCCccCCCCeEEEEcCeEEehhhhHH-hcCC
Confidence 99999998887443 34699998 4444
No 152
>KOG4443|consensus
Probab=20.47 E-value=22 Score=35.40 Aligned_cols=33 Identities=18% Similarity=0.606 Sum_probs=28.5
Q ss_pred CcCcccCCCCCCcccccccchhhHHHHHhhhcC
Q psy3092 56 HLCSICGDRASGKHYGVYSCEGCKGFFKRTVRK 88 (347)
Q Consensus 56 ~~C~VCg~~a~g~HyGv~sC~~Ck~FFRR~v~~ 88 (347)
..|.||+.-..|.--|..+|.-|..|+.+...+
T Consensus 19 ~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt 51 (694)
T KOG4443|consen 19 LMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVT 51 (694)
T ss_pred hhhhhhccccccccCcchhhhhhcccCCcchhh
Confidence 569999999999998999999999988887543
Done!