Query psy2636
Match_columns 335
No_of_seqs 203 out of 1613
Neff 10.1
Searched_HMMs 46136
Date Fri Aug 16 21:14:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2636.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2636hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4217|consensus 100.0 6.8E-64 1.5E-68 430.6 18.6 251 39-334 268-518 (605)
2 KOG4215|consensus 100.0 1.2E-62 2.6E-67 411.4 13.3 250 38-335 17-267 (432)
3 KOG4216|consensus 100.0 9.8E-55 2.1E-59 366.2 8.1 294 38-335 44-393 (479)
4 KOG4218|consensus 100.0 2.3E-49 5.1E-54 328.6 12.6 294 38-335 13-391 (475)
5 KOG4846|consensus 100.0 1.6E-44 3.5E-49 306.5 5.0 283 41-327 133-468 (538)
6 cd07170 NR_DBD_ERR DNA-binding 100.0 2.1E-37 4.5E-42 219.9 3.7 85 38-122 2-86 (97)
7 cd06964 NR_DBD_RAR DNA-binding 100.0 1.1E-36 2.5E-41 211.8 3.7 80 40-119 4-83 (85)
8 cd06962 NR_DBD_FXR DNA-binding 100.0 1.1E-36 2.3E-41 211.2 3.2 79 41-119 2-80 (84)
9 cd07160 NR_DBD_LXR DNA-binding 100.0 1.5E-36 3.3E-41 216.8 3.9 80 39-118 17-96 (101)
10 cd06970 NR_DBD_PNR DNA-binding 100.0 2E-36 4.4E-41 213.0 3.7 81 38-118 4-85 (92)
11 cd06956 NR_DBD_RXR DNA-binding 100.0 8.2E-37 1.8E-41 209.2 1.4 76 42-117 2-77 (77)
12 cd06961 NR_DBD_TR DNA-binding 100.0 1.1E-36 2.5E-41 212.1 2.0 80 42-121 1-80 (85)
13 cd06967 NR_DBD_TR2_like DNA-bi 100.0 3.5E-36 7.6E-41 210.3 3.9 81 39-119 2-82 (87)
14 cd07171 NR_DBD_ER DNA-binding 100.0 1.9E-36 4.2E-41 208.9 1.7 79 39-117 2-80 (82)
15 cd06969 NR_DBD_NGFI-B DNA-bind 100.0 4.9E-36 1.1E-40 204.2 3.2 75 41-115 1-75 (75)
16 cd07155 NR_DBD_ER_like DNA-bin 100.0 3.4E-36 7.5E-41 205.2 1.6 75 43-117 1-75 (75)
17 cd07163 NR_DBD_TLX DNA-binding 100.0 1E-35 2.3E-40 210.2 3.4 80 39-118 5-86 (92)
18 cd06957 NR_DBD_PNR_like_2 DNA- 100.0 9.3E-36 2E-40 206.3 3.0 76 43-118 1-77 (82)
19 cd07168 NR_DBD_DHR4_like DNA-b 100.0 7.9E-36 1.7E-40 209.9 2.7 83 39-121 5-87 (90)
20 cd07161 NR_DBD_EcR DNA-binding 100.0 6E-36 1.3E-40 210.4 2.0 78 41-118 2-79 (91)
21 cd07172 NR_DBD_GR_PR DNA-bindi 100.0 1.1E-35 2.4E-40 203.3 3.2 76 39-114 1-76 (78)
22 cd07169 NR_DBD_GCNF_like DNA-b 100.0 8.5E-36 1.8E-40 209.5 2.2 84 39-122 5-88 (90)
23 cd07166 NR_DBD_REV_ERB DNA-bin 100.0 9.8E-36 2.1E-40 209.0 2.3 80 40-119 3-83 (89)
24 cd06955 NR_DBD_VDR DNA-binding 100.0 9.2E-36 2E-40 214.8 1.6 78 40-117 6-83 (107)
25 cd07154 NR_DBD_PNR_like The DN 100.0 2.2E-35 4.7E-40 200.4 3.0 72 43-114 1-73 (73)
26 cd06959 NR_DBD_EcR_like The DN 100.0 1.4E-35 3.1E-40 201.1 2.0 73 42-114 1-73 (73)
27 cd07156 NR_DBD_VDR_like The DN 100.0 2E-35 4.3E-40 199.8 2.5 72 43-114 1-72 (72)
28 cd07167 NR_DBD_Lrh-1_like The 100.0 1.2E-35 2.6E-40 209.2 1.4 80 43-122 1-80 (93)
29 cd06960 NR_DBD_HNF4A DNA-bindi 100.0 2.9E-35 6.4E-40 201.7 3.0 75 43-117 1-75 (76)
30 cd06958 NR_DBD_COUP_TF DNA-bin 100.0 2.4E-35 5.1E-40 200.0 2.5 72 43-114 1-72 (73)
31 cd06916 NR_DBD_like DNA-bindin 100.0 3.3E-35 7.2E-40 199.0 3.1 72 43-114 1-72 (72)
32 cd07164 NR_DBD_PNR_like_1 DNA- 100.0 2.4E-35 5.2E-40 202.7 2.4 76 43-118 1-76 (78)
33 cd06963 NR_DBD_GR_like The DNA 100.0 2.9E-35 6.2E-40 199.1 2.7 72 43-114 1-72 (73)
34 cd06966 NR_DBD_CAR DNA-binding 100.0 2E-35 4.4E-40 209.3 1.5 80 41-120 1-80 (94)
35 cd07173 NR_DBD_AR DNA-binding 100.0 3E-35 6.6E-40 202.7 2.1 76 39-114 2-77 (82)
36 cd06968 NR_DBD_ROR DNA-binding 100.0 3.1E-35 6.7E-40 208.5 1.8 81 39-119 4-84 (95)
37 cd07179 2DBD_NR_DBD2 The secon 100.0 3.5E-35 7.5E-40 199.5 1.8 73 43-115 1-73 (74)
38 cd07157 2DBD_NR_DBD1 The first 100.0 1.1E-34 2.4E-39 202.3 4.0 76 42-117 2-79 (86)
39 cd07165 NR_DBD_DmE78_like DNA- 100.0 5.3E-35 1.1E-39 202.3 1.8 77 43-119 1-77 (81)
40 cd07162 NR_DBD_PXR DNA-binding 100.0 6.5E-35 1.4E-39 204.5 1.9 76 42-117 1-76 (87)
41 cd07158 NR_DBD_Ppar_like The D 100.0 7E-35 1.5E-39 198.2 1.8 72 43-114 1-73 (73)
42 cd06965 NR_DBD_Ppar DNA-bindin 100.0 1.1E-34 2.4E-39 201.6 2.3 76 42-119 1-77 (84)
43 smart00399 ZnF_C4 c4 zinc fing 100.0 1.5E-33 3.2E-38 190.5 3.1 70 42-111 1-70 (70)
44 PF00105 zf-C4: Zinc finger, C 100.0 1.9E-32 4.2E-37 185.7 0.2 70 41-110 1-70 (70)
45 cd07072 NR_LBD_DHR38_like Liga 99.9 7.5E-27 1.6E-31 196.1 16.0 127 208-335 27-153 (239)
46 cd07348 NR_LBD_NGFI-B The liga 99.9 1.4E-24 3E-29 182.3 15.4 116 219-335 37-152 (238)
47 cd07071 NR_LBD_Nurr1 The ligan 99.9 2.9E-24 6.2E-29 180.6 15.4 114 221-335 39-152 (238)
48 cd06940 NR_LBD_REV_ERB The lig 99.9 2.2E-23 4.7E-28 170.2 14.8 116 219-335 8-124 (189)
49 cd07076 NR_LBD_GR Ligand bindi 99.9 3.8E-23 8.2E-28 173.6 16.1 116 220-335 25-142 (247)
50 cd06935 NR_LBD_TR The ligand b 99.9 6.1E-23 1.3E-27 174.0 15.5 115 220-335 49-164 (243)
51 cd07075 NR_LBD_MR Ligand bindi 99.9 7.6E-23 1.7E-27 171.8 15.2 115 220-335 25-142 (248)
52 cd06945 NR_LBD_Nurr1_like The 99.9 7.6E-23 1.6E-27 172.8 14.9 116 219-335 37-152 (239)
53 cd06941 NR_LBD_DmE78_like The 99.9 1.1E-22 2.4E-27 167.6 14.1 112 224-335 3-114 (195)
54 cd06937 NR_LBD_RAR The ligand 99.9 2.9E-22 6.3E-27 168.5 14.8 115 220-335 35-150 (231)
55 cd06947 NR_LBD_GR_Like Ligand 99.9 6.3E-22 1.4E-26 167.1 16.0 115 220-335 25-142 (246)
56 cd07074 NR_LBD_PR Ligand bindi 99.9 7E-22 1.5E-26 165.8 15.3 115 220-335 25-142 (248)
57 cd06939 NR_LBD_ROR_like The li 99.9 5.4E-22 1.2E-26 167.6 14.0 114 220-335 45-159 (241)
58 cd06949 NR_LBD_ER Ligand bindi 99.9 2E-21 4.2E-26 163.9 16.9 116 219-335 28-145 (235)
59 cd07073 NR_LBD_AR Ligand bindi 99.9 1.8E-21 4E-26 164.3 15.9 114 221-335 26-142 (246)
60 cd06954 NR_LBD_LXR The ligand 99.9 1E-21 2.2E-26 166.7 13.8 113 223-335 43-156 (236)
61 cd06929 NR_LBD_F1 Ligand-bindi 99.9 2.1E-21 4.6E-26 157.6 12.9 113 223-335 2-114 (174)
62 cd06934 NR_LBD_PXR_like The li 99.9 2.1E-21 4.4E-26 162.8 12.7 113 222-335 34-147 (226)
63 cd06938 NR_LBD_EcR The ligand 99.9 4E-21 8.7E-26 162.1 14.3 113 222-335 38-151 (231)
64 cd06944 NR_LBD_Ftz-F1_like The 99.9 7.7E-21 1.7E-25 160.8 13.0 114 222-335 37-155 (237)
65 cd06942 NR_LBD_Sex_1_like The 99.9 8.6E-21 1.9E-25 155.6 12.6 109 224-335 3-113 (191)
66 cd06946 NR_LBD_ERR The ligand 99.9 2.5E-20 5.4E-25 156.6 15.4 116 220-335 24-139 (221)
67 cd07069 NR_LBD_Lrh-1 The ligan 99.9 8.4E-21 1.8E-25 160.4 12.6 113 222-335 39-157 (241)
68 cd07070 NR_LBD_SF-1 The ligand 99.8 1.3E-20 2.8E-25 159.1 13.1 115 221-335 36-155 (237)
69 cd06933 NR_LBD_VDR The ligand 99.8 1.8E-20 3.8E-25 158.4 13.7 115 221-335 35-151 (238)
70 cd06932 NR_LBD_PPAR The ligand 99.8 3.3E-20 7.2E-25 158.3 15.0 114 219-335 59-176 (259)
71 cd07068 NR_LBD_ER_like The lig 99.8 3.6E-20 7.7E-25 155.5 14.7 116 219-335 23-139 (221)
72 cd06930 NR_LBD_F2 Ligand-bindi 99.8 1.9E-20 4E-25 150.8 12.3 109 227-335 3-113 (165)
73 cd06943 NR_LBD_RXR_like The li 99.8 3E-20 6.4E-25 154.9 12.6 111 224-335 31-143 (207)
74 cd06950 NR_LBD_Tlx_PNR_like Th 99.8 3.2E-20 6.9E-25 153.8 12.5 111 225-335 28-138 (206)
75 cd06953 NR_LBD_DHR4_like The l 99.8 1.3E-19 2.7E-24 150.9 11.7 115 220-335 24-143 (213)
76 cd06931 NR_LBD_HNF4_like The l 99.8 1.6E-19 3.5E-24 152.0 12.4 111 224-335 33-144 (222)
77 cd06951 NR_LBD_Dax1_like The l 99.8 1.1E-19 2.3E-24 151.9 10.5 111 225-335 21-146 (222)
78 cd06936 NR_LBD_Fxr The ligand 99.8 6.3E-19 1.4E-23 147.5 12.1 109 222-335 35-145 (221)
79 cd07349 NR_LBD_SHP The ligand 99.8 3.9E-19 8.4E-24 148.1 10.6 110 225-335 21-143 (222)
80 cd07350 NR_LBD_Dax1 The ligand 99.8 5.5E-19 1.2E-23 148.1 10.4 111 225-335 21-155 (232)
81 cd06948 NR_LBD_COUP-TF Ligand 99.8 7.8E-19 1.7E-23 148.6 11.0 112 223-335 30-144 (236)
82 cd06952 NR_LBD_TR2_like The li 99.7 2.9E-17 6.3E-22 138.2 9.8 111 225-335 23-141 (222)
83 PF00104 Hormone_recep: Ligand 99.7 1.8E-16 4E-21 131.9 14.6 116 220-335 14-133 (203)
84 cd06157 NR_LBD The ligand bind 99.7 1E-16 2.2E-21 129.3 11.3 108 228-335 3-114 (168)
85 smart00430 HOLI Ligand binding 99.7 2.2E-16 4.9E-21 126.6 9.7 102 234-335 3-108 (163)
86 KOG4217|consensus 94.7 0.074 1.6E-06 48.2 5.6 49 159-207 405-453 (605)
87 KOG3277|consensus 85.7 0.62 1.3E-05 35.7 2.1 26 42-67 81-114 (165)
88 cd07072 NR_LBD_DHR38_like Liga 84.2 2 4.3E-05 36.5 4.8 51 156-206 36-86 (239)
89 PF10764 Gin: Inhibitor of sig 82.8 0.46 1E-05 28.7 0.3 23 42-64 1-25 (46)
90 PF03107 C1_2: C1 domain; Int 79.3 0.97 2.1E-05 24.5 0.8 21 42-64 2-22 (30)
91 PF01412 ArfGap: Putative GTPa 79.3 0.48 1.1E-05 35.3 -0.5 32 38-69 11-45 (116)
92 cd07348 NR_LBD_NGFI-B The liga 75.9 2.9 6.2E-05 35.5 3.1 45 162-206 41-85 (238)
93 cd06945 NR_LBD_Nurr1_like The 68.7 7.4 0.00016 33.1 4.0 47 160-206 39-85 (239)
94 PF09289 FOLN: Follistatin/Ost 67.5 0.85 1.8E-05 22.7 -1.1 19 77-95 4-22 (22)
95 PHA03124 dUTPase; Provisional 67.4 1.3 2.8E-05 39.5 -0.9 17 56-72 189-205 (418)
96 PF12760 Zn_Tnp_IS1595: Transp 64.9 0.98 2.1E-05 27.3 -1.5 12 90-101 35-46 (46)
97 PF13901 DUF4206: Domain of un 64.1 5.3 0.00012 33.0 2.2 31 40-70 152-185 (202)
98 PF00628 PHD: PHD-finger; Int 61.9 4.8 0.0001 24.6 1.2 26 43-70 2-27 (51)
99 PF10005 DUF2248: Uncharacteri 58.8 12 0.00025 33.4 3.4 57 43-102 2-84 (343)
100 PF00357 Integrin_alpha: Integ 58.4 2.1 4.5E-05 19.1 -0.6 7 65-71 3-9 (15)
101 PRK01343 zinc-binding protein; 58.0 9 0.00019 24.3 1.9 14 38-51 7-20 (57)
102 PTZ00218 40S ribosomal protein 58.0 3.8 8.2E-05 25.6 0.2 24 40-63 16-40 (54)
103 TIGR03655 anti_R_Lar restricti 55.6 7.4 0.00016 24.3 1.3 16 41-56 2-17 (53)
104 PF01286 XPA_N: XPA protein N- 55.5 4.7 0.0001 22.6 0.3 23 42-64 5-31 (34)
105 smart00105 ArfGap Putative GTP 55.5 3.7 8E-05 30.3 -0.1 31 40-70 3-36 (112)
106 PF07649 C1_3: C1-like domain; 55.3 4.7 0.0001 21.7 0.3 19 42-60 2-21 (30)
107 PF03002 Somatostatin: Somatos 55.1 4.9 0.00011 18.7 0.3 9 62-70 6-14 (18)
108 TIGR00269 conserved hypothetic 55.1 7.5 0.00016 28.2 1.4 20 40-64 80-99 (104)
109 PRK00420 hypothetical protein; 55.0 8.2 0.00018 28.4 1.6 27 39-65 22-48 (112)
110 cd06940 NR_LBD_REV_ERB The lig 54.1 18 0.00039 29.5 3.7 45 161-205 11-55 (189)
111 PF10013 DUF2256: Uncharacteri 53.8 7.1 0.00015 22.9 0.9 11 39-49 7-17 (42)
112 cd07071 NR_LBD_Nurr1 The ligan 53.6 19 0.0004 30.6 3.8 45 162-206 41-85 (238)
113 PF00645 zf-PARP: Poly(ADP-rib 53.2 14 0.0003 25.3 2.5 21 243-263 60-80 (82)
114 KOG3362|consensus 52.9 7 0.00015 29.8 1.0 22 38-65 116-137 (156)
115 PF01783 Ribosomal_L32p: Ribos 51.3 7.4 0.00016 24.6 0.8 23 41-68 27-49 (56)
116 KOG4399|consensus 49.3 4 8.7E-05 34.3 -0.8 49 42-99 263-311 (325)
117 smart00274 FOLN Follistatin-N- 48.7 7.9 0.00017 20.2 0.5 20 76-95 4-23 (26)
118 PF01753 zf-MYND: MYND finger; 47.9 11 0.00024 21.4 1.1 18 43-66 1-18 (37)
119 TIGR03124 ctirate_citX holo-AC 47.4 8 0.00017 30.7 0.6 22 30-51 120-141 (165)
120 KOG3715|consensus 47.0 16 0.00035 31.7 2.4 23 44-67 67-89 (344)
121 PF14569 zf-UDP: Zinc-binding 46.5 9.9 0.00022 25.7 0.8 14 37-50 6-19 (80)
122 COG4338 Uncharacterized protei 46.3 10 0.00022 22.9 0.8 14 37-50 9-22 (54)
123 PF03802 CitX: Apo-citrate lya 45.9 9.9 0.00021 30.4 0.9 23 29-51 121-143 (170)
124 COG1997 RPL43A Ribosomal prote 44.2 12 0.00026 26.0 0.9 28 40-67 35-63 (89)
125 smart00154 ZnF_AN1 AN1-like Zi 43.3 14 0.00031 21.3 1.1 22 43-67 1-22 (39)
126 smart00249 PHD PHD zinc finger 43.2 22 0.00047 20.7 2.0 26 43-70 2-27 (47)
127 PF05180 zf-DNL: DNL zinc fing 43.1 5 0.00011 26.3 -0.9 24 42-65 6-37 (66)
128 PF10080 DUF2318: Predicted me 43.0 11 0.00024 27.2 0.7 26 42-67 37-62 (102)
129 COG3677 Transposase and inacti 41.7 10 0.00022 28.8 0.4 39 51-101 24-62 (129)
130 cd00729 rubredoxin_SM Rubredox 40.6 11 0.00024 21.1 0.3 11 41-51 19-29 (34)
131 PF04216 FdhE: Protein involve 40.5 10 0.00022 33.3 0.3 12 55-66 236-247 (290)
132 smart00778 Prim_Zn_Ribbon Zinc 40.3 19 0.00041 20.6 1.3 9 41-49 4-12 (37)
133 PLN02638 cellulose synthase A 39.1 22 0.00049 36.7 2.4 25 38-64 15-43 (1079)
134 PRK01392 citX 2'-(5''-triphosp 38.5 11 0.00024 30.4 0.1 21 31-51 130-150 (180)
135 PF07282 OrfB_Zn_ribbon: Putat 38.3 25 0.00055 23.0 1.9 29 39-67 27-56 (69)
136 PF10330 Stb3: Putative Sin3 b 38.2 76 0.0017 22.3 4.1 23 241-263 29-51 (92)
137 PF13453 zf-TFIIB: Transcripti 38.0 11 0.00025 21.9 0.1 25 43-67 2-29 (41)
138 smart00401 ZnF_GATA zinc finge 37.9 18 0.00039 22.4 1.0 32 40-71 3-39 (52)
139 PF11494 Ta0938: Ta0938; Inte 37.9 13 0.00029 26.1 0.4 33 40-72 14-52 (105)
140 PF01780 Ribosomal_L37ae: Ribo 36.8 11 0.00024 26.4 -0.0 25 41-65 36-61 (90)
141 PF08273 Prim_Zn_Ribbon: Zinc- 36.7 16 0.00034 21.4 0.5 22 41-63 4-32 (40)
142 PF15446 zf-PHD-like: PHD/FYVE 35.8 20 0.00043 28.3 1.2 28 43-70 2-30 (175)
143 KOG0402|consensus 35.7 12 0.00026 25.5 -0.0 23 42-64 38-61 (92)
144 PF06147 DUF968: Protein of un 35.5 18 0.0004 29.7 1.0 16 40-55 127-143 (200)
145 KOG4327|consensus 35.2 43 0.00093 27.1 2.9 26 24-49 161-186 (218)
146 PLN02189 cellulose synthase 33.2 25 0.00053 36.3 1.6 24 39-64 33-60 (1040)
147 cd07075 NR_LBD_MR Ligand bindi 32.5 69 0.0015 27.4 4.0 43 163-205 29-71 (248)
148 COG2260 Predicted Zn-ribbon RN 32.2 24 0.00052 22.4 0.9 14 41-54 18-31 (59)
149 PTZ00255 60S ribosomal protein 31.6 23 0.0005 24.9 0.8 26 40-65 36-62 (90)
150 cd06935 NR_LBD_TR The ligand b 31.5 59 0.0013 27.7 3.5 46 161-206 51-96 (243)
151 PF02155 GCR: Glucocorticoid r 31.1 43 0.00093 30.1 2.6 20 42-61 289-308 (370)
152 KOG3490|consensus 30.8 23 0.0005 25.4 0.7 43 39-82 7-49 (111)
153 cd06939 NR_LBD_ROR_like The li 30.5 61 0.0013 27.6 3.4 45 162-206 48-92 (241)
154 PRK06424 transcription factor; 30.3 15 0.00033 28.4 -0.2 25 42-66 2-32 (144)
155 PRK03564 formate dehydrogenase 30.2 25 0.00054 31.1 1.0 14 51-64 220-233 (309)
156 PF14445 Prok-RING_2: Prokaryo 30.2 6.9 0.00015 23.8 -1.7 16 35-50 17-32 (57)
157 COG5204 SPT4 Transcription elo 29.4 21 0.00046 25.0 0.4 30 40-69 9-38 (112)
158 PF14354 Lar_restr_allev: Rest 29.0 37 0.00079 21.6 1.4 26 40-65 3-37 (61)
159 KOG1701|consensus 28.5 21 0.00046 32.6 0.3 49 41-102 335-392 (468)
160 cd06949 NR_LBD_ER Ligand bindi 28.5 99 0.0021 26.1 4.3 46 160-205 30-75 (235)
161 cd06933 NR_LBD_VDR The ligand 28.1 72 0.0016 27.0 3.5 42 164-205 39-80 (238)
162 PRK00564 hypA hydrogenase nick 28.1 40 0.00087 25.0 1.7 33 41-73 72-104 (117)
163 KOG1701|consensus 27.8 81 0.0018 29.0 3.7 34 41-78 275-319 (468)
164 KOG0703|consensus 27.1 28 0.00061 30.2 0.8 31 40-70 25-58 (287)
165 cd06941 NR_LBD_DmE78_like The 27.1 66 0.0014 26.2 3.0 40 166-205 6-45 (195)
166 cd06947 NR_LBD_GR_Like Ligand 27.0 1.2E+02 0.0026 25.9 4.6 43 163-205 29-71 (246)
167 TIGR00280 L37a ribosomal prote 26.7 29 0.00063 24.4 0.7 26 40-65 35-61 (91)
168 PF03811 Zn_Tnp_IS1: InsA N-te 26.7 24 0.00053 20.0 0.2 9 91-99 28-36 (36)
169 TIGR00311 aIF-2beta translatio 26.4 34 0.00074 26.1 1.1 29 41-71 98-130 (133)
170 PLN03114 ADP-ribosylation fact 26.4 30 0.00065 31.0 0.8 32 39-70 21-55 (395)
171 cd06929 NR_LBD_F1 Ligand-bindi 26.3 81 0.0018 24.9 3.3 40 166-205 6-45 (174)
172 KOG0706|consensus 26.1 26 0.00056 32.2 0.4 31 38-68 21-54 (454)
173 PLN02400 cellulose synthase 25.6 38 0.00083 35.2 1.5 25 38-64 34-62 (1085)
174 COG0675 Transposase and inacti 25.6 39 0.00084 30.1 1.5 28 38-69 307-334 (364)
175 KOG1044|consensus 25.5 38 0.00083 32.3 1.4 33 38-70 14-61 (670)
176 PF12156 ATPase-cat_bd: Putati 25.4 32 0.00069 24.1 0.7 26 42-67 2-36 (88)
177 TIGR01374 soxD sarcosine oxida 25.2 34 0.00074 23.7 0.8 17 42-58 3-20 (84)
178 KOG2879|consensus 25.2 51 0.0011 28.3 1.9 23 42-64 241-267 (298)
179 PF14260 zf-C4pol: C4-type zin 25.1 32 0.00068 22.9 0.6 26 41-70 46-73 (73)
180 PRK00418 DNA gyrase inhibitor; 24.9 53 0.0011 21.3 1.5 25 40-64 6-33 (62)
181 PRK03976 rpl37ae 50S ribosomal 24.6 34 0.00073 24.1 0.7 26 40-65 36-62 (90)
182 KOG3506|consensus 24.6 29 0.00062 21.7 0.3 26 38-63 16-42 (56)
183 KOG3002|consensus 24.3 73 0.0016 28.1 2.8 26 40-65 48-77 (299)
184 PF01586 Basic: Myogenic Basic 24.0 27 0.00059 24.3 0.1 15 54-71 69-83 (86)
185 PF14471 DUF4428: Domain of un 23.9 33 0.00071 21.2 0.4 9 42-50 1-9 (51)
186 cd06932 NR_LBD_PPAR The ligand 23.5 1E+02 0.0022 26.6 3.5 43 163-205 64-106 (259)
187 KOG3116|consensus 23.3 40 0.00087 25.9 0.9 12 99-110 29-40 (177)
188 PRK14282 chaperone protein Dna 23.2 86 0.0019 28.6 3.2 25 41-65 153-177 (369)
189 KOG4451|consensus 22.7 42 0.00091 27.9 1.0 26 39-67 248-273 (286)
190 cd07076 NR_LBD_GR Ligand bindi 22.7 1.6E+02 0.0034 25.2 4.5 29 177-205 43-71 (247)
191 PF09889 DUF2116: Uncharacteri 22.7 48 0.001 21.3 1.0 6 42-47 5-10 (59)
192 PF09788 Tmemb_55A: Transmembr 22.4 1.2E+02 0.0026 25.9 3.6 44 39-82 64-112 (256)
193 PLN02436 cellulose synthase A 22.4 50 0.0011 34.3 1.6 25 38-64 34-62 (1094)
194 cd06934 NR_LBD_PXR_like The li 22.2 98 0.0021 26.0 3.1 42 165-206 38-79 (226)
195 PHA02446 hypothetical protein 22.2 35 0.00077 24.9 0.4 21 39-59 61-81 (166)
196 KOG4323|consensus 22.2 32 0.00068 32.1 0.2 53 39-102 167-225 (464)
197 PF10146 zf-C4H2: Zinc finger- 22.1 50 0.0011 27.9 1.3 26 39-67 193-218 (230)
198 PF08271 TF_Zn_Ribbon: TFIIB z 21.8 32 0.0007 20.2 0.1 23 42-64 2-26 (43)
199 PRK12495 hypothetical protein; 21.8 48 0.001 27.5 1.1 29 39-68 41-69 (226)
200 PLN03119 putative ADP-ribosyla 21.7 50 0.0011 31.6 1.4 33 38-70 21-56 (648)
201 PRK14276 chaperone protein Dna 21.6 1.1E+02 0.0024 28.1 3.6 26 40-65 146-171 (380)
202 PF13913 zf-C2HC_2: zinc-finge 21.3 49 0.0011 16.9 0.7 9 41-49 3-11 (25)
203 PLN02195 cellulose synthase A 21.2 53 0.0012 33.8 1.5 25 38-64 4-32 (977)
204 cd06937 NR_LBD_RAR The ligand 21.2 1.2E+02 0.0026 25.6 3.5 42 165-206 41-82 (231)
205 cd00350 rubredoxin_like Rubred 21.1 59 0.0013 17.8 1.1 7 43-49 4-10 (33)
206 PF14205 Cys_rich_KTR: Cystein 21.0 36 0.00079 21.3 0.2 11 40-50 4-14 (55)
207 PRK05766 rps14P 30S ribosomal 21.0 62 0.0013 20.2 1.2 24 40-63 14-38 (52)
208 PF09150 Carot_N: Orange carot 20.9 94 0.002 24.4 2.5 20 248-267 21-40 (159)
209 cd07973 Spt4 Transcription elo 20.8 66 0.0014 23.1 1.5 39 41-79 4-42 (98)
210 COG4068 Uncharacterized protei 20.8 69 0.0015 20.3 1.4 8 40-47 8-15 (64)
211 PRK00432 30S ribosomal protein 20.8 54 0.0012 20.2 1.0 25 40-64 20-44 (50)
212 cd07073 NR_LBD_AR Ligand bindi 20.8 1.7E+02 0.0037 25.0 4.3 40 166-205 32-71 (246)
213 PF07191 zinc-ribbons_6: zinc- 20.6 40 0.00088 22.4 0.4 28 42-70 3-30 (70)
214 COG5347 GTPase-activating prot 20.5 43 0.00093 29.8 0.7 32 38-69 18-52 (319)
215 PF15472 DUF4638: Domain of un 20.1 41 0.00089 27.9 0.4 19 93-111 218-245 (268)
216 smart00109 C1 Protein kinase C 20.0 85 0.0018 18.4 1.8 24 41-65 12-35 (49)
217 PF11781 RRN7: RNA polymerase 20.0 45 0.00097 18.9 0.5 10 40-49 8-17 (36)
218 PLN02915 cellulose synthase A 20.0 47 0.001 34.4 0.9 24 39-64 14-41 (1044)
No 1
>KOG4217|consensus
Probab=100.00 E-value=6.8e-64 Score=430.61 Aligned_cols=251 Identities=66% Similarity=1.115 Sum_probs=224.0
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
.+..|.||||.|.--||||-+||||||||+|||++|.+|+|.+|++|.|||..||+||||||||||+|||-+|.|+.|..
T Consensus 268 ~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSL 347 (605)
T KOG4217|consen 268 AEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSL 347 (605)
T ss_pred ccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecccc
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCCCCCCCCCCCCcchhhhhhcCCCCCCCCCCChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHH
Q psy2636 119 KGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQEL 198 (335)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~ 198 (335)
++||+|.+++++++++.++++|..+++++.+++.+.. |+...+.
T Consensus 348 kGRRGRLpSKpKs~q~sppSpPi~LltalvrAh~Dst------------------------------p~~~~ld------ 391 (605)
T KOG4217|consen 348 KGRRGRLPSKPKSRQPSPPSPPISLLTALVRAHVDST------------------------------PSTMTLD------ 391 (605)
T ss_pred ccccCCCCCCCCCCCCCCCCCchHHHHHHHHHhhcCC------------------------------CCcchhh------
Confidence 9999999999999999899999999988887764322 2211111
Q ss_pred HHhhhhhccccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhc
Q psy2636 199 LFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTR 278 (335)
Q Consensus 199 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~ 278 (335)
+ ..| .+........+...+++|+++++-++..+..||..||+|.+|+.+||-+||.++++|+++|+.|||+.
T Consensus 392 -y------s~~-q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~ 463 (605)
T KOG4217|consen 392 -Y------SRF-QELVPHFSGTDALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSN 463 (605)
T ss_pred -H------HHh-ccccccccccHHHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcC
Confidence 0 000 01011112467788999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCeEEeeCCeEeeHHhhhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHc
Q psy2636 279 AEDTKLIFCNGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTL 334 (335)
Q Consensus 279 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l 334 (335)
..+++++|.+|..+++-++..+|| +|++.+.+|...|..|.+|..-|+||.||.+
T Consensus 464 ~~e~kliFcsG~vlhr~qC~rgfg-ewidsi~~FS~~l~~l~idi~AfacL~aLa~ 518 (605)
T KOG4217|consen 464 PSEDKLIFCSGLVLHRLQCLRGFG-EWIDSIREFSRSLHSLNIDISAFACLSALAL 518 (605)
T ss_pred CCCCeEEEecchhhhHHHHHHHHH-HHHHHHHHHHHHhhhchhhHHHHHHHHHHHh
Confidence 999999999999999999999999 9999999999999999999999999999986
No 2
>KOG4215|consensus
Probab=100.00 E-value=1.2e-62 Score=411.45 Aligned_cols=250 Identities=27% Similarity=0.515 Sum_probs=179.8
Q ss_pred CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
....+|.||||+|+|.||||.+|+||||||||+|+++..|+|+++.+|.|||+.||.|||||||||+++||+++|||.+|
T Consensus 17 ~~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnER 96 (432)
T KOG4215|consen 17 GVAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNER 96 (432)
T ss_pred cccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhccc
Confidence 34567999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCcchhhhhhcCCCCCCCCCCChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHH
Q psy2636 118 LKGRRGRLPSKPKSPQESPPSPPVSLITALYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQE 197 (335)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~ 197 (335)
++.+..+ +.... . ......+.++..+. ...+...............+
T Consensus 97 DrIg~Rr-~~~~~----~--n~~~~~id~L~~aE------------------------~~~~q~~~srs~~~~~~~~d-- 143 (432)
T KOG4215|consen 97 DRIGSRR-PSYEA----G--NENSPSIDALVQAE------------------------ALVRQLRSSRSGGVPGIDGD-- 143 (432)
T ss_pred ccccccC-CCCCC----C--CCCchhHHHHHhHH------------------------HHHhhhhccccccCcCcchh--
Confidence 6654311 11000 0 01111122221111 00000000000000000000
Q ss_pred HHHhhhhhccccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhh
Q psy2636 198 LLFQSASLELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT 277 (335)
Q Consensus 198 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~ 277 (335)
.++..+ ...........+.+.+.+..+|||||.+|.|.+|+.+||++|||++..++++|..|||+
T Consensus 144 ---------~r~~~~------n~~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RS 208 (432)
T KOG4215|consen 144 ---------IRQGPP------NKKIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRS 208 (432)
T ss_pred ---------hhcCcc------ccccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhcc
Confidence 000000 11122234556677888889999999999999999999999999999999999999999
Q ss_pred ccCCCeEEeeCCeEeeHHhhhh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 278 RAEDTKLIFCNGVVLEKQQCQR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 278 ~~~~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
....+.+++.|...+..+..+. ....-..+.+.|++.+|++|++|+.||++||||+||
T Consensus 209 m~l~~v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~Pmr~L~md~~Ey~cLKAi~Ff 267 (432)
T KOG4215|consen 209 MHLKDVCLLNNTYVLHRHAPDLPEISRVAPRIIDELVNPMRRLQMDEIEYVCLKAIAFF 267 (432)
T ss_pred ccccceEEecCceeeccCCCChHHHHHHHHHHHHHHhhHHHHhccchHHHHHHHHHHhc
Confidence 9888888888877777654433 223233455669999999999999999999999987
No 3
>KOG4216|consensus
Probab=100.00 E-value=9.8e-55 Score=366.17 Aligned_cols=294 Identities=25% Similarity=0.453 Sum_probs=182.3
Q ss_pred CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
++..+|+||||+++|.||||++||||||||||+.+.+..|.|.++.+|.||+.+||+||+||+||||++||.++||...|
T Consensus 44 IEvIPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGR 123 (479)
T KOG4216|consen 44 IEIIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGR 123 (479)
T ss_pred eEEEeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhcc
Confidence 34568999999999999999999999999999999999999999999999999999999999999999999999998765
Q ss_pred cccc-CC---------------C---CCCCC-CCCCCCCCCCCcchhhh-----hhc----CC-CCCCC-CCCChhHH-H
Q psy2636 118 LKGR-RG---------------R---LPSKP-KSPQESPPSPPVSLITA-----LYR----EP-NPLEP-PIAEPEKI-Q 165 (335)
Q Consensus 118 ~~~~-~~---------------~---~~~~~-~~~~~~~~~~~~~~~~~-----~~~----~~-~~~~~-~~~~~~~~-~ 165 (335)
..++ |. . .+... ...+.++..++...-.. ... .. ..... ...+|..- .
T Consensus 124 MSKKQRdsl~aEVq~h~~q~q~q~~a~~~~~~y~~s~p~~~~~l~~~~s~y~~g~~p~~~k~~~s~Ys~~~q~tPdq~~~ 203 (479)
T KOG4216|consen 124 MSKKQRDSLYAEVQKHRMQQQQQDEAEPLTPTYDISPPNGLTELHDDLSNYSDGHSPEGSKADSSFYSLDIQPTPDQSGL 203 (479)
T ss_pred ccHhhHHHHHHHHHHHHHHHHhhhhcCCcccccccCCCCCccccccCcccccCCcCCCCCCCCCCcceeccccCCCcccc
Confidence 3211 00 0 00000 00000000000000000 000 00 00000 00000000 0
Q ss_pred HHHHhhcchh---hhhhhcc----cCCCCCCCCCHHHHHHHHhhh---------hhccc----cCCCC----CCCCCCCh
Q psy2636 166 QFYSLLTTSV---DVIRHFA----DKIPGFSDLCKEDQELLFQSA---------SLELF----YREPN----PLEPPIAE 221 (335)
Q Consensus 166 ~~~~~l~~~~---~~i~~~~----~~~p~~~~l~~~~~~~l~~~~---------~~~~~----~~~~~----~~~~~~~~ 221 (335)
.++..+..+. .....-+ ...|. ..+. +.+.+.++. .++.. +..+. +.......
T Consensus 204 d~~g~~~d~t~~~~~~~~~s~~~~~~~p~-~~~~--e~d~laq~i~ksh~etq~~~e~lh~~~~~~~~~e~I~~yq~k~~ 280 (479)
T KOG4216|consen 204 DINGPICDSTPGSGYFPYCSFTNGETSPT-VSMA--ELDHLAQNIIKSHLETQYLLEELHQITWQTFDQEEIENYQNKGR 280 (479)
T ss_pred ccCCCcccCCCCCCcccccccCCCCCCCC-Cchh--HHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHhhhH
Confidence 0000000000 0000000 00111 1111 111111110 00000 00000 00111234
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhh
Q psy2636 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSF 301 (335)
Q Consensus 222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~ 301 (335)
.+.|+.++.-++..|+.||||||.|+||.+|+++||++|||.+.+|+.+++++..++...+.+.+ .|.+...+.+...-
T Consensus 281 e~mWe~cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~ntV~~-e~~~~g~~~f~a~~ 359 (479)
T KOG4216|consen 281 EEMWELCAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNNTVYF-EGKYAGPEVFYALG 359 (479)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhcccccceee-cccccchhheeccC
Confidence 45677777788999999999999999999999999999999999999999999998887776666 56666655444433
Q ss_pred cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
..+++..++++...|..|++++.|.||+.|+||+
T Consensus 360 ~~elis~vf~~~ksL~~Lq~te~EiAL~~alVL~ 393 (479)
T KOG4216|consen 360 CEELISRVFEFGKSLCSLQLTEDEIALFSALVLM 393 (479)
T ss_pred hHHHHHHHHhhhHHHHhhccCcHHHHHHHHHHhh
Confidence 3479999999999999999999999999999984
No 4
>KOG4218|consensus
Probab=100.00 E-value=2.3e-49 Score=328.57 Aligned_cols=294 Identities=29% Similarity=0.481 Sum_probs=182.5
Q ss_pred CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
..++.|.||||+.+|||||..+||+|||||+|||++|+.|+|..+.+|.||+..|.+|.+|||||||.|||+-+||+.||
T Consensus 13 dl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADR 92 (475)
T KOG4218|consen 13 DLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADR 92 (475)
T ss_pred ccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhh
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCCCC------------C----------CCCCC--CCCCCCc---chhhh--------h-------hcCCCCCC
Q psy2636 118 LKGRRGRLPSK------------P----------KSPQE--SPPSPPV---SLITA--------L-------YREPNPLE 155 (335)
Q Consensus 118 ~~~~~~~~~~~------------~----------~~~~~--~~~~~~~---~~~~~--------~-------~~~~~~~~ 155 (335)
.++.|.+...- . .-+.+ ....++. +.... + ..++-++.
T Consensus 93 MRGGRNKFGpmYKrDRAlkqQkkAqirAng~KlE~~~~~~~~~~psp~~~ss~~q~lh~~~~kgL~~~~aa~pp~~~~l~ 172 (475)
T KOG4218|consen 93 MRGGRNKFGPMYKRDRALKQQKKAQIRANGIKLEYIKTEYDAHLPSPTLSSSTNQQLHVSDFKGLAVLLAATPPDPLQLN 172 (475)
T ss_pred hcccccccCchhhhhHHHHHHHHHHhhhcceeeeccccccCCCCCCCcccccccccccCCCcccchhhhccCCCCCcccc
Confidence 87766543220 0 00000 0000000 00000 0 00000000
Q ss_pred CCCCCh-hH----HH---HHHHhhcch-hhhhh---------------------hcccCCCCCCCCCHHHHHHHHhhhh-
Q psy2636 156 PPIAEP-EK----IQ---QFYSLLTTS-VDVIR---------------------HFADKIPGFSDLCKEDQELLFQSAS- 204 (335)
Q Consensus 156 ~~~~~~-~~----~~---~~~~~l~~~-~~~i~---------------------~~~~~~p~~~~l~~~~~~~l~~~~~- 204 (335)
.....+ +. +. +-|...+.. .+++. ..+...|.+..+.-. +.+...
T Consensus 173 ~f~~~p~~ms~p~~HgsL~gY~tY~~fp~raikseyP~py~Sspqs~~~ygym~~~ss~sP~lP~lil~----llk~epd 248 (475)
T KOG4218|consen 173 EFKQEPFDMSEPFIHGSLHGYPTYTSFPTRAIKSEYPMPYVSSPQSLVTYGYMTEASSTSPILPLLILP----LLKTEPD 248 (475)
T ss_pred cccCCCccccCccCCCcccCCcccCCCcchhhhhcCCCCcCCCCcccccccccCccccCCCCccccchh----hhccCCh
Confidence 000000 00 00 000000000 00000 000001110000000 000000
Q ss_pred -------hccccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhh
Q psy2636 205 -------LELFYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRT 277 (335)
Q Consensus 205 -------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~ 277 (335)
...+..++.......+.++++.-........+..||+||++--.|.+|+.+||++||+++|.++.|++..|+.
T Consensus 249 E~qv~a~i~a~lq~~~ts~s~~~kp~~fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~Dhiyrq 328 (475)
T KOG4218|consen 249 EMQVTAPIDAQLQRIFTSVSGTSKPEKFGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQ 328 (475)
T ss_pred hhhhcchhHHHHhhhhhcccCCCchhhhhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHH
Confidence 0000000000111112233333334455667788999999999999999999999999999999999999998
Q ss_pred ccCC--CeEEeeCCeEeeHHhhhhh---hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 278 RAED--TKLIFCNGVVLEKQQCQRS---FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 278 ~~~~--~~~~~~~g~~~~~~~~~~~---~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+..+ ..+.+.+|+.+........ ....++....+++.+|+.|++|..||++||-|+||
T Consensus 329 V~hgkegsi~lvtGqeV~~~~vA~qags~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LF 391 (475)
T KOG4218|consen 329 VHHGKEGSIKLVTGQEVPVGLVALQAGSLLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALF 391 (475)
T ss_pred HhcCcccceEEecCCcccchhHhhhhhhHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHH
Confidence 8754 4688888887765432211 22467778889999999999999999999999987
No 5
>KOG4846|consensus
Probab=100.00 E-value=1.6e-44 Score=306.55 Aligned_cols=283 Identities=26% Similarity=0.396 Sum_probs=165.1
Q ss_pred CcccccCCCCCccccCCccccccccceecccccCCee-ecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK 119 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y-~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~ 119 (335)
.+|+||||+|+||||||.+||||||||||+|+.++.| .|.++++|.|.+++||+||+|||+|||+|||.+++|+..+.+
T Consensus 133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~ 212 (538)
T KOG4846|consen 133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMK 212 (538)
T ss_pred EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhcccc
Confidence 5799999999999999999999999999999999999 799999999999999999999999999999999999987655
Q ss_pred ccCCCCCCCCCCCCCCCCCCCc-----------chhhhhhcCCCCCCCCCCChhHHHHHHHh--------hcchhhhhhh
Q psy2636 120 GRRGRLPSKPKSPQESPPSPPV-----------SLITALYREPNPLEPPIAEPEKIQQFYSL--------LTTSVDVIRH 180 (335)
Q Consensus 120 ~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------l~~~~~~i~~ 180 (335)
.|.+......+.+ ....++.. ..+..+.+++..+... ...++...+.. ...-......
T Consensus 213 ~rnka~M~~~~~p-~~V~sp~~sq~~~Q~env~~V~~~V~rAh~t~~~y--~~~k~gsi~~~~fnv~~n~~s~P~~~~~~ 289 (538)
T KOG4846|consen 213 FRNKAAMRDDKSP-DSVFSPEISQLERQEENVDAVYEAVLRAHTTFSFY--TDIKIGSIVARPFNVRINEDSKPMNRLNA 289 (538)
T ss_pred cccccccCCCCCC-CCCCChhhhhhhhhhccHHHHHHHHHHhhcchhhe--ehhhcCcccCCCcccccccCCccccchhH
Confidence 4431110000001 00011111 1122222322111000 00000000000 0000011122
Q ss_pred cccC-CCCCCCCCHHHHHHHHhhhhh---------------------ccccCCCCCCCC--------CCChhHHHHHHHH
Q psy2636 181 FADK-IPGFSDLCKEDQELLFQSASL---------------------ELFYREPNPLEP--------PIAEPEKIQQFYS 230 (335)
Q Consensus 181 ~~~~-~p~~~~l~~~~~~~l~~~~~~---------------------~~~~~~~~~~~~--------~~~~~~~~~~~~~ 230 (335)
|... .|.+.+..++...-+.++... ...++.+..+.+ .......|+.+-.
T Consensus 290 w~n~~~pa~~di~qe~~n~l~q~pvfd~~~~~~g~a~~s~h~~n~~pty~~~~~~g~~Pn~~~~~rsgR~~qlp~~~~~l 369 (538)
T KOG4846|consen 290 WQNYAHPADVDIKQEVVNFLKQIPVFDKFNFINGNAKASLHRKNAFPTYLLRIVRGMSPNRGLMLRSGRLIQLPFKSLQL 369 (538)
T ss_pred HhhcCCCCcccchHHHHHHHHhCccccccccCCCccchhhhcCCCcchhhhhhcccCCcccccccccccccccCcchhhh
Confidence 2222 455555555554444443311 111111211111 0111122444555
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCC-HHHHHHHHHHhHHHHHHHHHhhhhccCCCeE-EeeCCeEeeHHhh-hhhhcHHHHH
Q psy2636 231 LLTTSVDVIRHFADKIPGFSDLC-KEDQELLFQSASLELFVLRLAYRTRAEDTKL-IFCNGVVLEKQQC-QRSFGDDWLN 307 (335)
Q Consensus 231 ~~~~~i~~vvefAk~~P~F~~L~-~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~-~~~~g~~~~~~~~-~~~~~~~~~~ 307 (335)
+....+..+++||+++++|..++ .-++.++|+.+-.......++-.+......+ +|.--..+..+.+ ..+.+ +...
T Consensus 370 l~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f~~~~Q~~~mfl~~~~~~~Q~~~~~~~g-d~~~ 448 (538)
T KOG4846|consen 370 LYGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNFKSQLQLLEMFLFYKKVLFQKMTCRIDG-DTYK 448 (538)
T ss_pred hhhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhch-HHHH
Confidence 56677888999999999999998 7899999999888877766654433222111 1100011111122 22445 7778
Q ss_pred HHHHHHHHhhcCCCCHHHHH
Q psy2636 308 AILEFCQSLHLMEIDISAFA 327 (335)
Q Consensus 308 ~~~~~~~~l~~l~l~~~E~~ 327 (335)
.++.+++++..|....+|.+
T Consensus 449 a~~~~~~~ln~L~~~~~~~~ 468 (538)
T KOG4846|consen 449 ALMKCIHELNRLNELHKQQL 468 (538)
T ss_pred HHHHhhcchhhcCchHHHHH
Confidence 88899999999998888763
No 6
>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=100.00 E-value=2.1e-37 Score=219.89 Aligned_cols=85 Identities=58% Similarity=1.125 Sum_probs=78.8
Q ss_pred CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
++..+|.|||++++|+||||++|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++
T Consensus 2 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r 81 (97)
T cd07170 2 IPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDR 81 (97)
T ss_pred CCCCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHccccc
Confidence 35567999999999999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred ccccC
Q psy2636 118 LKGRR 122 (335)
Q Consensus 118 ~~~~~ 122 (335)
....+
T Consensus 82 ~~~~~ 86 (97)
T cd07170 82 VRGGR 86 (97)
T ss_pred CCCCC
Confidence 55444
No 7
>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=100.00 E-value=1.1e-36 Score=211.81 Aligned_cols=80 Identities=55% Similarity=1.089 Sum_probs=75.7
Q ss_pred CCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636 40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK 119 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~ 119 (335)
..+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.+
T Consensus 4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~ 83 (85)
T cd06964 4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK 83 (85)
T ss_pred CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence 35799999999999999999999999999999999999999999999999999999999999999999999999987643
No 8
>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=100.00 E-value=1.1e-36 Score=211.17 Aligned_cols=79 Identities=44% Similarity=0.937 Sum_probs=75.2
Q ss_pred CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK 119 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~ 119 (335)
++|.||||+++|+||||.+|+|||+||||+|.++..|.|..+++|.|+...|..||+|||+|||+|||++++|+.++..
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~ 80 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQC 80 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHH
Confidence 5699999999999999999999999999999999999999999999999999999999999999999999999987543
No 9
>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=1.5e-36 Score=216.79 Aligned_cols=80 Identities=45% Similarity=0.976 Sum_probs=76.1
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
...+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus 17 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~ 96 (101)
T cd07160 17 GNEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQ 96 (101)
T ss_pred CCCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhh
Confidence 35679999999999999999999999999999999999999999999999999999999999999999999999998754
No 10
>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=100.00 E-value=2e-36 Score=212.97 Aligned_cols=81 Identities=51% Similarity=1.092 Sum_probs=75.6
Q ss_pred CCCCcccccCCCCCccccCCccccccccceecccccCCeeecCCC-CCCcccccccccccchhhHHHHhcCceeeeeeec
Q psy2636 38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLAD-KACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTD 116 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~-~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~ 116 (335)
.|..+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+ ++|.|++..|..||+|||+|||+|||++++||.+
T Consensus 4 ~p~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~ 83 (92)
T cd06970 4 NPGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNE 83 (92)
T ss_pred CCCCCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccc
Confidence 345579999999999999999999999999999999999999985 8999999999999999999999999999999987
Q ss_pred cc
Q psy2636 117 SL 118 (335)
Q Consensus 117 ~~ 118 (335)
+.
T Consensus 84 R~ 85 (92)
T cd06970 84 RQ 85 (92)
T ss_pred cC
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=100.00 E-value=8.2e-37 Score=209.18 Aligned_cols=76 Identities=59% Similarity=1.262 Sum_probs=73.4
Q ss_pred cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.+|
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 6999999999999999999999999999999999999999999999999999999999999999999999998763
No 12
>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=100.00 E-value=1.1e-36 Score=212.09 Aligned_cols=80 Identities=54% Similarity=1.053 Sum_probs=76.1
Q ss_pred cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccccc
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGR 121 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~~~ 121 (335)
+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||++++||.++.+..
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~ 80 (85)
T cd06961 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGA 80 (85)
T ss_pred CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCccc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999876543
No 13
>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=100.00 E-value=3.5e-36 Score=210.34 Aligned_cols=81 Identities=51% Similarity=1.112 Sum_probs=76.7
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
|.++|.||||+++|+||||.+|+|||+||||+|.++..|.|.++++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus 2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~ 81 (87)
T cd06967 2 PVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERK 81 (87)
T ss_pred CCCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccC
Confidence 45679999999999999999999999999999999999999999999999999999999999999999999999998764
Q ss_pred c
Q psy2636 119 K 119 (335)
Q Consensus 119 ~ 119 (335)
.
T Consensus 82 ~ 82 (87)
T cd06967 82 P 82 (87)
T ss_pred C
Confidence 3
No 14
>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=100.00 E-value=1.9e-36 Score=208.88 Aligned_cols=79 Identities=49% Similarity=1.074 Sum_probs=75.0
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
+.++|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||+|||++++|+.++
T Consensus 2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~ 80 (82)
T cd07171 2 DTHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER 80 (82)
T ss_pred CCCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhh
Confidence 3467999999999999999999999999999999999999999999999999999999999999999999999998764
No 15
>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=100.00 E-value=4.9e-36 Score=204.25 Aligned_cols=75 Identities=91% Similarity=1.615 Sum_probs=71.9
Q ss_pred CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeee
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRT 115 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~ 115 (335)
.+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||++||++++||.
T Consensus 1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~ 75 (75)
T cd06969 1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75 (75)
T ss_pred CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence 369999999999999999999999999999999999999999999999999999999999999999999999973
No 16
>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=100.00 E-value=3.4e-36 Score=205.25 Aligned_cols=75 Identities=60% Similarity=1.146 Sum_probs=72.5
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++
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 899999999999999999999999999999999999999999999999999999999999999999999998764
No 17
>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=100.00 E-value=1e-35 Score=210.22 Aligned_cols=80 Identities=45% Similarity=1.068 Sum_probs=75.0
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCC--CCCCcccccccccccchhhHHHHhcCceeeeeeec
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLA--DKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTD 116 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~--~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~ 116 (335)
++.+|.|||++++|+||||.+|+|||+||||+|..+..|.|.. +++|.|++..|..||+|||+||++|||++++||.+
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~ 84 (92)
T cd07163 5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHE 84 (92)
T ss_pred cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcc
Confidence 4667999999999999999999999999999999999999987 47899999999999999999999999999999986
Q ss_pred cc
Q psy2636 117 SL 118 (335)
Q Consensus 117 ~~ 118 (335)
+.
T Consensus 85 r~ 86 (92)
T cd07163 85 RG 86 (92)
T ss_pred cC
Confidence 54
No 18
>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=100.00 E-value=9.3e-36 Score=206.30 Aligned_cols=76 Identities=51% Similarity=1.089 Sum_probs=72.3
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecC-CCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCL-ADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~-~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
|.||||+++|+||||++|+|||+||||+|.++..|.|. .+++|.|++..|+.||+|||+|||+|||++++||.++.
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~ 77 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERG 77 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccC
Confidence 89999999999999999999999999999999999999 56899999999999999999999999999999998653
No 19
>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=100.00 E-value=7.9e-36 Score=209.94 Aligned_cols=83 Identities=52% Similarity=1.114 Sum_probs=77.4
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
...+|.|||++++|+||||++|+|||+||||++..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus 5 ~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~ 84 (90)
T cd07168 5 SPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRM 84 (90)
T ss_pred cCCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccC
Confidence 34569999999999999999999999999999999999999999999999999999999999999999999999998775
Q ss_pred ccc
Q psy2636 119 KGR 121 (335)
Q Consensus 119 ~~~ 121 (335)
+..
T Consensus 85 ~~~ 87 (90)
T cd07168 85 PGG 87 (90)
T ss_pred CCC
Confidence 543
No 20
>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=100.00 E-value=6e-36 Score=210.44 Aligned_cols=78 Identities=51% Similarity=0.998 Sum_probs=74.8
Q ss_pred CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
++|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||+|||++++||.++.
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~ 79 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQ 79 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhh
Confidence 569999999999999999999999999999999999999999999999999999999999999999999999998753
No 21
>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=100.00 E-value=1.1e-35 Score=203.34 Aligned_cols=76 Identities=46% Similarity=0.951 Sum_probs=72.1
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
|..+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||+..++.
T Consensus 1 ~~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 1 PQKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred CCCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence 3467999999999999999999999999999999999999999999999999999999999999999999988774
No 22
>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=100.00 E-value=8.5e-36 Score=209.49 Aligned_cols=84 Identities=48% Similarity=1.077 Sum_probs=78.0
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
...+|.|||++++|+||||++|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||+|||++++||.++.
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~ 84 (90)
T cd07169 5 EQRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGM 84 (90)
T ss_pred cCCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccC
Confidence 34569999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred cccC
Q psy2636 119 KGRR 122 (335)
Q Consensus 119 ~~~~ 122 (335)
++.+
T Consensus 85 ~~~~ 88 (90)
T cd07169 85 PGGR 88 (90)
T ss_pred CCCC
Confidence 5443
No 23
>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=100.00 E-value=9.8e-36 Score=209.01 Aligned_cols=80 Identities=50% Similarity=1.113 Sum_probs=75.7
Q ss_pred CCcccccCCCCCccccCCccccccccceecccccCCee-ecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y-~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
..+|.||||+++|+||||.+|+|||+||||+|..+..| .|..+++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~ 82 (89)
T cd07166 3 VVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRI 82 (89)
T ss_pred CCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCC
Confidence 45799999999999999999999999999999999999 59999999999999999999999999999999999998765
Q ss_pred c
Q psy2636 119 K 119 (335)
Q Consensus 119 ~ 119 (335)
+
T Consensus 83 ~ 83 (89)
T cd07166 83 P 83 (89)
T ss_pred C
Confidence 4
No 24
>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=100.00 E-value=9.2e-36 Score=214.79 Aligned_cols=78 Identities=41% Similarity=1.006 Sum_probs=74.4
Q ss_pred CCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
..+|.|||++++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||++++|+.++
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~ 83 (107)
T cd06955 6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDE 83 (107)
T ss_pred CCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCHH
Confidence 356999999999999999999999999999999999999999999999999999999999999999999999999863
No 25
>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=100.00 E-value=2.2e-35 Score=200.44 Aligned_cols=72 Identities=51% Similarity=1.151 Sum_probs=69.6
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecC-CCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCL-ADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~-~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
|.||||+++|+||||.+|+|||+||||+|..+..|.|. .+++|.|++..|..||+|||+|||+|||++++||
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 6889999999999999999999999999999885
No 26
>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=100.00 E-value=1.4e-35 Score=201.12 Aligned_cols=73 Identities=48% Similarity=1.012 Sum_probs=70.4
Q ss_pred cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||+++.|+
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 5999999999999999999999999999999999999999999999999999999999999999999999874
No 27
>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=100.00 E-value=2e-35 Score=199.83 Aligned_cols=72 Identities=44% Similarity=1.066 Sum_probs=69.8
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++|+
T Consensus 1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd07156 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL 72 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999873
No 28
>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=100.00 E-value=1.2e-35 Score=209.21 Aligned_cols=80 Identities=56% Similarity=1.204 Sum_probs=75.7
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccccccC
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKGRR 122 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~~~~ 122 (335)
|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|+...|+.||+|||+|||+|||++++||.++..+.+
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~ 80 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGR 80 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999998754433
No 29
>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=100.00 E-value=2.9e-35 Score=201.68 Aligned_cols=75 Identities=55% Similarity=1.178 Sum_probs=72.6
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
|.||||+++|+||||++|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||++||++++||.++
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r 75 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNER 75 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999765
No 30
>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=100.00 E-value=2.4e-35 Score=200.03 Aligned_cols=72 Identities=53% Similarity=1.232 Sum_probs=70.3
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||
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 899999999999999999999999999999999999999999999999999999999999999999999986
No 31
>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=100.00 E-value=3.3e-35 Score=198.97 Aligned_cols=72 Identities=64% Similarity=1.245 Sum_probs=70.1
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|+...|..||+|||+|||++||++++||
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 899999999999999999999999999999999999999999999999999999999999999999999885
No 32
>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=100.00 E-value=2.4e-35 Score=202.73 Aligned_cols=76 Identities=51% Similarity=1.142 Sum_probs=73.4
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
|.||||+++|+||||.+|+|||+||||++..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~ 76 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERA 76 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999998764
No 33
>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=100.00 E-value=2.9e-35 Score=199.11 Aligned_cols=72 Identities=44% Similarity=0.951 Sum_probs=69.7
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||++||+++++.
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 899999999999999999999999999999999999999999999999999999999999999999999873
No 34
>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=100.00 E-value=2e-35 Score=209.33 Aligned_cols=80 Identities=36% Similarity=0.826 Sum_probs=75.8
Q ss_pred CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccccc
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLKG 120 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~~ 120 (335)
.+|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.|+...|..|++|||+|||+|||++++||.++...
T Consensus 1 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~ 80 (94)
T cd06966 1 KICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS 80 (94)
T ss_pred CCCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhh
Confidence 36999999999999999999999999999999999999999999999999999999999999999999999999886543
No 35
>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=100.00 E-value=3e-35 Score=202.65 Aligned_cols=76 Identities=42% Similarity=0.947 Sum_probs=71.5
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
+..+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|+.||+|||+|||+|||+++...
T Consensus 2 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~ 77 (82)
T cd07173 2 PQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARK 77 (82)
T ss_pred CCCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHH
Confidence 4567999999999999999999999999999999999999999999999999999999999999999999977553
No 36
>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=100.00 E-value=3.1e-35 Score=208.53 Aligned_cols=81 Identities=47% Similarity=1.021 Sum_probs=76.1
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeeccc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSL 118 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~ 118 (335)
...+|.||||+++|+||||.+|+||++||||+|..+..|.|..+++|.|+...|..||+|||+||++|||++++||.++.
T Consensus 4 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~ 83 (95)
T cd06968 4 EVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRM 83 (95)
T ss_pred cccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcC
Confidence 34579999999999999999999999999999999999999999999999999999999999999999999999998754
Q ss_pred c
Q psy2636 119 K 119 (335)
Q Consensus 119 ~ 119 (335)
.
T Consensus 84 ~ 84 (95)
T cd06968 84 S 84 (95)
T ss_pred C
Confidence 4
No 37
>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=100.00 E-value=3.5e-35 Score=199.51 Aligned_cols=73 Identities=47% Similarity=1.021 Sum_probs=70.9
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeee
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRT 115 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~ 115 (335)
|.||||+++|+||||++|+|||+||||++..+..|.|..+++|.|++..|..||+|||+|||++||++++|+.
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 8999999999999999999999999999999999999999999999999999999999999999999999974
No 38
>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=100.00 E-value=1.1e-34 Score=202.30 Aligned_cols=76 Identities=42% Similarity=0.789 Sum_probs=71.3
Q ss_pred cccccCCCCCccccCCccccccccceecccccCC--eeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGS--KYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~--~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
+|.|||++++|+||||++|+|||+||||++..+. .|.|.++++|.|+...|+.||+|||+|||+|||+++.++.++
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~ 79 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGR 79 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccc
Confidence 5999999999999999999999999999998664 899999999999999999999999999999999999987654
No 39
>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=100.00 E-value=5.3e-35 Score=202.29 Aligned_cols=77 Identities=55% Similarity=1.156 Sum_probs=74.1
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK 119 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~ 119 (335)
|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.|++..|..||+|||+|||+|||++++||.++.+
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~ 77 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIP 77 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999987654
No 40
>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=100.00 E-value=6.5e-35 Score=204.46 Aligned_cols=76 Identities=45% Similarity=1.041 Sum_probs=73.3
Q ss_pred cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceeeeeeecc
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDS 117 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~ 117 (335)
+|.||||+++|+||||.+|+||++||||++..+..|.|..+++|.|++..|+.||+|||+|||++||++++|+.++
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~ 76 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDE 76 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHH
Confidence 4999999999999999999999999999999999999999999999999999999999999999999999999874
No 41
>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=100.00 E-value=7e-35 Score=198.19 Aligned_cols=72 Identities=57% Similarity=1.257 Sum_probs=69.9
Q ss_pred ccccCCCCCccccCCccccccccceecccccCCee-ecCCCCCCcccccccccccchhhHHHHhcCceeeeee
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKY-VCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVR 114 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y-~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 114 (335)
|.||||+++|+||||.+|+|||+||||+|..+..| .|..+++|.|++..|..||+|||+|||+|||++++|+
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 8999999999999999999999999999999999885
No 42
>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=100.00 E-value=1.1e-34 Score=201.63 Aligned_cols=76 Identities=51% Similarity=1.104 Sum_probs=71.0
Q ss_pred cccccCCCCCccccCCccccccccceecccccCCeee-cCCCCCCcccccccccccchhhHHHHhcCceeeeeeecccc
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYV-CLADKACPVDKRRRNRCQFCRFQKCLQVGMVKEVVRTDSLK 119 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~-C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~~~~ 119 (335)
+|.||||+++|+||||.+|+|||+||||+|..+..|. |..+ |.|++..|+.||+|||+|||+|||++++||.++.+
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~ 77 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMP 77 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCC
Confidence 4999999999999999999999999999999999995 9753 99999999999999999999999999999987654
No 43
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.98 E-value=1.5e-33 Score=190.46 Aligned_cols=70 Identities=51% Similarity=1.047 Sum_probs=67.4
Q ss_pred cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCceee
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVKE 111 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 111 (335)
+|.||||+++|+||||.+|+|||+||||+|..+..|.|..+++|.|++..|..||+|||+|||++||+++
T Consensus 1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 4999999999999999999999999999999999999999999999999999999999999999999864
No 44
>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=99.97 E-value=1.9e-32 Score=185.73 Aligned_cols=70 Identities=51% Similarity=1.086 Sum_probs=62.9
Q ss_pred CcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHHHHhcCcee
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQKCLQVGMVK 110 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~ 110 (335)
++|+||||+++|+||||.+|++|+.||||++..+..|.|..+++|.|++..+..|++|||+|||+|||++
T Consensus 1 ~~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 1 KKCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp -BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred CCCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence 4699999999999999999999999999999999999999999999999999999999999999999974
No 45
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.95 E-value=7.5e-27 Score=196.11 Aligned_cols=127 Identities=83% Similarity=1.350 Sum_probs=116.3
Q ss_pred ccCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEee
Q psy2636 208 FYREPNPLEPPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFC 287 (335)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~ 287 (335)
+|.++.+.++...+.+.|++++++.+..|+.+|+|||++|||.+|+.+||++|||++|+|+++|+.||++.+.++++++.
T Consensus 27 ~~~~~~~~~~~~~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~ 106 (239)
T cd07072 27 QYREPSPLEPPMSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFC 106 (239)
T ss_pred ccCCCCcccCCcchHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEee
Confidence 34555555666788899999999999999999999999999999999999999999999999999999999988899999
Q ss_pred CCeEeeHHhhhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 288 NGVVLEKQQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 288 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+|..+.+.+...+++ ++++.+++|+.+|++|++|.+||+|||||+||
T Consensus 107 ~g~~~~~~~~~~~~~-~~~~~i~ef~~~l~~L~ld~~E~a~LkAivLf 153 (239)
T cd07072 107 NGVVLHKQQCQRSFG-DWLHAILEFSKSLHAMDIDISAFACLCALTLI 153 (239)
T ss_pred CCeeecHHHHHhhHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 999998887766777 68999999999999999999999999999986
No 46
>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=99.92 E-value=1.4e-24 Score=182.31 Aligned_cols=116 Identities=64% Similarity=1.139 Sum_probs=107.5
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636 219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ 298 (335)
Q Consensus 219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~ 298 (335)
..+...++++++..+..++.+|+|||++|||.+|+.+||++|||++|.|+++|+.||++.+.+++++|.+|..+.+.+..
T Consensus 37 ~~~~~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~~~ 116 (238)
T cd07348 37 KEDASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQCV 116 (238)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHHHH
Confidence 34557789999999999999999999999999999999999999999999999999999999899999999999887655
Q ss_pred hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+++ ++++.+++|+.+|++|+||.+||+|||||+||
T Consensus 117 ~~~~-~~~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf 152 (238)
T cd07348 117 RGFG-DWIDSILEFSQSLHRMNLDVSAFSCLAALVII 152 (238)
T ss_pred hhHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 5676 88999999999999999999999999999987
No 47
>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=99.92 E-value=2.9e-24 Score=180.59 Aligned_cols=114 Identities=60% Similarity=1.076 Sum_probs=105.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhh
Q psy2636 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRS 300 (335)
Q Consensus 221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~ 300 (335)
....++++++..+..++.+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++...++.+++.+|..+.+.+...+
T Consensus 39 ~~~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~~ 118 (238)
T cd07071 39 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVRG 118 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhhhhhc
Confidence 45778899999999999999999999999999999999999999999999999999999889999999999887665456
Q ss_pred hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
++ ++++.+++|+.+|++|+||.+||+|||||+||
T Consensus 119 ~~-~~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf 152 (238)
T cd07071 119 FG-EWIDSIVEFSSNLQNMNIDISAFSCIAALAMV 152 (238)
T ss_pred HH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc
Confidence 66 78899999999999999999999999999986
No 48
>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=99.91 E-value=2.2e-23 Score=170.16 Aligned_cols=116 Identities=25% Similarity=0.461 Sum_probs=106.3
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636 219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ 298 (335)
Q Consensus 219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~ 298 (335)
....+.|++|...++..|+.+|+|||++|+|.+|+.+||++|||++|+++++++.|+++....+.+.+.+|..++.+...
T Consensus 8 ~~~~~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~l~~~~~~~~~~~~~~ 87 (189)
T cd06940 8 KSGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLH 87 (189)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCcEEcHHHHH
Confidence 45667899999999999999999999999999999999999999999999999999998888888999999999887754
Q ss_pred h-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 R-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 ~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
. +++ ++++.+++|+.+|++|++|.+||++||||+||
T Consensus 88 ~~~~~-~~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf 124 (189)
T cd06940 88 SMGAG-DLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLV 124 (189)
T ss_pred HcCcH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh
Confidence 4 444 78899999999999999999999999999986
No 49
>cd07076 NR_LBD_GR Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription
Probab=99.91 E-value=3.8e-23 Score=173.57 Aligned_cols=116 Identities=22% Similarity=0.338 Sum_probs=101.8
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCC--eEEeeCCeEeeHHhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT--KLIFCNGVVLEKQQC 297 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~--~~~~~~g~~~~~~~~ 297 (335)
+....+..+.++..+.+..+|+|||++|+|.+|+.+||++|||++|.++++++.||++....+ .+++++|..++.+..
T Consensus 25 ~~~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~ 104 (247)
T cd07076 25 STWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRM 104 (247)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHH
Confidence 445666778888899999999999999999999999999999999999999999999886443 488999999988765
Q ss_pred hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 298 QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 298 ~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
......++.+.+++++.+|++|++|.+||+|||||+||
T Consensus 105 ~~~~~~~~~~~l~e~~~~~r~L~ld~~EfacLKAIvLf 142 (247)
T cd07076 105 TLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLL 142 (247)
T ss_pred hhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 54444467788899999999999999999999999997
No 50
>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=99.90 E-value=6.1e-23 Score=173.97 Aligned_cols=115 Identities=27% Similarity=0.437 Sum_probs=106.1
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR 299 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~ 299 (335)
.+.+.|.++++..+..++.+|+|||++|||.+|+.+||++|||++|+++++|+.|+++...++.+.+++|..+..+....
T Consensus 49 ~~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (243)
T cd06935 49 VDLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKN 128 (243)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCeEeeHHHHHh
Confidence 35677889999999999999999999999999999999999999999999999999998888899999999988877644
Q ss_pred -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+++ ++.+.+++|+.+|++|+||++||+||+||+||
T Consensus 129 ~~~~-~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf 164 (243)
T cd06935 129 GGLG-VVSDAIFDLGVSLSSFNLDDTEVALLQAVLLM 164 (243)
T ss_pred cChH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh
Confidence 555 78999999999999999999999999999986
No 51
>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=99.90 E-value=7.6e-23 Score=171.82 Aligned_cols=115 Identities=17% Similarity=0.295 Sum_probs=101.7
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC--CeEEeeCCeEeeHHhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED--TKLIFCNGVVLEKQQC 297 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~--~~~~~~~g~~~~~~~~ 297 (335)
.....+..+++..++.+..+|+|||++|||.+|+.+||++|||++|.|+++++.||++...+ +.+.+.+|..++.+..
T Consensus 25 ~~~~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~ 104 (248)
T cd07075 25 TAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERM 104 (248)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHH
Confidence 44566788899999999999999999999999999999999999999999999999987643 3588899998887765
Q ss_pred hh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 298 QR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 298 ~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.. +.+ ++.+.+++++.+|++|+||.+||+|||||+||
T Consensus 105 ~~~~~~-~~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLf 142 (248)
T cd07075 105 HQSAMY-ELCQGMHQISLQFVRLQLTFEEYTIMKVLLLL 142 (248)
T ss_pred hhccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 44 555 67888999999999999999999999999997
No 52
>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=99.90 E-value=7.6e-23 Score=172.80 Aligned_cols=116 Identities=56% Similarity=0.959 Sum_probs=107.1
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636 219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ 298 (335)
Q Consensus 219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~ 298 (335)
..+...+..+++..+..+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.+.++.+++++|..+.+.+..
T Consensus 37 ~~~~~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~~~ 116 (239)
T cd06945 37 KPDSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQCV 116 (239)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHHHH
Confidence 34467788899999999999999999999999999999999999999999999999999998889999999999887765
Q ss_pred hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+++ ++++.+++|+.+|++|++|++||++||||+||
T Consensus 117 ~~~~-~~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~ 152 (239)
T cd06945 117 RGFG-EWLDSILAFSSSLQSLLLDDISAFCCLALLLL 152 (239)
T ss_pred HhHH-HHHHHHHHHHHHHHHHhCChHHHHHHHHHHHh
Confidence 5666 88999999999999999999999999999986
No 53
>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=99.89 E-value=1.1e-22 Score=167.57 Aligned_cols=112 Identities=29% Similarity=0.563 Sum_probs=103.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhcH
Q psy2636 224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD 303 (335)
Q Consensus 224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~ 303 (335)
.|.++++..+..++.+|+|||++|+|.+|+.+||++|||++|+++++++.++++....+.+.+.+|..+..+....+.+.
T Consensus 3 ~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (195)
T cd06941 3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDS 82 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCeEEecCCeEeeHHHHHhccch
Confidence 47788999999999999999999999999999999999999999999999998888778899999999988776555666
Q ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 304 DWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 304 ~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
++.+.+++|+.+|++|++|++||+|||||+||
T Consensus 83 ~~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf 114 (195)
T cd06941 83 DFVKALFEFSDSFNSLGLSDTEVALFCAVVLL 114 (195)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc
Confidence 78899999999999999999999999999987
No 54
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=99.89 E-value=2.9e-22 Score=168.53 Aligned_cols=115 Identities=29% Similarity=0.515 Sum_probs=104.6
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR 299 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~ 299 (335)
.+...+.++++..+..+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.+..+.+.+.+|..+..+....
T Consensus 35 ~~~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~ 114 (231)
T cd06937 35 LDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHN 114 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhh
Confidence 35567788889999999999999999999999999999999999999999999999999888899999999888776544
Q ss_pred -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+++ .+.+.+++|+.+|++|+||.+||+|||||+||
T Consensus 115 ~~~~-~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf 150 (231)
T cd06937 115 AGFG-PLTDLVFTFANQLLPLEMDDTEIGLLSAICLI 150 (231)
T ss_pred cChH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 455 77888999999999999999999999999997
No 55
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=99.89 E-value=6.3e-22 Score=167.08 Aligned_cols=115 Identities=20% Similarity=0.362 Sum_probs=99.8
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC--CeEEeeCCeEeeHHhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED--TKLIFCNGVVLEKQQC 297 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~--~~~~~~~g~~~~~~~~ 297 (335)
.....+..++++.++.+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.||++.... +.+.+.+|..+..+..
T Consensus 25 ~~~~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~~ 104 (246)
T cd06947 25 TTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRM 104 (246)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHHh
Confidence 34556778899999999999999999999999999999999999999999999999987543 3477888888887765
Q ss_pred hh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 298 QR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 298 ~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.. +.+ ++.+.+.+++.+|++|++|.+||+|||||+||
T Consensus 105 ~~~~~~-~~~~~~~e~~~~l~~L~ld~~E~acLKAIvLf 142 (246)
T cd06947 105 HQSAMY-SLCLGMRQISQEFVRLQVTYEEFLCMKVLLLL 142 (246)
T ss_pred hhccHH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc
Confidence 33 455 57778889999999999999999999999997
No 56
>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=99.88 E-value=7e-22 Score=165.80 Aligned_cols=115 Identities=22% Similarity=0.392 Sum_probs=97.9
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQC 297 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~ 297 (335)
.....+..+.++..+.+..+|||||++|||.+|+.+||++|||++|+++++|+.||++... ++.+.|.+|..+..+..
T Consensus 25 ~~~~~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~ 104 (248)
T cd07074 25 TPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM 104 (248)
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhh
Confidence 4455567778888899999999999999999999999999999999999999999998764 34578878888777654
Q ss_pred hh-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 298 QR-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 298 ~~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.. +.. ++...+++++.+|++|++|.+||+|||||+||
T Consensus 105 ~~~~~~-~~~~~m~e~~~~~~~L~ld~~Ey~cLKAIvLf 142 (248)
T cd07074 105 KESSFY-SLCLTMWQIPQEFVKLQVSQEEFLCMKALLLL 142 (248)
T ss_pred hhccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHC
Confidence 33 333 46777889999999999999999999999997
No 57
>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely r
Probab=99.88 E-value=5.4e-22 Score=167.65 Aligned_cols=114 Identities=26% Similarity=0.495 Sum_probs=100.9
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR 299 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~ 299 (335)
...+.|.++...++..|+.+|+|||++|||.+|+.+||++|||++|+|+++++.|+++...++.+.+ +|.++..+....
T Consensus 45 ~~~~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~~~-~~~~~~~~~~~~ 123 (241)
T cd06939 45 SREEMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLF-DGKYAPIDLFKS 123 (241)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCEEEE-CCccccHHHHHH
Confidence 3557889999999999999999999999999999999999999999999999999888877777777 566666665443
Q ss_pred -hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 300 -SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 300 -~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+.+ ++++.+++|+.+|+.|+||++||+||+||+||
T Consensus 124 ~~~~-~~~~~~~~f~~~l~~L~ld~~E~all~AivL~ 159 (241)
T cd06939 124 LGCD-DLISAVFDFAKSLCELKLTEDEIALFSALVLI 159 (241)
T ss_pred cCcH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh
Confidence 444 78899999999999999999999999999986
No 58
>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal doma
Probab=99.88 E-value=2e-21 Score=163.94 Aligned_cols=116 Identities=27% Similarity=0.472 Sum_probs=103.4
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636 219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ 298 (335)
Q Consensus 219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~ 298 (335)
.+..+.+..++++..+.+..+|+|||++|||.+|+.+||++|||++|+++++|+.||++....+.+++.+|..+..+...
T Consensus 28 ~~~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~~~~~~~~~~~~~~ 107 (235)
T cd06949 28 FTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQGS 107 (235)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCceecHHHhh
Confidence 35567778889999999999999999999999999999999999999999999999999888788999999888876543
Q ss_pred --hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 --RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 --~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+. .++.+.+++++.+|++|++|.+||+|||||+||
T Consensus 108 ~~~~~-~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLf 145 (235)
T cd06949 108 CVEGM-VEIFDMLLATASRFRELQLQREEYVCLKAIILL 145 (235)
T ss_pred hcccH-HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence 233 367888999999999999999999999999987
No 59
>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=99.88 E-value=1.8e-21 Score=164.25 Aligned_cols=114 Identities=19% Similarity=0.332 Sum_probs=98.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhh
Q psy2636 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQ 298 (335)
Q Consensus 221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~ 298 (335)
....+..++++..+.+..+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++... .+.+.+.+|..++.+...
T Consensus 26 ~~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~~~ 105 (246)
T cd07073 26 FAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMH 105 (246)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhhhc
Confidence 445567788889999999999999999999999999999999999999999999998764 446999999888866543
Q ss_pred h-hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 R-SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 ~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
. +.. +....+++++.+|++|++|.+||+|||||+||
T Consensus 106 ~~~~~-~~~~~l~~~~~~l~~L~ld~~EyacLKAIiLf 142 (246)
T cd07073 106 KSRMY-SQCVRMRHLSQEFGWLQITPQEFLCMKALLLF 142 (246)
T ss_pred cccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 3 333 55566789999999999999999999999997
No 60
>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=99.87 E-value=1e-21 Score=166.65 Aligned_cols=113 Identities=27% Similarity=0.503 Sum_probs=103.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-hhh
Q psy2636 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-RSF 301 (335)
Q Consensus 223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~~~ 301 (335)
..+.+++++.+..++.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+.+++|..+.+++.. .+.
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 5677888999999999999999999999999999999999999999999999999888889999999988877654 344
Q ss_pred cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
..++.+.+.+|+.+|++|++|.+||+||+||+||
T Consensus 123 ~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf 156 (236)
T cd06954 123 QVEFINPIFEFSKSMRELQLDDAEYALLIAINIF 156 (236)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence 5588999999999999999999999999999987
No 61
>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=99.87 E-value=2.1e-21 Score=157.60 Aligned_cols=113 Identities=27% Similarity=0.489 Sum_probs=101.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhc
Q psy2636 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFG 302 (335)
Q Consensus 223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 302 (335)
+.|..+++..+..+..+|+|||++|+|.+|+.+||++|||++|+++++++.|+++....+.+.+++|.....+.......
T Consensus 2 ~~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (174)
T cd06929 2 EKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSRDVLLNGGF 81 (174)
T ss_pred cHHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcccCCeEEecCCceecHHHHHHccc
Confidence 35778888899999999999999999999999999999999999999999999888888889999999877665444334
Q ss_pred HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 303 DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 303 ~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
..+.+.+.+++.+|++|++|.+||++||||+||
T Consensus 82 ~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~ 114 (174)
T cd06929 82 GEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLF 114 (174)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 578899999999999999999999999999986
No 62
>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=99.86 E-value=2.1e-21 Score=162.83 Aligned_cols=113 Identities=21% Similarity=0.304 Sum_probs=96.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHh-hhhh
Q psy2636 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQ-CQRS 300 (335)
Q Consensus 222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~-~~~~ 300 (335)
...+.++++..+..++.+|+|||++|||.+|+.+||++|||++|+|+++++.++++....+.+.+ +|..+...+ ...+
T Consensus 34 ~~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~~~~~~~-~~~~~~~~~~~~~g 112 (226)
T cd06934 34 FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWEC-GPLTYCIEDAARAG 112 (226)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhcccCCeEee-CCEeecHHHHHHcc
Confidence 45577888888999999999999999999999999999999999999999999988876665555 555555443 3345
Q ss_pred hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
++..+.+.+++|+.+|++|++|.+||+|||||+||
T Consensus 113 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf 147 (226)
T cd06934 113 FQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLF 147 (226)
T ss_pred chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 66567888999999999999999999999999987
No 63
>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=99.86 E-value=4e-21 Score=162.15 Aligned_cols=113 Identities=27% Similarity=0.549 Sum_probs=102.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh-h
Q psy2636 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR-S 300 (335)
Q Consensus 222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~-~ 300 (335)
...+.+++++.+..++.+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++....+.+.+++|..+.++.... +
T Consensus 38 ~~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~~~~~~f~~g~~~~~~~~~~~~ 117 (231)
T cd06938 38 DMRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYRKAG 117 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEeeCCEEecHHHHhhcC
Confidence 356778888889999999999999999999999999999999999999999999988888889999999988876533 4
Q ss_pred hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 301 FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 301 ~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+ ++.+.+++|+.+|++|+||++||++|+||+||
T Consensus 118 ~~-~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf 151 (231)
T cd06938 118 MG-DSAEDLFRFCRAMCSMKVDNAEYALLTAIVIF 151 (231)
T ss_pred HH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 44 77888999999999999999999999999986
No 64
>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=99.85 E-value=7.7e-21 Score=160.81 Aligned_cols=114 Identities=21% Similarity=0.318 Sum_probs=98.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCC--CeEEeeCCeEeeHHhhhh
Q psy2636 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAED--TKLIFCNGVVLEKQQCQR 299 (335)
Q Consensus 222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~--~~~~~~~g~~~~~~~~~~ 299 (335)
.+.+..+..+....+..+|||||++|+|.+|+.+||++|||++|+++++|+.||++...+ +.+.+++|..+.......
T Consensus 37 ~~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~ 116 (237)
T cd06944 37 LDTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLAS 116 (237)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhh
Confidence 445667777888889999999999999999999999999999999999999999988654 679999999888775432
Q ss_pred --hhc-HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 300 --SFG-DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 300 --~~~-~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+.+ .++++.+.+++.+|++|++|.+||+|||||+||
T Consensus 117 ~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaIiL~ 155 (237)
T cd06944 117 QAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILF 155 (237)
T ss_pred hccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 222 367888899999999999999999999999986
No 65
>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.85 E-value=8.6e-21 Score=155.60 Aligned_cols=109 Identities=24% Similarity=0.455 Sum_probs=95.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-h-hh
Q psy2636 224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-R-SF 301 (335)
Q Consensus 224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~-~~ 301 (335)
.|.++.+..+..++.+|+|||++|||.+|+.+||++|||++|+++++++.++++..+ .+++++|..+..+... . +.
T Consensus 3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~--~~~~~~g~~~~~~~~~~~~~~ 80 (191)
T cd06942 3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNE--GTVLCDFRPVEFASLLSQLLH 80 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcC--CeEEeCCccccHHHHHHhcch
Confidence 577888899999999999999999999999999999999999999999988766655 5778889888776542 2 23
Q ss_pred cHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 302 GDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 302 ~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+ ++++.+.+++.+|++|+||++||+||+||+||
T Consensus 81 ~-~~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~ 113 (191)
T cd06942 81 G-KLIDEMLQFANKILTLNLTNAELALLCAAELL 113 (191)
T ss_pred H-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 3 77888899999999999999999999999986
No 66
>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=99.85 E-value=2.5e-20 Score=156.59 Aligned_cols=116 Identities=25% Similarity=0.405 Sum_probs=100.4
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQR 299 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~ 299 (335)
...+.+..++++.+..+..+|+|||++|||.+|+.+||++|||++|+++++|+.||++.+.++.+++.+|.+........
T Consensus 24 ~~~~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~ 103 (221)
T cd06946 24 SDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEELARE 103 (221)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCceeecCCeEEcHHHHhh
Confidence 34566788899999999999999999999999999999999999999999999999999887788888887776554332
Q ss_pred hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.....+.+.+.+++.+|++|++|.+||+|||||+||
T Consensus 104 ~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~L~ 139 (221)
T cd06946 104 AGLLELYSACLQLVRRLQRLRLEKEEYVLLKALALA 139 (221)
T ss_pred cCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 222366778889999999999999999999999986
No 67
>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=99.85 E-value=8.4e-21 Score=160.41 Aligned_cols=113 Identities=20% Similarity=0.302 Sum_probs=95.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhh--
Q psy2636 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQC-- 297 (335)
Q Consensus 222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~-- 297 (335)
.+.+..++++....+..+|+|||++|+|.+|+.+||++|||++|.++++++.||++... .+.+++.+|..++....
T Consensus 39 ~~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~ 118 (241)
T cd07069 39 LSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIAS 118 (241)
T ss_pred cchHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhh
Confidence 44566778888889999999999999999999999999999999999999999998753 45788999987665331
Q ss_pred hh--hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 298 QR--SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 298 ~~--~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.. ++. .+++.+.+++.+|++|++|.+||+|||||+||
T Consensus 119 ~~~~~~~-~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLf 157 (241)
T cd07069 119 QAGATLN-NLMSHAQELVAKLRSLQFDQREFVCLKFLVLF 157 (241)
T ss_pred hhhhHHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 11 233 56788889999999999999999999999997
No 68
>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=99.85 E-value=1.3e-20 Score=159.14 Aligned_cols=115 Identities=23% Similarity=0.338 Sum_probs=97.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhh
Q psy2636 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQ 298 (335)
Q Consensus 221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~ 298 (335)
..+.+..++++....+..+|+|||++|+|.+|+.+||++|||++|.++++|+.||++... .+.+++++|..+..+...
T Consensus 36 ~~~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~ 115 (237)
T cd07070 36 QPAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVA 115 (237)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHH
Confidence 445567788888899999999999999999999999999999999999999999998753 467999999988866543
Q ss_pred hhhc---HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 RSFG---DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 ~~~~---~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
...+ ..++..+.+++.+|++|++|.+||+|||||+||
T Consensus 116 ~~~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLf 155 (237)
T cd07070 116 AQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILF 155 (237)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhc
Confidence 2222 234455678999999999999999999999997
No 69
>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=99.85 E-value=1.8e-20 Score=158.45 Aligned_cols=115 Identities=21% Similarity=0.334 Sum_probs=95.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCC-eEeeHHhhh-
Q psy2636 221 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNG-VVLEKQQCQ- 298 (335)
Q Consensus 221 ~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g-~~~~~~~~~- 298 (335)
....+.++++..+..++.+|+|||++|||.+|+.+||++|||++|+|+++++.++.+..++..+.+.++ ..+..++..
T Consensus 35 ~~~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (238)
T cd06933 35 RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQSFSLDDMSWTCGSPDFKYKVSDVTK 114 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHhcCcCCCeeEecCCceeecHHHHHH
Confidence 355678889999999999999999999999999999999999999999999999876555555665543 334444432
Q ss_pred hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 ~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+...++++.+++|+.+|++|++|.+||+|||||+||
T Consensus 115 ~g~~~~~~~~l~~~~~~l~~L~ld~~E~alLkAivLf 151 (238)
T cd06933 115 AGHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICIL 151 (238)
T ss_pred ccCcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 3445578899999999999999999999999999986
No 70
>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=99.84 E-value=3.3e-20 Score=158.34 Aligned_cols=114 Identities=22% Similarity=0.357 Sum_probs=95.7
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCC-eEeeHHhh
Q psy2636 219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNG-VVLEKQQC 297 (335)
Q Consensus 219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g-~~~~~~~~ 297 (335)
..+.+.|..+....+..|+.+|||||++|||.+|+.+||++|||++|+|++++..|.++. .+.+.+.+| .++.++..
T Consensus 59 ~~~~~~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~--~~~~~~~~~~~~~~~~~~ 136 (259)
T cd06932 59 TIRIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYN--KDGLLFPEGNGYVTREFL 136 (259)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcC--CCCeEEeCCCEEeeHHHH
Confidence 346677888888888999999999999999999999999999999999999999997754 334666655 55666654
Q ss_pred hh---hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 298 QR---SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 298 ~~---~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.. +++ ++++.+++|+.+|++|+||++||+|||||+||
T Consensus 137 ~~~~~~~~-~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf 176 (259)
T cd06932 137 ESLRKPFC-DIMEPKFEFAEKFNALELTDSELALFCAVIIL 176 (259)
T ss_pred HHhcccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 33 233 67888999999999999999999999999997
No 71
>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin
Probab=99.84 E-value=3.6e-20 Score=155.53 Aligned_cols=116 Identities=28% Similarity=0.474 Sum_probs=102.2
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh
Q psy2636 219 IAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ 298 (335)
Q Consensus 219 ~~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~ 298 (335)
....+.+..++.+..+.+..+|||||++|+|.+|+.+||++|||++|++++++..||++...++.+.+.+|..+..+...
T Consensus 23 ~~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~ 102 (221)
T cd07068 23 DTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQAR 102 (221)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCCeEEeCCCceECHHHHh
Confidence 34567788889999999999999999999999999999999999999999999999999887778999898887765433
Q ss_pred -hhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 -RSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 -~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.++. ++.+.+.+++.+|++|++|++||++||||+||
T Consensus 103 ~~~~~-~~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~ 139 (221)
T cd07068 103 VEGLL-EIFDMLLQLVRRFRELGLQREEYVCLKAIILA 139 (221)
T ss_pred hccHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 2443 66778889999999999999999999999986
No 72
>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=99.84 E-value=1.9e-20 Score=150.79 Aligned_cols=109 Identities=23% Similarity=0.285 Sum_probs=95.1
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccC--CCeEEeeCCeEeeHHhhhhhhcHH
Q psy2636 227 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAE--DTKLIFCNGVVLEKQQCQRSFGDD 304 (335)
Q Consensus 227 ~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~ 304 (335)
.+.++..+.+..+|||||++|+|.+|+.+||++|||++|.++++|+.||++... .+.+.+++|..+..+........+
T Consensus 3 ~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (165)
T cd06930 3 SLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAE 82 (165)
T ss_pred hHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHHH
Confidence 345667788889999999999999999999999999999999999999999865 456899999988876654433336
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 305 WLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 305 ~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+.+.+.+++.+|++|++|++||++||||+||
T Consensus 83 ~~~~~~~~~~~l~~L~l~~~E~~lLkai~l~ 113 (165)
T cd06930 83 LVQRLQELLSKLRSLQLDPKEYACLKAIVLF 113 (165)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 7888899999999999999999999999986
No 73
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=99.84 E-value=3e-20 Score=154.85 Aligned_cols=111 Identities=21% Similarity=0.401 Sum_probs=96.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhh-hhhc
Q psy2636 224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQ-RSFG 302 (335)
Q Consensus 224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~-~~~~ 302 (335)
.+..++.+....+..+|+|||++|+|.+|+.+||++|||++|++++++..||++....+.+++.+|..+..+... .+++
T Consensus 31 ~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 (207)
T cd06943 31 PVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQAGVG 110 (207)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCceeccchhhhccch
Confidence 356778888899999999999999999999999999999999999999999999887778889999888765542 2444
Q ss_pred HHHHHH-HHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 303 DDWLNA-ILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 303 ~~~~~~-~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+... +.+++.+|++|+||++||++||||+||
T Consensus 111 -~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~ 143 (207)
T cd06943 111 -AIFDRILTELVVKMRDLKMDRTELGCLRAIILF 143 (207)
T ss_pred -HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 44445 458999999999999999999999987
No 74
>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=99.84 E-value=3.2e-20 Score=153.77 Aligned_cols=111 Identities=22% Similarity=0.224 Sum_probs=88.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhcHH
Q psy2636 225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGDD 304 (335)
Q Consensus 225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 304 (335)
+..++++..+.+..+|+|||++|+|.+|+.+||++|||++|.++++|+.|+++...+...++.++...............
T Consensus 28 ~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~~~~~~~~~~~ 107 (206)
T cd06950 28 PESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLS 107 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCcccccccchhhHHHH
Confidence 45677788888999999999999999999999999999999999999999998876655555443322221111112224
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 305 WLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 305 ~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
..+.+.+++.+|++|+||.+||++||||+||
T Consensus 108 ~~~~i~~~~~~~~~L~ld~~EyalLKai~L~ 138 (206)
T cd06950 108 EVRALQETLSRFRQLRVDATEFACLKAIVLF 138 (206)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 4567889999999999999999999999986
No 75
>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=99.82 E-value=1.3e-19 Score=150.89 Aligned_cols=115 Identities=14% Similarity=0.178 Sum_probs=90.6
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe-----EEeeCCeEeeH
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK-----LIFCNGVVLEK 294 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~-----~~~~~g~~~~~ 294 (335)
+..+.+..+++.....+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++...... +....|.....
T Consensus 24 ~~~~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~ 103 (213)
T cd06953 24 DQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDEL 103 (213)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhH
Confidence 3446677788888899999999999999999999999999999999999999999999864321 11122222111
Q ss_pred HhhhhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 295 QQCQRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 295 ~~~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+.....+ ++++.+.+++.+|++|++|.+||+|||||+||
T Consensus 104 ~~~~~~~~-~~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLf 143 (213)
T cd06953 104 ERFGDEGG-EVVERLTYLLAKFRQLKVSNEEYVCLKVINFL 143 (213)
T ss_pred HHHHhhHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 11222233 67888899999999999999999999999986
No 76
>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal lig
Probab=99.81 E-value=1.6e-19 Score=152.02 Aligned_cols=111 Identities=23% Similarity=0.351 Sum_probs=95.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeHHhhhhhhcH
Q psy2636 224 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEKQQCQRSFGD 303 (335)
Q Consensus 224 ~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~~~ 303 (335)
.+..+...+...+..+++|||.||+|.+|+.+||++|||++|+++++++.||++....+.+++++|..+..+.....++
T Consensus 33 ~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~l~~~~g~~~~~~~~~~~~~- 111 (222)
T cd06931 33 SINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHCPEPEIS- 111 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCCeeeeCCCcccccccccchHH-
Confidence 3566777888999999999999999999999999999999999999999999998877889999998877654433444
Q ss_pred HHHHH-HHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 304 DWLNA-ILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 304 ~~~~~-~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+... +.+++.+|++|++|++||++||||+||
T Consensus 112 ~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~ 144 (222)
T cd06931 112 RVANRILDELVLPLRDLNIDDNEYACLKAIVFF 144 (222)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 34444 458999999999999999999999987
No 77
>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=99.81 E-value=1.1e-19 Score=151.92 Aligned_cols=111 Identities=18% Similarity=0.151 Sum_probs=86.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe----------EEeeCCeEeeH
Q psy2636 225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK----------LIFCNGVVLEK 294 (335)
Q Consensus 225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~----------~~~~~g~~~~~ 294 (335)
+..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++.+.+.. ++..++..+..
T Consensus 21 ~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (222)
T cd06951 21 PQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMHWGG 100 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhcccccccc
Confidence 45567777888999999999999999999999999999999999999999998765432 22333333322
Q ss_pred Hhh---hhh--hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 295 QQC---QRS--FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 295 ~~~---~~~--~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
... ..+ ....+++.+++|+.+|++|+||.+||++||||+||
T Consensus 101 ~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLf 146 (222)
T cd06951 101 TPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLF 146 (222)
T ss_pred ccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 110 111 12245788899999999999999999999999997
No 78
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=99.80 E-value=6.3e-19 Score=147.46 Aligned_cols=109 Identities=23% Similarity=0.404 Sum_probs=90.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEEeeCCeEeeH-Hhhh-h
Q psy2636 222 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLIFCNGVVLEK-QQCQ-R 299 (335)
Q Consensus 222 ~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~~~~g~~~~~-~~~~-~ 299 (335)
.+.+..+++|.+..+..+|+|||++|||.+|+.+||++|||++|+++++|+.|+++... +++|..+.. +... .
T Consensus 35 ~~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~~-----~~~~~~~~~~~~~~~~ 109 (221)
T cd06936 35 EENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKK-----LPAGHADLLEERIRSS 109 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhccc-----ccCCCchhhHHHHHhc
Confidence 46678889999999999999999999999999999999999999999999999765421 444543222 2222 2
Q ss_pred hhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 300 SFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 300 ~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
+...++++.+++|+.+|++|+||.+||+||+||+||
T Consensus 110 ~~~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~ 145 (221)
T cd06936 110 GISDEFITPMFNFYKSMGELKMTQEEYALLTAITIL 145 (221)
T ss_pred cchHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 334578999999999999999999999999999986
No 79
>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=99.79 E-value=3.9e-19 Score=148.13 Aligned_cols=110 Identities=16% Similarity=0.135 Sum_probs=83.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe----------EEeeCCeEeeH
Q psy2636 225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK----------LIFCNGVVLEK 294 (335)
Q Consensus 225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~----------~~~~~g~~~~~ 294 (335)
+..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.+.+.. +.+. |.....
T Consensus 21 ~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~-~~~~~~ 99 (222)
T cd07349 21 PHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLE-GQSSSG 99 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhc-cccccc
Confidence 44556666788889999999999999999999999999999999999999998654321 2222 222111
Q ss_pred Hh-h--hhhhcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 295 QQ-C--QRSFGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 295 ~~-~--~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.. . ..+.....++.+.+|+.+|++|++|.+||++||||+||
T Consensus 100 ~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf 143 (222)
T cd07349 100 GSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILF 143 (222)
T ss_pred ccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 10 0 11222345667789999999999999999999999997
No 80
>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=99.79 E-value=5.5e-19 Score=148.10 Aligned_cols=111 Identities=22% Similarity=0.174 Sum_probs=84.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCeEE---------eeCCeEeeHH
Q psy2636 225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTKLI---------FCNGVVLEKQ 295 (335)
Q Consensus 225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~~~---------~~~g~~~~~~ 295 (335)
+..+++...+.+..+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++.+.+...+ +.++......
T Consensus 21 ~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~~~~~~ 100 (232)
T cd07350 21 PQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPPPTSG 100 (232)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhcccccccc
Confidence 4566777788889999999999999999999999999999999999999999876543221 2222111000
Q ss_pred -------------hhhhh--hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 296 -------------QCQRS--FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 296 -------------~~~~~--~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
....+ .....++.+++|+.+|+.|+||.+||++||||+||
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf 155 (232)
T cd07350 101 AEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLF 155 (232)
T ss_pred cccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 00111 11235677889999999999999999999999997
No 81
>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=99.79 E-value=7.8e-19 Score=148.60 Aligned_cols=112 Identities=25% Similarity=0.295 Sum_probs=91.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCC-eEEeeCCeEeeHHhhhhhh
Q psy2636 223 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT-KLIFCNGVVLEKQQCQRSF 301 (335)
Q Consensus 223 ~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~-~~~~~~g~~~~~~~~~~~~ 301 (335)
..+..++++..+.+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|+++..... .+.+++|..+..... ...
T Consensus 30 ~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~-~~~ 108 (236)
T cd06948 30 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSA-DRV 108 (236)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccch-hhH
Confidence 446778888899999999999999999999999999999999999999999999876443 477778887653321 111
Q ss_pred c--HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 302 G--DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 302 ~--~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
. .+.++.+.+++.+|++|+||++||++||||+||
T Consensus 109 ~~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~ 144 (236)
T cd06948 109 VAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLF 144 (236)
T ss_pred hHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 1 133445668999999999999999999999986
No 82
>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=99.72 E-value=2.9e-17 Score=138.17 Aligned_cols=111 Identities=23% Similarity=0.297 Sum_probs=82.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCC-eEEeeCCeEeeHH----hhh-
Q psy2636 225 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT-KLIFCNGVVLEKQ----QCQ- 298 (335)
Q Consensus 225 ~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~-~~~~~~g~~~~~~----~~~- 298 (335)
+..+.++..+.+..+++|||++|+|.+|+.+||++|||++|.++++++.++++...+. .+....+.++... ...
T Consensus 23 ~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (222)
T cd06952 23 VHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQDKLSA 102 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhhhHhcCCCch
Confidence 4556777788899999999999999999999999999999999999999877654332 2332333322111 110
Q ss_pred hhhc--HHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 RSFG--DDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 ~~~~--~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
...+ .+.+..+.+++.+|++|++|.+||++||||+||
T Consensus 103 ~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf 141 (222)
T cd06952 103 DKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLF 141 (222)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh
Confidence 0111 133445678999999999999999999999997
No 83
>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=99.72 E-value=1.8e-16 Score=131.86 Aligned_cols=116 Identities=28% Similarity=0.498 Sum_probs=101.4
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhc-cCCCeEEeeCCeEeeHHhhh
Q psy2636 220 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTR-AEDTKLIFCNGVVLEKQQCQ 298 (335)
Q Consensus 220 ~~~~~~~~~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~-~~~~~~~~~~g~~~~~~~~~ 298 (335)
.....+..+..++...+..+++|||++|+|.+|+.+||++|||++|+++++|+.++++. ...+.+.+.+|..+..+...
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 45666788888899999999999999999999999999999999999999999999988 56678999999999877654
Q ss_pred hh---hcHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 299 RS---FGDDWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 299 ~~---~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.. ...+..+.+.+++.+|.+|++|.+||++|+||+||
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~ 133 (203)
T PF00104_consen 94 DFITGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILF 133 (203)
T ss_dssp HTSTTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHS
T ss_pred cccccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhh
Confidence 32 34477888999999999999999999999999987
No 84
>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=99.71 E-value=1e-16 Score=129.27 Aligned_cols=108 Identities=31% Similarity=0.461 Sum_probs=88.5
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCCe-EEeeCCeE---eeHHhhhhhhcH
Q psy2636 228 FYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDTK-LIFCNGVV---LEKQQCQRSFGD 303 (335)
Q Consensus 228 ~~~~~~~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~~-~~~~~g~~---~~~~~~~~~~~~ 303 (335)
+..++...+..+++|||++|+|.+|+.+||+.|||++|+++++|+.+|++...... ...+++.. ...+.....+.+
T Consensus 3 ~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (168)
T cd06157 3 LCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKG 82 (168)
T ss_pred HHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHHH
Confidence 45567788889999999999999999999999999999999999999999876543 44444442 223333344555
Q ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 304 DWLNAILEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 304 ~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+.+.+.+++.+|.+|++|++||++|+||+||
T Consensus 83 ~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~ 114 (168)
T cd06157 83 ELIRLLFEFVNPLRALKLDDEEYALLKAIVLF 114 (168)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 77788889999999999999999999999987
No 85
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=99.68 E-value=2.2e-16 Score=126.56 Aligned_cols=102 Identities=22% Similarity=0.371 Sum_probs=86.3
Q ss_pred HHHHHHHHHhhcCCCCCCCCHHHHHHHHHHhHHHHHHHHHhhhhccCCC-eEEeeCCeEeeHHhhh---hhhcHHHHHHH
Q psy2636 234 TSVDVIRHFADKIPGFSDLCKEDQELLFQSASLELFVLRLAYRTRAEDT-KLIFCNGVVLEKQQCQ---RSFGDDWLNAI 309 (335)
Q Consensus 234 ~~i~~vvefAk~~P~F~~L~~~DQ~~LLk~~~~~~~~l~~a~~~~~~~~-~~~~~~g~~~~~~~~~---~~~~~~~~~~~ 309 (335)
..+..+++|||++|+|.+|+.+||+.|||++|+++++|+.++++...+. .+.+++|.++..+... ..+.+.+.+.+
T Consensus 3 ~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (163)
T smart00430 3 RDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRIL 82 (163)
T ss_pred hHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHHH
Confidence 4567789999999999999999999999999999999999999987655 5666777666544322 34555777888
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHHcC
Q psy2636 310 LEFCQSLHLMEIDISAFACLCALTLI 335 (335)
Q Consensus 310 ~~~~~~l~~l~l~~~E~~ll~ai~l~ 335 (335)
.+++.+|++|++|++||++|+||++|
T Consensus 83 ~~~~~~l~~L~l~~~E~~~l~ai~l~ 108 (163)
T smart00430 83 QELVKPLRELKLDDEEYALLKAILLF 108 (163)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 89999999999999999999999986
No 86
>KOG4217|consensus
Probab=94.65 E-value=0.074 Score=48.18 Aligned_cols=49 Identities=55% Similarity=0.887 Sum_probs=44.2
Q ss_pred CChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhcc
Q psy2636 159 AEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLEL 207 (335)
Q Consensus 159 ~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~~ 207 (335)
.....+++||++++.+.++++.|...+|.|.++.++|+++|+..+.+++
T Consensus 405 tdA~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflel 453 (605)
T KOG4217|consen 405 TDALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLEL 453 (605)
T ss_pred cHHHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHH
Confidence 3457899999999999999999999999999999999999998887653
No 87
>KOG3277|consensus
Probab=85.67 E-value=0.62 Score=35.74 Aligned_cols=26 Identities=35% Similarity=0.752 Sum_probs=21.0
Q ss_pred cccccCCCCCc------cccCCc--cccccccce
Q psy2636 42 LCAVCGDIAAC------QHYGVR--TCEGCKGFF 67 (335)
Q Consensus 42 ~C~VCgd~a~g------~HyGv~--sC~gCk~FF 67 (335)
.|.|||-+.+. ||=||. +|.||+.+.
T Consensus 81 TCkvCntRs~ktisk~AY~~GvVivqC~gC~~~H 114 (165)
T KOG3277|consen 81 TCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH 114 (165)
T ss_pred EeeccCCccccccChhhhhCceEEEECCCCccce
Confidence 59999988754 888874 699999864
No 88
>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=84.20 E-value=2 Score=36.54 Aligned_cols=51 Identities=80% Similarity=1.291 Sum_probs=43.7
Q ss_pred CCCCChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636 156 PPIAEPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206 (335)
Q Consensus 156 ~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~ 206 (335)
++....+.+++++...+.....+..|++.+|.|.+|..+|+..+++.+..+
T Consensus 36 ~~~~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~E 86 (239)
T cd07072 36 PPMSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLE 86 (239)
T ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHH
Confidence 345566788899999888888889999999999999999999999888644
No 89
>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=82.76 E-value=0.46 Score=28.73 Aligned_cols=23 Identities=35% Similarity=0.908 Sum_probs=19.4
Q ss_pred cccccCCCC-Cccc-cCCccccccc
Q psy2636 42 LCAVCGDIA-ACQH-YGVRTCEGCK 64 (335)
Q Consensus 42 ~C~VCgd~a-~g~H-yGv~sC~gCk 64 (335)
.|.|||..- .|.| ||..-|..|-
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE 25 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCE 25 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHH
Confidence 499999775 5988 9999999985
No 90
>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=79.32 E-value=0.97 Score=24.50 Aligned_cols=21 Identities=24% Similarity=0.504 Sum_probs=16.8
Q ss_pred cccccCCCCCccccCCccccccc
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCK 64 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk 64 (335)
.|.||+.+.+|.. ...|+.|-
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 3889999998886 67777775
No 91
>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=79.26 E-value=0.48 Score=35.26 Aligned_cols=32 Identities=28% Similarity=0.732 Sum_probs=22.2
Q ss_pred CCCCcccccCCCCCc---cccCCccccccccceec
Q psy2636 38 SPSQLCAVCGDIAAC---QHYGVRTCEGCKGFFKR 69 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g---~HyGv~sC~gCk~FFRR 69 (335)
..+..|.-||.+... ..||+..|..|+|..|-
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~ 45 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRS 45 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHH
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHH
Confidence 346789999988754 68999999999998654
No 92
>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=75.85 E-value=2.9 Score=35.53 Aligned_cols=45 Identities=67% Similarity=1.091 Sum_probs=38.9
Q ss_pred hHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636 162 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206 (335)
Q Consensus 162 ~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~ 206 (335)
..+++++...+.....+..|++.+|.|.+|+.+|+..|++.+..+
T Consensus 41 ~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~E 85 (238)
T cd07348 41 SDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVE 85 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHH
Confidence 567788888888788888999999999999999999999887643
No 93
>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=68.72 E-value=7.4 Score=33.06 Aligned_cols=47 Identities=64% Similarity=1.029 Sum_probs=38.6
Q ss_pred ChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636 160 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206 (335)
Q Consensus 160 ~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~ 206 (335)
....+..++...+.....+..|++.+|.|.+|..+|+..+++.+..+
T Consensus 39 ~~~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~E 85 (239)
T cd06945 39 DSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLE 85 (239)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHH
Confidence 34566777777777777788899999999999999999999877643
No 94
>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=67.53 E-value=0.85 Score=22.70 Aligned_cols=19 Identities=32% Similarity=0.875 Sum_probs=13.6
Q ss_pred eecCCCCCCcccccccccc
Q psy2636 77 YVCLADKACPVDKRRRNRC 95 (335)
Q Consensus 77 y~C~~~~~C~i~~~~r~~C 95 (335)
+.|+.+.-|.+|+.++..|
T Consensus 4 ~~Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 4 FHCKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp ---BTTEEEEEETTTCEEE
T ss_pred cccCCCCEeeeCCCCCcCC
Confidence 5698899999998887765
No 95
>PHA03124 dUTPase; Provisional
Probab=67.41 E-value=1.3 Score=39.46 Aligned_cols=17 Identities=41% Similarity=1.007 Sum_probs=13.8
Q ss_pred CCccccccccceecccc
Q psy2636 56 GVRTCEGCKGFFKRTVQ 72 (335)
Q Consensus 56 Gv~sC~gCk~FFRR~v~ 72 (335)
|-.-|.|||+||||...
T Consensus 189 ~~~~~~~~~~~~~~~~~ 205 (418)
T PHA03124 189 GNFGCMGCKAFYRRLFE 205 (418)
T ss_pred ccccccchHHHHHHHHH
Confidence 44569999999999863
No 96
>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=64.86 E-value=0.98 Score=27.31 Aligned_cols=12 Identities=58% Similarity=1.054 Sum_probs=7.7
Q ss_pred cccccccchhhH
Q psy2636 90 RRRNRCQFCRFQ 101 (335)
Q Consensus 90 ~~r~~Cr~CR~~ 101 (335)
..+.+|+.||.|
T Consensus 35 ~~~~~C~~C~~q 46 (46)
T PF12760_consen 35 RGRYRCKACRKQ 46 (46)
T ss_pred CCeEECCCCCCc
Confidence 455677777754
No 97
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=64.12 E-value=5.3 Score=32.97 Aligned_cols=31 Identities=19% Similarity=0.572 Sum_probs=24.4
Q ss_pred CCcccccCCCCCc--ccc-CCccccccccceecc
Q psy2636 40 SQLCAVCGDIAAC--QHY-GVRTCEGCKGFFKRT 70 (335)
Q Consensus 40 ~~~C~VCgd~a~g--~Hy-Gv~sC~gCk~FFRR~ 70 (335)
.-+|.+|++..-- ++- ++..|+.|++.|-|.
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~ 185 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKS 185 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchh
Confidence 3569999977544 556 778899999999887
No 98
>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=61.92 E-value=4.8 Score=24.65 Aligned_cols=26 Identities=23% Similarity=0.837 Sum_probs=19.7
Q ss_pred ccccCCCCCccccCCccccccccceecc
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFFKRT 70 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FFRR~ 70 (335)
|.|||. .+.--..+.|++|...|-..
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 44455778899998777554
No 99
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=58.75 E-value=12 Score=33.41 Aligned_cols=57 Identities=25% Similarity=0.700 Sum_probs=34.3
Q ss_pred ccccCCCCCccccCCccccccc--------------------cceecccccCCee-ecCCC--CCCc--ccc-ccccccc
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCK--------------------GFFKRTVQKGSKY-VCLAD--KACP--VDK-RRRNRCQ 96 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk--------------------~FFRR~v~~~~~y-~C~~~--~~C~--i~~-~~r~~Cr 96 (335)
|..||.. .+|.-..|..|. +.++........| .|... +.|- |.. ....-|+
T Consensus 2 C~~Cg~~---v~FeNt~C~~Cg~~LGf~p~~~~~~al~~~~~~~~~~~~~~~~~~~~C~N~~~~~CNWlvp~~~~~~~C~ 78 (343)
T PF10005_consen 2 CPNCGQP---VFFENTRCLSCGSALGFDPDRREMVALEPDGDGRWRAPAAPGRRYRRCANAEHAVCNWLVPADDPDALCR 78 (343)
T ss_pred CCCCCCc---ceeCCCccccCCccccCCCCCCcEEeeccCCCCcccccCCCCceeeeCCCCCccccceeecCCCCCCcch
Confidence 7778765 677777888886 2344333344556 58653 2352 211 2245899
Q ss_pred chhhHH
Q psy2636 97 FCRFQK 102 (335)
Q Consensus 97 ~CR~~K 102 (335)
+||+.+
T Consensus 79 aCrlnr 84 (343)
T PF10005_consen 79 ACRLNR 84 (343)
T ss_pred hhhccC
Confidence 999875
No 100
>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=58.38 E-value=2.1 Score=19.15 Aligned_cols=7 Identities=71% Similarity=1.260 Sum_probs=5.2
Q ss_pred cceeccc
Q psy2636 65 GFFKRTV 71 (335)
Q Consensus 65 ~FFRR~v 71 (335)
|||+|.-
T Consensus 3 GFFKR~~ 9 (15)
T PF00357_consen 3 GFFKRQR 9 (15)
T ss_dssp CHHHHHH
T ss_pred ccccccC
Confidence 6888864
No 101
>PRK01343 zinc-binding protein; Provisional
Probab=58.04 E-value=9 Score=24.30 Aligned_cols=14 Identities=29% Similarity=0.850 Sum_probs=10.6
Q ss_pred CCCCcccccCCCCC
Q psy2636 38 SPSQLCAVCGDIAA 51 (335)
Q Consensus 38 ~~~~~C~VCgd~a~ 51 (335)
.+...|.|||....
T Consensus 7 ~p~~~CP~C~k~~~ 20 (57)
T PRK01343 7 RPTRPCPECGKPST 20 (57)
T ss_pred CCCCcCCCCCCcCc
Confidence 45567999998764
No 102
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=58.04 E-value=3.8 Score=25.58 Aligned_cols=24 Identities=33% Similarity=0.934 Sum_probs=18.9
Q ss_pred CCcccccCCCCCc-cccCCcccccc
Q psy2636 40 SQLCAVCGDIAAC-QHYGVRTCEGC 63 (335)
Q Consensus 40 ~~~C~VCgd~a~g-~HyGv~sC~gC 63 (335)
..-|.|||.+-.- -.||..-|+-|
T Consensus 16 sr~C~vCg~~~gliRkygL~~CRqC 40 (54)
T PTZ00218 16 SRQCRVCSNRHGLIRKYGLNVCRQC 40 (54)
T ss_pred CCeeecCCCcchhhhhcCcchhhHH
Confidence 4679999987533 55999999888
No 103
>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=55.64 E-value=7.4 Score=24.26 Aligned_cols=16 Identities=25% Similarity=0.659 Sum_probs=12.0
Q ss_pred CcccccCCCCCccccC
Q psy2636 41 QLCAVCGDIAACQHYG 56 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyG 56 (335)
++|.-||.++-.+|+|
T Consensus 2 kPCPfCGg~~~~~~~~ 17 (53)
T TIGR03655 2 KPCPFCGGADVYLRRG 17 (53)
T ss_pred CCCCCCCCcceeeEec
Confidence 5799999888766643
No 104
>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=55.54 E-value=4.7 Score=22.58 Aligned_cols=23 Identities=22% Similarity=0.775 Sum_probs=12.0
Q ss_pred cccccCCCC----CccccCCccccccc
Q psy2636 42 LCAVCGDIA----ACQHYGVRTCEGCK 64 (335)
Q Consensus 42 ~C~VCgd~a----~g~HyGv~sC~gCk 64 (335)
.|.-||+.- ---||+...|..|+
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 488888663 23789999999996
No 105
>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=55.54 E-value=3.7 Score=30.29 Aligned_cols=31 Identities=26% Similarity=0.590 Sum_probs=25.2
Q ss_pred CCcccccCCCCCc---cccCCccccccccceecc
Q psy2636 40 SQLCAVCGDIAAC---QHYGVRTCEGCKGFFKRT 70 (335)
Q Consensus 40 ~~~C~VCgd~a~g---~HyGv~sC~gCk~FFRR~ 70 (335)
+..|.=||.+.-. .-||+..|..|+|..|..
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~l 36 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSL 36 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHHhc
Confidence 5679999987643 689999999999987654
No 106
>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=55.34 E-value=4.7 Score=21.68 Aligned_cols=19 Identities=26% Similarity=0.653 Sum_probs=7.1
Q ss_pred cccccCCCCCc-cccCCccc
Q psy2636 42 LCAVCGDIAAC-QHYGVRTC 60 (335)
Q Consensus 42 ~C~VCgd~a~g-~HyGv~sC 60 (335)
.|.+||.+..| .-|.-..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~C 21 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSEC 21 (30)
T ss_dssp --TTTS----S--EEE-TTT
T ss_pred cCCcCCCcCCCCceEECccC
Confidence 58888888877 55554333
No 107
>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=55.09 E-value=4.9 Score=18.68 Aligned_cols=9 Identities=67% Similarity=1.383 Sum_probs=6.6
Q ss_pred ccccceecc
Q psy2636 62 GCKGFFKRT 70 (335)
Q Consensus 62 gCk~FFRR~ 70 (335)
|||-||=.+
T Consensus 6 ~CknffWK~ 14 (18)
T PF03002_consen 6 GCKNFFWKT 14 (18)
T ss_pred cccceeecc
Confidence 788888544
No 108
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=55.05 E-value=7.5 Score=28.22 Aligned_cols=20 Identities=30% Similarity=0.890 Sum_probs=16.0
Q ss_pred CCcccccCCCCCccccCCccccccc
Q psy2636 40 SQLCAVCGDIAACQHYGVRTCEGCK 64 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyGv~sC~gCk 64 (335)
...|.+||.+++|- .|..|+
T Consensus 80 ~~~C~~CG~pss~~-----iC~~C~ 99 (104)
T TIGR00269 80 LRRCERCGEPTSGR-----ICKACK 99 (104)
T ss_pred CCcCCcCcCcCCcc-----ccHhhh
Confidence 35699999999863 788885
No 109
>PRK00420 hypothetical protein; Validated
Probab=55.01 E-value=8.2 Score=28.37 Aligned_cols=27 Identities=26% Similarity=0.283 Sum_probs=21.9
Q ss_pred CCCcccccCCCCCccccCCcccccccc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKG 65 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~ 65 (335)
....|.|||.+-.+.+=|-.-|-.|..
T Consensus 22 l~~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred ccCCCCCCCCcceecCCCceECCCCCC
Confidence 346799999888887778888888865
No 110
>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=54.15 E-value=18 Score=29.45 Aligned_cols=45 Identities=33% Similarity=0.572 Sum_probs=36.3
Q ss_pred hhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 161 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 161 ~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
.+..+++.+..+.....+-+|...+|.|.+|..+|+..+++....
T Consensus 11 ~~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~ 55 (189)
T cd06940 11 HEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTF 55 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhH
Confidence 455666777777666777889999999999999999999887754
No 111
>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=53.82 E-value=7.1 Score=22.92 Aligned_cols=11 Identities=55% Similarity=1.346 Sum_probs=8.5
Q ss_pred CCCcccccCCC
Q psy2636 39 PSQLCAVCGDI 49 (335)
Q Consensus 39 ~~~~C~VCgd~ 49 (335)
|..+|.|||.+
T Consensus 7 p~K~C~~C~rp 17 (42)
T PF10013_consen 7 PSKICPVCGRP 17 (42)
T ss_pred CCCcCcccCCc
Confidence 45679999965
No 112
>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=53.61 E-value=19 Score=30.63 Aligned_cols=45 Identities=64% Similarity=1.013 Sum_probs=37.4
Q ss_pred hHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636 162 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206 (335)
Q Consensus 162 ~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~ 206 (335)
..+++++...+.....+..|++.+|.|.+|+.+|+..|++.+..+
T Consensus 41 ~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~E 85 (238)
T cd07071 41 QHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLE 85 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHH
Confidence 456677777777777788899999999999999999999887643
No 113
>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=53.18 E-value=14 Score=25.31 Aligned_cols=21 Identities=38% Similarity=0.563 Sum_probs=16.2
Q ss_pred hhcCCCCCCCCHHHHHHHHHH
Q psy2636 243 ADKIPGFSDLCKEDQELLFQS 263 (335)
Q Consensus 243 Ak~~P~F~~L~~~DQ~~LLk~ 263 (335)
+..|+||.+|..+||..|.+.
T Consensus 60 ~~~i~G~~~L~~~Dq~~i~~~ 80 (82)
T PF00645_consen 60 IEEIKGFDELKPEDQEKIRKL 80 (82)
T ss_dssp GGGCETCCCS-HHHHHHHHHH
T ss_pred HHHCCChHHCCHHHHHHHHHH
Confidence 345899999999999988653
No 114
>KOG3362|consensus
Probab=52.89 E-value=7 Score=29.76 Aligned_cols=22 Identities=32% Similarity=0.750 Sum_probs=15.6
Q ss_pred CCCCcccccCCCCCccccCCcccccccc
Q psy2636 38 SPSQLCAVCGDIAACQHYGVRTCEGCKG 65 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~ 65 (335)
.....|.||| -.+..+|-.|-+
T Consensus 116 P~r~fCaVCG------~~S~ysC~~CG~ 137 (156)
T KOG3362|consen 116 PLRKFCAVCG------YDSKYSCVNCGT 137 (156)
T ss_pred CcchhhhhcC------CCchhHHHhcCC
Confidence 3456699999 345668888854
No 115
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=51.33 E-value=7.4 Score=24.64 Aligned_cols=23 Identities=35% Similarity=0.989 Sum_probs=15.6
Q ss_pred CcccccCCCCCccccCCcccccccccee
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFK 68 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFR 68 (335)
..|..||...-.. ..|.+| ||++
T Consensus 27 ~~c~~cg~~~~~H----~vc~~c-G~y~ 49 (56)
T PF01783_consen 27 VKCPNCGEPKLPH----RVCPSC-GYYK 49 (56)
T ss_dssp EESSSSSSEESTT----SBCTTT-BBSS
T ss_pred eeeccCCCEeccc----EeeCCC-CeEC
Confidence 4599999544333 378888 6765
No 116
>KOG4399|consensus
Probab=49.31 E-value=4 Score=34.33 Aligned_cols=49 Identities=18% Similarity=0.301 Sum_probs=21.9
Q ss_pred cccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchh
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCR 99 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR 99 (335)
.|.|||.-.+.. .+|..|++ =|.+...+--.|+....|.- .-+.|-+||
T Consensus 263 ~C~iC~~~~~~R----~~C~~~kA--~~~~~Q~K~N~~~~~~~~~q---~~~H~s~~~ 311 (325)
T KOG4399|consen 263 GCFICGELDHKR----STCPNIKA--VRKQKQRKSNKMKMETTKGQ---SMNHTSATR 311 (325)
T ss_pred ceeecccccccc----ccCccHHH--HHHHHhcccchhhhhhhhhh---hhHHHHHHH
Confidence 355555444332 45666655 24444444444544333433 223444444
No 117
>smart00274 FOLN Follistatin-N-terminal domain-like. Follistatin-N-terminal domain-like, EGF-like. Region distinct from the kazal-like sequence
Probab=48.67 E-value=7.9 Score=20.19 Aligned_cols=20 Identities=40% Similarity=0.728 Sum_probs=15.7
Q ss_pred eeecCCCCCCcccccccccc
Q psy2636 76 KYVCLADKACPVDKRRRNRC 95 (335)
Q Consensus 76 ~y~C~~~~~C~i~~~~r~~C 95 (335)
.+.|..+..|.+|+.++-+|
T Consensus 4 ~v~C~~G~~C~~d~~g~p~C 23 (26)
T smart00274 4 NVQCPFGKVCVVDKGGNARC 23 (26)
T ss_pred CEECCCCCEEEeCCCCCEEE
Confidence 35698999999987777666
No 118
>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=47.93 E-value=11 Score=21.36 Aligned_cols=18 Identities=50% Similarity=1.219 Sum_probs=10.7
Q ss_pred ccccCCCCCccccCCccccccccc
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGF 66 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~F 66 (335)
|.+||.++ ...|.+|+..
T Consensus 1 C~~C~~~~------~~~C~~C~~~ 18 (37)
T PF01753_consen 1 CAVCGKPA------LKRCSRCKSV 18 (37)
T ss_dssp -TTTSSCS------SEEETTTSSS
T ss_pred CcCCCCCc------CCcCCCCCCE
Confidence 66787733 2378888543
No 119
>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=47.42 E-value=8 Score=30.73 Aligned_cols=22 Identities=27% Similarity=0.475 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCCcccccCCCCC
Q psy2636 30 DTSRPTPPSPSQLCAVCGDIAA 51 (335)
Q Consensus 30 ~~~~~~~~~~~~~C~VCgd~a~ 51 (335)
..|.....-+.+.|+|||+.|.
T Consensus 120 ~iSR~~lg~~~R~CliC~~~Ak 141 (165)
T TIGR03124 120 SLSRTDLGLPPRKCLLCEEDAK 141 (165)
T ss_pred CcCHHHcCCCCCeeecCCchHH
Confidence 3444455567789999999984
No 120
>KOG3715|consensus
Probab=47.03 E-value=16 Score=31.66 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=19.3
Q ss_pred cccCCCCCccccCCccccccccce
Q psy2636 44 AVCGDIAACQHYGVRTCEGCKGFF 67 (335)
Q Consensus 44 ~VCgd~a~g~HyGv~sC~gCk~FF 67 (335)
.-|.|.+.|+|| -..|+||..+|
T Consensus 67 ~~~E~~s~~p~~-e~~C~aCss~~ 89 (344)
T KOG3715|consen 67 LGEEDLSPGPPT-ESYCEACSSQF 89 (344)
T ss_pred ccccccCCCCCc-ccHHHHHHhhc
Confidence 457788999999 78999998776
No 121
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=46.48 E-value=9.9 Score=25.66 Aligned_cols=14 Identities=36% Similarity=0.845 Sum_probs=5.5
Q ss_pred CCCCCcccccCCCC
Q psy2636 37 PSPSQLCAVCGDIA 50 (335)
Q Consensus 37 ~~~~~~C~VCgd~a 50 (335)
.-..++|.||||.-
T Consensus 6 ~~~~qiCqiCGD~V 19 (80)
T PF14569_consen 6 NLNGQICQICGDDV 19 (80)
T ss_dssp --SS-B-SSS--B-
T ss_pred hcCCcccccccCcc
Confidence 34457899999864
No 122
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.32 E-value=10 Score=22.86 Aligned_cols=14 Identities=29% Similarity=0.736 Sum_probs=10.5
Q ss_pred CCCCCcccccCCCC
Q psy2636 37 PSPSQLCAVCGDIA 50 (335)
Q Consensus 37 ~~~~~~C~VCgd~a 50 (335)
.-+.++|.|||.+=
T Consensus 9 ~lp~KICpvCqRPF 22 (54)
T COG4338 9 TLPDKICPVCQRPF 22 (54)
T ss_pred ccchhhhhhhcCch
Confidence 35678899999763
No 123
>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=45.86 E-value=9.9 Score=30.41 Aligned_cols=23 Identities=30% Similarity=0.520 Sum_probs=16.1
Q ss_pred CCCCCCCCCCCCCcccccCCCCC
Q psy2636 29 CDTSRPTPPSPSQLCAVCGDIAA 51 (335)
Q Consensus 29 ~~~~~~~~~~~~~~C~VCgd~a~ 51 (335)
...|....-.+.+.|+|||+.|.
T Consensus 121 ~~iSR~~lg~~~R~CliC~~~Ak 143 (170)
T PF03802_consen 121 KQISREDLGLPPRRCLICGRPAK 143 (170)
T ss_pred CccCHHHcCCCCCcccCCChhHH
Confidence 33444444567789999999874
No 124
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=44.17 E-value=12 Score=25.95 Aligned_cols=28 Identities=25% Similarity=0.704 Sum_probs=20.6
Q ss_pred CCcccccCCCCCc-cccCCccccccccce
Q psy2636 40 SQLCAVCGDIAAC-QHYGVRTCEGCKGFF 67 (335)
Q Consensus 40 ~~~C~VCgd~a~g-~HyGv~sC~gCk~FF 67 (335)
...|..||.++-- .--|+..|+.|..-|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3469999988533 558899999997544
No 125
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=43.28 E-value=14 Score=21.32 Aligned_cols=22 Identities=23% Similarity=0.647 Sum_probs=13.1
Q ss_pred ccccCCCCCccccCCccccccccce
Q psy2636 43 CAVCGDIAACQHYGVRTCEGCKGFF 67 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~sC~gCk~FF 67 (335)
|.+|+.+..-. ...|+.|+.-|
T Consensus 1 C~~C~~~~~l~---~f~C~~C~~~F 22 (39)
T smart00154 1 CHFCRKKVGLT---GFKCRHCGNLF 22 (39)
T ss_pred CcccCCccccc---CeECCccCCcc
Confidence 56666655433 45677777655
No 126
>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 PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=43.11 E-value=5 Score=26.35 Aligned_cols=24 Identities=46% Similarity=0.982 Sum_probs=14.4
Q ss_pred cccccCCCCC------ccccCCc--ccccccc
Q psy2636 42 LCAVCGDIAA------CQHYGVR--TCEGCKG 65 (335)
Q Consensus 42 ~C~VCgd~a~------g~HyGv~--sC~gCk~ 65 (335)
.|.+||-++. .||-|+. .|.||+.
T Consensus 6 TC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~ 37 (66)
T PF05180_consen 6 TCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKN 37 (66)
T ss_dssp EETTTTEEEEEEEEHHHHHTSEEEEE-TTS--
T ss_pred EcCCCCCccceeeCHHHHhCCeEEEECCCCcc
Confidence 3888886653 2777764 4888875
No 128
>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=42.98 E-value=11 Score=27.20 Aligned_cols=26 Identities=27% Similarity=0.590 Sum_probs=17.0
Q ss_pred cccccCCCCCccccCCccccccccce
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFF 67 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FF 67 (335)
.|.|||+..-...=+.+.|..|..=|
T Consensus 37 aCeiC~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 37 ACEICGPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred eccccCCCceEEECCEEEEecCCCEE
Confidence 48888665544456677788887543
No 129
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.69 E-value=10 Score=28.76 Aligned_cols=39 Identities=15% Similarity=0.194 Sum_probs=26.0
Q ss_pred CccccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhH
Q psy2636 51 ACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQ 101 (335)
Q Consensus 51 ~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~ 101 (335)
.+.+.+-..|.-|+.|. +.. ...+.+ ...|.+|+.|+..
T Consensus 24 ~~~~~~~~~cP~C~s~~-~~k--~g~~~~---------~~qRyrC~~C~~t 62 (129)
T COG3677 24 IRMQITKVNCPRCKSSN-VVK--IGGIRR---------GHQRYKCKSCGST 62 (129)
T ss_pred HhhhcccCcCCCCCccc-eee--ECCccc---------cccccccCCcCcc
Confidence 46777888999999987 222 112221 1578899999855
No 130
>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=40.60 E-value=11 Score=21.06 Aligned_cols=11 Identities=27% Similarity=0.887 Sum_probs=7.1
Q ss_pred CcccccCCCCC
Q psy2636 41 QLCAVCGDIAA 51 (335)
Q Consensus 41 ~~C~VCgd~a~ 51 (335)
..|.|||.+++
T Consensus 19 ~~CP~Cg~~~~ 29 (34)
T cd00729 19 EKCPICGAPKE 29 (34)
T ss_pred CcCcCCCCchH
Confidence 45777776554
No 131
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=40.48 E-value=10 Score=33.28 Aligned_cols=12 Identities=42% Similarity=1.165 Sum_probs=5.8
Q ss_pred cCCccccccccc
Q psy2636 55 YGVRTCEGCKGF 66 (335)
Q Consensus 55 yGv~sC~gCk~F 66 (335)
|.|.+|+.|++.
T Consensus 236 ~rve~C~~C~~Y 247 (290)
T PF04216_consen 236 YRVEVCESCGSY 247 (290)
T ss_dssp EEEEEETTTTEE
T ss_pred EEEEECCcccch
Confidence 344455555543
No 132
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=40.28 E-value=19 Score=20.61 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=6.4
Q ss_pred CcccccCCC
Q psy2636 41 QLCAVCGDI 49 (335)
Q Consensus 41 ~~C~VCgd~ 49 (335)
.+|.+||.+
T Consensus 4 ~pCP~CGG~ 12 (37)
T smart00778 4 GPCPNCGGS 12 (37)
T ss_pred cCCCCCCCc
Confidence 468888854
No 133
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=39.07 E-value=22 Score=36.72 Aligned_cols=25 Identities=28% Similarity=0.829 Sum_probs=18.3
Q ss_pred CCCCcccccCCC----CCccccCCccccccc
Q psy2636 38 SPSQLCAVCGDI----AACQHYGVRTCEGCK 64 (335)
Q Consensus 38 ~~~~~C~VCgd~----a~g~HyGv~sC~gCk 64 (335)
-..+.|.||||. ++|-=| .+|+.|.
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~F--VAC~eC~ 43 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPF--VACDVCA 43 (1079)
T ss_pred cCCceeeecccccCcCCCCCEE--EEeccCC
Confidence 345689999987 577656 6787774
No 134
>PRK01392 citX 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase; Reviewed
Probab=38.53 E-value=11 Score=30.44 Aligned_cols=21 Identities=33% Similarity=0.577 Sum_probs=14.8
Q ss_pred CCCCCCCCCCCcccccCCCCC
Q psy2636 31 TSRPTPPSPSQLCAVCGDIAA 51 (335)
Q Consensus 31 ~~~~~~~~~~~~C~VCgd~a~ 51 (335)
.|.....-+.+.|+|||+.|.
T Consensus 130 iSR~~lg~p~R~CliC~~~Ak 150 (180)
T PRK01392 130 LSRTDLGLPPRRCLLCGQDAK 150 (180)
T ss_pred cCHHHcCCCCCeeecCCchHH
Confidence 344444457788999999984
No 135
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=38.32 E-value=25 Score=23.03 Aligned_cols=29 Identities=31% Similarity=0.454 Sum_probs=19.8
Q ss_pred CCCcccccCCCCCc-cccCCccccccccce
Q psy2636 39 PSQLCAVCGDIAAC-QHYGVRTCEGCKGFF 67 (335)
Q Consensus 39 ~~~~C~VCgd~a~g-~HyGv~sC~gCk~FF 67 (335)
+.+.|.+||..... ....+..|..|..-+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEE
Confidence 55679999987655 566666777775433
No 136
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=38.19 E-value=76 Score=22.26 Aligned_cols=23 Identities=35% Similarity=0.608 Sum_probs=18.4
Q ss_pred HHhhcCCCCCCCCHHHHHHHHHH
Q psy2636 241 HFADKIPGFSDLCKEDQELLFQS 263 (335)
Q Consensus 241 efAk~~P~F~~L~~~DQ~~LLk~ 263 (335)
.-+..+|+|.+|+..-|--|+-+
T Consensus 29 ~Lt~~vPgF~~ls~sKqRRLi~~ 51 (92)
T PF10330_consen 29 YLTTSVPGFSDLSPSKQRRLIMA 51 (92)
T ss_pred HHhccCCCcccCCHHHHHHHHHH
Confidence 44566999999999999887654
No 137
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=38.00 E-value=11 Score=21.92 Aligned_cols=25 Identities=24% Similarity=0.723 Sum_probs=15.7
Q ss_pred ccccCCCCCc---cccCCccccccccce
Q psy2636 43 CAVCGDIAAC---QHYGVRTCEGCKGFF 67 (335)
Q Consensus 43 C~VCgd~a~g---~HyGv~sC~gCk~FF 67 (335)
|..|+..-.. ..+-+..|.+|.|.|
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCeEE
Confidence 7777764322 234466788888865
No 138
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=37.94 E-value=18 Score=22.43 Aligned_cols=32 Identities=22% Similarity=0.561 Sum_probs=22.0
Q ss_pred CCcccccCCCCCc-c---ccCC-ccccccccceeccc
Q psy2636 40 SQLCAVCGDIAAC-Q---HYGV-RTCEGCKGFFKRTV 71 (335)
Q Consensus 40 ~~~C~VCgd~a~g-~---HyGv-~sC~gCk~FFRR~v 71 (335)
...|..||...+- . =.|. .-|++|-.+|++.-
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 3569999976554 2 2443 77999999887643
No 139
>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=37.87 E-value=13 Score=26.13 Aligned_cols=33 Identities=27% Similarity=0.484 Sum_probs=14.9
Q ss_pred CCcccccCCCCCccccCC------ccccccccceecccc
Q psy2636 40 SQLCAVCGDIAACQHYGV------RTCEGCKGFFKRTVQ 72 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyGv------~sC~gCk~FFRR~v~ 72 (335)
..-|.+||..=.+||=-+ .+|.-|+.=|++.|+
T Consensus 14 e~~CalCG~tWg~~y~Ev~G~rLfFCCd~ca~EF~nmi~ 52 (105)
T PF11494_consen 14 EMGCALCGATWGDYYEEVDGERLFFCCDDCAKEFKNMIN 52 (105)
T ss_dssp GGS-SS---S---SS-B-TT--BSSS--SSSS-TTS-TH
T ss_pred cccccccCCcHHHHHHhhcCCEEEEEcHHHHHHHHHHHH
Confidence 345999999988888654 468888888888775
No 140
>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=36.80 E-value=11 Score=26.38 Aligned_cols=25 Identities=24% Similarity=0.670 Sum_probs=20.4
Q ss_pred CcccccCCCCCc-cccCCcccccccc
Q psy2636 41 QLCAVCGDIAAC-QHYGVRTCEGCKG 65 (335)
Q Consensus 41 ~~C~VCgd~a~g-~HyGv~sC~gCk~ 65 (335)
-.|..||..+-. .--|+..|..|.-
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~ 61 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCGK 61 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTTE
T ss_pred CcCCCCCCceeEEeeeEEeecCCCCC
Confidence 469999988855 5589999999973
No 141
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=36.67 E-value=16 Score=21.37 Aligned_cols=22 Identities=27% Similarity=0.835 Sum_probs=10.6
Q ss_pred CcccccCCCCCccc-c------CCcccccc
Q psy2636 41 QLCAVCGDIAACQH-Y------GVRTCEGC 63 (335)
Q Consensus 41 ~~C~VCgd~a~g~H-y------Gv~sC~gC 63 (335)
.+|.+||.+. .++ | |..-|+.|
T Consensus 4 ~pCP~CGG~D-rFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGKD-RFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-TT-TEEEETT----S-EEETTT
T ss_pred CCCCCCcCcc-ccccCcCcccCCCEECCCC
Confidence 3688998643 222 3 55667776
No 142
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=35.81 E-value=20 Score=28.32 Aligned_cols=28 Identities=25% Similarity=0.738 Sum_probs=21.9
Q ss_pred ccccCCCCCccccCCcc-ccccccceecc
Q psy2636 43 CAVCGDIAACQHYGVRT-CEGCKGFFKRT 70 (335)
Q Consensus 43 C~VCgd~a~g~HyGv~s-C~gCk~FFRR~ 70 (335)
|-+|+....+..=|.+. |-||..-|-+.
T Consensus 2 C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~ 30 (175)
T PF15446_consen 2 CDTCGYEGDDRNKGPLVYCQGCSSSYHKA 30 (175)
T ss_pred cccccCCCCCccCCCeEEcCccChHHHhh
Confidence 88998777777777765 99998776665
No 143
>KOG0402|consensus
Probab=35.73 E-value=12 Score=25.53 Aligned_cols=23 Identities=30% Similarity=0.861 Sum_probs=18.3
Q ss_pred cccccCCCCCc-cccCCccccccc
Q psy2636 42 LCAVCGDIAAC-QHYGVRTCEGCK 64 (335)
Q Consensus 42 ~C~VCgd~a~g-~HyGv~sC~gCk 64 (335)
.|.-||...-. ---|...|.+|+
T Consensus 38 ~CsfCGK~~vKR~AvGiW~C~~C~ 61 (92)
T KOG0402|consen 38 TCSFCGKKTVKRKAVGIWKCGSCK 61 (92)
T ss_pred hhhhcchhhhhhhceeEEecCCcc
Confidence 59999987744 457899999996
No 144
>PF06147 DUF968: Protein of unknown function (DUF968); InterPro: IPR010373 This is a family of uncharacterised prophage proteins that are also found in bacteria and humans.
Probab=35.50 E-value=18 Score=29.75 Aligned_cols=16 Identities=31% Similarity=0.781 Sum_probs=12.0
Q ss_pred CCcccccCCCC-Ccccc
Q psy2636 40 SQLCAVCGDIA-ACQHY 55 (335)
Q Consensus 40 ~~~C~VCgd~a-~g~Hy 55 (335)
.++|.|||.++ .-.|+
T Consensus 127 ~~~C~iCGk~~~d~hH~ 143 (200)
T PF06147_consen 127 SRPCVICGKPPADIHHI 143 (200)
T ss_pred cCccccCCCCcccccee
Confidence 57899999864 45666
No 145
>KOG4327|consensus
Probab=35.15 E-value=43 Score=27.15 Aligned_cols=26 Identities=31% Similarity=0.512 Sum_probs=16.1
Q ss_pred CCCCCCCCCCCCCCCCCCcccccCCC
Q psy2636 24 SSSPGCDTSRPTPPSPSQLCAVCGDI 49 (335)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~C~VCgd~ 49 (335)
++.|+-++..|+|..+..+|.+=.|.
T Consensus 161 ~s~p~~sfmpppPP~pp~i~p~~~de 186 (218)
T KOG4327|consen 161 KSAPWNSFMPPPPPMPPPICPDSLDE 186 (218)
T ss_pred ccCCccccCCCCCCCCcccCCCCchH
Confidence 55666666666666666666665555
No 146
>PLN02189 cellulose synthase
Probab=33.15 E-value=25 Score=36.30 Aligned_cols=24 Identities=29% Similarity=0.852 Sum_probs=18.6
Q ss_pred CCCcccccCCC----CCccccCCccccccc
Q psy2636 39 PSQLCAVCGDI----AACQHYGVRTCEGCK 64 (335)
Q Consensus 39 ~~~~C~VCgd~----a~g~HyGv~sC~gCk 64 (335)
..+.|.||||. +.|--| .+|..|.
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~f--vaC~~C~ 60 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLF--VACNECG 60 (1040)
T ss_pred cCccccccccccCcCCCCCEE--EeeccCC
Confidence 45689999998 788766 6787774
No 147
>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=32.51 E-value=69 Score=27.42 Aligned_cols=43 Identities=26% Similarity=0.345 Sum_probs=32.3
Q ss_pred HHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 163 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 163 ~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
....++.........+-.|++.+|.|.+|..+|+..|++.+..
T Consensus 29 ~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~ 71 (248)
T cd07075 29 LLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWM 71 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHH
Confidence 3444555544444556778999999999999999999988753
No 148
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=32.24 E-value=24 Score=22.39 Aligned_cols=14 Identities=36% Similarity=0.838 Sum_probs=11.3
Q ss_pred CcccccCCCCCccc
Q psy2636 41 QLCAVCGDIAACQH 54 (335)
Q Consensus 41 ~~C~VCgd~a~g~H 54 (335)
+.|.|||..+--.|
T Consensus 18 e~Cp~CG~~t~~~~ 31 (59)
T COG2260 18 EKCPVCGGDTKVPH 31 (59)
T ss_pred ccCCCCCCccccCC
Confidence 68999998876665
No 149
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=31.61 E-value=23 Score=24.85 Aligned_cols=26 Identities=38% Similarity=0.897 Sum_probs=19.6
Q ss_pred CCcccccCCCCCc-cccCCcccccccc
Q psy2636 40 SQLCAVCGDIAAC-QHYGVRTCEGCKG 65 (335)
Q Consensus 40 ~~~C~VCgd~a~g-~HyGv~sC~gCk~ 65 (335)
...|..||..+-. .--|+..|..|.-
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQAVGIWRCKGCKK 62 (90)
T ss_pred CccCCCCCCCceeeeeeEEEEcCCCCC
Confidence 3469999977654 4469999999963
No 150
>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=31.51 E-value=59 Score=27.65 Aligned_cols=46 Identities=30% Similarity=0.549 Sum_probs=35.2
Q ss_pred hhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636 161 PEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206 (335)
Q Consensus 161 ~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~ 206 (335)
.+...++....+.....+-.|.+.+|.|.+|..+|+..+++.+..+
T Consensus 51 ~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~E 96 (243)
T cd06935 51 LEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCME 96 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHH
Confidence 3445556666655556677889999999999999999999887643
No 151
>PF02155 GCR: Glucocorticoid receptor; InterPro: IPR001409 Steroid or nuclear hormone receptors (NRs) constitute an important super- family of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity. NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed "orphan" receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members. The glucocorticoid receptor consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domain that mediates specific binding to target DNA sequences (ligand-responsive elements); and a hormone binding domain. The N-terminal domain is unique to the glucocorticoid receptors; it spans the first 440 residues, and is primarily responsible for transcriptional activation. The smaller (around 65 residues), highly-conserved central portion of the protein is the DNA binding domain, which plays a role in DNA binding specificity, homo- dimerisation and in interactions with other proteins. The hormone binding domain comprises approximately 250 residues at the C terminus of the receptor. This domain mediates receptor activity via interaction with heat shock proteins and cyclophilins, or with hormone.; GO: 0003677 DNA binding, 0004883 glucocorticoid receptor activity, 0005496 steroid binding, 0006355 regulation of transcription, DNA-dependent, 0042921 glucocorticoid receptor signaling pathway, 0043402 glucocorticoid mediated signaling pathway, 0005634 nucleus
Probab=31.08 E-value=43 Score=30.11 Aligned_cols=20 Identities=25% Similarity=0.536 Sum_probs=13.1
Q ss_pred cccccCCCCCccccCCcccc
Q psy2636 42 LCAVCGDIAACQHYGVRTCE 61 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~ 61 (335)
+|-|+---..+|||||..=-
T Consensus 289 v~GVstSgGq~Yhy~~n~ss 308 (370)
T PF02155_consen 289 VCGVSTSGGQSYHYGANPSS 308 (370)
T ss_pred ccccccCCCcccccCCCccc
Confidence 35555444556999998753
No 152
>KOG3490|consensus
Probab=30.79 E-value=23 Score=25.45 Aligned_cols=43 Identities=16% Similarity=0.464 Sum_probs=33.1
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCC
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLAD 82 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~ 82 (335)
..+.|++|+-.-+---|.-.-|+.|- +|+=--.....|.|...
T Consensus 7 ~lRACllCs~Vkt~~~F~~dGC~Nc~-~l~mkgn~e~V~ecTS~ 49 (111)
T KOG3490|consen 7 KLRACLLCSIVKTLNGFRKDGCENCP-MLNMKGNVENVYECTSP 49 (111)
T ss_pred hhhhhhhhhhhhhhhhhhhcCCCCch-hhhhccCcceeEEecCC
Confidence 44679999988877778888999999 77655455678888643
No 153
>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=30.49 E-value=61 Score=27.57 Aligned_cols=45 Identities=38% Similarity=0.665 Sum_probs=34.6
Q ss_pred hHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636 162 EKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206 (335)
Q Consensus 162 ~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~ 206 (335)
+...++....+.....+-.|++.+|.|.+|..+|+..|++.+..+
T Consensus 48 ~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~E 92 (241)
T cd06939 48 EMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLE 92 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHH
Confidence 344455555566666777899999999999999999999877543
No 154
>PRK06424 transcription factor; Provisional
Probab=30.34 E-value=15 Score=28.42 Aligned_cols=25 Identities=28% Similarity=0.809 Sum_probs=16.8
Q ss_pred cccccCCCCCcccc----CC--ccccccccc
Q psy2636 42 LCAVCGDIAACQHY----GV--RTCEGCKGF 66 (335)
Q Consensus 42 ~C~VCgd~a~g~Hy----Gv--~sC~gCk~F 66 (335)
.|-+||....+.|. |+ ..|..|+-|
T Consensus 2 ~CE~CG~~~~~~~~v~ieg~~l~vC~~Ca~~ 32 (144)
T PRK06424 2 ECEMCGKKVPQTTKVMIDGAILNVCDDCAKF 32 (144)
T ss_pred cccccCcccCCceEEEEcCeeeehhHHHHHc
Confidence 39999999888742 11 347777654
No 155
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=30.25 E-value=25 Score=31.10 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=10.3
Q ss_pred CccccCCccccccc
Q psy2636 51 ACQHYGVRTCEGCK 64 (335)
Q Consensus 51 ~g~HyGv~sC~gCk 64 (335)
+..||.=..|-.|-
T Consensus 220 teW~~~R~~C~~Cg 233 (309)
T PRK03564 220 SEWHVVRVKCSNCE 233 (309)
T ss_pred CcccccCccCCCCC
Confidence 44677778888885
No 156
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=30.24 E-value=6.9 Score=23.84 Aligned_cols=16 Identities=38% Similarity=0.750 Sum_probs=10.8
Q ss_pred CCCCCCCcccccCCCC
Q psy2636 35 TPPSPSQLCAVCGDIA 50 (335)
Q Consensus 35 ~~~~~~~~C~VCgd~a 50 (335)
.|.+.-+.|.+||.=|
T Consensus 17 ~p~~~LRQCvlCGRWa 32 (57)
T PF14445_consen 17 HPISELRQCVLCGRWA 32 (57)
T ss_pred CcHHHHHHHhhhchhh
Confidence 3445567899998643
No 157
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=29.44 E-value=21 Score=25.03 Aligned_cols=30 Identities=20% Similarity=0.500 Sum_probs=23.6
Q ss_pred CCcccccCCCCCccccCCccccccccceec
Q psy2636 40 SQLCAVCGDIAACQHYGVRTCEGCKGFFKR 69 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR 69 (335)
.+.|++||-.-+---|.-.-|..|.+.|--
T Consensus 9 sRACl~Cgiv~t~n~F~~dGCpNc~~l~~~ 38 (112)
T COG5204 9 SRACLGCGIVKTLNGFRKDGCPNCPMLNMK 38 (112)
T ss_pred hhhhhhcceeeecccccccCCCCCcccccc
Confidence 467999998887777788888888877643
No 158
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=28.99 E-value=37 Score=21.60 Aligned_cols=26 Identities=19% Similarity=0.531 Sum_probs=16.5
Q ss_pred CCcccccCCCCCccccC---------Ccccccccc
Q psy2636 40 SQLCAVCGDIAACQHYG---------VRTCEGCKG 65 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyG---------v~sC~gCk~ 65 (335)
-++|..||...-..++. .+.|..|.+
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 35799998776554432 244777765
No 159
>KOG1701|consensus
Probab=28.50 E-value=21 Score=32.58 Aligned_cols=49 Identities=31% Similarity=0.502 Sum_probs=25.8
Q ss_pred CcccccCC-------CCCc--cccCCccccccccceecccccCCeeecCCCCCCcccccccccccchhhHH
Q psy2636 41 QLCAVCGD-------IAAC--QHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRRRNRCQFCRFQK 102 (335)
Q Consensus 41 ~~C~VCgd-------~a~g--~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~K 102 (335)
+.|-+||. +|.| ||=|..+|--|+- |..+..-.+|..++..|=-|-.+|
T Consensus 335 ekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r-------------~ldgipFtvd~~n~v~Cv~dfh~k 392 (468)
T KOG1701|consen 335 EKCNKCGEPIMDRILRALGKAYHPGCFTCVVCAR-------------CLDGIPFTVDSQNNVYCVPDFHKK 392 (468)
T ss_pred HHHhhhhhHHHHHHHHhcccccCCCceEEEEecc-------------ccCCccccccCCCceeeehhhhhh
Confidence 45666663 2444 6666666666642 333444455555555555554444
No 160
>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=28.45 E-value=99 Score=26.15 Aligned_cols=46 Identities=35% Similarity=0.447 Sum_probs=34.4
Q ss_pred ChhHHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 160 EPEKIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 160 ~~~~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
..+.+..++.........+-.|.+.+|.|..++.+|+..+.+.+..
T Consensus 30 ~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~ 75 (235)
T cd06949 30 EASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWL 75 (235)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHH
Confidence 3445555555555555566778999999999999999999887754
No 161
>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=28.13 E-value=72 Score=27.03 Aligned_cols=42 Identities=36% Similarity=0.607 Sum_probs=32.3
Q ss_pred HHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 164 IQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 164 ~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
..++..........+-.|++.+|.|.+|..+|+..+++.+..
T Consensus 39 ~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ 80 (238)
T cd06933 39 LPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAI 80 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHH
Confidence 344455555555566788999999999999999999987764
No 162
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.12 E-value=40 Score=25.05 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=22.8
Q ss_pred CcccccCCCCCccccCCccccccccceeccccc
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQK 73 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~ 73 (335)
-.|.-||....-..|+...|..|.++.-+.+.+
T Consensus 72 ~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 72 LECKDCSHVFKPNALDYGVCEKCHSKNVIITQG 104 (117)
T ss_pred EEhhhCCCccccCCccCCcCcCCCCCceEEecC
Confidence 359999966544334445799999987666654
No 163
>KOG1701|consensus
Probab=27.76 E-value=81 Score=29.03 Aligned_cols=34 Identities=29% Similarity=0.589 Sum_probs=27.3
Q ss_pred CcccccCCCCCc-----------cccCCccccccccceecccccCCeee
Q psy2636 41 QLCAVCGDIAAC-----------QHYGVRTCEGCKGFFKRTVQKGSKYV 78 (335)
Q Consensus 41 ~~C~VCgd~a~g-----------~HyGv~sC~gCk~FFRR~v~~~~~y~ 78 (335)
.+|.-||..-+| ||-...+|..| ||..+.+.-|.
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C----~r~L~Gq~FY~ 319 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTC----RRQLAGQSFYQ 319 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhh----hhhhccccccc
Confidence 489999987665 89999999999 67777666664
No 164
>KOG0703|consensus
Probab=27.15 E-value=28 Score=30.22 Aligned_cols=31 Identities=32% Similarity=0.711 Sum_probs=25.8
Q ss_pred CCcccccCCCC---CccccCCccccccccceecc
Q psy2636 40 SQLCAVCGDIA---ACQHYGVRTCEGCKGFFKRT 70 (335)
Q Consensus 40 ~~~C~VCgd~a---~g~HyGv~sC~gCk~FFRR~ 70 (335)
+..|.=||.+. ..+.+||.-|--|.|-.|--
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 67899999874 34799999999999988753
No 165
>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=27.10 E-value=66 Score=26.18 Aligned_cols=40 Identities=43% Similarity=0.677 Sum_probs=29.9
Q ss_pred HHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 166 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 166 ~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
++++........+-.|++.+|.|.++..+|+..+.+....
T Consensus 6 ~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~ 45 (195)
T cd06941 6 QLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFF 45 (195)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHH
Confidence 3344444444556778999999999999999999887753
No 166
>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=27.02 E-value=1.2e+02 Score=25.89 Aligned_cols=43 Identities=23% Similarity=0.362 Sum_probs=32.6
Q ss_pred HHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 163 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 163 ~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
.+..++.........+-.|++.+|.|.+|..+|+..+++....
T Consensus 29 ~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ 71 (246)
T cd06947 29 LLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWM 71 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHH
Confidence 4445555555445556778999999999999999999987754
No 167
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=26.72 E-value=29 Score=24.39 Aligned_cols=26 Identities=27% Similarity=0.714 Sum_probs=19.7
Q ss_pred CCcccccCCCCCc-cccCCcccccccc
Q psy2636 40 SQLCAVCGDIAAC-QHYGVRTCEGCKG 65 (335)
Q Consensus 40 ~~~C~VCgd~a~g-~HyGv~sC~gCk~ 65 (335)
...|..||..+-. .--|+..|..|.-
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~~C~~ 61 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCRKCGA 61 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcCCCCC
Confidence 3469999976644 5688999999964
No 168
>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=26.71 E-value=24 Score=20.00 Aligned_cols=9 Identities=56% Similarity=1.265 Sum_probs=5.5
Q ss_pred ccccccchh
Q psy2636 91 RRNRCQFCR 99 (335)
Q Consensus 91 ~r~~Cr~CR 99 (335)
.|.+|+.||
T Consensus 28 qryrC~~C~ 36 (36)
T PF03811_consen 28 QRYRCKDCR 36 (36)
T ss_pred EeEecCcCC
Confidence 455666665
No 169
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=26.45 E-value=34 Score=26.09 Aligned_cols=29 Identities=24% Similarity=0.489 Sum_probs=20.2
Q ss_pred CcccccCCCCCcccc--CC--ccccccccceeccc
Q psy2636 41 QLCAVCGDIAACQHY--GV--RTCEGCKGFFKRTV 71 (335)
Q Consensus 41 ~~C~VCgd~a~g~Hy--Gv--~sC~gCk~FFRR~v 71 (335)
-+|..||.+.+-+.= .+ ..|+||.+ +|.|
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa--~~~v 130 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGA--KAPL 130 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCC--CCcc
Confidence 579999988877543 22 47888876 4554
No 170
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=26.38 E-value=30 Score=30.99 Aligned_cols=32 Identities=22% Similarity=0.583 Sum_probs=26.1
Q ss_pred CCCcccccCCCC---CccccCCccccccccceecc
Q psy2636 39 PSQLCAVCGDIA---ACQHYGVRTCEGCKGFFKRT 70 (335)
Q Consensus 39 ~~~~C~VCgd~a---~g~HyGv~sC~gCk~FFRR~ 70 (335)
.+..|.=||.+. ...-||+..|-.|.|..|..
T Consensus 21 gNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsL 55 (395)
T PLN03114 21 DNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 55 (395)
T ss_pred CCCcCccCCCCCCCceeeccceeehhhhhHhhccC
Confidence 467899999775 34789999999999987763
No 171
>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=26.26 E-value=81 Score=24.88 Aligned_cols=40 Identities=33% Similarity=0.679 Sum_probs=29.4
Q ss_pred HHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 166 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 166 ~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
.+..........+-.|...+|.|..|..+|+..+++....
T Consensus 6 ~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~ 45 (174)
T cd06929 6 HFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCF 45 (174)
T ss_pred HHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHH
Confidence 3344444444456678899999999999999999887643
No 172
>KOG0706|consensus
Probab=26.09 E-value=26 Score=32.23 Aligned_cols=31 Identities=29% Similarity=0.699 Sum_probs=26.2
Q ss_pred CCCCcccccCCCC---CccccCCcccccccccee
Q psy2636 38 SPSQLCAVCGDIA---ACQHYGVRTCEGCKGFFK 68 (335)
Q Consensus 38 ~~~~~C~VCgd~a---~g~HyGv~sC~gCk~FFR 68 (335)
+.++.|.=||.+. +..-||+.-|--|.+-.|
T Consensus 21 ~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHR 54 (454)
T KOG0706|consen 21 SENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHR 54 (454)
T ss_pred CCCceecccCCCCCCceeecceEEEEEecchhhh
Confidence 5678899999987 568899999999997654
No 173
>PLN02400 cellulose synthase
Probab=25.61 E-value=38 Score=35.16 Aligned_cols=25 Identities=28% Similarity=0.803 Sum_probs=18.1
Q ss_pred CCCCcccccCCC----CCccccCCccccccc
Q psy2636 38 SPSQLCAVCGDI----AACQHYGVRTCEGCK 64 (335)
Q Consensus 38 ~~~~~C~VCgd~----a~g~HyGv~sC~gCk 64 (335)
-..+.|.||||. ++|-=| .+|+.|+
T Consensus 34 ~~gqiCqICGD~VG~t~dGe~F--VAC~eCa 62 (1085)
T PLN02400 34 LNGQICQICGDDVGVTETGDVF--VACNECA 62 (1085)
T ss_pred cCCceeeecccccCcCCCCCEE--EEEccCC
Confidence 345689999987 566555 6787775
No 174
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.59 E-value=39 Score=30.08 Aligned_cols=28 Identities=25% Similarity=0.515 Sum_probs=20.0
Q ss_pred CCCCcccccCCCCCccccCCccccccccceec
Q psy2636 38 SPSQLCAVCGDIAACQHYGVRTCEGCKGFFKR 69 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR 69 (335)
.....|.+||. .+-+...|..|...+-|
T Consensus 307 ~tS~~C~~cg~----~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 307 YTSKTCPCCGH----LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred CCcccccccCC----ccceeEECCCCCCeehh
Confidence 34456999998 66677778888766555
No 175
>KOG1044|consensus
Probab=25.49 E-value=38 Score=32.32 Aligned_cols=33 Identities=24% Similarity=0.604 Sum_probs=26.6
Q ss_pred CCCCcccccCCCCCc---------cccCCccccccc------cceecc
Q psy2636 38 SPSQLCAVCGDIAAC---------QHYGVRTCEGCK------GFFKRT 70 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g---------~HyGv~sC~gCk------~FFRR~ 70 (335)
+....|.+|+++-+| +|.....|..|+ |||-+-
T Consensus 14 ~~~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~ 61 (670)
T KOG1044|consen 14 KQGIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKP 61 (670)
T ss_pred ccceehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecc
Confidence 445679999999887 888999999997 888553
No 176
>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=25.43 E-value=32 Score=24.08 Aligned_cols=26 Identities=27% Similarity=0.669 Sum_probs=17.0
Q ss_pred cccccCCCCC-cccc-----C---Cccccccccce
Q psy2636 42 LCAVCGDIAA-CQHY-----G---VRTCEGCKGFF 67 (335)
Q Consensus 42 ~C~VCgd~a~-g~Hy-----G---v~sC~gCk~FF 67 (335)
.|.=||.+.. +.++ | ..+|.||++-+
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~ 36 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVY 36 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHH
Confidence 4888887763 3322 3 67888887655
No 177
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=25.25 E-value=34 Score=23.70 Aligned_cols=17 Identities=29% Similarity=0.561 Sum_probs=12.9
Q ss_pred cccccCCCC-CccccCCc
Q psy2636 42 LCAVCGDIA-ACQHYGVR 58 (335)
Q Consensus 42 ~C~VCgd~a-~g~HyGv~ 58 (335)
.|..||.+. +.++||..
T Consensus 3 ~CP~CG~R~~~EF~y~G~ 20 (84)
T TIGR01374 3 PCPYCGPRPEEEFTYGGD 20 (84)
T ss_pred cCCCCCCccHhhEeccce
Confidence 599999765 66999843
No 178
>KOG2879|consensus
Probab=25.18 E-value=51 Score=28.33 Aligned_cols=23 Identities=30% Similarity=0.540 Sum_probs=15.3
Q ss_pred cccccCCCCCccccCC----ccccccc
Q psy2636 42 LCAVCGDIAACQHYGV----RTCEGCK 64 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv----~sC~gCk 64 (335)
.|.|||...+-.|-+. +.|-=|.
T Consensus 241 ~C~~Cg~~PtiP~~~~~C~HiyCY~Ci 267 (298)
T KOG2879|consen 241 ECPVCGEPPTIPHVIGKCGHIYCYYCI 267 (298)
T ss_pred eeeccCCCCCCCeeeccccceeehhhh
Confidence 4999998887766443 4455553
No 179
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=25.11 E-value=32 Score=22.93 Aligned_cols=26 Identities=23% Similarity=0.690 Sum_probs=15.3
Q ss_pred CcccccCCCCCccccCCcccc--ccccceecc
Q psy2636 41 QLCAVCGDIAACQHYGVRTCE--GCKGFFKRT 70 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~--gCk~FFRR~ 70 (335)
..|.-|. |...+.+.|. .|-.||+|.
T Consensus 46 ~iC~~C~----~~~~~~~~C~s~DCpV~Y~R~ 73 (73)
T PF14260_consen 46 TICQSCS----GSLHEEIECDSLDCPVFYERV 73 (73)
T ss_pred HHHHHhc----CcCCCCCcccCCCCCcceeeC
Confidence 4566666 4444555554 477777763
No 180
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=24.95 E-value=53 Score=21.30 Aligned_cols=25 Identities=16% Similarity=0.465 Sum_probs=15.4
Q ss_pred CCcccccCCCC---CccccCCccccccc
Q psy2636 40 SQLCAVCGDIA---ACQHYGVRTCEGCK 64 (335)
Q Consensus 40 ~~~C~VCgd~a---~g~HyGv~sC~gCk 64 (335)
...|.+||... ...-|.-.+.+-||
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk 33 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQ 33 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHH
Confidence 34699999875 23455555555554
No 181
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=24.64 E-value=34 Score=24.06 Aligned_cols=26 Identities=27% Similarity=0.709 Sum_probs=19.6
Q ss_pred CCcccccCCCCCc-cccCCcccccccc
Q psy2636 40 SQLCAVCGDIAAC-QHYGVRTCEGCKG 65 (335)
Q Consensus 40 ~~~C~VCgd~a~g-~HyGv~sC~gCk~ 65 (335)
...|..||..+-. .--|+..|..|.-
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCGA 62 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCCC
Confidence 3469999877644 5688999999963
No 182
>KOG3506|consensus
Probab=24.60 E-value=29 Score=21.69 Aligned_cols=26 Identities=31% Similarity=0.838 Sum_probs=19.1
Q ss_pred CCCCcccccCCCCCc-cccCCcccccc
Q psy2636 38 SPSQLCAVCGDIAAC-QHYGVRTCEGC 63 (335)
Q Consensus 38 ~~~~~C~VCgd~a~g-~HyGv~sC~gC 63 (335)
.-...|.||+..-.- --||-..|+-|
T Consensus 16 ~GsrsC~vCsn~~gLIrKYGL~vcr~c 42 (56)
T KOG3506|consen 16 QGSRSCRVCSNRHGLIRKYGLNVCRQC 42 (56)
T ss_pred CCCcceeeeccchhHHHHhhhHHhHHH
Confidence 344669999976543 56999999877
No 183
>KOG3002|consensus
Probab=24.35 E-value=73 Score=28.10 Aligned_cols=26 Identities=23% Similarity=0.450 Sum_probs=17.6
Q ss_pred CCcccccCCCCCc----cccCCcccccccc
Q psy2636 40 SQLCAVCGDIAAC----QHYGVRTCEGCKG 65 (335)
Q Consensus 40 ~~~C~VCgd~a~g----~HyGv~sC~gCk~ 65 (335)
..-|.||.+.=+- .+=|=++|..|+.
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~ 77 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRT 77 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhh
Confidence 3459999976433 5567788888843
No 184
>PF01586 Basic: Myogenic Basic domain; InterPro: IPR002546 This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding []. With 12 residues of the basic domain involved in DNA binding []. The basic domain forms an extended alpha helix in the structure.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007517 muscle organ development, 0005634 nucleus; PDB: 1MDY_C.
Probab=23.96 E-value=27 Score=24.28 Aligned_cols=15 Identities=33% Similarity=0.807 Sum_probs=1.3
Q ss_pred ccCCccccccccceeccc
Q psy2636 54 HYGVRTCEGCKGFFKRTV 71 (335)
Q Consensus 54 HyGv~sC~gCk~FFRR~v 71 (335)
|-=.++|.+|| |.|+
T Consensus 69 ~CL~WACKaCK---RKt~ 83 (86)
T PF01586_consen 69 QCLLWACKACK---RKTV 83 (86)
T ss_dssp ----------S------T
T ss_pred cchHHHhHhhh---ccCc
Confidence 33467899988 6654
No 185
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.86 E-value=33 Score=21.22 Aligned_cols=9 Identities=44% Similarity=1.132 Sum_probs=7.0
Q ss_pred cccccCCCC
Q psy2636 42 LCAVCGDIA 50 (335)
Q Consensus 42 ~C~VCgd~a 50 (335)
.|.|||++.
T Consensus 1 ~C~iCg~ki 9 (51)
T PF14471_consen 1 KCAICGKKI 9 (51)
T ss_pred CCCcccccc
Confidence 488888876
No 186
>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=23.46 E-value=1e+02 Score=26.59 Aligned_cols=43 Identities=23% Similarity=0.339 Sum_probs=31.8
Q ss_pred HHHHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 163 KIQQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 163 ~~~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
...++....+.....+-.|++.+|.|.+|..+|+..|++.+..
T Consensus 64 ~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~ 106 (259)
T cd06932 64 LFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVH 106 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhH
Confidence 3334444444445567779999999999999999999987754
No 187
>KOG3116|consensus
Probab=23.29 E-value=40 Score=25.91 Aligned_cols=12 Identities=58% Similarity=0.858 Sum_probs=9.8
Q ss_pred hhHHHHhcCcee
Q psy2636 99 RFQKCLQVGMVK 110 (335)
Q Consensus 99 R~~KCl~vGM~~ 110 (335)
|-||||++|-..
T Consensus 29 rCQKClq~GHWt 40 (177)
T KOG3116|consen 29 RCQKCLQAGHWT 40 (177)
T ss_pred hHHHHHhhccce
Confidence 668999999854
No 188
>PRK14282 chaperone protein DnaJ; Provisional
Probab=23.25 E-value=86 Score=28.61 Aligned_cols=25 Identities=32% Similarity=0.753 Sum_probs=17.3
Q ss_pred CcccccCCCCCccccCCcccccccc
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKG 65 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~ 65 (335)
..|..|.......+-....|..|.|
T Consensus 153 ~~C~~C~G~G~~~~~~~~~C~~C~G 177 (369)
T PRK14282 153 ETCPHCGGTGVEPGSGYVTCPKCHG 177 (369)
T ss_pred ccCCCCCccCCCCCCCCcCCCCCCC
Confidence 5788888765444444678999975
No 189
>KOG4451|consensus
Probab=22.73 E-value=42 Score=27.86 Aligned_cols=26 Identities=27% Similarity=0.570 Sum_probs=21.3
Q ss_pred CCCcccccCCCCCccccCCccccccccce
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFF 67 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FF 67 (335)
+.+.|+-||. ..|-++..|-=||+=-
T Consensus 248 pMK~ClsChq---qIHRNAPiCPlCKaKs 273 (286)
T KOG4451|consen 248 PMKVCLSCHQ---QIHRNAPICPLCKAKS 273 (286)
T ss_pred cchHHHHHHH---HHhcCCCCCcchhhcc
Confidence 4566999985 5899999999999854
No 190
>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=22.72 E-value=1.6e+02 Score=25.21 Aligned_cols=29 Identities=34% Similarity=0.529 Sum_probs=25.0
Q ss_pred hhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 177 VIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 177 ~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
.+-.|++.+|.|.+|..+|+..+++.+..
T Consensus 43 ~~VeWAK~IPgF~~L~l~DQi~LLk~sW~ 71 (247)
T cd07076 43 AAVKWAKAIPGFRNLHLDDQMTLLQYSWM 71 (247)
T ss_pred HHHHHHhcCCCcccCCHHHHHHHHHHhHH
Confidence 45678999999999999999999987753
No 191
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.65 E-value=48 Score=21.26 Aligned_cols=6 Identities=67% Similarity=1.741 Sum_probs=2.9
Q ss_pred cccccC
Q psy2636 42 LCAVCG 47 (335)
Q Consensus 42 ~C~VCg 47 (335)
.|.|||
T Consensus 5 HC~~CG 10 (59)
T PF09889_consen 5 HCPVCG 10 (59)
T ss_pred cCCcCC
Confidence 355554
No 192
>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=22.44 E-value=1.2e+02 Score=25.88 Aligned_cols=44 Identities=25% Similarity=0.468 Sum_probs=29.6
Q ss_pred CCCcccccC---CCCCccccCCcccccccc--ceecccccCCeeecCCC
Q psy2636 39 PSQLCAVCG---DIAACQHYGVRTCEGCKG--FFKRTVQKGSKYVCLAD 82 (335)
Q Consensus 39 ~~~~C~VCg---d~a~g~HyGv~sC~gCk~--FFRR~v~~~~~y~C~~~ 82 (335)
+...|.||+ |-....|=-|.-|.-|.- --|++=.+|+..+|.-|
T Consensus 64 p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCPCN 112 (256)
T PF09788_consen 64 PVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCPCN 112 (256)
T ss_pred ceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecCCc
Confidence 345699999 455668989999999963 34444445555577543
No 193
>PLN02436 cellulose synthase A
Probab=22.42 E-value=50 Score=34.31 Aligned_cols=25 Identities=28% Similarity=0.792 Sum_probs=17.8
Q ss_pred CCCCcccccCCC----CCccccCCccccccc
Q psy2636 38 SPSQLCAVCGDI----AACQHYGVRTCEGCK 64 (335)
Q Consensus 38 ~~~~~C~VCgd~----a~g~HyGv~sC~gCk 64 (335)
...+.|.||||. +.|-=| .+|+-|.
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~F--VACn~C~ 62 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPF--VACNECA 62 (1094)
T ss_pred cCCccccccccccCcCCCCCEE--EeeccCC
Confidence 345689999986 567555 6777774
No 194
>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=22.23 E-value=98 Score=25.99 Aligned_cols=42 Identities=36% Similarity=0.469 Sum_probs=31.2
Q ss_pred HHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636 165 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206 (335)
Q Consensus 165 ~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~ 206 (335)
.++..........+-.|++.+|.|.++..+|+..+++.+..+
T Consensus 38 ~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~E 79 (226)
T cd06934 38 PHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFE 79 (226)
T ss_pred HHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHH
Confidence 344444444444567789999999999999999999877543
No 195
>PHA02446 hypothetical protein
Probab=22.21 E-value=35 Score=24.93 Aligned_cols=21 Identities=33% Similarity=0.607 Sum_probs=16.9
Q ss_pred CCCcccccCCCCCccccCCcc
Q psy2636 39 PSQLCAVCGDIAACQHYGVRT 59 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~s 59 (335)
..+.|.|||..|--.|-|..-
T Consensus 61 ~~q~cp~cg~dawv~~~g~~e 81 (166)
T PHA02446 61 EQQQCPLCGQDAWVIHTGIVE 81 (166)
T ss_pred hhhcCCCcccceeEeecCccc
Confidence 346799999999989988653
No 196
>KOG4323|consensus
Probab=22.18 E-value=32 Score=32.12 Aligned_cols=53 Identities=15% Similarity=0.413 Sum_probs=37.6
Q ss_pred CCCcccccCCCCCccccCCccccccccceecccccCCeeecCCCCCCcccccc------cccccchhhHH
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLADKACPVDKRR------RNRCQFCRFQK 102 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C~~~~~C~i~~~~------r~~Cr~CR~~K 102 (335)
.++.|.||+---.|.-|.++-|.+|...|-+. | .+|.|++.. ...|--|+.++
T Consensus 167 ~n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~--------C---hqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 167 VNLQCSVCYCGGPGAGNRMLQCDKCRQWYHQA--------C---HQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred ccceeeeeecCCcCccceeeeecccccHHHHH--------h---ccCCCCHhhccCccceEeehhhccch
Confidence 35669999977777777999999999999887 4 234444432 23677787553
No 197
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=22.09 E-value=50 Score=27.87 Aligned_cols=26 Identities=27% Similarity=0.543 Sum_probs=21.5
Q ss_pred CCCcccccCCCCCccccCCccccccccce
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFF 67 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FF 67 (335)
|.+.|..|+. -+|-+|..|-=||+=-
T Consensus 193 PMK~C~sC~q---qIHRNAPiCPlCK~Ks 218 (230)
T PF10146_consen 193 PMKTCQSCHQ---QIHRNAPICPLCKAKS 218 (230)
T ss_pred CcchhHhHHH---HHhcCCCCCccccccc
Confidence 3567999986 5899999999999843
No 198
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.83 E-value=32 Score=20.19 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=15.1
Q ss_pred cccccCCCCC--ccccCCccccccc
Q psy2636 42 LCAVCGDIAA--CQHYGVRTCEGCK 64 (335)
Q Consensus 42 ~C~VCgd~a~--g~HyGv~sC~gCk 64 (335)
.|..||.+.. -.+-|-..|..|-
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-
T ss_pred CCcCCcCCceEEcCCCCeEECCCCC
Confidence 4888887652 2456777788873
No 199
>PRK12495 hypothetical protein; Provisional
Probab=21.75 E-value=48 Score=27.50 Aligned_cols=29 Identities=28% Similarity=0.594 Sum_probs=22.4
Q ss_pred CCCcccccCCCCCccccCCcccccccccee
Q psy2636 39 PSQLCAVCGDIAACQHYGVRTCEGCKGFFK 68 (335)
Q Consensus 39 ~~~~C~VCgd~a~g~HyGv~sC~gCk~FFR 68 (335)
....|.+||.+=- .+=|+..|-.|...+-
T Consensus 41 sa~hC~~CG~PIp-a~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIF-RHDGQEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCccc-CCCCeeECCCCCCccc
Confidence 3467999999977 3369999999986554
No 200
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=21.74 E-value=50 Score=31.62 Aligned_cols=33 Identities=21% Similarity=0.725 Sum_probs=26.7
Q ss_pred CCCCcccccCCCCC---ccccCCccccccccceecc
Q psy2636 38 SPSQLCAVCGDIAA---CQHYGVRTCEGCKGFFKRT 70 (335)
Q Consensus 38 ~~~~~C~VCgd~a~---g~HyGv~sC~gCk~FFRR~ 70 (335)
..++.|.=||.+.- ..-||+..|-.|.|..|..
T Consensus 21 PgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsL 56 (648)
T PLN03119 21 PPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREF 56 (648)
T ss_pred cCCCccccCCCCCCCceeeccceEEeccchhhhccC
Confidence 34678999997763 3679999999999987765
No 201
>PRK14276 chaperone protein DnaJ; Provisional
Probab=21.61 E-value=1.1e+02 Score=28.07 Aligned_cols=26 Identities=27% Similarity=0.560 Sum_probs=18.6
Q ss_pred CCcccccCCCCCccccCCcccccccc
Q psy2636 40 SQLCAVCGDIAACQHYGVRTCEGCKG 65 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyGv~sC~gCk~ 65 (335)
...|..|.......+.-..+|..|.|
T Consensus 146 ~~~C~~C~G~G~~~~~~~~~C~~C~G 171 (380)
T PRK14276 146 EATCHTCNGSGAKPGTSPVTCGKCHG 171 (380)
T ss_pred cccCCCCcCcccCCCCCCccCCCCCC
Confidence 35799998765444444678999987
No 202
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.27 E-value=49 Score=16.86 Aligned_cols=9 Identities=33% Similarity=0.992 Sum_probs=5.6
Q ss_pred CcccccCCC
Q psy2636 41 QLCAVCGDI 49 (335)
Q Consensus 41 ~~C~VCgd~ 49 (335)
.+|.+||.+
T Consensus 3 ~~C~~CgR~ 11 (25)
T PF13913_consen 3 VPCPICGRK 11 (25)
T ss_pred CcCCCCCCE
Confidence 357777754
No 203
>PLN02195 cellulose synthase A
Probab=21.19 E-value=53 Score=33.75 Aligned_cols=25 Identities=28% Similarity=0.817 Sum_probs=16.3
Q ss_pred CCCCcccccCC----CCCccccCCccccccc
Q psy2636 38 SPSQLCAVCGD----IAACQHYGVRTCEGCK 64 (335)
Q Consensus 38 ~~~~~C~VCgd----~a~g~HyGv~sC~gCk 64 (335)
+..++|.|||| .++|--| .+|+.|.
T Consensus 4 ~~~~~c~~cgd~~~~~~~g~~f--vaC~eC~ 32 (977)
T PLN02195 4 SGAPICATCGEEVGVDSNGEAF--VACHECS 32 (977)
T ss_pred CCCccceecccccCcCCCCCeE--EEeccCC
Confidence 34457999998 3566444 5677764
No 204
>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=21.19 E-value=1.2e+02 Score=25.58 Aligned_cols=42 Identities=36% Similarity=0.580 Sum_probs=31.0
Q ss_pred HHHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhhc
Q psy2636 165 QQFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASLE 206 (335)
Q Consensus 165 ~~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~~ 206 (335)
.++..........+-.|++.+|.|.+|+.+|+..+++.+..+
T Consensus 41 ~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~E 82 (231)
T cd06937 41 DKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLD 82 (231)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHH
Confidence 344444444444566789999999999999999999877643
No 205
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain 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), but iron can also be replaced by cobalt, nickel or zinc 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=21.11 E-value=59 Score=17.85 Aligned_cols=7 Identities=71% Similarity=1.640 Sum_probs=3.3
Q ss_pred ccccCCC
Q psy2636 43 CAVCGDI 49 (335)
Q Consensus 43 C~VCgd~ 49 (335)
|.|||-.
T Consensus 4 C~~CGy~ 10 (33)
T cd00350 4 CPVCGYI 10 (33)
T ss_pred CCCCCCE
Confidence 5555533
No 206
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=20.96 E-value=36 Score=21.27 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=8.2
Q ss_pred CCcccccCCCC
Q psy2636 40 SQLCAVCGDIA 50 (335)
Q Consensus 40 ~~~C~VCgd~a 50 (335)
+..|.|||.+.
T Consensus 4 Wi~CP~CgnKT 14 (55)
T PF14205_consen 4 WILCPICGNKT 14 (55)
T ss_pred EEECCCCCCcc
Confidence 45688888766
No 207
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=20.96 E-value=62 Score=20.16 Aligned_cols=24 Identities=29% Similarity=0.850 Sum_probs=17.8
Q ss_pred CCcccccCCCCCc-cccCCcccccc
Q psy2636 40 SQLCAVCGDIAAC-QHYGVRTCEGC 63 (335)
Q Consensus 40 ~~~C~VCgd~a~g-~HyGv~sC~gC 63 (335)
..-|.|||..-.- -.||..-|+-|
T Consensus 14 ~nrC~~~Gr~rgvirkf~l~lcR~~ 38 (52)
T PRK05766 14 ARECQRCGRKQGLIRKYGLYLCRQC 38 (52)
T ss_pred CceeecCCCCceeHHhhCCcccHHH
Confidence 3469999986533 45888888777
No 208
>PF09150 Carot_N: Orange carotenoid protein, N-terminal ; InterPro: IPR015233 Carotenoids such as beta-carotene, lycopene, lutein and beta-cryptoxanthine are produced in plants and certain bacteria, algae and fungi, where they function as accessory photosynthetic pigments and as scavengers of oxygen radicals for photoprotection. They are also essential dietary nutrients in animals. Orange carotenoid-binding proteins (OCP) were first identified in cyanobacterial species, where they occur associated with phycobilisome in the cellular thylakoid membrane. These proteins function in photoprotection, and are essential for inhibiting white and blue-green light non-photochemical quenching (NPQ) [, ]. Carotenoids improve the photoprotectant activity by broadening OCP's absorption spectrum and facilitating the dissipation of absorbed energy. OCP acts as a homodimer, and binds one molecule of carotenoid (3'-hydroxyechinenone) and one chloride ion per subunit, where the carotenoid binding site is lined with a striking number of methionine residues. The carotenoid 3'-hydroxyechinenone is not found in higher plants. OCP has two domains: an N-terminal helical domain and a C-terminal domain that resembles a NTF2 (nuclear transport factor 2) domain. OCP can be proteolytically cleaved into a red form (RCP), which lacks 15 residues from the N terminus and approximately 150 residues from the C terminus []. This entry represents the N-terminal domain found predominantly in prokaryotic orange carotenoid proteins and related carotenoid-binding proteins. It adopts an alpha-helical structure consisting of two four-helix bundles [].; GO: 0031404 chloride ion binding, 0016037 light absorption, 0030089 phycobilisome; PDB: 3MG3_B 3MG1_A 3MG2_A 1M98_A.
Probab=20.91 E-value=94 Score=24.39 Aligned_cols=20 Identities=35% Similarity=0.328 Sum_probs=14.6
Q ss_pred CCCCCCHHHHHHHHHHhHHH
Q psy2636 248 GFSDLCKEDQELLFQSASLE 267 (335)
Q Consensus 248 ~F~~L~~~DQ~~LLk~~~~~ 267 (335)
-|..|+.|||..||=..+.+
T Consensus 21 ~F~~Ls~DdqLAlLWf~Y~e 40 (159)
T PF09150_consen 21 RFNQLSVDDQLALLWFAYTE 40 (159)
T ss_dssp HHCCS-HHHHHHHHHHHHHH
T ss_pred HHHcCCHHHHHHHHHHHHHH
Confidence 59999999999987554444
No 209
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=20.84 E-value=66 Score=23.08 Aligned_cols=39 Identities=21% Similarity=0.623 Sum_probs=26.4
Q ss_pred CcccccCCCCCccccCCccccccccceecccccCCeeec
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKGFFKRTVQKGSKYVC 79 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~FFRR~v~~~~~y~C 79 (335)
+-|+.|+-.-+.-.|-..-|..|.+|+..--...+.+.|
T Consensus 4 rAC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~~~v~~~ 42 (98)
T cd07973 4 RACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDC 42 (98)
T ss_pred chhccCCcccccccccCCCCCCCcchhccCCCccccccc
Confidence 459999988777667778899998777544333334444
No 210
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=20.80 E-value=69 Score=20.33 Aligned_cols=8 Identities=50% Similarity=1.352 Sum_probs=3.9
Q ss_pred CCcccccC
Q psy2636 40 SQLCAVCG 47 (335)
Q Consensus 40 ~~~C~VCg 47 (335)
...|.|||
T Consensus 8 H~HC~VCg 15 (64)
T COG4068 8 HRHCVVCG 15 (64)
T ss_pred CccccccC
Confidence 34455555
No 211
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.79 E-value=54 Score=20.16 Aligned_cols=25 Identities=24% Similarity=0.663 Sum_probs=16.9
Q ss_pred CCcccccCCCCCccccCCccccccc
Q psy2636 40 SQLCAVCGDIAACQHYGVRTCEGCK 64 (335)
Q Consensus 40 ~~~C~VCgd~a~g~HyGv~sC~gCk 64 (335)
.+.|..||..-...|-+...|..|.
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCG 44 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcC
Confidence 4568888864444666777777774
No 212
>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=20.76 E-value=1.7e+02 Score=25.00 Aligned_cols=40 Identities=23% Similarity=0.362 Sum_probs=29.6
Q ss_pred HHHHhhcchhhhhhhcccCCCCCCCCCHHHHHHHHhhhhh
Q psy2636 166 QFYSLLTTSVDVIRHFADKIPGFSDLCKEDQELLFQSASL 205 (335)
Q Consensus 166 ~~~~~l~~~~~~i~~~~~~~p~~~~l~~~~~~~l~~~~~~ 205 (335)
.++.......-.+-.|++.+|.|.+|+.+||..+++.+..
T Consensus 32 ~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ 71 (246)
T cd07073 32 SLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWM 71 (246)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHH
Confidence 3444433333456678999999999999999999987754
No 213
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=20.62 E-value=40 Score=22.40 Aligned_cols=28 Identities=25% Similarity=0.527 Sum_probs=15.9
Q ss_pred cccccCCCCCccccCCccccccccceecc
Q psy2636 42 LCAVCGDIAACQHYGVRTCEGCKGFFKRT 70 (335)
Q Consensus 42 ~C~VCgd~a~g~HyGv~sC~gCk~FFRR~ 70 (335)
.|.+|+.. -..-.|...|.+|..-|++-
T Consensus 3 ~CP~C~~~-L~~~~~~~~C~~C~~~~~~~ 30 (70)
T PF07191_consen 3 TCPKCQQE-LEWQGGHYHCEACQKDYKKE 30 (70)
T ss_dssp B-SSS-SB-EEEETTEEEETTT--EEEEE
T ss_pred cCCCCCCc-cEEeCCEEECccccccceec
Confidence 58888876 33333677788888877654
No 214
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=20.53 E-value=43 Score=29.80 Aligned_cols=32 Identities=34% Similarity=0.683 Sum_probs=26.4
Q ss_pred CCCCcccccCCCC---CccccCCccccccccceec
Q psy2636 38 SPSQLCAVCGDIA---ACQHYGVRTCEGCKGFFKR 69 (335)
Q Consensus 38 ~~~~~C~VCgd~a---~g~HyGv~sC~gCk~FFRR 69 (335)
..+..|.=||.+. ...-|||.-|--|+|-.|-
T Consensus 18 ~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRs 52 (319)
T COG5347 18 SSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRS 52 (319)
T ss_pred cccCccccCCCCCCceEecccCeEEEeecchhhhc
Confidence 3467899999887 4589999999999987654
No 215
>PF15472 DUF4638: Domain of unknown function (DUF4638)
Probab=20.10 E-value=41 Score=27.94 Aligned_cols=19 Identities=32% Similarity=0.753 Sum_probs=16.0
Q ss_pred ccccchhhHH---------HHhcCceee
Q psy2636 93 NRCQFCRFQK---------CLQVGMVKE 111 (335)
Q Consensus 93 ~~Cr~CR~~K---------Cl~vGM~~~ 111 (335)
..|||=|+.| |-++||+.+
T Consensus 218 l~crylrl~~nNi~Tl~~lCkdaG~~vd 245 (268)
T PF15472_consen 218 LSCRYLRLSKNNIRTLLKLCKDAGMDVD 245 (268)
T ss_pred hccceeeechhhHHHHHHHHHHcCCCcc
Confidence 4799999766 999999865
No 216
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=20.02 E-value=85 Score=18.37 Aligned_cols=24 Identities=25% Similarity=0.398 Sum_probs=15.0
Q ss_pred CcccccCCCCCccccCCcccccccc
Q psy2636 41 QLCAVCGDIAACQHYGVRTCEGCKG 65 (335)
Q Consensus 41 ~~C~VCgd~a~g~HyGv~sC~gCk~ 65 (335)
..|.||++.-.+.. -+.-|..|+.
T Consensus 12 ~~C~~C~~~i~~~~-~~~~C~~C~~ 35 (49)
T smart00109 12 TKCCVCRKSIWGSF-QGLRCSWCKV 35 (49)
T ss_pred CCccccccccCcCC-CCcCCCCCCc
Confidence 35888887765533 2456777753
No 217
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=20.01 E-value=45 Score=18.90 Aligned_cols=10 Identities=40% Similarity=1.056 Sum_probs=6.7
Q ss_pred CCcccccCCC
Q psy2636 40 SQLCAVCGDI 49 (335)
Q Consensus 40 ~~~C~VCgd~ 49 (335)
..+|.|||..
T Consensus 8 ~~~C~~C~~~ 17 (36)
T PF11781_consen 8 NEPCPVCGSR 17 (36)
T ss_pred CCcCCCCCCe
Confidence 3458888855
No 218
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=20.01 E-value=47 Score=34.39 Aligned_cols=24 Identities=33% Similarity=0.792 Sum_probs=17.2
Q ss_pred CCCcccccCCC----CCccccCCccccccc
Q psy2636 39 PSQLCAVCGDI----AACQHYGVRTCEGCK 64 (335)
Q Consensus 39 ~~~~C~VCgd~----a~g~HyGv~sC~gCk 64 (335)
..+.|.||||. ++|--| .+|+.|.
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~F--VAC~eC~ 41 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPF--VACHVCG 41 (1044)
T ss_pred CcchhhccccccCcCCCCCEE--EEeccCC
Confidence 34679999987 566555 6777774
Done!