Query psy16825
Match_columns 183
No_of_seqs 142 out of 1246
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 23:00:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16825.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16825hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 100.0 3.7E-51 8.1E-56 323.8 8.8 173 9-181 18-299 (432)
2 KOG4217|consensus 100.0 4.2E-40 9.1E-45 267.9 9.7 172 10-181 269-548 (605)
3 KOG4216|consensus 100.0 8.9E-39 1.9E-43 255.1 8.4 82 12-93 48-129 (479)
4 KOG4218|consensus 100.0 3.5E-37 7.6E-42 242.8 4.6 85 10-94 15-99 (475)
5 cd07170 NR_DBD_ERR DNA-binding 100.0 4.6E-34 9.9E-39 192.4 4.4 89 9-97 3-91 (97)
6 cd06961 NR_DBD_TR DNA-binding 100.0 6.9E-34 1.5E-38 187.8 3.1 83 12-94 1-83 (85)
7 cd06964 NR_DBD_RAR DNA-binding 100.0 1.1E-33 2.4E-38 186.6 3.2 82 9-90 3-84 (85)
8 cd07160 NR_DBD_LXR DNA-binding 100.0 2.8E-33 6.1E-38 189.7 4.0 82 10-91 18-99 (101)
9 cd07168 NR_DBD_DHR4_like DNA-b 100.0 2.6E-33 5.6E-38 186.8 3.7 85 8-92 4-88 (90)
10 cd06967 NR_DBD_TR2_like DNA-bi 100.0 2.2E-33 4.8E-38 186.0 3.0 83 9-91 2-84 (87)
11 cd06956 NR_DBD_RXR DNA-binding 100.0 2.4E-33 5.2E-38 182.1 2.8 76 12-87 2-77 (77)
12 cd06970 NR_DBD_PNR DNA-binding 100.0 4.5E-33 9.7E-38 186.0 3.2 84 8-91 4-88 (92)
13 cd06957 NR_DBD_PNR_like_2 DNA- 100.0 3.1E-33 6.7E-38 183.6 2.3 80 13-92 1-81 (82)
14 cd07171 NR_DBD_ER DNA-binding 100.0 4.1E-33 8.9E-38 182.6 2.9 79 9-87 2-80 (82)
15 cd07163 NR_DBD_TLX DNA-binding 100.0 4.9E-33 1.1E-37 186.2 3.1 83 9-91 5-89 (92)
16 cd07169 NR_DBD_GCNF_like DNA-b 100.0 7.3E-33 1.6E-37 184.5 3.8 84 10-93 6-89 (90)
17 cd07155 NR_DBD_ER_like DNA-bin 100.0 5.8E-33 1.2E-37 179.5 2.8 75 13-87 1-75 (75)
18 cd07166 NR_DBD_REV_ERB DNA-bin 100.0 5.2E-33 1.1E-37 185.0 2.4 83 10-92 3-86 (89)
19 cd07165 NR_DBD_DmE78_like DNA- 100.0 9E-33 2E-37 181.1 3.2 79 13-91 1-79 (81)
20 cd07164 NR_DBD_PNR_like_1 DNA- 100.0 9.7E-33 2.1E-37 179.8 3.1 78 13-90 1-78 (78)
21 cd07167 NR_DBD_Lrh-1_like The 100.0 9.6E-33 2.1E-37 184.6 2.6 82 13-94 1-82 (93)
22 cd07161 NR_DBD_EcR DNA-binding 100.0 1E-32 2.2E-37 184.1 2.4 82 11-92 2-83 (91)
23 cd06962 NR_DBD_FXR DNA-binding 100.0 1.1E-32 2.4E-37 181.4 2.4 80 11-90 2-81 (84)
24 cd06960 NR_DBD_HNF4A DNA-bindi 100.0 2.4E-32 5.2E-37 177.2 2.8 76 13-88 1-76 (76)
25 cd06969 NR_DBD_NGFI-B DNA-bind 100.0 2.5E-32 5.5E-37 176.4 2.6 74 11-84 1-74 (75)
26 cd06968 NR_DBD_ROR DNA-binding 100.0 3.7E-32 7.9E-37 182.7 3.4 84 10-93 5-88 (95)
27 cd07179 2DBD_NR_DBD2 The secon 100.0 4.1E-32 8.8E-37 175.0 3.3 74 13-86 1-74 (74)
28 cd06966 NR_DBD_CAR DNA-binding 100.0 1.4E-32 3.1E-37 184.5 1.1 82 12-93 2-83 (94)
29 KOG4846|consensus 100.0 8E-32 1.7E-36 216.8 5.5 82 11-92 133-215 (538)
30 cd07172 NR_DBD_GR_PR DNA-bindi 100.0 7.1E-32 1.5E-36 175.3 4.1 76 9-84 1-76 (78)
31 cd07156 NR_DBD_VDR_like The DN 100.0 4.9E-32 1.1E-36 173.8 3.0 72 13-84 1-72 (72)
32 cd06958 NR_DBD_COUP_TF DNA-bin 100.0 5.9E-32 1.3E-36 173.9 3.2 72 13-84 1-72 (73)
33 cd07173 NR_DBD_AR DNA-binding 100.0 6.5E-32 1.4E-36 176.8 3.4 78 9-86 2-79 (82)
34 cd06959 NR_DBD_EcR_like The DN 100.0 7.7E-32 1.7E-36 173.4 3.1 73 12-84 1-73 (73)
35 cd06965 NR_DBD_Ppar DNA-bindin 100.0 7.3E-32 1.6E-36 177.7 2.5 80 12-93 1-81 (84)
36 cd06963 NR_DBD_GR_like The DNA 100.0 1.3E-31 2.8E-36 172.1 3.5 72 13-84 1-72 (73)
37 cd07154 NR_DBD_PNR_like The DN 100.0 7.5E-32 1.6E-36 173.5 2.3 72 13-84 1-73 (73)
38 cd07157 2DBD_NR_DBD1 The first 100.0 1.2E-31 2.6E-36 177.3 3.2 78 12-89 2-81 (86)
39 cd06955 NR_DBD_VDR DNA-binding 100.0 8.5E-32 1.8E-36 184.1 2.5 77 10-86 6-82 (107)
40 cd06916 NR_DBD_like DNA-bindin 100.0 8.9E-32 1.9E-36 172.7 2.3 72 13-84 1-72 (72)
41 cd07162 NR_DBD_PXR DNA-binding 100.0 8.4E-32 1.8E-36 178.7 2.2 78 12-89 1-78 (87)
42 cd07158 NR_DBD_Ppar_like The D 100.0 1.7E-31 3.7E-36 172.0 2.9 72 13-84 1-73 (73)
43 smart00399 ZnF_C4 c4 zinc fing 100.0 6.2E-30 1.3E-34 163.5 3.3 70 12-81 1-70 (70)
44 PF00105 zf-C4: Zinc finger, C 99.9 3.4E-29 7.3E-34 160.4 1.8 70 11-80 1-70 (70)
45 cd07076 NR_LBD_GR Ligand bindi 99.4 1.6E-13 3.5E-18 107.6 5.9 57 126-182 116-174 (247)
46 cd06934 NR_LBD_PXR_like The li 99.4 5.9E-13 1.3E-17 103.5 6.9 58 126-183 121-179 (226)
47 cd06937 NR_LBD_RAR The ligand 99.4 5.5E-13 1.2E-17 104.0 6.4 57 126-182 124-181 (231)
48 cd06940 NR_LBD_REV_ERB The lig 99.4 7.5E-13 1.6E-17 100.3 6.8 57 126-182 98-155 (189)
49 cd06935 NR_LBD_TR The ligand b 99.4 7.2E-13 1.6E-17 104.1 6.7 76 108-183 71-196 (243)
50 cd07073 NR_LBD_AR Ligand bindi 99.4 1E-12 2.3E-17 103.2 6.3 57 126-182 116-174 (246)
51 cd06939 NR_LBD_ROR_like The li 99.4 1.1E-12 2.4E-17 102.9 6.4 75 108-182 67-190 (241)
52 cd06933 NR_LBD_VDR The ligand 99.4 1.3E-12 2.9E-17 102.3 6.6 57 126-182 125-182 (238)
53 cd07349 NR_LBD_SHP The ligand 99.4 1.6E-12 3.4E-17 100.8 6.5 57 126-182 117-174 (222)
54 cd07069 NR_LBD_Lrh-1 The ligan 99.4 1.4E-12 3.1E-17 102.3 6.3 56 127-182 132-188 (241)
55 cd06947 NR_LBD_GR_Like Ligand 99.3 1.5E-12 3.3E-17 102.3 6.2 56 127-182 117-174 (246)
56 cd06932 NR_LBD_PPAR The ligand 99.3 1.8E-12 3.8E-17 102.7 6.6 57 127-183 151-208 (259)
57 cd07070 NR_LBD_SF-1 The ligand 99.3 1.5E-12 3.3E-17 101.9 6.1 56 127-182 130-186 (237)
58 cd06950 NR_LBD_Tlx_PNR_like Th 99.3 2E-12 4.4E-17 99.2 6.2 57 126-182 112-169 (206)
59 cd06951 NR_LBD_Dax1_like The l 99.3 2.1E-12 4.6E-17 100.1 6.2 56 126-182 120-176 (222)
60 cd07348 NR_LBD_NGFI-B The liga 99.3 2.8E-12 6.1E-17 100.3 6.7 73 108-181 60-181 (238)
61 cd07075 NR_LBD_MR Ligand bindi 99.3 2.4E-12 5.1E-17 101.1 6.3 56 126-181 116-173 (248)
62 cd06954 NR_LBD_LXR The ligand 99.3 3.1E-12 6.6E-17 100.2 6.5 57 126-182 130-187 (236)
63 cd06953 NR_LBD_DHR4_like The l 99.3 3.7E-12 8.1E-17 98.2 6.2 56 127-182 118-174 (213)
64 cd06941 NR_LBD_DmE78_like The 99.3 4E-12 8.6E-17 96.8 6.3 58 125-182 87-145 (195)
65 cd06936 NR_LBD_Fxr The ligand 99.3 4.7E-12 1E-16 98.2 6.6 57 126-182 119-176 (221)
66 cd06945 NR_LBD_Nurr1_like The 99.3 5.2E-12 1.1E-16 99.0 6.0 74 109-182 61-183 (239)
67 cd07074 NR_LBD_PR Ligand bindi 99.3 4.8E-12 1E-16 99.3 5.7 56 127-182 117-174 (248)
68 cd07071 NR_LBD_Nurr1 The ligan 99.3 7.7E-12 1.7E-16 97.9 6.7 73 109-182 61-182 (238)
69 cd06943 NR_LBD_RXR_like The li 99.3 9.1E-12 2E-16 95.6 6.3 57 126-182 117-174 (207)
70 cd06944 NR_LBD_Ftz-F1_like The 99.3 8.1E-12 1.8E-16 97.8 6.1 57 126-182 129-186 (237)
71 cd07072 NR_LBD_DHR38_like Liga 99.3 9.6E-12 2.1E-16 97.4 6.4 73 108-181 61-182 (239)
72 cd06949 NR_LBD_ER Ligand bindi 99.3 8.3E-12 1.8E-16 97.6 6.0 57 126-182 119-181 (235)
73 cd06948 NR_LBD_COUP-TF Ligand 99.2 1E-11 2.3E-16 97.2 5.9 56 127-182 119-175 (236)
74 cd06946 NR_LBD_ERR The ligand 99.2 1.9E-11 4.1E-16 94.8 6.3 57 126-182 113-170 (221)
75 cd06929 NR_LBD_F1 Ligand-bindi 99.2 2.6E-11 5.5E-16 90.4 6.7 57 126-182 88-145 (174)
76 cd06930 NR_LBD_F2 Ligand-bindi 99.2 5.2E-11 1.1E-15 87.9 6.4 58 125-182 86-144 (165)
77 cd07068 NR_LBD_ER_like The lig 99.2 6E-11 1.3E-15 92.0 6.2 57 126-182 113-170 (221)
78 cd06942 NR_LBD_Sex_1_like The 99.2 8.2E-11 1.8E-15 89.3 6.5 55 127-181 88-145 (191)
79 cd07350 NR_LBD_Dax1 The ligand 99.1 8.8E-11 1.9E-15 91.6 6.3 58 125-182 128-186 (232)
80 cd06938 NR_LBD_EcR The ligand 99.1 1.4E-10 3E-15 90.5 6.7 58 126-183 125-182 (231)
81 cd06952 NR_LBD_TR2_like The li 99.1 1.4E-10 3E-15 90.0 6.2 56 127-182 116-172 (222)
82 cd06931 NR_LBD_HNF4_like The l 99.0 1.1E-09 2.4E-14 85.0 6.3 56 126-181 118-174 (222)
83 cd06157 NR_LBD The ligand bind 98.7 4.4E-08 9.5E-13 71.6 6.1 59 124-182 86-146 (168)
84 smart00430 HOLI Ligand binding 98.7 2.7E-08 5.8E-13 72.4 4.6 59 124-182 80-141 (163)
85 PF00104 Hormone_recep: Ligand 98.1 9.2E-06 2E-10 61.1 6.0 55 125-179 106-163 (203)
86 PF01412 ArfGap: Putative GTPa 89.5 0.2 4.3E-06 34.8 1.4 33 8-40 11-46 (116)
87 smart00105 ArfGap Putative GTP 78.4 1.3 2.9E-05 30.5 1.5 31 10-40 3-36 (112)
88 KOG3277|consensus 78.1 0.9 2E-05 33.0 0.6 32 12-45 81-120 (165)
89 PF03107 C1_2: C1 domain; Int 65.1 3.3 7.2E-05 21.3 0.8 21 12-34 2-22 (30)
90 PF01286 XPA_N: XPA protein N- 62.1 2.5 5.5E-05 22.7 -0.0 24 11-34 4-31 (34)
91 PF03002 Somatostatin: Somatos 60.8 2.8 6.1E-05 18.9 0.0 11 32-42 6-16 (18)
92 PF10764 Gin: Inhibitor of sig 58.2 4.4 9.6E-05 23.3 0.5 23 12-34 1-25 (46)
93 PF09289 FOLN: Follistatin/Ost 57.2 2.6 5.6E-05 20.3 -0.4 19 47-65 4-22 (22)
94 PF00628 PHD: PHD-finger; Int 55.9 4.9 0.00011 23.0 0.5 27 12-40 1-27 (51)
95 PRK00420 hypothetical protein; 55.5 6.2 0.00013 27.3 1.0 26 11-36 24-49 (112)
96 KOG0703|consensus 54.7 6.6 0.00014 31.7 1.2 32 9-40 24-58 (287)
97 smart00249 PHD PHD zinc finger 53.9 13 0.00029 20.1 2.1 27 12-40 1-27 (47)
98 smart00401 ZnF_GATA zinc finge 50.7 14 0.00031 21.6 1.9 33 10-42 3-40 (52)
99 PF10013 DUF2256: Uncharacteri 49.1 13 0.00028 20.9 1.4 16 5-20 3-18 (42)
100 PF12760 Zn_Tnp_IS1595: Transp 47.7 8 0.00017 21.9 0.5 39 32-71 5-46 (46)
101 COG1997 RPL43A Ribosomal prote 47.5 8.1 0.00017 25.4 0.5 27 11-37 36-63 (89)
102 PF09889 DUF2116: Uncharacteri 47.1 11 0.00024 22.9 1.1 28 9-40 2-31 (59)
103 PF00357 Integrin_alpha: Integ 46.8 6.7 0.00014 17.0 0.0 7 35-41 3-9 (15)
104 PLN03114 ADP-ribosylation fact 45.9 13 0.00028 31.1 1.6 32 9-40 21-55 (395)
105 PHA03124 dUTPase; Provisional 45.4 8.2 0.00018 32.4 0.4 14 29-42 192-205 (418)
106 COG4338 Uncharacterized protei 45.0 11 0.00023 21.9 0.7 18 3-20 5-22 (54)
107 PTZ00218 40S ribosomal protein 43.7 11 0.00023 22.5 0.6 23 11-33 17-40 (54)
108 COG4068 Uncharacterized protei 40.9 15 0.00034 22.2 1.0 13 8-20 6-18 (64)
109 PF07649 C1_3: C1-like domain; 40.7 12 0.00026 19.0 0.5 20 12-34 2-22 (30)
110 PRK01343 zinc-binding protein; 39.2 29 0.00064 20.9 2.0 26 8-34 7-32 (57)
111 PF08273 Prim_Zn_Ribbon: Zinc- 38.5 14 0.00031 20.5 0.6 23 11-33 4-32 (40)
112 KOG4443|consensus 38.3 7.9 0.00017 34.7 -0.7 38 6-43 14-51 (694)
113 PLN02189 cellulose synthase 37.3 20 0.00043 34.1 1.6 23 9-33 33-59 (1040)
114 COG5347 GTPase-activating prot 37.1 20 0.00043 29.5 1.4 31 10-40 20-53 (319)
115 PF08394 Arc_trans_TRASH: Arch 34.1 23 0.00051 19.3 0.9 27 13-39 1-35 (37)
116 smart00274 FOLN Follistatin-N- 33.9 24 0.00052 17.6 0.9 19 47-65 5-23 (26)
117 PF01780 Ribosomal_L37ae: Ribo 33.6 14 0.0003 24.5 -0.0 25 11-35 36-61 (90)
118 PRK12495 hypothetical protein; 33.6 20 0.00043 27.8 0.8 29 10-39 42-70 (226)
119 PF01783 Ribosomal_L32p: Ribos 33.2 17 0.00038 21.6 0.4 25 9-38 25-49 (56)
120 PLN02638 cellulose synthase A 33.0 26 0.00056 33.6 1.6 23 9-33 16-42 (1079)
121 PF10080 DUF2318: Predicted me 32.7 16 0.00035 24.8 0.2 26 12-37 37-62 (102)
122 COG5204 SPT4 Transcription elo 32.5 17 0.00037 24.3 0.3 29 11-39 10-38 (112)
123 PF14569 zf-UDP: Zinc-binding 32.4 27 0.00059 22.4 1.2 14 7-20 6-19 (80)
124 KOG4399|consensus 32.2 15 0.00033 29.2 -0.0 19 13-35 264-282 (325)
125 cd02249 ZZ Zinc finger, ZZ typ 32.1 26 0.00057 19.7 1.0 13 13-25 3-15 (46)
126 KOG1734|consensus 31.1 26 0.00057 28.1 1.1 20 1-20 215-234 (328)
127 PTZ00255 60S ribosomal protein 30.9 22 0.00048 23.5 0.6 24 11-34 37-61 (90)
128 PLN03119 putative ADP-ribosyla 30.8 31 0.00067 30.7 1.6 32 9-40 22-56 (648)
129 PLN03131 hypothetical protein; 30.5 31 0.00067 31.0 1.6 32 9-40 22-56 (705)
130 PF07282 OrfB_Zn_ribbon: Putat 30.1 36 0.00078 20.7 1.5 26 9-34 27-53 (69)
131 smart00778 Prim_Zn_Ribbon Zinc 29.9 35 0.00075 18.6 1.2 23 10-33 3-31 (37)
132 PF01753 zf-MYND: MYND finger; 29.8 22 0.00047 18.9 0.4 18 13-36 1-18 (37)
133 PLN02915 cellulose synthase A 29.6 28 0.00061 33.2 1.3 25 8-34 13-41 (1044)
134 KOG4323|consensus 29.6 24 0.00053 30.5 0.8 51 11-72 169-225 (464)
135 KOG3490|consensus 28.0 38 0.00082 23.1 1.4 43 10-53 8-50 (111)
136 KOG0706|consensus 28.0 34 0.00073 29.4 1.4 33 8-40 21-56 (454)
137 KOG2879|consensus 28.0 58 0.0013 26.2 2.6 38 11-51 240-281 (298)
138 cd00729 rubredoxin_SM Rubredox 27.7 27 0.00058 18.5 0.5 12 10-21 18-29 (34)
139 PLN02400 cellulose synthase 27.7 34 0.00074 32.8 1.5 24 9-34 35-62 (1085)
140 PF14471 DUF4428: Domain of un 27.4 28 0.0006 20.4 0.6 22 12-34 1-27 (51)
141 cd02340 ZZ_NBR1_like Zinc fing 27.3 36 0.00078 19.0 1.0 6 29-34 2-7 (43)
142 smart00291 ZnF_ZZ Zinc-binding 27.2 36 0.00079 19.0 1.0 13 13-25 7-19 (44)
143 PRK03976 rpl37ae 50S ribosomal 27.0 27 0.00059 23.1 0.5 24 11-34 37-61 (90)
144 TIGR00280 L37a ribosomal prote 26.3 28 0.00061 23.1 0.5 25 11-35 36-61 (91)
145 PF04216 FdhE: Protein involve 25.9 22 0.00048 28.6 -0.0 9 10-18 172-180 (290)
146 TIGR00598 rad14 DNA repair pro 25.9 24 0.00053 26.3 0.2 23 13-35 1-27 (172)
147 smart00154 ZnF_AN1 AN1-like Zi 25.8 36 0.00079 18.6 0.8 22 13-37 1-22 (39)
148 PF05180 zf-DNL: DNL zinc fing 25.8 14 0.00031 23.0 -0.9 26 12-37 6-39 (66)
149 PLN02195 cellulose synthase A 25.8 35 0.00077 32.3 1.2 26 7-34 3-32 (977)
150 PF00320 GATA: GATA zinc finge 25.8 28 0.00061 18.6 0.4 28 13-40 1-33 (36)
151 TIGR03655 anti_R_Lar restricti 25.5 45 0.00097 19.4 1.2 15 11-25 2-16 (53)
152 cd00202 ZnF_GATA Zinc finger D 25.4 39 0.00085 19.9 1.0 30 12-41 1-35 (54)
153 PF05596 Taeniidae_ag: Taeniid 24.7 1.2E+02 0.0026 18.7 3.1 19 164-182 43-61 (64)
154 PLN02436 cellulose synthase A 24.6 41 0.00088 32.3 1.4 23 9-33 35-61 (1094)
155 PLN03207 stomagen; Provisional 24.5 27 0.00059 23.5 0.2 11 61-71 77-87 (113)
156 PF11494 Ta0938: Ta0938; Inte 24.5 33 0.00071 23.0 0.5 32 11-42 15-52 (105)
157 KOG0402|consensus 24.4 23 0.0005 23.0 -0.2 24 11-34 37-61 (92)
158 PRK05766 rps14P 30S ribosomal 23.9 56 0.0012 19.2 1.4 24 10-33 14-38 (52)
159 PRK08359 transcription factor; 23.9 42 0.00091 25.2 1.1 27 11-37 7-40 (176)
160 COG3677 Transposase and inacti 23.4 29 0.00063 24.5 0.2 44 21-76 24-67 (129)
161 PRK00418 DNA gyrase inhibitor; 23.1 71 0.0015 19.6 1.8 26 10-35 6-34 (62)
162 PF08201 BssC_TutF: BssC/TutF 22.3 31 0.00068 20.5 0.1 11 28-38 2-12 (57)
163 PF01586 Basic: Myogenic Basic 22.1 31 0.00067 22.6 0.1 12 27-41 72-83 (86)
164 PF08271 TF_Zn_Ribbon: TFIIB z 21.8 38 0.00082 18.7 0.4 23 12-34 2-26 (43)
165 PF14446 Prok-RING_1: Prokaryo 21.6 50 0.0011 19.7 0.9 30 10-40 5-34 (54)
166 PF09986 DUF2225: Uncharacteri 21.5 44 0.00096 25.7 0.9 7 12-18 7-13 (214)
167 PF11261 IRF-2BP1_2: Interfero 21.3 44 0.00096 19.6 0.6 27 10-36 3-33 (54)
168 COG2260 Predicted Zn-ribbon RN 21.1 51 0.0011 19.9 0.9 14 11-24 18-31 (59)
169 cd02336 ZZ_RSC8 Zinc finger, Z 20.9 57 0.0012 18.5 1.0 14 12-25 2-15 (45)
170 KOG1701|consensus 20.7 63 0.0014 27.7 1.6 34 11-48 275-319 (468)
171 PRK00432 30S ribosomal protein 20.5 58 0.0013 18.9 1.0 25 10-34 20-44 (50)
172 PF06147 DUF968: Protein of un 20.4 50 0.0011 25.2 0.9 16 10-25 127-143 (200)
173 KOG0704|consensus 20.1 48 0.001 27.6 0.8 29 10-38 19-50 (386)
No 1
>KOG4215|consensus
Probab=100.00 E-value=3.7e-51 Score=323.82 Aligned_cols=173 Identities=34% Similarity=0.661 Sum_probs=152.7
Q ss_pred CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 88 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~ 88 (183)
....|.||||++.|.|||+.+|+||||||||+|.++..|+|+.+.+|.|||+.|+.||+|||+||+++||+++|||.+|+
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERD 97 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERD 97 (432)
T ss_pred ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccc
Confidence 34679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccCCCCC--CC---------------------------CC---CC------------------------CCCCC
Q psy16825 89 RGGRQKYRRNPDL--LS---------------------------QQ---WP------------------------PNKSI 112 (183)
Q Consensus 89 ~~~~~~~~~~~~~--~~---------------------------~~---~~------------------------~~k~i 112 (183)
+.+.++....... .+ .+ -+ |.|.+
T Consensus 98 rIg~Rr~~~~~~n~~~~~id~L~~aE~~~~q~~~srs~~~~~~~~d~r~~~~n~~~at~~Dv~eSm~qqLlllVEWAK~i 177 (432)
T KOG4215|consen 98 RIGSRRPSYEAGNENSPSIDALVQAEALVRQLRSSRSGGVPGIDGDIRQGPPNKKIATENDVCESMKQQLLLLVEWAKYI 177 (432)
T ss_pred cccccCCCCCCCCCCchhHHHHHhHHHHHhhhhccccccCcCcchhhhcCccccccccHHHHHHHHHHHHHHHHHHHHhc
Confidence 9877654433211 00 00 00 11889
Q ss_pred CCccccccccc--------------------------------------------------chhhhhhhhchhcccChhH
Q psy16825 113 PSLEDLERNTE--------------------------------------------------ISCTQVIDRLEHVAVSKEE 142 (183)
Q Consensus 113 P~f~~L~~~dq--------------------------------------------------~~~~~lv~~~~~l~~~~~E 142 (183)
|.|.+++.+|| +++.+++..|++|++|..|
T Consensus 178 ~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~Pmr~L~md~~E 257 (432)
T KOG4215|consen 178 PPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLNNTYVLHRHAPDLPEISRVAPRIIDELVNPMRRLQMDEIE 257 (432)
T ss_pred cchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEecCceeeccCCCChHHHHHHHHHHHHHHhhHHHHhccchHH
Confidence 99999999999 5678999999999999999
Q ss_pred HHHHHHHHhcCCCCC-CCchh--HHHHHHHHHHHHHHHHHHh
Q psy16825 143 YYFLKALVLANSDVK-LDEFS--SLKKFRNSILSSLGDCIYV 181 (183)
Q Consensus 143 ~~~lkai~L~~~d~~-L~~~~--~v~~~~~~~~~~L~~~~~~ 181 (183)
|+|||||+||+||+. |++.. .|++.+++++.+|..||.-
T Consensus 258 y~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d 299 (432)
T KOG4215|consen 258 YVCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISD 299 (432)
T ss_pred HHHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhh
Confidence 999999999999986 99988 8999999999999999964
No 2
>KOG4217|consensus
Probab=100.00 E-value=4.2e-40 Score=267.88 Aligned_cols=172 Identities=38% Similarity=0.699 Sum_probs=149.7
Q ss_pred CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 89 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~ 89 (183)
.+.|.||||.+.-.||||-+|+|||+||+|+|+++..|+|.++.+|.|||..||+||+|||||||+|||-++-|+.+--+
T Consensus 269 e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLk 348 (605)
T KOG4217|consen 269 EGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLK 348 (605)
T ss_pred cceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheeccccc
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999988777
Q ss_pred cccccccCCCCCCCCC--CCCC----------------------------------------------------------
Q psy16825 90 GGRQKYRRNPDLLSQQ--WPPN---------------------------------------------------------- 109 (183)
Q Consensus 90 ~~~~~~~~~~~~~~~~--~~~~---------------------------------------------------------- 109 (183)
+++.+....+...... .|+.
T Consensus 349 GRRGRLpSKpKs~q~sppSpPi~LltalvrAh~Dstp~~~~ldys~~q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~a 428 (605)
T KOG4217|consen 349 GRRGRLPSKPKSRQPSPPSPPISLLTALVRAHVDSTPSTMTLDYSRFQELVPHFSGTDALHVQQFYDLLTGSLEVIRKWA 428 (605)
T ss_pred cccCCCCCCCCCCCCCCCCCchHHHHHHHHHhhcCCCCcchhhHHHhccccccccccHHHHHHHHHHHhhhhHHHHHHHH
Confidence 7776655444331110 1110
Q ss_pred CCCCCccccccccc------------------------------------------------chhhhhhhhchhcccChh
Q psy16825 110 KSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSKE 141 (183)
Q Consensus 110 k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~~ 141 (183)
..||+|.+|+..|| +.+.+|...+..+++|..
T Consensus 429 ekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~e~kliFcsG~vlhr~qC~rgfgewidsi~~FS~~l~~l~idi~ 508 (605)
T KOG4217|consen 429 EKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPSEDKLIFCSGLVLHRLQCLRGFGEWIDSIREFSRSLHSLNIDIS 508 (605)
T ss_pred HhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEecchhhhHHHHHHHHHHHHHHHHHHHHHhhhchhhHH
Confidence 56999999999999 334567888889999999
Q ss_pred HHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHh
Q psy16825 142 EYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYV 181 (183)
Q Consensus 142 E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~ 181 (183)
-|+||.|+.+..--++|.++..||++|++|+.+|.||+..
T Consensus 509 AfacL~aLa~iTErhGL~epkrVeelqnkIi~~LKDHvt~ 548 (605)
T KOG4217|consen 509 AFACLSALALITERHGLKEPKRVEELQNKIINCLKDHVTG 548 (605)
T ss_pred HHHHHHHHHhhhhhhcCCCcchHHHHHHHHHHHHHHHhhh
Confidence 9999999999998888999999999999999999999853
No 3
>KOG4216|consensus
Probab=100.00 E-value=8.9e-39 Score=255.06 Aligned_cols=82 Identities=45% Similarity=1.053 Sum_probs=78.5
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 91 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~ 91 (183)
+|.||||.++|.||||++|+|||+||||+-..+..|.|+...+|.||...||+||+||+||||++||.++||.++|+..+
T Consensus 48 PCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKK 127 (479)
T KOG4216|consen 48 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKK 127 (479)
T ss_pred eeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHh
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999997665
Q ss_pred cc
Q psy16825 92 RQ 93 (183)
Q Consensus 92 ~~ 93 (183)
.+
T Consensus 128 QR 129 (479)
T KOG4216|consen 128 QR 129 (479)
T ss_pred hH
Confidence 54
No 4
>KOG4218|consensus
Probab=100.00 E-value=3.5e-37 Score=242.83 Aligned_cols=85 Identities=59% Similarity=1.193 Sum_probs=81.5
Q ss_pred CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 89 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~ 89 (183)
.+.|.||||+.+|+|||-.+|+.||+||+|+|++++.|.|....+|.|||..|.+|.+|||||||.+||+.+||+.+|++
T Consensus 15 ~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMR 94 (475)
T KOG4218|consen 15 GELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMR 94 (475)
T ss_pred ccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhc
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccc
Q psy16825 90 GGRQK 94 (183)
Q Consensus 90 ~~~~~ 94 (183)
+++.+
T Consensus 95 GGRNK 99 (475)
T KOG4218|consen 95 GGRNK 99 (475)
T ss_pred ccccc
Confidence 87753
No 5
>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=4.6e-34 Score=192.37 Aligned_cols=89 Identities=87% Similarity=1.599 Sum_probs=82.2
Q ss_pred CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 88 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~ 88 (183)
+...|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|+
T Consensus 3 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~ 82 (97)
T cd07170 3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRV 82 (97)
T ss_pred CCCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccC
Confidence 45679999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccccC
Q psy16825 89 RGGRQKYRR 97 (183)
Q Consensus 89 ~~~~~~~~~ 97 (183)
..++.+...
T Consensus 83 ~~~~~~~~~ 91 (97)
T cd07170 83 RGGRQKYKR 91 (97)
T ss_pred CCCCCCccC
Confidence 777655443
No 6
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=99.98 E-value=6.9e-34 Score=187.77 Aligned_cols=83 Identities=49% Similarity=1.070 Sum_probs=79.2
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 91 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~ 91 (183)
+|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..++.|++|||+||+++||++++||.+|++..
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 49999999999999999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred ccc
Q psy16825 92 RQK 94 (183)
Q Consensus 92 ~~~ 94 (183)
+++
T Consensus 81 ~~~ 83 (85)
T cd06961 81 KRK 83 (85)
T ss_pred ccc
Confidence 654
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=99.98 E-value=1.1e-33 Score=186.63 Aligned_cols=82 Identities=52% Similarity=1.037 Sum_probs=77.6
Q ss_pred CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 88 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~ 88 (183)
....|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|+
T Consensus 3 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~ 82 (85)
T cd06964 3 IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN 82 (85)
T ss_pred cCCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhcccc
Confidence 34679999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cc
Q psy16825 89 RG 90 (183)
Q Consensus 89 ~~ 90 (183)
+.
T Consensus 83 ~~ 84 (85)
T cd06964 83 KK 84 (85)
T ss_pred CC
Confidence 63
No 8
>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=99.98 E-value=2.8e-33 Score=189.69 Aligned_cols=82 Identities=40% Similarity=0.881 Sum_probs=77.7
Q ss_pred CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 89 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~ 89 (183)
...|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|++
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~ 97 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI 97 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence 45799999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred cc
Q psy16825 90 GG 91 (183)
Q Consensus 90 ~~ 91 (183)
..
T Consensus 98 ~~ 99 (101)
T cd07160 98 RL 99 (101)
T ss_pred hh
Confidence 53
No 9
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=99.97 E-value=2.6e-33 Score=186.80 Aligned_cols=85 Identities=53% Similarity=1.102 Sum_probs=80.1
Q ss_pred CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825 8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 87 (183)
Q Consensus 8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r 87 (183)
+....|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+.+|
T Consensus 4 ~~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R 83 (90)
T cd07168 4 ESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDR 83 (90)
T ss_pred ccCCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhccc
Confidence 34567999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccc
Q psy16825 88 VRGGR 92 (183)
Q Consensus 88 ~~~~~ 92 (183)
+|+.+
T Consensus 84 ~~~~~ 88 (90)
T cd07168 84 MPGGR 88 (90)
T ss_pred CCCCC
Confidence 98664
No 10
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=99.97 E-value=2.2e-33 Score=185.99 Aligned_cols=83 Identities=54% Similarity=1.056 Sum_probs=78.7
Q ss_pred CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 88 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~ 88 (183)
|...|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++||.+|+
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 45679999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccc
Q psy16825 89 RGG 91 (183)
Q Consensus 89 ~~~ 91 (183)
+..
T Consensus 82 ~~~ 84 (87)
T cd06967 82 PID 84 (87)
T ss_pred CCC
Confidence 754
No 11
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=99.97 E-value=2.4e-33 Score=182.07 Aligned_cols=76 Identities=57% Similarity=1.167 Sum_probs=73.6
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 87 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r 87 (183)
.|.|||++++|+||||.+|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+||+++||++++||.+|
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 5999999999999999999999999999999999999999999999999999999999999999999999999876
No 12
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=99.97 E-value=4.5e-33 Score=185.96 Aligned_cols=84 Identities=44% Similarity=0.965 Sum_probs=78.2
Q ss_pred CCCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCC-CCccccccccccccchhhhHHhhhcccccceeec
Q psy16825 8 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPAS-NDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 86 (183)
Q Consensus 8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~-~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~ 86 (183)
.|...|.|||++++|+||||.+|+||++||||+|..+..|.|..+ ++|.+++..+..|++|||+||+++||++++||.+
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 345579999999999999999999999999999999999999885 8999999999999999999999999999999999
Q ss_pred ccccc
Q psy16825 87 RVRGG 91 (183)
Q Consensus 87 r~~~~ 91 (183)
|++..
T Consensus 84 R~~~~ 88 (92)
T cd06970 84 RQPRN 88 (92)
T ss_pred cCccc
Confidence 98654
No 13
>cd06957 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members
Probab=99.97 E-value=3.1e-33 Score=183.56 Aligned_cols=80 Identities=43% Similarity=0.904 Sum_probs=75.7
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecC-CCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 91 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~-~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~ 91 (183)
|.|||++++|+||||++|+||++||||+|..+..|.|. .+++|.+++..++.|++|||+||+++||++++|+.+|+|..
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~ 80 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRK 80 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCC
Confidence 89999999999999999999999999999999999998 46899999999999999999999999999999999998765
Q ss_pred c
Q psy16825 92 R 92 (183)
Q Consensus 92 ~ 92 (183)
+
T Consensus 81 ~ 81 (82)
T cd06957 81 L 81 (82)
T ss_pred C
Confidence 4
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=99.97 E-value=4.1e-33 Score=182.60 Aligned_cols=79 Identities=61% Similarity=1.244 Sum_probs=75.2
Q ss_pred CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 87 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r 87 (183)
+...|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+|||++||++++|+.+|
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 4567999999999999999999999999999999999999999999999999999999999999999999999998876
No 15
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=4.9e-33 Score=186.22 Aligned_cols=83 Identities=41% Similarity=0.920 Sum_probs=77.5
Q ss_pred CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCC--CCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPA--SNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 86 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~--~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~ 86 (183)
....|.|||++++|+||||.+|+||++||||++..+..|.|.. +++|.+++..+..|++|||+||+++||++++||.+
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 3567999999999999999999999999999999999999987 47999999999999999999999999999999999
Q ss_pred ccccc
Q psy16825 87 RVRGG 91 (183)
Q Consensus 87 r~~~~ 91 (183)
|+|..
T Consensus 85 r~p~~ 89 (92)
T cd07163 85 RGPRN 89 (92)
T ss_pred cCcCC
Confidence 98754
No 16
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=7.3e-33 Score=184.49 Aligned_cols=84 Identities=46% Similarity=1.068 Sum_probs=79.6
Q ss_pred CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 89 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~ 89 (183)
...|.|||++++|+||||++|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+.+|++
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 85 (90)
T cd07169 6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP 85 (90)
T ss_pred CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccCC
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccc
Q psy16825 90 GGRQ 93 (183)
Q Consensus 90 ~~~~ 93 (183)
+.+.
T Consensus 86 ~~~~ 89 (90)
T cd07169 86 GGRN 89 (90)
T ss_pred CCCC
Confidence 7653
No 17
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=99.97 E-value=5.8e-33 Score=179.52 Aligned_cols=75 Identities=79% Similarity=1.549 Sum_probs=72.7
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecc
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDR 87 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r 87 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|+.+++|.+++..+..|++|||+||+++||++++||.+|
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 899999999999999999999999999999999999999999999999999999999999999999999999876
No 18
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=99.97 E-value=5.2e-33 Score=184.98 Aligned_cols=83 Identities=51% Similarity=1.064 Sum_probs=78.2
Q ss_pred CCcccccCCCCcccccccccccchhhhhhccccCCcee-ecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 88 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~-~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~ 88 (183)
...|.|||++++|+||||.+|+||++||||+|..+..| .|..+++|.+++..+..|++|||+||+++||++++||.+|+
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 35699999999999999999999999999999999999 59999999999999999999999999999999999999998
Q ss_pred cccc
Q psy16825 89 RGGR 92 (183)
Q Consensus 89 ~~~~ 92 (183)
|.+.
T Consensus 83 ~~~~ 86 (89)
T cd07166 83 PKRE 86 (89)
T ss_pred CCcc
Confidence 8655
No 19
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=99.97 E-value=9e-33 Score=181.06 Aligned_cols=79 Identities=56% Similarity=1.129 Sum_probs=76.3
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 91 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~ 91 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|+|++
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~ 79 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR 79 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999998854
No 20
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=99.97 E-value=9.7e-33 Score=179.76 Aligned_cols=78 Identities=49% Similarity=1.070 Sum_probs=75.3
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 90 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~ 90 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+|||++||++++||.+|+|.
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~ 78 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAPR 78 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCCC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999999863
No 21
>cd07167 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regu
Probab=99.97 E-value=9.6e-33 Score=184.56 Aligned_cols=82 Identities=59% Similarity=1.187 Sum_probs=77.9
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccccc
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGGR 92 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~~ 92 (183)
|.|||++++|+||||.+|+||++||||+|..+..|.|+.+++|.+++..++.|++|||+||+++||++++||.+|.++.+
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 89999999999999999999999999999999999999999999999999999999999999999999999999987665
Q ss_pred cc
Q psy16825 93 QK 94 (183)
Q Consensus 93 ~~ 94 (183)
.+
T Consensus 81 ~~ 82 (93)
T cd07167 81 NK 82 (93)
T ss_pred cc
Confidence 43
No 22
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=99.97 E-value=1e-32 Score=184.07 Aligned_cols=82 Identities=43% Similarity=0.912 Sum_probs=77.0
Q ss_pred CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 90 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~ 90 (183)
..|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+||+++||++++||.+++..
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~ 81 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCA 81 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhh
Confidence 45999999999999999999999999999999999999999999999999999999999999999999999999997654
Q ss_pred cc
Q psy16825 91 GR 92 (183)
Q Consensus 91 ~~ 92 (183)
.+
T Consensus 82 ~~ 83 (91)
T cd07161 82 IK 83 (91)
T ss_pred HH
Confidence 44
No 23
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=99.97 E-value=1.1e-32 Score=181.40 Aligned_cols=80 Identities=44% Similarity=0.956 Sum_probs=75.4
Q ss_pred CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 90 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~ 90 (183)
..|.|||++++|+||||++|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+.++...
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~ 81 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCK 81 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHHh
Confidence 35999999999999999999999999999999999999999999999999999999999999999999999999887543
No 24
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=99.97 E-value=2.4e-32 Score=177.24 Aligned_cols=76 Identities=50% Similarity=1.060 Sum_probs=73.5
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeeccc
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRV 88 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~ 88 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+|||++||++++|+.+|+
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999875
No 25
>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B. DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcrip
Probab=99.97 E-value=2.5e-32 Score=176.40 Aligned_cols=74 Identities=61% Similarity=1.182 Sum_probs=71.2
Q ss_pred CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
++|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++||
T Consensus 1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 74 (75)
T cd06969 1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74 (75)
T ss_pred CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHcc
Confidence 36999999999999999999999999999999999999999999999999999999999999999999999986
No 26
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=99.97 E-value=3.7e-32 Score=182.74 Aligned_cols=84 Identities=44% Similarity=1.023 Sum_probs=79.2
Q ss_pred CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 89 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~ 89 (183)
...|.|||++++|+||||++|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+.+|.+
T Consensus 5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~ 84 (95)
T cd06968 5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMS 84 (95)
T ss_pred ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCC
Confidence 45799999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred cccc
Q psy16825 90 GGRQ 93 (183)
Q Consensus 90 ~~~~ 93 (183)
.+.+
T Consensus 85 ~~~~ 88 (95)
T cd06968 85 KKQR 88 (95)
T ss_pred hhhh
Confidence 6654
No 27
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=99.97 E-value=4.1e-32 Score=175.00 Aligned_cols=74 Identities=47% Similarity=1.108 Sum_probs=71.2
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 86 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~ 86 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++|+++
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~ 74 (74)
T cd07179 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRIG 74 (74)
T ss_pred CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999863
No 28
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=99.97 E-value=1.4e-32 Score=184.49 Aligned_cols=82 Identities=41% Similarity=0.909 Sum_probs=77.9
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccccc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRGG 91 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~~ 91 (183)
.|.|||++++|+||||++|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+|+...
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~ 81 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSE 81 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhH
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999987765
Q ss_pred cc
Q psy16825 92 RQ 93 (183)
Q Consensus 92 ~~ 93 (183)
++
T Consensus 82 ~r 83 (94)
T cd06966 82 KR 83 (94)
T ss_pred HH
Confidence 54
No 29
>KOG4846|consensus
Probab=99.97 E-value=8e-32 Score=216.78 Aligned_cols=82 Identities=51% Similarity=1.093 Sum_probs=77.8
Q ss_pred CcccccCCCCcccccccccccchhhhhhccccCCcee-ecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 89 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~-~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~ 89 (183)
-.|.||||+++|+||||.+|+|||+||||+|+.+..| .|-+..+|.|.++.||+||+|||+|||.|||.+++|++++++
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 3699999999999999999999999999999999999 699999999999999999999999999999999999999876
Q ss_pred ccc
Q psy16825 90 GGR 92 (183)
Q Consensus 90 ~~~ 92 (183)
.+.
T Consensus 213 ~rn 215 (538)
T KOG4846|consen 213 FRN 215 (538)
T ss_pred ccc
Confidence 544
No 30
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=99.97 E-value=7.1e-32 Score=175.25 Aligned_cols=76 Identities=53% Similarity=1.127 Sum_probs=71.7
Q ss_pred CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
|...|.|||++++|+||||++|+||++||||++..+..|.|..+++|.+++..++.|++|||+||+++||+..++.
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 3567999999999999999999999999999999999999999999999999999999999999999999988764
No 31
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=99.97 E-value=4.9e-32 Score=173.85 Aligned_cols=72 Identities=50% Similarity=1.118 Sum_probs=69.4
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..++.|++|||+||+++||++++|.
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 32
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=99.97 E-value=5.9e-32 Score=173.90 Aligned_cols=72 Identities=50% Similarity=1.152 Sum_probs=70.0
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..++.|++|||+|||++||++++||
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (73)
T cd06958 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 899999999999999999999999999999999999999999999999999999999999999999999987
No 33
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=99.97 E-value=6.5e-32 Score=176.79 Aligned_cols=78 Identities=49% Similarity=1.096 Sum_probs=72.3
Q ss_pred CCCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 86 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~ 86 (183)
+...|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..++.|++|||+||+++||++.....+
T Consensus 2 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~ 79 (82)
T cd07173 2 PQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK 79 (82)
T ss_pred CCCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence 456799999999999999999999999999999999999999999999999999999999999999999988765443
No 34
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=99.97 E-value=7.7e-32 Score=173.37 Aligned_cols=73 Identities=48% Similarity=1.043 Sum_probs=70.0
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
+|.|||++++|+||||.+|+||++||||++..+..|.|+.+++|.+++..+..|++|||+||+++||+++.|+
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 5999999999999999999999999999999999999999999999999999999999999999999998873
No 35
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=99.97 E-value=7.3e-32 Score=177.72 Aligned_cols=80 Identities=53% Similarity=1.074 Sum_probs=74.2
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCceee-cCCCCCccccccccccccchhhhHHhhhcccccceeeccccc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYT-CPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVRG 90 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~-C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~~ 90 (183)
.|.|||++++|+||||.+|+||++||||++..+..|. |... |.+++..++.|++|||+||+++||++++|+.+|++.
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~ 78 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPR 78 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCc
Confidence 4999999999999999999999999999999999995 9753 999999999999999999999999999999999976
Q ss_pred ccc
Q psy16825 91 GRQ 93 (183)
Q Consensus 91 ~~~ 93 (183)
..+
T Consensus 79 ~~~ 81 (84)
T cd06965 79 VEK 81 (84)
T ss_pred hhh
Confidence 553
No 36
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=99.97 E-value=1.3e-31 Score=172.12 Aligned_cols=72 Identities=53% Similarity=1.120 Sum_probs=69.3
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
|.|||++++|+||||++|+||++||||++..+..|.|+.+++|.+++..++.|++|||+||+++||+++++.
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 899999999999999999999999999999999999999999999999999999999999999999998863
No 37
>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear
Probab=99.97 E-value=7.5e-32 Score=173.51 Aligned_cols=72 Identities=51% Similarity=1.106 Sum_probs=69.2
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecC-CCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCP-ASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~-~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|. .+++|.+++..+..|++|||+||+++||++++||
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 89999999999999999999999999999999999998 6789999999999999999999999999999886
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=99.97 E-value=1.2e-31 Score=177.32 Aligned_cols=78 Identities=46% Similarity=0.925 Sum_probs=73.2
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCc--eeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNI--EYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 89 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~--~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~ 89 (183)
.|.|||++++|+||||.+|+||++||||++..+. .|.|..+++|.+++..++.|++|||+|||++||++++++.+|+.
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~ 81 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS 81 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence 5999999999999999999999999999998764 89999999999999999999999999999999999999988763
No 39
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=99.97 E-value=8.5e-32 Score=184.13 Aligned_cols=77 Identities=47% Similarity=1.072 Sum_probs=73.3
Q ss_pred CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeec
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLD 86 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~ 86 (183)
...|.|||++++|+||||++|+||++||||+|..+..|.|..+++|.+++..++.|++|||+|||++||++++|+.+
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 82 (107)
T cd06955 6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82 (107)
T ss_pred CCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence 35699999999999999999999999999999999999999999999999999999999999999999999888877
No 40
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or hetero
Probab=99.97 E-value=8.9e-32 Score=172.74 Aligned_cols=72 Identities=63% Similarity=1.309 Sum_probs=69.7
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..+..|++|||+||+++||++++||
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 41
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=99.97 E-value=8.4e-32 Score=178.69 Aligned_cols=78 Identities=45% Similarity=0.990 Sum_probs=74.1
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccccceeecccc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVRLDRVR 89 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~~~r~~ 89 (183)
+|.|||++++|+||||.+|+||++||||++..+..|.|..+++|.+++..++.|++|||+||+++||++++|+.++..
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~ 78 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEAV 78 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHHH
Confidence 499999999999999999999999999999999999999999999999999999999999999999999999988543
No 42
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=1.7e-31 Score=171.96 Aligned_cols=72 Identities=58% Similarity=1.207 Sum_probs=69.5
Q ss_pred ccccCCCCcccccccccccchhhhhhccccCCcee-ecCCCCCccccccccccccchhhhHHhhhccccccee
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY-TCPASNDCEINKRRRKACQACRFQKCLRKGMLKEGVR 84 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~-~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~~v~ 84 (183)
|.|||++++|+||||.+|+||++||||++..+..| .|+.+++|.+++..+..|++|||+|||++||++++|+
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 8999999999999999999999999999999999875
No 43
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.96 E-value=6.2e-30 Score=163.54 Aligned_cols=70 Identities=60% Similarity=1.177 Sum_probs=67.0
Q ss_pred cccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhccccc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLKE 81 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~~ 81 (183)
.|.|||++++|+||||.+|+||++||||+|..+..|.|..+++|.+++..+..|++|||+||+++||+++
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=99.95 E-value=3.4e-29 Score=160.35 Aligned_cols=70 Identities=53% Similarity=1.186 Sum_probs=62.5
Q ss_pred CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhhcccc
Q psy16825 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRKGMLK 80 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~GM~~ 80 (183)
..|.|||++++|+||||.+|++|++||||++..+..+.|..+++|.+++..+..|++|||+||+++||++
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 3699999999999999999999999999999999889999999999999999999999999999999974
No 45
>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=99.44 E-value=1.6e-13 Score=107.60 Aligned_cols=57 Identities=26% Similarity=0.355 Sum_probs=53.6
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+++++.+|++|++|.+||+|||||+|||| |.+ |.+...|+.+|++++.+|.+||..+
T Consensus 116 l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~ 174 (247)
T cd07076 116 MLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKR 174 (247)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 56899999999999999999999999999 875 9999999999999999999999865
No 46
>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=99.40 E-value=5.9e-13 Score=103.54 Aligned_cols=58 Identities=17% Similarity=0.297 Sum_probs=53.4
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR 183 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~ 183 (183)
+.+++.+|+.|++|..||+||+||+||+||++ |.+...|+.+|++++.+|.+|+..+|
T Consensus 121 ~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~ 179 (226)
T cd06934 121 LLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKR 179 (226)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcChHHHHHHHHHHHHHHHHHHHHcC
Confidence 35678899999999999999999999999986 99999999999999999999997653
No 47
>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=99.40 E-value=5.5e-13 Score=104.03 Aligned_cols=57 Identities=19% Similarity=0.232 Sum_probs=53.4
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|+.|++|..||+||+||+||+||.+ |.+...|+++|++++.+|.+|+...
T Consensus 124 ~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 181 (231)
T cd06937 124 VFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKR 181 (231)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 45799999999999999999999999999986 9999999999999999999999754
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=99.39 E-value=7.5e-13 Score=100.29 Aligned_cols=57 Identities=19% Similarity=0.329 Sum_probs=53.4
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|+.+++|.+||++|+||+|+|||.+ |.+...|+++|++++.+|.+|+...
T Consensus 98 ~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~ 155 (189)
T cd06940 98 MFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKN 155 (189)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 46789999999999999999999999999986 9999999999999999999998753
No 49
>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=99.39 E-value=7.2e-13 Score=104.10 Aligned_cols=76 Identities=20% Similarity=0.254 Sum_probs=69.1
Q ss_pred CCCCCCCccccccccc-------------------------------------------------chhhhhhhhchhccc
Q psy16825 108 PNKSIPSLEDLERNTE-------------------------------------------------ISCTQVIDRLEHVAV 138 (183)
Q Consensus 108 ~~k~iP~f~~L~~~dq-------------------------------------------------~~~~~lv~~~~~l~~ 138 (183)
+.|.+|+|.+|+.+|| ..+.+++.+|+.|++
T Consensus 71 fAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~f~~~l~~L~l 150 (243)
T cd06935 71 FAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKNGGLGVVSDAIFDLGVSLSSFNL 150 (243)
T ss_pred HHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCeEeeHHHHHhcChHHHHHHHHHHHHHHHhcCC
Confidence 3599999999999999 234579999999999
Q ss_pred ChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825 139 SKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR 183 (183)
Q Consensus 139 ~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~ 183 (183)
|.+||++|+||+||+||++ |.+...|+++|++++.+|.+|+..+|
T Consensus 151 d~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~ 196 (243)
T cd06935 151 DDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRK 196 (243)
T ss_pred CHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999999986 99999999999999999999997643
No 50
>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=99.37 E-value=1e-12 Score=103.22 Aligned_cols=57 Identities=18% Similarity=0.289 Sum_probs=52.6
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.++++|++|.+||+|||||+|||| |++ |.+.+.|+.+|++++.+|.+||...
T Consensus 116 l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 174 (246)
T cd07073 116 MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACK 174 (246)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhc
Confidence 34788999999999999999999999999 875 9999999999999999999999764
No 51
>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=99.36 E-value=1.1e-12 Score=102.86 Aligned_cols=75 Identities=23% Similarity=0.298 Sum_probs=68.7
Q ss_pred CCCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccC
Q psy16825 108 PNKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVS 139 (183)
Q Consensus 108 ~~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~ 139 (183)
+.|.+|+|.+|+.+|| ..+.+++.+++.|++|
T Consensus 67 fAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l~~L~ld 146 (241)
T cd06939 67 FAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFDGKYAPIDLFKSLGCDDLISAVFDFAKSLCELKLT 146 (241)
T ss_pred HHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCEEEECCccccHHHHHHcCcHHHHHHHHHHHHHHHhcCCC
Confidence 3488999999999999 2256889999999999
Q ss_pred hhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 140 KEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 140 ~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
..||+||+||+|++||++ |.+...|+++|++++.+|.+|+...
T Consensus 147 ~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 190 (241)
T cd06939 147 EDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKN 190 (241)
T ss_pred HHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999987 9999999999999999999999764
No 52
>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=99.36 E-value=1.3e-12 Score=102.28 Aligned_cols=57 Identities=14% Similarity=0.240 Sum_probs=52.6
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|+.|++|.+||+||+||+||+||++ |.+...|+.+|++++.+|.+|+..+
T Consensus 125 l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 182 (238)
T cd06933 125 LVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCR 182 (238)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCCCCcchHHHHHHHHHHHHHHHHHHHhc
Confidence 34677889999999999999999999999986 9999999999999999999999764
No 53
>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=99.35 E-value=1.6e-12 Score=100.81 Aligned_cols=57 Identities=23% Similarity=0.328 Sum_probs=53.0
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+++++.+|++|++|.+||++||||+|||||.+ |.+...|+.+|++++.+|.+|+...
T Consensus 117 l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~ 174 (222)
T cd07349 117 LQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPL 174 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778899999999999999999999999987 9999999999999999999999754
No 54
>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=99.35 E-value=1.4e-12 Score=102.26 Aligned_cols=56 Identities=25% Similarity=0.405 Sum_probs=52.6
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
++++.+|+.|++|..||+|||||+|||||++ |.+...|+.+|++++.+|.+|+...
T Consensus 132 ~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 188 (241)
T cd07069 132 QELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCN 188 (241)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 4688999999999999999999999999987 9999999999999999999999753
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=99.35 E-value=1.5e-12 Score=102.31 Aligned_cols=56 Identities=20% Similarity=0.331 Sum_probs=52.0
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.+++.+|++|++|.+||+|||||+|||+ |.+ |.+...|+++|++++.+|.+||..+
T Consensus 117 ~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~ 174 (246)
T cd06947 117 RQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKR 174 (246)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4678999999999999999999999999 765 9999999999999999999999754
No 56
>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=99.35 E-value=1.8e-12 Score=102.75 Aligned_cols=57 Identities=11% Similarity=0.213 Sum_probs=53.3
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVLR 183 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~~ 183 (183)
.+++.+|+.|++|.+||+||+||+|++||++ |.+...|+++|++++.+|.+|+...+
T Consensus 151 ~e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~ 208 (259)
T cd06932 151 FEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNH 208 (259)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhC
Confidence 4789999999999999999999999999987 99999999999999999999997653
No 57
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.35 E-value=1.5e-12 Score=101.89 Aligned_cols=56 Identities=25% Similarity=0.353 Sum_probs=52.5
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.+++.+|++|++|.+||+||+||+|||||++ |++.+.|+.+|++++.+|.+||...
T Consensus 130 ~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~ 186 (237)
T cd07070 130 QELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCH 186 (237)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 4689999999999999999999999999986 9999999999999999999999753
No 58
>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge
Probab=99.34 E-value=2e-12 Score=99.19 Aligned_cols=57 Identities=19% Similarity=0.335 Sum_probs=53.1
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|++|++|.+||++||||+|+|||++ |++...|+++|++++.+|.+|+...
T Consensus 112 i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~ 169 (206)
T cd06950 112 LQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTR 169 (206)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 45788999999999999999999999999986 9999999999999999999999753
No 59
>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=99.33 E-value=2.1e-12 Score=100.14 Aligned_cols=56 Identities=16% Similarity=0.176 Sum_probs=52.7
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+++++.+|++|++|..||++||||+|||||.+ | +...|+++|++++.+|.+||...
T Consensus 120 l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~ 176 (222)
T cd06951 120 IQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMT 176 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhh
Confidence 56899999999999999999999999999987 9 99999999999999999999754
No 60
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=99.33 E-value=2.8e-12 Score=100.33 Aligned_cols=73 Identities=21% Similarity=0.327 Sum_probs=66.6
Q ss_pred CCCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccC
Q psy16825 108 PNKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVS 139 (183)
Q Consensus 108 ~~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~ 139 (183)
+.|.+|+|.+|+.+|| ..+.+++.+|+.|++|
T Consensus 60 wAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~~~~~~~~~~~~i~ef~~~l~~L~ld 139 (238)
T cd07348 60 WAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQCVRGFGDWIDSILEFSQSLHRMNLD 139 (238)
T ss_pred HHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHHHHhhHHHHHHHHHHHHHHHHHcCCC
Confidence 3499999999999999 2246789999999999
Q ss_pred hhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825 140 KEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYV 181 (183)
Q Consensus 140 ~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~ 181 (183)
.+||+||+||+|+ +|++ |.+...|+.+|++++.+|.+|+..
T Consensus 140 ~~E~a~LkAIvLf-~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~ 181 (238)
T cd07348 140 VSAFSCLAALVII-TDRHGLKEPKRVEELQNRLISCLKEHVSG 181 (238)
T ss_pred HHHHHHHHHHHHc-CCCcCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999 7876 999999999999999999999975
No 61
>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=99.33 E-value=2.4e-12 Score=101.09 Aligned_cols=56 Identities=18% Similarity=0.288 Sum_probs=51.6
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCC-C-CCCchhHHHHHHHHHHHHHHHHHHh
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSD-V-KLDEFSSLKKFRNSILSSLGDCIYV 181 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d-~-~L~~~~~v~~~~~~~~~~L~~~~~~ 181 (183)
+.+++.+|++|++|.+||+|||||+||||| . +|++...|+.+|++++.+|.+||..
T Consensus 116 ~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~ 173 (248)
T cd07075 116 MHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTK 173 (248)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999999999999996 4 4999999999999999999999974
No 62
>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=99.32 E-value=3.1e-12 Score=100.16 Aligned_cols=57 Identities=12% Similarity=0.294 Sum_probs=53.3
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|++|++|.+||++|+||+|||||++ |.+...|+.+|++++.+|.+|+...
T Consensus 130 i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~ 187 (236)
T cd06954 130 IFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIK 187 (236)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 35789999999999999999999999999986 9999999999999999999999754
No 63
>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=99.31 E-value=3.7e-12 Score=98.22 Aligned_cols=56 Identities=27% Similarity=0.393 Sum_probs=52.0
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.+++.+|+++++|.+||++|+||+|||||.+ |++.+.|+++|++++.+|.+||...
T Consensus 118 ~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~ 174 (213)
T cd06953 118 TYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELN 174 (213)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3678899999999999999999999999986 9999999999999999999999754
No 64
>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=99.31 E-value=4e-12 Score=96.76 Aligned_cols=58 Identities=19% Similarity=0.212 Sum_probs=53.6
Q ss_pred hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.+.+++.+|++|++|.+||++|+||+||+||.+ |.+.+.|+++|++++.+|.+||...
T Consensus 87 ~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~ 145 (195)
T cd06941 87 ALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRN 145 (195)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 356789999999999999999999999999985 9999999999999999999998754
No 65
>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=99.30 E-value=4.7e-12 Score=98.16 Aligned_cols=57 Identities=18% Similarity=0.314 Sum_probs=52.2
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|++|++|.+||+||+||+|||||++ |++...|+.+|++++.+|.+||...
T Consensus 119 i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~ 176 (221)
T cd06936 119 MFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLY 176 (221)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 34678888999999999999999999999986 9999999999999999999999654
No 66
>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=99.29 E-value=5.2e-12 Score=99.02 Aligned_cols=74 Identities=23% Similarity=0.324 Sum_probs=67.3
Q ss_pred CCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccCh
Q psy16825 109 NKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSK 140 (183)
Q Consensus 109 ~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~ 140 (183)
.|.+|+|.+|+.+|| ..+.+++.+|+.|+++.
T Consensus 61 AK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~f~~~l~~L~ld~ 140 (239)
T cd06945 61 AEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQCVRGFGEWLDSILAFSSSLQSLLLDD 140 (239)
T ss_pred HHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHHHHHhHHHHHHHHHHHHHHHHHHhCCh
Confidence 488999999999999 22456778999999999
Q ss_pred hHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 141 EEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 141 ~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.||++|+||+|++||++ |.+.+.|+++|++++.+|.+|+...
T Consensus 141 ~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~ 183 (239)
T cd06945 141 ISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSN 183 (239)
T ss_pred HHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999986 9999999999999999999999764
No 67
>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=99.28 E-value=4.8e-12 Score=99.31 Aligned_cols=56 Identities=27% Similarity=0.387 Sum_probs=51.0
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCC-CCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANS-DVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~-d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
++++.+|+++++|.+||+|||||+|||| |++ |++...|+++|++|+.+|.+||..+
T Consensus 117 ~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~ 174 (248)
T cd07074 117 WQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLR 174 (248)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 3578899999999999999999999999 665 9999999999999999999997543
No 68
>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=99.28 E-value=7.7e-12 Score=97.89 Aligned_cols=73 Identities=19% Similarity=0.359 Sum_probs=66.1
Q ss_pred CCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccCh
Q psy16825 109 NKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVSK 140 (183)
Q Consensus 109 ~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~~ 140 (183)
.|.+|+|.+|+.+|| ..+.+++.+|+.|++|.
T Consensus 61 AK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~i~ef~~~l~~L~ld~ 140 (238)
T cd07071 61 AEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVRGFGEWIDSIVEFSSNLQNMNIDI 140 (238)
T ss_pred hccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhhhhhcHHHHHHHHHHHHHHHHhcCCCH
Confidence 499999999999999 22468999999999999
Q ss_pred hHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 141 EEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 141 ~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+||+||+||+|++ |.+ |.+...|+++|++++.+|.+|+..+
T Consensus 141 ~E~alLkAIvLf~-D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 182 (238)
T cd07071 141 SAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLKDHVTFN 182 (238)
T ss_pred HHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999995 765 9999999999999999999999753
No 69
>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=99.27 E-value=9.1e-12 Score=95.59 Aligned_cols=57 Identities=23% Similarity=0.388 Sum_probs=52.8
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|++|++|.+||++|+||+|||||.. |++...|+++|++++.+|.+|+...
T Consensus 117 ~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~ 174 (207)
T cd06943 117 LTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQK 174 (207)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 45789999999999999999999999999985 9999999999999999999999653
No 70
>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=99.26 E-value=8.1e-12 Score=97.84 Aligned_cols=57 Identities=23% Similarity=0.412 Sum_probs=53.1
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|++|++|.+||+|||||+|||||++ |++...|+++|++++.+|.+|+...
T Consensus 129 i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~ 186 (237)
T cd06944 129 AQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCN 186 (237)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 45889999999999999999999999999986 9999999999999999999998654
No 71
>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=99.26 E-value=9.6e-12 Score=97.37 Aligned_cols=73 Identities=22% Similarity=0.310 Sum_probs=65.8
Q ss_pred CCCCCCCccccccccc------------------------------------------------chhhhhhhhchhcccC
Q psy16825 108 PNKSIPSLEDLERNTE------------------------------------------------ISCTQVIDRLEHVAVS 139 (183)
Q Consensus 108 ~~k~iP~f~~L~~~dq------------------------------------------------~~~~~lv~~~~~l~~~ 139 (183)
+.|.+|+|.+|+.+|| ..+.+++.+|+.|++|
T Consensus 61 wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~i~ef~~~l~~L~ld 140 (239)
T cd07072 61 FAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQRSFGDWLHAILEFSKSLHAMDID 140 (239)
T ss_pred HhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEeeCCeeecHHHHHhhHHHHHHHHHHHHHHHHHcCCC
Confidence 3599999999999999 2245889999999999
Q ss_pred hhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825 140 KEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYV 181 (183)
Q Consensus 140 ~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~ 181 (183)
.+||+||+||+||+ |.+ |.+...|+++|++++.+|.+|+..
T Consensus 141 ~~E~a~LkAivLf~-dr~gL~~~~~Ve~lQe~~~~aL~~yi~~ 182 (239)
T cd07072 141 ISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTY 182 (239)
T ss_pred HHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999996 664 999999999999999999999974
No 72
>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=99.26 E-value=8.3e-12 Score=97.63 Aligned_cols=57 Identities=25% Similarity=0.368 Sum_probs=51.8
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCC-C-----CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDV-K-----LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~-~-----L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|+.+++|.+||+|||||+|||||+ + |++...|+++|++++.+|.+||...
T Consensus 119 ~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~ 181 (235)
T cd06949 119 LLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKR 181 (235)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhc
Confidence 3568889999999999999999999999997 4 6788999999999999999999754
No 73
>cd06948 NR_LBD_COUP-TF Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family. The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone
Probab=99.25 E-value=1e-11 Score=97.17 Aligned_cols=56 Identities=21% Similarity=0.371 Sum_probs=52.3
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.+++.+|++|++|.+||++||||+|+|||.+ |++...|+++|++++.+|.+|+...
T Consensus 119 ~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~ 175 (236)
T cd06948 119 QEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQ 175 (236)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4788999999999999999999999999985 9999999999999999999999754
No 74
>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=99.23 E-value=1.9e-11 Score=94.79 Aligned_cols=57 Identities=37% Similarity=0.648 Sum_probs=52.7
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|++|++|.+||++|+||+|+|||.. +.+...|+++|++|+.+|.+||...
T Consensus 113 ~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~ 170 (221)
T cd06946 113 CLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGR 170 (221)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 45799999999999999999999999999975 9999999999999999999999643
No 75
>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=99.22 E-value=2.6e-11 Score=90.43 Aligned_cols=57 Identities=21% Similarity=0.427 Sum_probs=52.8
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+++++++|.+||++|+||+||+||.. |++...|++.|++++.+|.+|+...
T Consensus 88 ~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~ 145 (174)
T cd06929 88 LFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVN 145 (174)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 45789999999999999999999999999985 9999999999999999999998654
No 76
>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=99.18 E-value=5.2e-11 Score=87.87 Aligned_cols=58 Identities=22% Similarity=0.385 Sum_probs=53.3
Q ss_pred hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.+.+++.+|+++++|.+||++|+||+|++||.. |++...|++.|++++.+|.+|+...
T Consensus 86 ~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~ 144 (165)
T cd06930 86 RLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKR 144 (165)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhh
Confidence 346799999999999999999999999999985 9999999999999999999999753
No 77
>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=99.16 E-value=6e-11 Score=92.00 Aligned_cols=57 Identities=35% Similarity=0.581 Sum_probs=52.9
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
+.+++.+|+++++|.+||++|+||+|+|||+. |.+...|++.|++++.+|.+||...
T Consensus 113 ~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~ 170 (221)
T cd07068 113 LLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKR 170 (221)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHh
Confidence 45789999999999999999999999999986 8999999999999999999998754
No 78
>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=99.15 E-value=8.2e-11 Score=89.27 Aligned_cols=55 Identities=16% Similarity=0.189 Sum_probs=51.7
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCCC--CC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANSD--VK-LDEFSSLKKFRNSILSSLGDCIYV 181 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d--~~-L~~~~~v~~~~~~~~~~L~~~~~~ 181 (183)
.+++.+|++|++|.+||++|+||+|++|| .. |++...|+.+|+.++.+|.+|+..
T Consensus 88 ~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~ 145 (191)
T cd06942 88 LQFANKILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFK 145 (191)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHh
Confidence 47999999999999999999999999999 76 999999999999999999999864
No 79
>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=99.14 E-value=8.8e-11 Score=91.60 Aligned_cols=58 Identities=19% Similarity=0.330 Sum_probs=54.7
Q ss_pred hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.+++++.+|+.|++|..||++||||+|||||++ |.+...|+++|++++.+|.+|+...
T Consensus 128 ~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~ 186 (232)
T cd07350 128 AIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMI 186 (232)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 467999999999999999999999999999987 9999999999999999999999754
No 80
>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=99.12 E-value=1.4e-10 Score=90.54 Aligned_cols=58 Identities=19% Similarity=0.216 Sum_probs=51.9
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHhcC
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVKLDEFSSLKKFRNSILSSLGDCIYVLR 183 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~L~~~~~v~~~~~~~~~~L~~~~~~~~ 183 (183)
+.+++.+|++|++|.+||++|+||+||++..+|++...|+++|++++.+|.+||..++
T Consensus 125 l~~~~~~l~~L~ld~~E~~lL~AI~Lf~d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~ 182 (231)
T cd06938 125 LFRFCRAMCSMKVDNAEYALLTAIVIFSDRPGLLQPKKVEKIQEIYLEALRAYVDNRR 182 (231)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3457999999999999999999999998555699999999999999999999997653
No 81
>cd06952 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2. The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D
Probab=99.11 E-value=1.4e-10 Score=90.03 Aligned_cols=56 Identities=23% Similarity=0.394 Sum_probs=52.0
Q ss_pred hhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 127 TQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 127 ~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
.+++.+|+++++|..||++|+||+|++||+. +++...|+++|++++.+|.+|+...
T Consensus 116 ~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~ 172 (222)
T cd06952 116 QEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKT 172 (222)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4678999999999999999999999999986 9999999999999999999999643
No 82
>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal lig
Probab=98.98 E-value=1.1e-09 Score=84.95 Aligned_cols=56 Identities=29% Similarity=0.430 Sum_probs=52.1
Q ss_pred hhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCchhHHHHHHHHHHHHHHHHHHh
Q psy16825 126 CTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEFSSLKKFRNSILSSLGDCIYV 181 (183)
Q Consensus 126 ~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~~~v~~~~~~~~~~L~~~~~~ 181 (183)
+.+++.+|+++++|.+||++|+||+|++||.. |++.+.++.+|++++.+|.+|+..
T Consensus 118 ~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~ 174 (222)
T cd06931 118 LDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYIND 174 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 45789999999999999999999999999986 999999999999999999999853
No 83
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=98.69 E-value=4.4e-08 Score=71.65 Aligned_cols=59 Identities=25% Similarity=0.395 Sum_probs=52.9
Q ss_pred chhhhhhhhchhcccChhHHHHHHHHHhcCCCCC--CCchhHHHHHHHHHHHHHHHHHHhc
Q psy16825 124 ISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK--LDEFSSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 124 ~~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~--L~~~~~v~~~~~~~~~~L~~~~~~~ 182 (183)
..+.+++.+|.++++|.+|+++|+|++|++|+.. +.....+++.|+++..+|.+|+...
T Consensus 86 ~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~ 146 (168)
T cd06157 86 RLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLRKN 146 (168)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3456899999999999999999999999999975 6777889999999999999998653
No 84
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=98.67 E-value=2.7e-08 Score=72.43 Aligned_cols=59 Identities=25% Similarity=0.344 Sum_probs=52.9
Q ss_pred chhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CCch--hHHHHHHHHHHHHHHHHHHhc
Q psy16825 124 ISCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LDEF--SSLKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 124 ~~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~~~--~~v~~~~~~~~~~L~~~~~~~ 182 (183)
..+.+++.+|++|+++.+|+++|+++++++|+.. +.+. ..++++|+.+..+|.+|+...
T Consensus 80 ~~~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~ 141 (163)
T smart00430 80 RILQELVKPLRELKLDDEEYALLKAILLFNPAGPGLSEEGKEILEKLQEKLANALHDYYLKN 141 (163)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHcChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4456899999999999999999999999999875 8877 789999999999999998653
No 85
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=98.07 E-value=9.2e-06 Score=61.14 Aligned_cols=55 Identities=27% Similarity=0.478 Sum_probs=48.1
Q ss_pred hhhhhhhhchhcccChhHHHHHHHHHhcCCCCC-CC-chhH-HHHHHHHHHHHHHHHH
Q psy16825 125 SCTQVIDRLEHVAVSKEEYYFLKALVLANSDVK-LD-EFSS-LKKFRNSILSSLGDCI 179 (183)
Q Consensus 125 ~~~~lv~~~~~l~~~~~E~~~lkai~L~~~d~~-L~-~~~~-v~~~~~~~~~~L~~~~ 179 (183)
.+..++.+|.++++|.+||+++++++|++|+.. +. +... ++.+|+++..+|.+|+
T Consensus 106 ~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~ 163 (203)
T PF00104_consen 106 YMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYY 163 (203)
T ss_dssp HHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHH
Confidence 455789999999999999999999999999876 66 5555 8899999999999998
No 86
>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=89.51 E-value=0.2 Score=34.79 Aligned_cols=33 Identities=21% Similarity=0.642 Sum_probs=23.9
Q ss_pred CCCCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825 8 LPRRLCLVCGDVAS---GFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 8 ~~~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~ 40 (183)
+....|.-||.+.. ...||++.|..|++.+|-.
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~l 46 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSL 46 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHH
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHh
Confidence 44678999998775 3789999999999997764
No 87
>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=78.35 E-value=1.3 Score=30.46 Aligned_cols=31 Identities=23% Similarity=0.623 Sum_probs=26.2
Q ss_pred CCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825 10 RRLCLVCGDVAS---GFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 10 ~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~ 40 (183)
...|.-||.+.. ..-||++.|-.|++..|..
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~l 36 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSL 36 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHHhc
Confidence 567999998764 4799999999999998875
No 88
>KOG3277|consensus
Probab=78.09 E-value=0.9 Score=33.02 Aligned_cols=32 Identities=31% Similarity=0.745 Sum_probs=24.4
Q ss_pred cccccCCCCcc------cccccc--cccchhhhhhccccCCc
Q psy16825 12 LCLVCGDVASG------FHYGVA--SCEACKAFFKRTIQGNI 45 (183)
Q Consensus 12 ~C~vC~~~~~~------~hyg~~--~C~~C~~FFrR~v~~~~ 45 (183)
.|.||+.+++. ||-|++ +|.||+.+. .+..++
T Consensus 81 TCkvCntRs~ktisk~AY~~GvVivqC~gC~~~H--liaDnL 120 (165)
T KOG3277|consen 81 TCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH--LIADNL 120 (165)
T ss_pred EeeccCCccccccChhhhhCceEEEECCCCccce--eehhhh
Confidence 59999988753 888876 899999886 444443
No 89
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=65.14 E-value=3.3 Score=21.29 Aligned_cols=21 Identities=33% Similarity=0.760 Sum_probs=16.0
Q ss_pred cccccCCCCcccccccccccchh
Q psy16825 12 LCLVCGDVASGFHYGVASCEACK 34 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~ 34 (183)
.|.||+...+|.. ...|..|-
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 4888988888885 55777775
No 90
>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=62.06 E-value=2.5 Score=22.66 Aligned_cols=24 Identities=21% Similarity=0.607 Sum_probs=12.8
Q ss_pred CcccccCCCCc----ccccccccccchh
Q psy16825 11 RLCLVCGDVAS----GFHYGVASCEACK 34 (183)
Q Consensus 11 ~~C~vC~~~~~----~~hyg~~~C~~C~ 34 (183)
..|.-||++-. -.||+..+|..|+
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 46888887653 3789999999995
No 91
>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=60.78 E-value=2.8 Score=18.90 Aligned_cols=11 Identities=45% Similarity=0.957 Sum_probs=8.4
Q ss_pred chhhhhhcccc
Q psy16825 32 ACKAFFKRTIQ 42 (183)
Q Consensus 32 ~C~~FFrR~v~ 42 (183)
+|+.||..+..
T Consensus 6 ~CknffWK~~t 16 (18)
T PF03002_consen 6 GCKNFFWKTFT 16 (18)
T ss_pred cccceeecccc
Confidence 79999987643
No 92
>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=58.15 E-value=4.4 Score=23.27 Aligned_cols=23 Identities=35% Similarity=0.996 Sum_probs=18.9
Q ss_pred cccccCCCCc-c-cccccccccchh
Q psy16825 12 LCLVCGDVAS-G-FHYGVASCEACK 34 (183)
Q Consensus 12 ~C~vC~~~~~-~-~hyg~~~C~~C~ 34 (183)
.|.||+.+.. | .-||.+.|..|-
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE 25 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCE 25 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHH
Confidence 3899999886 6 558999999996
No 93
>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=57.18 E-value=2.6 Score=20.26 Aligned_cols=19 Identities=16% Similarity=0.805 Sum_probs=13.2
Q ss_pred eecCCCCCccccccccccc
Q psy16825 47 YTCPASNDCEINKRRRKAC 65 (183)
Q Consensus 47 ~~C~~~~~C~~~k~~r~~C 65 (183)
+.|+.+..|.+|+..+..|
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 4588888899988877765
No 94
>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=55.95 E-value=4.9 Score=23.03 Aligned_cols=27 Identities=26% Similarity=0.797 Sum_probs=20.0
Q ss_pred cccccCCCCcccccccccccchhhhhhcc
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FFrR~ 40 (183)
.|.||+. .+..-.++.|..|..+|...
T Consensus 1 ~C~vC~~--~~~~~~~i~C~~C~~~~H~~ 27 (51)
T PF00628_consen 1 YCPVCGQ--SDDDGDMIQCDSCNRWYHQE 27 (51)
T ss_dssp EBTTTTS--SCTTSSEEEBSTTSCEEETT
T ss_pred eCcCCCC--cCCCCCeEEcCCCChhhCcc
Confidence 3889998 44555677899998887654
No 95
>PRK00420 hypothetical protein; Validated
Probab=55.49 E-value=6.2 Score=27.29 Aligned_cols=26 Identities=23% Similarity=0.423 Sum_probs=20.2
Q ss_pred CcccccCCCCcccccccccccchhhh
Q psy16825 11 RLCLVCGDVASGFHYGVASCEACKAF 36 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~~~C~~C~~F 36 (183)
..|++||.+-.+.+=|-.-|-.|..+
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 57999998887777777778888643
No 96
>KOG0703|consensus
Probab=54.70 E-value=6.6 Score=31.66 Aligned_cols=32 Identities=22% Similarity=0.640 Sum_probs=27.0
Q ss_pred CCCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825 9 PRRLCLVCGDVAS---GFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 9 ~~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~ 40 (183)
....|.-||.+.- .+.+||+.|-.|++.+|..
T Consensus 24 ~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~l 58 (287)
T KOG0703|consen 24 DNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSL 58 (287)
T ss_pred ccCcccccCCCCCCeEEeecCeEEEeecccccccc
Confidence 3678999998764 4899999999999998765
No 97
>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 smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=50.68 E-value=14 Score=21.62 Aligned_cols=33 Identities=27% Similarity=0.653 Sum_probs=23.1
Q ss_pred CCcccccCCCCcc-c---cccc-ccccchhhhhhcccc
Q psy16825 10 RRLCLVCGDVASG-F---HYGV-ASCEACKAFFKRTIQ 42 (183)
Q Consensus 10 ~~~C~vC~~~~~~-~---hyg~-~~C~~C~~FFrR~v~ 42 (183)
...|..|+...+- . -.|. .-|++|-.||++.-.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 3569999876653 2 3443 679999999987544
No 99
>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=49.07 E-value=13 Score=20.93 Aligned_cols=16 Identities=38% Similarity=0.947 Sum_probs=11.7
Q ss_pred CCCCCCCcccccCCCC
Q psy16825 5 EEELPRRLCLVCGDVA 20 (183)
Q Consensus 5 ~~~~~~~~C~vC~~~~ 20 (183)
.+..+..+|.|||.+-
T Consensus 3 K~~lp~K~C~~C~rpf 18 (42)
T PF10013_consen 3 KSNLPSKICPVCGRPF 18 (42)
T ss_pred cccCCCCcCcccCCcc
Confidence 3456778899999753
No 100
>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=47.68 E-value=8 Score=21.95 Aligned_cols=39 Identities=28% Similarity=0.690 Sum_probs=19.0
Q ss_pred chhhhhhccccCCceeecCCC---CCccccccccccccchhhh
Q psy16825 32 ACKAFFKRTIQGNIEYTCPAS---NDCEINKRRRKACQACRFQ 71 (183)
Q Consensus 32 ~C~~FFrR~v~~~~~~~C~~~---~~C~~~k~~r~~C~~CR~~ 71 (183)
.|..||...--.+- ++|+.= ....+....+..|+.||.|
T Consensus 5 ~c~~~l~~~RW~~g-~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 5 ACREYLEEIRWPDG-FVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred HHHHHHHHhcCCCC-CCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 34555555444433 445431 1223333356678888754
No 101
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=47.54 E-value=8.1 Score=25.39 Aligned_cols=27 Identities=30% Similarity=0.748 Sum_probs=21.3
Q ss_pred CcccccCCCCc-ccccccccccchhhhh
Q psy16825 11 RLCLVCGDVAS-GFHYGVASCEACKAFF 37 (183)
Q Consensus 11 ~~C~vC~~~~~-~~hyg~~~C~~C~~FF 37 (183)
-.|..|+..+. -.-.|++.|+.|..-|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 35999999875 3788999999997544
No 102
>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=47.15 E-value=11 Score=22.86 Aligned_cols=28 Identities=25% Similarity=0.836 Sum_probs=18.3
Q ss_pred CCCcccccCCCCc-ccccccccc-cchhhhhhcc
Q psy16825 9 PRRLCLVCGDVAS-GFHYGVASC-EACKAFFKRT 40 (183)
Q Consensus 9 ~~~~C~vC~~~~~-~~hyg~~~C-~~C~~FFrR~ 40 (183)
++..|.+||.+.. ...| | ..|+.-+++.
T Consensus 2 ~HkHC~~CG~~Ip~~~~f----CS~~C~~~~~k~ 31 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDESF----CSPKCREEYRKR 31 (59)
T ss_pred CCCcCCcCCCcCCcchhh----hCHHHHHHHHHH
Confidence 5778999998774 3444 6 3676555443
No 103
>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=46.83 E-value=6.7 Score=16.99 Aligned_cols=7 Identities=57% Similarity=0.951 Sum_probs=5.1
Q ss_pred hhhhccc
Q psy16825 35 AFFKRTI 41 (183)
Q Consensus 35 ~FFrR~v 41 (183)
+||+|.-
T Consensus 3 GFFKR~~ 9 (15)
T PF00357_consen 3 GFFKRQR 9 (15)
T ss_dssp CHHHHHH
T ss_pred ccccccC
Confidence 6888863
No 104
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=45.88 E-value=13 Score=31.08 Aligned_cols=32 Identities=22% Similarity=0.653 Sum_probs=26.8
Q ss_pred CCCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825 9 PRRLCLVCGDVAS---GFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 9 ~~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~ 40 (183)
....|.-||.+.. ...||++.|-.|.+..|..
T Consensus 21 gNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsL 55 (395)
T PLN03114 21 DNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 55 (395)
T ss_pred CCCcCccCCCCCCCceeeccceeehhhhhHhhccC
Confidence 4677999998764 4899999999999998864
No 105
>PHA03124 dUTPase; Provisional
Probab=45.42 E-value=8.2 Score=32.35 Aligned_cols=14 Identities=43% Similarity=1.151 Sum_probs=12.1
Q ss_pred cccchhhhhhcccc
Q psy16825 29 SCEACKAFFKRTIQ 42 (183)
Q Consensus 29 ~C~~C~~FFrR~v~ 42 (183)
-|-||++||||...
T Consensus 192 ~~~~~~~~~~~~~~ 205 (418)
T PHA03124 192 GCMGCKAFYRRLFE 205 (418)
T ss_pred cccchHHHHHHHHH
Confidence 49999999999854
No 106
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.96 E-value=11 Score=21.89 Aligned_cols=18 Identities=28% Similarity=0.623 Sum_probs=13.4
Q ss_pred CCCCCCCCCcccccCCCC
Q psy16825 3 IKEEELPRRLCLVCGDVA 20 (183)
Q Consensus 3 ~~~~~~~~~~C~vC~~~~ 20 (183)
.+.+..+..+|.||+.+-
T Consensus 5 r~Ka~lp~KICpvCqRPF 22 (54)
T COG4338 5 RPKATLPDKICPVCQRPF 22 (54)
T ss_pred CcccccchhhhhhhcCch
Confidence 345667778999999764
No 107
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=43.69 E-value=11 Score=22.52 Aligned_cols=23 Identities=35% Similarity=0.847 Sum_probs=18.2
Q ss_pred CcccccCCCCc-ccccccccccch
Q psy16825 11 RLCLVCGDVAS-GFHYGVASCEAC 33 (183)
Q Consensus 11 ~~C~vC~~~~~-~~hyg~~~C~~C 33 (183)
+.|.|||.+.. --.||...|+-|
T Consensus 17 r~C~vCg~~~gliRkygL~~CRqC 40 (54)
T PTZ00218 17 RQCRVCSNRHGLIRKYGLNVCRQC 40 (54)
T ss_pred CeeecCCCcchhhhhcCcchhhHH
Confidence 56999999753 267888888888
No 108
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=40.95 E-value=15 Score=22.16 Aligned_cols=13 Identities=46% Similarity=1.214 Sum_probs=9.6
Q ss_pred CCCCcccccCCCC
Q psy16825 8 LPRRLCLVCGDVA 20 (183)
Q Consensus 8 ~~~~~C~vC~~~~ 20 (183)
.|++.|.|||...
T Consensus 6 ~PH~HC~VCg~aI 18 (64)
T COG4068 6 VPHRHCVVCGKAI 18 (64)
T ss_pred CCCccccccCCcC
Confidence 3567899998754
No 109
>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=40.72 E-value=12 Score=19.02 Aligned_cols=20 Identities=35% Similarity=1.041 Sum_probs=7.7
Q ss_pred cccccCCCCcc-cccccccccchh
Q psy16825 12 LCLVCGDVASG-FHYGVASCEACK 34 (183)
Q Consensus 12 ~C~vC~~~~~~-~hyg~~~C~~C~ 34 (183)
.|.+|+.+..+ ..|. |..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~---C~~Cd 22 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYR---CSECD 22 (30)
T ss_dssp --TTTS----S--EEE----TTT-
T ss_pred cCCcCCCcCCCCceEE---CccCC
Confidence 58888888887 6664 55553
No 110
>PRK01343 zinc-binding protein; Provisional
Probab=39.22 E-value=29 Score=20.88 Aligned_cols=26 Identities=27% Similarity=0.524 Sum_probs=15.4
Q ss_pred CCCCcccccCCCCcccccccccccchh
Q psy16825 8 LPRRLCLVCGDVASGFHYGVASCEACK 34 (183)
Q Consensus 8 ~~~~~C~vC~~~~~~~hyg~~~C~~C~ 34 (183)
.+...|.|||.+... .|-.++-..|+
T Consensus 7 ~p~~~CP~C~k~~~~-~~rPFCS~RC~ 32 (57)
T PRK01343 7 RPTRPCPECGKPSTR-EAYPFCSERCR 32 (57)
T ss_pred CCCCcCCCCCCcCcC-CCCcccCHHHh
Confidence 356679999988642 33344444443
No 111
>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=38.52 E-value=14 Score=20.48 Aligned_cols=23 Identities=26% Similarity=0.637 Sum_probs=11.1
Q ss_pred CcccccCCCCccccc------ccccccch
Q psy16825 11 RLCLVCGDVASGFHY------GVASCEAC 33 (183)
Q Consensus 11 ~~C~vC~~~~~~~hy------g~~~C~~C 33 (183)
.+|.+||....-..| |.+.|+.|
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCC
Confidence 468899875432213 55667777
No 112
>KOG4443|consensus
Probab=38.27 E-value=7.9 Score=34.66 Aligned_cols=38 Identities=16% Similarity=0.376 Sum_probs=31.4
Q ss_pred CCCCCCcccccCCCCcccccccccccchhhhhhccccC
Q psy16825 6 EELPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQG 43 (183)
Q Consensus 6 ~~~~~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~ 43 (183)
.......|.||+....+.--++.+|.-|..|+.+...+
T Consensus 14 ~~~~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt 51 (694)
T KOG4443|consen 14 AIIVCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVT 51 (694)
T ss_pred hhhhhhhhhhhccccccccCcchhhhhhcccCCcchhh
Confidence 34445679999999999999999999999999887554
No 113
>PLN02189 cellulose synthase
Probab=37.30 E-value=20 Score=34.12 Aligned_cols=23 Identities=30% Similarity=0.946 Sum_probs=16.3
Q ss_pred CCCcccccCCC----Ccccccccccccch
Q psy16825 9 PRRLCLVCGDV----ASGFHYGVASCEAC 33 (183)
Q Consensus 9 ~~~~C~vC~~~----~~~~hyg~~~C~~C 33 (183)
..+.|+||||. .+|--| .+|+.|
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~f--vaC~~C 59 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLF--VACNEC 59 (1040)
T ss_pred cCccccccccccCcCCCCCEE--EeeccC
Confidence 34589999997 567655 456666
No 114
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=37.12 E-value=20 Score=29.52 Aligned_cols=31 Identities=23% Similarity=0.570 Sum_probs=26.7
Q ss_pred CCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825 10 RRLCLVCGDVAS---GFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 10 ~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~ 40 (183)
...|.-||.+.- ...|||+-|--|++-+|-.
T Consensus 20 Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsL 53 (319)
T COG5347 20 NKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSL 53 (319)
T ss_pred cCccccCCCCCCceEecccCeEEEeecchhhhcc
Confidence 567999999884 5999999999999998754
No 115
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=34.07 E-value=23 Score=19.31 Aligned_cols=27 Identities=33% Similarity=0.811 Sum_probs=16.8
Q ss_pred ccccCCCCcc----cccc----cccccchhhhhhc
Q psy16825 13 CLVCGDVASG----FHYG----VASCEACKAFFKR 39 (183)
Q Consensus 13 C~vC~~~~~~----~hyg----~~~C~~C~~FFrR 39 (183)
|..||+...| +.+| .+.|+.|..=|+.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~fk~ 35 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQFKK 35 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHHHh
Confidence 6778877665 2221 2478888877764
No 116
>smart00274 FOLN Follistatin-N-terminal domain-like. Follistatin-N-terminal domain-like, EGF-like. Region distinct from the kazal-like sequence
Probab=33.92 E-value=24 Score=17.57 Aligned_cols=19 Identities=26% Similarity=0.718 Sum_probs=15.0
Q ss_pred eecCCCCCccccccccccc
Q psy16825 47 YTCPASNDCEINKRRRKAC 65 (183)
Q Consensus 47 ~~C~~~~~C~~~k~~r~~C 65 (183)
+.|+.+..|.+|+..+..|
T Consensus 5 v~C~~G~~C~~d~~g~p~C 23 (26)
T smart00274 5 VQCPFGKVCVVDKGGNARC 23 (26)
T ss_pred EECCCCCEEEeCCCCCEEE
Confidence 4688888999987776666
No 117
>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=33.61 E-value=14 Score=24.50 Aligned_cols=25 Identities=24% Similarity=0.664 Sum_probs=20.0
Q ss_pred CcccccCCCCc-ccccccccccchhh
Q psy16825 11 RLCLVCGDVAS-GFHYGVASCEACKA 35 (183)
Q Consensus 11 ~~C~vC~~~~~-~~hyg~~~C~~C~~ 35 (183)
-.|..||..+- -.-.|++.|..|.-
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 35999999885 47789999999963
No 118
>PRK12495 hypothetical protein; Provisional
Probab=33.57 E-value=20 Score=27.80 Aligned_cols=29 Identities=28% Similarity=0.535 Sum_probs=23.2
Q ss_pred CCcccccCCCCcccccccccccchhhhhhc
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKR 39 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR 39 (183)
...|.+||.+..- +=|+..|-.|...+-+
T Consensus 42 a~hC~~CG~PIpa-~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 42 NAHCDECGDPIFR-HDGQEFCPTCQQPVTE 70 (226)
T ss_pred hhhcccccCcccC-CCCeeECCCCCCcccc
Confidence 4679999999984 4799999999866543
No 119
>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=33.23 E-value=17 Score=21.61 Aligned_cols=25 Identities=24% Similarity=0.689 Sum_probs=15.8
Q ss_pred CCCcccccCCCCcccccccccccchhhhhh
Q psy16825 9 PRRLCLVCGDVASGFHYGVASCEACKAFFK 38 (183)
Q Consensus 9 ~~~~C~vC~~~~~~~hyg~~~C~~C~~FFr 38 (183)
....|..||...-.+| .|.+| +||+
T Consensus 25 ~l~~c~~cg~~~~~H~----vc~~c-G~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPHR----VCPSC-GYYK 49 (56)
T ss_dssp SEEESSSSSSEESTTS----BCTTT-BBSS
T ss_pred ceeeeccCCCEecccE----eeCCC-CeEC
Confidence 3456999996554433 48888 5664
No 120
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=33.00 E-value=26 Score=33.55 Aligned_cols=23 Identities=30% Similarity=0.993 Sum_probs=14.4
Q ss_pred CCCcccccCCC----Ccccccccccccch
Q psy16825 9 PRRLCLVCGDV----ASGFHYGVASCEAC 33 (183)
Q Consensus 9 ~~~~C~vC~~~----~~~~hyg~~~C~~C 33 (183)
..+.|+||||. ++|--| ++|+.|
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~F--VAC~eC 42 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPF--VACDVC 42 (1079)
T ss_pred CCceeeecccccCcCCCCCEE--EEeccC
Confidence 34689999996 345444 345555
No 121
>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=32.69 E-value=16 Score=24.80 Aligned_cols=26 Identities=23% Similarity=0.485 Sum_probs=16.4
Q ss_pred cccccCCCCcccccccccccchhhhh
Q psy16825 12 LCLVCGDVASGFHYGVASCEACKAFF 37 (183)
Q Consensus 12 ~C~vC~~~~~~~hyg~~~C~~C~~FF 37 (183)
-|.||++..-...=+.+.|..|.+=|
T Consensus 37 aCeiC~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 37 ACEICGPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred eccccCCCceEEECCEEEEecCCCEE
Confidence 47888655544555666777776543
No 122
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=32.50 E-value=17 Score=24.28 Aligned_cols=29 Identities=28% Similarity=0.566 Sum_probs=24.8
Q ss_pred CcccccCCCCcccccccccccchhhhhhc
Q psy16825 11 RLCLVCGDVASGFHYGVASCEACKAFFKR 39 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR 39 (183)
+-|++||....-.-|.-.-|..|.+.|-.
T Consensus 10 RACl~Cgiv~t~n~F~~dGCpNc~~l~~~ 38 (112)
T COG5204 10 RACLGCGIVKTLNGFRKDGCPNCPMLNMK 38 (112)
T ss_pred hhhhhcceeeecccccccCCCCCcccccc
Confidence 56999999988888888889999988865
No 123
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=32.39 E-value=27 Score=22.45 Aligned_cols=14 Identities=36% Similarity=0.959 Sum_probs=5.4
Q ss_pred CCCCCcccccCCCC
Q psy16825 7 ELPRRLCLVCGDVA 20 (183)
Q Consensus 7 ~~~~~~C~vC~~~~ 20 (183)
....++|+|||+..
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 34457899999854
No 124
>KOG4399|consensus
Probab=32.21 E-value=15 Score=29.24 Aligned_cols=19 Identities=32% Similarity=0.915 Sum_probs=8.8
Q ss_pred ccccCCCCcccccccccccchhh
Q psy16825 13 CLVCGDVASGFHYGVASCEACKA 35 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~ 35 (183)
|-|||.-.+.. .+|..|++
T Consensus 264 C~iC~~~~~~R----~~C~~~kA 282 (325)
T KOG4399|consen 264 CFICGELDHKR----STCPNIKA 282 (325)
T ss_pred eeecccccccc----ccCccHHH
Confidence 44555433332 34555543
No 125
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=32.12 E-value=26 Score=19.73 Aligned_cols=13 Identities=31% Similarity=0.598 Sum_probs=5.5
Q ss_pred ccccCCCCccccc
Q psy16825 13 CLVCGDVASGFHY 25 (183)
Q Consensus 13 C~vC~~~~~~~hy 25 (183)
|.+|+.+..|.+|
T Consensus 3 C~~C~~~i~g~r~ 15 (46)
T cd02249 3 CDGCLKPIVGVRY 15 (46)
T ss_pred CcCCCCCCcCCEE
Confidence 4444444344333
No 126
>KOG1734|consensus
Probab=31.06 E-value=26 Score=28.13 Aligned_cols=20 Identities=30% Similarity=0.782 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCcccccCCCC
Q psy16825 1 DGIKEEELPRRLCLVCGDVA 20 (183)
Q Consensus 1 ~~~~~~~~~~~~C~vC~~~~ 20 (183)
||.+........|.|||+.-
T Consensus 215 ~glPtkhl~d~vCaVCg~~~ 234 (328)
T KOG1734|consen 215 SGLPTKHLSDSVCAVCGQQI 234 (328)
T ss_pred CCCCCCCCCcchhHhhcchh
Confidence 56777777888999999765
No 127
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.93 E-value=22 Score=23.53 Aligned_cols=24 Identities=33% Similarity=0.775 Sum_probs=18.4
Q ss_pred CcccccCCCCc-ccccccccccchh
Q psy16825 11 RLCLVCGDVAS-GFHYGVASCEACK 34 (183)
Q Consensus 11 ~~C~vC~~~~~-~~hyg~~~C~~C~ 34 (183)
-.|+.||..+- ..--|++.|+.|.
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~ 61 (90)
T PTZ00255 37 YFCPFCGKHAVKRQAVGIWRCKGCK 61 (90)
T ss_pred ccCCCCCCCceeeeeeEEEEcCCCC
Confidence 46999987764 3666899999995
No 128
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=30.83 E-value=31 Score=30.69 Aligned_cols=32 Identities=22% Similarity=0.591 Sum_probs=26.6
Q ss_pred CCCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825 9 PRRLCLVCGDVAS---GFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 9 ~~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~ 40 (183)
....|.-||.... ...||++.|-.|++..|..
T Consensus 22 gNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsL 56 (648)
T PLN03119 22 PNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREF 56 (648)
T ss_pred CCCccccCCCCCCCceeeccceEEeccchhhhccC
Confidence 3567999998664 4789999999999998776
No 129
>PLN03131 hypothetical protein; Provisional
Probab=30.51 E-value=31 Score=31.00 Aligned_cols=32 Identities=19% Similarity=0.580 Sum_probs=26.6
Q ss_pred CCCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825 9 PRRLCLVCGDVAS---GFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 9 ~~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~ 40 (183)
....|.-||.... ...||++.|-.|++..|..
T Consensus 22 gNk~CADCga~~P~WASiNlGIFICi~CSGIHRsL 56 (705)
T PLN03131 22 PNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREF 56 (705)
T ss_pred CCCccccCCCCCCCeeEeccceEEchhchhhhccc
Confidence 3567999998664 4789999999999998876
No 130
>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=30.09 E-value=36 Score=20.75 Aligned_cols=26 Identities=23% Similarity=0.485 Sum_probs=15.2
Q ss_pred CCCcccccCCCCcc-cccccccccchh
Q psy16825 9 PRRLCLVCGDVASG-FHYGVASCEACK 34 (183)
Q Consensus 9 ~~~~C~vC~~~~~~-~hyg~~~C~~C~ 34 (183)
+.+.|..||..... ....++.|..|-
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCG 53 (69)
T ss_pred CccCccCcccccccccccceEEcCCCC
Confidence 34568888877654 444445555553
No 131
>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=29.93 E-value=35 Score=18.60 Aligned_cols=23 Identities=30% Similarity=0.829 Sum_probs=13.5
Q ss_pred CCcccccCCCCccccc------ccccccch
Q psy16825 10 RRLCLVCGDVASGFHY------GVASCEAC 33 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hy------g~~~C~~C 33 (183)
...|.+||.... +.| |.+.|+.|
T Consensus 3 ~~pCP~CGG~Dr-Fr~~d~~g~G~~~C~~C 31 (37)
T smart00778 3 HGPCPNCGGSDR-FRFDDKDGRGTWFCSVC 31 (37)
T ss_pred ccCCCCCCCccc-cccccCCCCcCEEeCCC
Confidence 356889987442 212 55566666
No 132
>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=29.79 E-value=22 Score=18.94 Aligned_cols=18 Identities=44% Similarity=1.058 Sum_probs=9.4
Q ss_pred ccccCCCCcccccccccccchhhh
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAF 36 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~F 36 (183)
|.+|+.++. ..|.+|+..
T Consensus 1 C~~C~~~~~------~~C~~C~~~ 18 (37)
T PF01753_consen 1 CAVCGKPAL------KRCSRCKSV 18 (37)
T ss_dssp -TTTSSCSS------EEETTTSSS
T ss_pred CcCCCCCcC------CcCCCCCCE
Confidence 556766332 267777543
No 133
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=29.63 E-value=28 Score=33.18 Aligned_cols=25 Identities=32% Similarity=0.861 Sum_probs=17.0
Q ss_pred CCCCcccccCCC----Ccccccccccccchh
Q psy16825 8 LPRRLCLVCGDV----ASGFHYGVASCEACK 34 (183)
Q Consensus 8 ~~~~~C~vC~~~----~~~~hyg~~~C~~C~ 34 (183)
.+.+.|+||||. ++|--| ++|+.|+
T Consensus 13 ~~~~~c~iCGd~vg~~~~Ge~F--VAC~eC~ 41 (1044)
T PLN02915 13 ADAKTCRVCGDEVGVKEDGQPF--VACHVCG 41 (1044)
T ss_pred CCcchhhccccccCcCCCCCEE--EEeccCC
Confidence 345789999996 455555 5677664
No 134
>KOG4323|consensus
Probab=29.58 E-value=24 Score=30.49 Aligned_cols=51 Identities=20% Similarity=0.465 Sum_probs=37.9
Q ss_pred CcccccCCCCcccccccccccchhhhhhccccCCceeecCCCCCccccc------cccccccchhhhH
Q psy16825 11 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINK------RRRKACQACRFQK 72 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k------~~r~~C~~CR~~K 72 (183)
..|.||.-.-.|.-|.++-|.+|..+|... |. +|.+.. ...+.|--|...+
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~--------Ch---qp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDKCRQWYHQA--------CH---QPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred ceeeeeecCCcCccceeeeecccccHHHHH--------hc---cCCCCHhhccCccceEeehhhccch
Confidence 349999877777777999999999999987 63 344433 3346888887655
No 135
>KOG3490|consensus
Probab=28.05 E-value=38 Score=23.08 Aligned_cols=43 Identities=26% Similarity=0.520 Sum_probs=32.0
Q ss_pred CCcccccCCCCcccccccccccchhhhhhccccCCceeecCCCC
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEYTCPASN 53 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~ 53 (183)
.+-|++|+-..+---|.-.-|..|. +|+=--.....|.|-..+
T Consensus 8 lRACllCs~Vkt~~~F~~dGC~Nc~-~l~mkgn~e~V~ecTS~n 50 (111)
T KOG3490|consen 8 LRACLLCSIVKTLNGFRKDGCENCP-MLNMKGNVENVYECTSPN 50 (111)
T ss_pred hhhhhhhhhhhhhhhhhhcCCCCch-hhhhccCcceeEEecCCC
Confidence 4569999999987778778899999 664433335778886544
No 136
>KOG0706|consensus
Probab=28.01 E-value=34 Score=29.38 Aligned_cols=33 Identities=24% Similarity=0.672 Sum_probs=27.4
Q ss_pred CCCCcccccCCCCc---ccccccccccchhhhhhcc
Q psy16825 8 LPRRLCLVCGDVAS---GFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 8 ~~~~~C~vC~~~~~---~~hyg~~~C~~C~~FFrR~ 40 (183)
+....|.-||.+.. ..-||++-|--|.+-+|..
T Consensus 21 ~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnL 56 (454)
T KOG0706|consen 21 SENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNL 56 (454)
T ss_pred CCCceecccCCCCCCceeecceEEEEEecchhhhcc
Confidence 44678999999885 5899999999999987653
No 137
>KOG2879|consensus
Probab=27.95 E-value=58 Score=26.25 Aligned_cols=38 Identities=26% Similarity=0.473 Sum_probs=23.5
Q ss_pred CcccccCCCCcccccc----cccccchhhhhhccccCCceeecCC
Q psy16825 11 RLCLVCGDVASGFHYG----VASCEACKAFFKRTIQGNIEYTCPA 51 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg----~~~C~~C~~FFrR~v~~~~~~~C~~ 51 (183)
-.|.+||.+..-.|-+ ...|..|. +-+......+.|+.
T Consensus 240 ~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci---~ts~~~~asf~Cp~ 281 (298)
T KOG2879|consen 240 TECPVCGEPPTIPHVIGKCGHIYCYYCI---ATSRLWDASFTCPL 281 (298)
T ss_pred ceeeccCCCCCCCeeeccccceeehhhh---hhhhcchhhcccCc
Confidence 4699999988765443 35677776 23333334456754
No 138
>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=27.75 E-value=27 Score=18.49 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=7.7
Q ss_pred CCcccccCCCCc
Q psy16825 10 RRLCLVCGDVAS 21 (183)
Q Consensus 10 ~~~C~vC~~~~~ 21 (183)
...|.|||.+..
T Consensus 18 p~~CP~Cg~~~~ 29 (34)
T cd00729 18 PEKCPICGAPKE 29 (34)
T ss_pred CCcCcCCCCchH
Confidence 346777776653
No 139
>PLN02400 cellulose synthase
Probab=27.73 E-value=34 Score=32.80 Aligned_cols=24 Identities=29% Similarity=0.926 Sum_probs=15.9
Q ss_pred CCCcccccCCC----Ccccccccccccchh
Q psy16825 9 PRRLCLVCGDV----ASGFHYGVASCEACK 34 (183)
Q Consensus 9 ~~~~C~vC~~~----~~~~hyg~~~C~~C~ 34 (183)
..+.|+||||. .+|--| ++|+.|+
T Consensus 35 ~gqiCqICGD~VG~t~dGe~F--VAC~eCa 62 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVF--VACNECA 62 (1085)
T ss_pred CCceeeecccccCcCCCCCEE--EEEccCC
Confidence 34689999996 355555 4666664
No 140
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=27.35 E-value=28 Score=20.37 Aligned_cols=22 Identities=32% Similarity=0.797 Sum_probs=12.8
Q ss_pred cccccCCCCcccc-----cccccccchh
Q psy16825 12 LCLVCGDVASGFH-----YGVASCEACK 34 (183)
Q Consensus 12 ~C~vC~~~~~~~h-----yg~~~C~~C~ 34 (183)
.|.|||+...-+. =| ..|..|.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~ 27 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCL 27 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHH
Confidence 4889988763322 23 4566664
No 141
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=27.29 E-value=36 Score=19.02 Aligned_cols=6 Identities=33% Similarity=1.436 Sum_probs=2.9
Q ss_pred cccchh
Q psy16825 29 SCEACK 34 (183)
Q Consensus 29 ~C~~C~ 34 (183)
.|++|+
T Consensus 2 ~Cd~C~ 7 (43)
T cd02340 2 ICDGCQ 7 (43)
T ss_pred CCCCCC
Confidence 355554
No 142
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=27.19 E-value=36 Score=18.96 Aligned_cols=13 Identities=38% Similarity=0.963 Sum_probs=6.3
Q ss_pred ccccCCCCccccc
Q psy16825 13 CLVCGDVASGFHY 25 (183)
Q Consensus 13 C~vC~~~~~~~hy 25 (183)
|.+|+.+..|.+|
T Consensus 7 C~~C~~~i~g~ry 19 (44)
T smart00291 7 CDTCGKPIVGVRY 19 (44)
T ss_pred CCCCCCCCcCCEE
Confidence 5555544444444
No 143
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=27.04 E-value=27 Score=23.12 Aligned_cols=24 Identities=29% Similarity=0.744 Sum_probs=18.5
Q ss_pred CcccccCCCCc-ccccccccccchh
Q psy16825 11 RLCLVCGDVAS-GFHYGVASCEACK 34 (183)
Q Consensus 11 ~~C~vC~~~~~-~~hyg~~~C~~C~ 34 (183)
-.|+.||..+- ..-.|++.|..|.
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~ 61 (90)
T PRK03976 37 HVCPVCGRPKVKRVGTGIWECRKCG 61 (90)
T ss_pred ccCCCCCCCceEEEEEEEEEcCCCC
Confidence 45899987764 4778888898885
No 144
>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=26.27 E-value=28 Score=23.09 Aligned_cols=25 Identities=28% Similarity=0.659 Sum_probs=18.8
Q ss_pred CcccccCCCCc-ccccccccccchhh
Q psy16825 11 RLCLVCGDVAS-GFHYGVASCEACKA 35 (183)
Q Consensus 11 ~~C~vC~~~~~-~~hyg~~~C~~C~~ 35 (183)
-.|+.||..+- ..--|++.|..|.-
T Consensus 36 y~CpfCgk~~vkR~a~GIW~C~~C~~ 61 (91)
T TIGR00280 36 YVCPFCGKKTVKRGSTGIWTCRKCGA 61 (91)
T ss_pred ccCCCCCCCceEEEeeEEEEcCCCCC
Confidence 45899987764 47788888988853
No 145
>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=25.92 E-value=22 Score=28.61 Aligned_cols=9 Identities=56% Similarity=1.291 Sum_probs=2.8
Q ss_pred CCcccccCC
Q psy16825 10 RRLCLVCGD 18 (183)
Q Consensus 10 ~~~C~vC~~ 18 (183)
.+.|.|||.
T Consensus 172 ~g~CPvCGs 180 (290)
T PF04216_consen 172 RGYCPVCGS 180 (290)
T ss_dssp -SS-TTT--
T ss_pred CCcCCCCCC
Confidence 445555554
No 146
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.91 E-value=24 Score=26.26 Aligned_cols=23 Identities=30% Similarity=0.804 Sum_probs=16.2
Q ss_pred ccccCCCCc----ccccccccccchhh
Q psy16825 13 CLVCGDVAS----GFHYGVASCEACKA 35 (183)
Q Consensus 13 C~vC~~~~~----~~hyg~~~C~~C~~ 35 (183)
|.-||..-. -.|||+.+|++|+-
T Consensus 1 C~eCg~~~~D~~l~~~F~~~vC~~C~~ 27 (172)
T TIGR00598 1 CEECGKIFMDSYLFDHFDCAVCDNCRD 27 (172)
T ss_pred CccccchhhhHHHHHHCCChhhhhhhc
Confidence 566776432 27889999999963
No 147
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=25.81 E-value=36 Score=18.60 Aligned_cols=22 Identities=23% Similarity=0.570 Sum_probs=11.2
Q ss_pred ccccCCCCcccccccccccchhhhh
Q psy16825 13 CLVCGDVASGFHYGVASCEACKAFF 37 (183)
Q Consensus 13 C~vC~~~~~~~hyg~~~C~~C~~FF 37 (183)
|.+|+....-. ...|+.|..-|
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 44555544322 34566666554
No 148
>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=25.80 E-value=14 Score=22.97 Aligned_cols=26 Identities=35% Similarity=0.848 Sum_probs=15.6
Q ss_pred cccccCCCCc------ccccccc--cccchhhhh
Q psy16825 12 LCLVCGDVAS------GFHYGVA--SCEACKAFF 37 (183)
Q Consensus 12 ~C~vC~~~~~------~~hyg~~--~C~~C~~FF 37 (183)
.|.+|+.++. .||-|++ .|.+|+..+
T Consensus 6 TC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 6 TCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp EETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EE
T ss_pred EcCCCCCccceeeCHHHHhCCeEEEECCCCccee
Confidence 4788877664 2777775 688887543
No 149
>PLN02195 cellulose synthase A
Probab=25.79 E-value=35 Score=32.32 Aligned_cols=26 Identities=27% Similarity=0.822 Sum_probs=16.4
Q ss_pred CCCCCcccccCCC----Ccccccccccccchh
Q psy16825 7 ELPRRLCLVCGDV----ASGFHYGVASCEACK 34 (183)
Q Consensus 7 ~~~~~~C~vC~~~----~~~~hyg~~~C~~C~ 34 (183)
++..+.|.||||. .+|--| ++|+.|.
T Consensus 3 ~~~~~~c~~cgd~~~~~~~g~~f--vaC~eC~ 32 (977)
T PLN02195 3 ESGAPICATCGEEVGVDSNGEAF--VACHECS 32 (977)
T ss_pred cCCCccceecccccCcCCCCCeE--EEeccCC
Confidence 3446789999993 345444 4566663
No 150
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=25.77 E-value=28 Score=18.59 Aligned_cols=28 Identities=29% Similarity=0.808 Sum_probs=15.8
Q ss_pred ccccCCCCcc-cc---cccc-cccchhhhhhcc
Q psy16825 13 CLVCGDVASG-FH---YGVA-SCEACKAFFKRT 40 (183)
Q Consensus 13 C~vC~~~~~~-~h---yg~~-~C~~C~~FFrR~ 40 (183)
|..|+...+. .+ .|.. -|++|-.+|++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~ 33 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKY 33 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHh
Confidence 5566655432 22 4444 799999998875
No 151
>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=25.50 E-value=45 Score=19.41 Aligned_cols=15 Identities=20% Similarity=0.523 Sum_probs=10.8
Q ss_pred CcccccCCCCccccc
Q psy16825 11 RLCLVCGDVASGFHY 25 (183)
Q Consensus 11 ~~C~vC~~~~~~~hy 25 (183)
..|.-||..+..+++
T Consensus 2 kPCPfCGg~~~~~~~ 16 (53)
T TIGR03655 2 KPCPFCGGADVYLRR 16 (53)
T ss_pred CCCCCCCCcceeeEe
Confidence 469999987765553
No 152
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=25.43 E-value=39 Score=19.94 Aligned_cols=30 Identities=27% Similarity=0.697 Sum_probs=19.5
Q ss_pred cccccCCCCcc-cc----cccccccchhhhhhccc
Q psy16825 12 LCLVCGDVASG-FH----YGVASCEACKAFFKRTI 41 (183)
Q Consensus 12 ~C~vC~~~~~~-~h----yg~~~C~~C~~FFrR~v 41 (183)
.|..|+...+- .+ -+..-|++|-.+++..-
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 37777775542 22 34457999988887763
No 153
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=24.67 E-value=1.2e+02 Score=18.68 Aligned_cols=19 Identities=21% Similarity=0.267 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q psy16825 164 LKKFRNSILSSLGDCIYVL 182 (183)
Q Consensus 164 v~~~~~~~~~~L~~~~~~~ 182 (183)
++..+.++..+|.+|+..+
T Consensus 43 ~~~~r~KiR~~L~ey~k~L 61 (64)
T PF05596_consen 43 CQEVRKKIRAALAEYCKGL 61 (64)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 5578999999999999764
No 154
>PLN02436 cellulose synthase A
Probab=24.60 E-value=41 Score=32.28 Aligned_cols=23 Identities=30% Similarity=0.954 Sum_probs=14.7
Q ss_pred CCCcccccCCC----Ccccccccccccch
Q psy16825 9 PRRLCLVCGDV----ASGFHYGVASCEAC 33 (183)
Q Consensus 9 ~~~~C~vC~~~----~~~~hyg~~~C~~C 33 (183)
..+.|+||||. ..|--| ++|+.|
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~F--VACn~C 61 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPF--VACNEC 61 (1094)
T ss_pred CCccccccccccCcCCCCCEE--EeeccC
Confidence 34689999996 345444 455555
No 155
>PLN03207 stomagen; Provisional
Probab=24.51 E-value=27 Score=23.47 Aligned_cols=11 Identities=27% Similarity=1.062 Sum_probs=8.4
Q ss_pred ccccccchhhh
Q psy16825 61 RRKACQACRFQ 71 (183)
Q Consensus 61 ~r~~C~~CR~~ 71 (183)
..+.||.||++
T Consensus 77 tynecrgcr~k 87 (113)
T PLN03207 77 TYNECRGCRYK 87 (113)
T ss_pred ccccccCcccc
Confidence 35679999985
No 156
>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=24.45 E-value=33 Score=23.03 Aligned_cols=32 Identities=28% Similarity=0.590 Sum_probs=13.6
Q ss_pred CcccccCCCCccccccc------ccccchhhhhhcccc
Q psy16825 11 RLCLVCGDVASGFHYGV------ASCEACKAFFKRTIQ 42 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~------~~C~~C~~FFrR~v~ 42 (183)
..|.+||.+=.++|=-+ ++|.-|+.=|++.+.
T Consensus 15 ~~CalCG~tWg~~y~Ev~G~rLfFCCd~ca~EF~nmi~ 52 (105)
T PF11494_consen 15 MGCALCGATWGDYYEEVDGERLFFCCDDCAKEFKNMIN 52 (105)
T ss_dssp GS-SS---S---SS-B-TT--BSSS--SSSS-TTS-TH
T ss_pred ccccccCCcHHHHHHhhcCCEEEEEcHHHHHHHHHHHH
Confidence 35999999887766544 378888888887665
No 157
>KOG0402|consensus
Probab=24.38 E-value=23 Score=23.04 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=19.0
Q ss_pred CcccccCCCCc-ccccccccccchh
Q psy16825 11 RLCLVCGDVAS-GFHYGVASCEACK 34 (183)
Q Consensus 11 ~~C~vC~~~~~-~~hyg~~~C~~C~ 34 (183)
-.|.-||...- -.--|++.|+.|+
T Consensus 37 y~CsfCGK~~vKR~AvGiW~C~~C~ 61 (92)
T KOG0402|consen 37 YTCSFCGKKTVKRKAVGIWKCGSCK 61 (92)
T ss_pred hhhhhcchhhhhhhceeEEecCCcc
Confidence 46999998774 4778999999984
No 158
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=23.88 E-value=56 Score=19.23 Aligned_cols=24 Identities=33% Similarity=0.744 Sum_probs=17.8
Q ss_pred CCcccccCCCCcc-cccccccccch
Q psy16825 10 RRLCLVCGDVASG-FHYGVASCEAC 33 (183)
Q Consensus 10 ~~~C~vC~~~~~~-~hyg~~~C~~C 33 (183)
...|.+||.+..- ..||..-|+-|
T Consensus 14 ~nrC~~~Gr~rgvirkf~l~lcR~~ 38 (52)
T PRK05766 14 ARECQRCGRKQGLIRKYGLYLCRQC 38 (52)
T ss_pred CceeecCCCCceeHHhhCCcccHHH
Confidence 4569999987643 67887778777
No 159
>PRK08359 transcription factor; Validated
Probab=23.86 E-value=42 Score=25.16 Aligned_cols=27 Identities=26% Similarity=0.683 Sum_probs=19.9
Q ss_pred CcccccCCCCccccccc-------ccccchhhhh
Q psy16825 11 RLCLVCGDVASGFHYGV-------ASCEACKAFF 37 (183)
Q Consensus 11 ~~C~vC~~~~~~~hyg~-------~~C~~C~~FF 37 (183)
..|=+||.+..|.-|=| .+|+.|+.=|
T Consensus 7 ~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~ 40 (176)
T PRK08359 7 RYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKY 40 (176)
T ss_pred ceeecCCCccCCCCeEEEEcCeEEehHHHHHHHh
Confidence 34999999999874443 4899998444
No 160
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.45 E-value=29 Score=24.51 Aligned_cols=44 Identities=16% Similarity=0.289 Sum_probs=25.9
Q ss_pred cccccccccccchhhhhhccccCCceeecCCCCCccccccccccccchhhhHHhhh
Q psy16825 21 SGFHYGVASCEACKAFFKRTIQGNIEYTCPASNDCEINKRRRKACQACRFQKCLRK 76 (183)
Q Consensus 21 ~~~hyg~~~C~~C~~FFrR~v~~~~~~~C~~~~~C~~~k~~r~~C~~CR~~KCl~~ 76 (183)
.+.+.+...|..|+.|. +...+ .+. . +..|..|+.|...--++.
T Consensus 24 ~~~~~~~~~cP~C~s~~-~~k~g--~~~------~---~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 24 IRMQITKVNCPRCKSSN-VVKIG--GIR------R---GHQRYKCKSCGSTFTVET 67 (129)
T ss_pred HhhhcccCcCCCCCccc-eeeEC--Ccc------c---cccccccCCcCcceeeec
Confidence 35677778899999887 32221 111 1 145677777766654443
No 161
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=23.11 E-value=71 Score=19.60 Aligned_cols=26 Identities=15% Similarity=0.326 Sum_probs=17.5
Q ss_pred CCcccccCCCC---cccccccccccchhh
Q psy16825 10 RRLCLVCGDVA---SGFHYGVASCEACKA 35 (183)
Q Consensus 10 ~~~C~vC~~~~---~~~hyg~~~C~~C~~ 35 (183)
...|.+||.+. ....|-.++...|+.
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~ 34 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQL 34 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHh
Confidence 45699999875 245666666666664
No 162
>PF08201 BssC_TutF: BssC/TutF protein; InterPro: IPR013161 BssC short protein (57 amino acids) has been described as the gamma-subunit of benzylsuccinate synthase from Thauera aromatica strain K172 []. TutF has been identified and described as highly similar to BssC in T. aromatica strain T1 [].
Probab=22.34 E-value=31 Score=20.53 Aligned_cols=11 Identities=36% Similarity=1.213 Sum_probs=8.9
Q ss_pred ccccchhhhhh
Q psy16825 28 ASCEACKAFFK 38 (183)
Q Consensus 28 ~~C~~C~~FFr 38 (183)
.+|.-|+-||-
T Consensus 2 ttCkeC~~fF~ 12 (57)
T PF08201_consen 2 TTCKECRFFFP 12 (57)
T ss_pred cchhhhHhhcC
Confidence 57899998883
No 163
>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=22.14 E-value=31 Score=22.64 Aligned_cols=12 Identities=42% Similarity=1.113 Sum_probs=1.4
Q ss_pred cccccchhhhhhccc
Q psy16825 27 VASCEACKAFFKRTI 41 (183)
Q Consensus 27 ~~~C~~C~~FFrR~v 41 (183)
.++|.+|| |.+|
T Consensus 72 ~WACKaCK---RKt~ 83 (86)
T PF01586_consen 72 LWACKACK---RKTV 83 (86)
T ss_dssp -------S------T
T ss_pred HHHhHhhh---ccCc
Confidence 56899998 6665
No 164
>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=21.76 E-value=38 Score=18.73 Aligned_cols=23 Identities=26% Similarity=0.559 Sum_probs=14.5
Q ss_pred cccccCCCCc--ccccccccccchh
Q psy16825 12 LCLVCGDVAS--GFHYGVASCEACK 34 (183)
Q Consensus 12 ~C~vC~~~~~--~~hyg~~~C~~C~ 34 (183)
.|..||.... -..-|-..|..|-
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 4788887652 3455666777774
No 165
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=21.57 E-value=50 Score=19.65 Aligned_cols=30 Identities=27% Similarity=0.512 Sum_probs=22.3
Q ss_pred CCcccccCCCCcccccccccccchhhhhhcc
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACKAFFKRT 40 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~~FFrR~ 40 (183)
...|.+||++-. .--.++.|..|.+=+.|.
T Consensus 5 ~~~C~~Cg~~~~-~~dDiVvCp~CgapyHR~ 34 (54)
T PF14446_consen 5 GCKCPVCGKKFK-DGDDIVVCPECGAPYHRD 34 (54)
T ss_pred CccChhhCCccc-CCCCEEECCCCCCcccHH
Confidence 456999998762 123466899999998887
No 166
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=21.52 E-value=44 Score=25.70 Aligned_cols=7 Identities=57% Similarity=1.421 Sum_probs=5.2
Q ss_pred cccccCC
Q psy16825 12 LCLVCGD 18 (183)
Q Consensus 12 ~C~vC~~ 18 (183)
.|+||+.
T Consensus 7 ~CPvC~~ 13 (214)
T PF09986_consen 7 TCPVCGK 13 (214)
T ss_pred ECCCCCC
Confidence 4888875
No 167
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=21.25 E-value=44 Score=19.62 Aligned_cols=27 Identities=19% Similarity=0.631 Sum_probs=18.8
Q ss_pred CCcccccCCCCc----ccccccccccchhhh
Q psy16825 10 RRLCLVCGDVAS----GFHYGVASCEACKAF 36 (183)
Q Consensus 10 ~~~C~vC~~~~~----~~hyg~~~C~~C~~F 36 (183)
...|-.|.-+.- -.-|+-.+|+||-.|
T Consensus 3 Rq~CyLCdlPr~PWami~df~EpVCRgCvNy 33 (54)
T PF11261_consen 3 RQQCYLCDLPRMPWAMIWDFSEPVCRGCVNY 33 (54)
T ss_pred ceeEEeccCCCCchHHHhhccchhhhhhcCc
Confidence 445777776653 266788899999655
No 168
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=21.13 E-value=51 Score=19.93 Aligned_cols=14 Identities=36% Similarity=0.615 Sum_probs=10.4
Q ss_pred CcccccCCCCcccc
Q psy16825 11 RLCLVCGDVASGFH 24 (183)
Q Consensus 11 ~~C~vC~~~~~~~h 24 (183)
..|.+||..+...|
T Consensus 18 e~Cp~CG~~t~~~~ 31 (59)
T COG2260 18 EKCPVCGGDTKVPH 31 (59)
T ss_pred ccCCCCCCccccCC
Confidence 47999998776544
No 169
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=20.92 E-value=57 Score=18.54 Aligned_cols=14 Identities=29% Similarity=0.916 Sum_probs=10.0
Q ss_pred cccccCCCCccccc
Q psy16825 12 LCLVCGDVASGFHY 25 (183)
Q Consensus 12 ~C~vC~~~~~~~hy 25 (183)
.|.+||...+..+|
T Consensus 2 ~C~~Cg~D~t~vry 15 (45)
T cd02336 2 HCFTCGNDCTRVRY 15 (45)
T ss_pred cccCCCCccCceEE
Confidence 47788877776666
No 170
>KOG1701|consensus
Probab=20.65 E-value=63 Score=27.72 Aligned_cols=34 Identities=32% Similarity=0.835 Sum_probs=26.9
Q ss_pred CcccccCCCCcc-----------cccccccccchhhhhhccccCCceee
Q psy16825 11 RLCLVCGDVASG-----------FHYGVASCEACKAFFKRTIQGNIEYT 48 (183)
Q Consensus 11 ~~C~vC~~~~~~-----------~hyg~~~C~~C~~FFrR~v~~~~~~~ 48 (183)
.+|.-|++...| +|-+-++|..| +|.++++..|.
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 479999987665 89999999999 67777766664
No 171
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.49 E-value=58 Score=18.91 Aligned_cols=25 Identities=24% Similarity=0.553 Sum_probs=14.6
Q ss_pred CCcccccCCCCcccccccccccchh
Q psy16825 10 RRLCLVCGDVASGFHYGVASCEACK 34 (183)
Q Consensus 10 ~~~C~vC~~~~~~~hyg~~~C~~C~ 34 (183)
...|+.||..--..|.+-..|..|-
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCG 44 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcC
Confidence 3467777764223555666666663
No 172
>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=20.37 E-value=50 Score=25.19 Aligned_cols=16 Identities=31% Similarity=0.769 Sum_probs=11.8
Q ss_pred CCcccccCCCC-ccccc
Q psy16825 10 RRLCLVCGDVA-SGFHY 25 (183)
Q Consensus 10 ~~~C~vC~~~~-~~~hy 25 (183)
.+.|.|||.+. .-.|+
T Consensus 127 ~~~C~iCGk~~~d~hH~ 143 (200)
T PF06147_consen 127 SRPCVICGKPPADIHHI 143 (200)
T ss_pred cCccccCCCCcccccee
Confidence 46799999854 45776
No 173
>KOG0704|consensus
Probab=20.10 E-value=48 Score=27.62 Aligned_cols=29 Identities=24% Similarity=0.717 Sum_probs=24.2
Q ss_pred CCcccccCCCCc---ccccccccccchhhhhh
Q psy16825 10 RRLCLVCGDVAS---GFHYGVASCEACKAFFK 38 (183)
Q Consensus 10 ~~~C~vC~~~~~---~~hyg~~~C~~C~~FFr 38 (183)
...|.-|+.+-. ..-||++.|--|++-+|
T Consensus 19 Nk~CfeC~a~NPQWvSvsyGIfICLECSG~HR 50 (386)
T KOG0704|consen 19 NKKCFECGAPNPQWVSVSYGIFICLECSGKHR 50 (386)
T ss_pred CCceeecCCCCCCeEeecccEEEEEecCCccc
Confidence 457999998764 58999999999998754
Done!