Query psy7884
Match_columns 240
No_of_seqs 115 out of 1485
Neff 10.6
Searched_HMMs 46136
Date Fri Aug 16 21:16:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7884.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7884hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 100.0 7.1E-40 1.5E-44 250.9 9.7 180 2-230 42-222 (432)
2 KOG4216|consensus 100.0 1.9E-39 4.2E-44 250.1 4.3 226 2-239 69-359 (479)
3 KOG4217|consensus 100.0 8.8E-35 1.9E-39 229.4 13.0 186 2-232 292-479 (605)
4 KOG4218|consensus 100.0 9.5E-34 2.1E-38 215.6 8.1 62 2-63 38-99 (475)
5 KOG4846|consensus 100.0 2.5E-31 5.4E-36 206.9 5.0 209 2-239 155-371 (538)
6 cd06961 NR_DBD_TR DNA-binding 99.9 2.7E-25 5.7E-30 141.5 2.2 61 2-62 22-82 (85)
7 cd07170 NR_DBD_ERR DNA-binding 99.9 1.7E-24 3.6E-29 140.5 3.6 61 2-62 27-87 (97)
8 cd06957 NR_DBD_PNR_like_2 DNA- 99.9 8.8E-25 1.9E-29 138.3 1.5 60 2-61 21-81 (82)
9 cd06964 NR_DBD_RAR DNA-binding 99.9 1E-24 2.2E-29 138.7 1.7 58 2-59 27-84 (85)
10 cd06956 NR_DBD_RXR DNA-binding 99.9 1.2E-24 2.7E-29 136.1 1.9 55 2-56 23-77 (77)
11 cd07155 NR_DBD_ER_like DNA-bin 99.9 1.6E-24 3.6E-29 135.0 2.2 55 2-56 21-75 (75)
12 cd07164 NR_DBD_PNR_like_1 DNA- 99.9 2E-24 4.2E-29 135.7 2.3 58 2-59 21-78 (78)
13 cd06967 NR_DBD_TR2_like DNA-bi 99.9 1.6E-24 3.5E-29 138.4 1.6 59 2-60 26-84 (87)
14 cd07160 NR_DBD_LXR DNA-binding 99.9 1.9E-24 4E-29 141.2 1.7 59 2-60 41-99 (101)
15 cd07167 NR_DBD_Lrh-1_like The 99.9 2.5E-24 5.5E-29 138.6 1.8 62 2-63 21-82 (93)
16 cd07166 NR_DBD_REV_ERB DNA-bin 99.9 1.9E-24 4E-29 138.7 1.1 61 2-62 26-87 (89)
17 cd06970 NR_DBD_PNR DNA-binding 99.9 2.9E-24 6.2E-29 138.2 2.0 59 2-60 29-88 (92)
18 cd07168 NR_DBD_DHR4_like DNA-b 99.9 3.4E-24 7.3E-29 137.8 2.3 59 2-60 29-87 (90)
19 cd07165 NR_DBD_DmE78_like DNA- 99.9 3.2E-24 7E-29 135.6 2.1 59 2-60 21-79 (81)
20 cd07163 NR_DBD_TLX DNA-binding 99.9 2.4E-24 5.3E-29 139.1 1.4 59 2-60 29-89 (92)
21 cd07169 NR_DBD_GCNF_like DNA-b 99.9 4.9E-24 1.1E-28 136.9 2.2 60 2-61 29-88 (90)
22 cd06968 NR_DBD_ROR DNA-binding 99.9 4E-24 8.6E-29 138.6 1.7 62 2-63 28-89 (95)
23 cd06960 NR_DBD_HNF4A DNA-bindi 99.9 5.2E-24 1.1E-28 133.4 1.9 56 2-57 21-76 (76)
24 cd07171 NR_DBD_ER DNA-binding 99.9 4.2E-24 9.2E-29 134.8 1.5 55 2-56 26-80 (82)
25 cd06962 NR_DBD_FXR DNA-binding 99.9 4.2E-24 9.2E-29 135.4 0.8 58 2-59 24-81 (84)
26 cd07161 NR_DBD_EcR DNA-binding 99.9 6.2E-24 1.3E-28 136.6 1.3 59 2-60 24-82 (91)
27 cd07179 2DBD_NR_DBD2 The secon 99.9 1.5E-23 3.2E-28 130.2 2.1 53 2-54 21-73 (74)
28 cd06969 NR_DBD_NGFI-B DNA-bind 99.9 1.1E-23 2.4E-28 131.1 1.4 53 2-54 23-75 (75)
29 cd07156 NR_DBD_VDR_like The DN 99.9 1.9E-23 4.1E-28 129.2 1.9 52 2-53 21-72 (72)
30 cd06958 NR_DBD_COUP_TF DNA-bin 99.9 2.6E-23 5.6E-28 128.9 2.3 52 2-53 21-72 (73)
31 cd06966 NR_DBD_CAR DNA-binding 99.9 1E-23 2.3E-28 136.5 0.3 62 2-63 23-84 (94)
32 cd06959 NR_DBD_EcR_like The DN 99.9 2.8E-23 6.1E-28 128.7 2.1 52 2-53 22-73 (73)
33 cd06916 NR_DBD_like DNA-bindin 99.9 2.1E-23 4.6E-28 129.1 1.3 52 2-53 21-72 (72)
34 cd06963 NR_DBD_GR_like The DNA 99.9 4.1E-23 9E-28 127.7 2.6 52 2-53 21-72 (73)
35 cd07154 NR_DBD_PNR_like The DN 99.9 2.5E-23 5.4E-28 129.1 1.5 52 2-53 21-73 (73)
36 cd06965 NR_DBD_Ppar DNA-bindin 99.9 2.4E-23 5.2E-28 132.3 1.3 59 2-62 22-81 (84)
37 cd07158 NR_DBD_Ppar_like The D 99.9 3.9E-23 8.4E-28 128.4 1.8 52 2-53 21-73 (73)
38 cd07162 NR_DBD_PXR DNA-binding 99.9 2.2E-23 4.8E-28 133.5 0.6 56 2-57 22-77 (87)
39 cd06955 NR_DBD_VDR DNA-binding 99.9 2.1E-23 4.6E-28 137.5 0.3 54 2-55 29-82 (107)
40 cd07157 2DBD_NR_DBD1 The first 99.9 8.3E-23 1.8E-27 130.2 2.3 57 2-58 23-81 (86)
41 cd07172 NR_DBD_GR_PR DNA-bindi 99.9 1.8E-22 3.8E-27 126.3 2.8 52 2-53 25-76 (78)
42 cd07173 NR_DBD_AR DNA-binding 99.8 2.8E-22 6.1E-27 126.3 2.1 54 2-55 26-79 (82)
43 smart00399 ZnF_C4 c4 zinc fing 99.8 1.3E-21 2.9E-26 120.7 2.5 49 2-50 22-70 (70)
44 PF00105 zf-C4: Zinc finger, C 99.8 5.3E-20 1.1E-24 113.9 1.1 48 2-49 23-70 (70)
45 cd06939 NR_LBD_ROR_like The li 99.8 8.7E-18 1.9E-22 129.0 12.3 121 107-238 3-124 (241)
46 cd06932 NR_LBD_PPAR The ligand 99.7 2.4E-16 5.3E-21 122.2 12.3 130 107-238 3-139 (259)
47 cd06935 NR_LBD_TR The ligand b 99.7 1.1E-15 2.3E-20 117.8 11.0 78 160-237 49-128 (243)
48 cd07072 NR_LBD_DHR38_like Liga 99.6 1.6E-15 3.4E-20 116.1 11.0 77 160-236 39-117 (239)
49 cd06954 NR_LBD_LXR The ligand 99.6 2.6E-15 5.7E-20 115.6 10.8 114 109-236 3-118 (236)
50 cd07348 NR_LBD_NGFI-B The liga 99.6 3.8E-15 8.1E-20 113.9 11.2 72 163-234 41-114 (238)
51 cd06940 NR_LBD_REV_ERB The lig 99.6 1.8E-15 3.8E-20 112.4 8.9 78 160-237 9-88 (189)
52 cd07071 NR_LBD_Nurr1 The ligan 99.6 7.6E-15 1.7E-19 112.3 10.9 73 162-234 40-114 (238)
53 cd06941 NR_LBD_DmE78_like The 99.6 2.6E-15 5.5E-20 112.4 8.0 74 163-236 2-77 (195)
54 cd06938 NR_LBD_EcR The ligand 99.6 1.1E-14 2.3E-19 111.8 11.5 74 163-236 39-114 (231)
55 cd06937 NR_LBD_RAR The ligand 99.6 1.9E-14 4.1E-19 110.1 10.7 78 160-237 35-114 (231)
56 cd06934 NR_LBD_PXR_like The li 99.6 4.3E-14 9.3E-19 107.8 11.3 101 106-232 4-105 (226)
57 cd06945 NR_LBD_Nurr1_like The 99.5 7.3E-14 1.6E-18 107.4 10.7 72 163-234 41-114 (239)
58 cd06933 NR_LBD_VDR The ligand 99.5 1.3E-13 2.9E-18 105.9 11.6 97 107-227 5-103 (238)
59 cd06942 NR_LBD_Sex_1_like The 99.5 3.7E-14 7.9E-19 105.7 7.8 72 164-235 3-74 (191)
60 cd07075 NR_LBD_MR Ligand bindi 99.5 4.6E-14 9.9E-19 108.1 8.2 74 163-236 28-105 (248)
61 cd06929 NR_LBD_F1 Ligand-bindi 99.5 5.7E-14 1.2E-18 103.5 8.2 74 164-237 3-78 (174)
62 cd07076 NR_LBD_GR Ligand bindi 99.5 1.5E-13 3.2E-18 105.3 8.8 75 162-236 27-105 (247)
63 cd06947 NR_LBD_GR_Like Ligand 99.5 2E-13 4.2E-18 105.0 8.7 73 163-235 28-104 (246)
64 cd07074 NR_LBD_PR Ligand bindi 99.4 3E-13 6.5E-18 103.6 8.0 72 164-235 29-104 (248)
65 cd07073 NR_LBD_AR Ligand bindi 99.4 4.2E-13 9.1E-18 103.2 8.8 72 163-234 28-103 (246)
66 cd06949 NR_LBD_ER Ligand bindi 99.4 4.7E-13 1E-17 102.7 8.6 74 162-235 31-106 (235)
67 cd07070 NR_LBD_SF-1 The ligand 99.4 7.7E-13 1.7E-17 101.6 7.8 71 165-235 40-114 (237)
68 cd06944 NR_LBD_Ftz-F1_like The 99.4 7.6E-13 1.7E-17 101.8 7.5 73 164-236 39-115 (237)
69 cd07068 NR_LBD_ER_like The lig 99.4 1.1E-12 2.5E-17 100.0 8.3 74 162-235 26-101 (221)
70 cd06946 NR_LBD_ERR The ligand 99.4 1.8E-12 3.9E-17 98.9 8.8 72 163-234 27-100 (221)
71 cd06936 NR_LBD_Fxr The ligand 99.4 3.2E-12 6.9E-17 97.3 9.9 97 107-229 3-99 (221)
72 cd06930 NR_LBD_F2 Ligand-bindi 99.4 1.3E-12 2.8E-17 95.4 7.2 70 167-236 3-76 (165)
73 cd06943 NR_LBD_RXR_like The li 99.4 1.4E-12 3.1E-17 98.6 7.2 71 165-235 32-104 (207)
74 cd07069 NR_LBD_Lrh-1 The ligan 99.4 2.5E-12 5.4E-17 99.0 7.5 70 164-233 41-114 (241)
75 cd06931 NR_LBD_HNF4_like The l 99.3 2.1E-12 4.6E-17 98.7 5.9 72 163-234 32-105 (222)
76 cd06950 NR_LBD_Tlx_PNR_like Th 99.3 1.4E-11 3.1E-16 92.8 8.0 53 164-216 27-79 (206)
77 cd06948 NR_LBD_COUP-TF Ligand 99.3 7.6E-12 1.6E-16 96.3 5.8 68 164-231 31-101 (236)
78 cd07350 NR_LBD_Dax1 The ligand 99.2 1.2E-11 2.7E-16 94.4 4.5 56 161-216 17-72 (232)
79 cd06953 NR_LBD_DHR4_like The l 99.2 4.3E-11 9.3E-16 90.6 6.2 54 163-216 27-80 (213)
80 PF00104 Hormone_recep: Ligand 99.2 9.9E-11 2.2E-15 88.2 8.2 77 161-237 15-94 (203)
81 cd06951 NR_LBD_Dax1_like The l 99.2 5.1E-11 1.1E-15 90.6 5.8 53 164-216 20-72 (222)
82 cd07349 NR_LBD_SHP The ligand 99.1 1E-10 2.2E-15 88.8 5.7 53 164-216 20-72 (222)
83 cd06952 NR_LBD_TR2_like The li 99.0 3.1E-10 6.7E-15 86.7 4.8 52 165-216 23-74 (222)
84 cd06157 NR_LBD The ligand bind 98.9 2.8E-09 6.1E-14 77.7 6.8 63 167-229 2-67 (168)
85 smart00430 HOLI Ligand binding 98.9 2.2E-09 4.8E-14 77.9 4.6 60 174-233 3-65 (163)
86 PF09289 FOLN: Follistatin/Ost 91.3 0.07 1.5E-06 24.3 0.3 20 15-34 3-22 (22)
87 PF00357 Integrin_alpha: Integ 79.8 0.73 1.6E-05 18.9 0.3 7 4-10 3-9 (15)
88 KOG4846|consensus 75.3 4.6 0.0001 33.5 3.9 48 163-210 362-410 (538)
89 smart00274 FOLN Follistatin-N- 74.1 2 4.2E-05 20.6 1.0 20 15-34 4-23 (26)
90 PF12760 Zn_Tnp_IS1595: Transp 67.5 2 4.2E-05 23.7 0.2 38 2-40 6-46 (46)
91 PF00645 zf-PARP: Poly(ADP-rib 58.6 9.4 0.0002 23.9 2.2 22 182-203 59-80 (82)
92 PF09150 Carot_N: Orange carot 56.4 11 0.00023 27.0 2.3 23 186-208 19-41 (159)
93 KOG4033|consensus 42.9 15 0.00033 28.3 1.4 57 174-231 130-190 (314)
94 KOG4004|consensus 41.7 10 0.00022 28.2 0.4 28 16-44 56-83 (259)
95 PF06594 HCBP_related: Haemoly 40.6 18 0.0004 19.4 1.2 19 217-235 25-43 (43)
96 PF03002 Somatostatin: Somatos 40.1 9.3 0.0002 16.3 -0.0 8 2-9 7-14 (18)
97 PF10330 Stb3: Putative Sin3 b 37.8 66 0.0014 20.7 3.5 28 179-207 26-54 (92)
98 PF05528 Coronavirus_5: Corona 33.5 35 0.00076 20.7 1.7 32 6-37 9-43 (82)
99 PF05924 SAMP: SAMP Motif; In 32.2 27 0.00058 15.5 0.8 11 39-49 6-16 (20)
100 KOG3116|consensus 32.0 21 0.00045 25.2 0.6 10 38-47 29-38 (177)
101 PF08723 Gag_p15: Gag protein 31.5 22 0.00047 23.8 0.6 16 42-57 83-98 (123)
102 PF13451 zf-trcl: Probable zin 30.8 21 0.00046 20.0 0.4 12 30-41 32-43 (49)
103 PF08209 Sgf11: Sgf11 (transcr 29.5 17 0.00038 18.5 -0.0 9 39-47 23-31 (33)
104 PHA03124 dUTPase; Provisional 25.1 24 0.00052 29.2 0.0 9 2-10 196-204 (418)
105 PF15612 WHIM1: WSTF, HB1, Itc 24.4 72 0.0016 17.6 1.9 20 187-206 12-31 (50)
106 PF15472 DUF4638: Domain of un 21.7 46 0.00099 25.5 0.9 18 33-50 219-245 (268)
107 PF03811 Zn_Tnp_IS1: InsA N-te 20.9 35 0.00076 17.7 0.1 8 31-38 29-36 (36)
108 cd00435 ACBP Acyl CoA binding 20.4 1.6E+02 0.0034 18.7 3.0 25 176-202 5-29 (85)
109 PF08483 IstB_IS21_ATP: IstB-l 20.0 91 0.002 15.5 1.5 17 186-202 6-22 (30)
No 1
>KOG4215|consensus
Probab=100.00 E-value=7.1e-40 Score=250.85 Aligned_cols=180 Identities=27% Similarity=0.416 Sum_probs=121.3
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccccccCCCcccCCCCCC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEP 81 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (240)
|||||||||.++..|+|+++++|.|||+.|+.||+|||+||+.+||+++|||++|++.+.++........
T Consensus 42 CKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg~Rr~~~~~~n~---------- 111 (432)
T KOG4215|consen 42 CKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIGSRRPSYEAGNE---------- 111 (432)
T ss_pred chHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccccccccCCCCCCCCC----------
Confidence 9999999999999999999999999999999999999999999999999999999999875432211000
Q ss_pred CCCCCCCCCCCCCCCCcccCcchhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhH
Q psy7884 82 PSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQR 161 (240)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (240)
....+..+..+....-+..... ..+. +... .. .........
T Consensus 112 -------------------------~~~~id~L~~aE~~~~q~~~sr-s~~~------~~~~----~d---~r~~~~n~~ 152 (432)
T KOG4215|consen 112 -------------------------NSPSIDALVQAEALVRQLRSSR-SGGV------PGID----GD---IRQGPPNKK 152 (432)
T ss_pred -------------------------CchhHHHHHhHHHHHhhhhccc-cccC------cCcc----hh---hhcCccccc
Confidence 0111112222111110000000 0000 0000 00 000000011
Q ss_pred HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeee
Q psy7884 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYV 230 (240)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i 230 (240)
...-.++.+.+..+|..+|||||.+|.|..|+.+||+.|||+.+-++++|..+++ .....+.+.+.+++
T Consensus 153 ~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~N~~v 222 (432)
T KOG4215|consen 153 IATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLNNTYV 222 (432)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEecCcee
Confidence 1224577888889999999999999999999999999999999999999999999 44434444444443
No 2
>KOG4216|consensus
Probab=100.00 E-value=1.9e-39 Score=250.09 Aligned_cols=226 Identities=32% Similarity=0.589 Sum_probs=157.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccc-----------cc--
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSD-----------SE-- 68 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~-----------~~-- 68 (240)
|||||||+-+.+..|.|.+.++|.||+.+|++|++||||||+++||+++||.++|+.++.+.... ..
T Consensus 69 CKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKKQRdsl~aEVq~h~~q~q~q~~ 148 (479)
T KOG4216|consen 69 CKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQQDE 148 (479)
T ss_pred chHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHhhHHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999988765210 00
Q ss_pred cC---CCcccC-CCCCC--------------CCCCCCC-C----CCCCCCCC--------------------------cc
Q psy7884 69 TG---STRVST-TGAEP--------------PSSLETA-G----PVQSLPSS--------------------------TE 99 (240)
Q Consensus 69 ~~---~~~~~~-~~~~~--------------~~~~~~~-~----~~~~~~~~--------------------------~~ 99 (240)
.. .+-..+ ++..+ |...... + ..++.|.. .+
T Consensus 149 a~~~~~~y~~s~p~~~~~l~~~~s~y~~g~~p~~~k~~~s~Ys~~~q~tPdq~~~d~~g~~~d~t~~~~~~~~~s~~~~~ 228 (479)
T KOG4216|consen 149 AEPLTPTYDISPPNGLTELHDDLSNYSDGHSPEGSKADSSFYSLDIQPTPDQSGLDINGPICDSTPGSGYFPYCSFTNGE 228 (479)
T ss_pred cCCcccccccCCCCCccccccCcccccCCcCCCCCCCCCCcceeccccCCCccccccCCCcccCCCCCCcccccccCCCC
Confidence 00 000000 00000 0000000 0 00000000 01
Q ss_pred cCcc-hhhhHH-HHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHH
Q psy7884 100 LDTK-QLLTYD-VILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQ 177 (240)
Q Consensus 100 ~~~~-~~~~~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 177 (240)
+.+. +....+ ++++|+.+|.++ .+.-+.+..+.+..+ ++.. +..-....+-.+|+.++.-++..|+
T Consensus 229 ~~p~~~~~e~d~laq~i~ksh~et-q~~~e~lh~~~~~~~--------~~e~---I~~yq~k~~e~mWe~cA~~lt~~IQ 296 (479)
T KOG4216|consen 229 TSPTVSMAELDHLAQNIIKSHLET-QYLLEELHQITWQTF--------DQEE---IENYQNKGREEMWELCAIKLTPAIQ 296 (479)
T ss_pred CCCCCchhHHHHHHHHHHHHHHHH-HHHHHHHHHHHhccC--------CHHH---HHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 1111 122244 789999999998 555555555544332 1111 2233344566789999999999999
Q ss_pred HHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeeecHHHHhhhc
Q psy7884 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYVTRQQLEVMY 239 (240)
Q Consensus 178 ~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i~~~~~~~~~ 239 (240)
.+|||||.++||..|+.+||++|||.+.||+.+.+.+++ ...+.-++.+|.+.+++.+.+++
T Consensus 297 ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~ntV~~e~~~~g~~~f~a~~ 359 (479)
T KOG4216|consen 297 YVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNNTVYFEGKYAGPEVFYALG 359 (479)
T ss_pred HHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhcccccceeecccccchhheeccC
Confidence 999999999999999999999999999999999998887 55666678888888887766543
No 3
>KOG4217|consensus
Probab=100.00 E-value=8.8e-35 Score=229.36 Aligned_cols=186 Identities=32% Similarity=0.564 Sum_probs=130.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccccccCCCcccCCCCCC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEP 81 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (240)
|||||+|||++|.+|+|-.+++|+|||..|++||+|||||||+|||-+|-|+.+-...++ -|..+..+.. ++
T Consensus 292 CKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLkGRR-GRLpSKpKs~--q~----- 363 (605)
T KOG4217|consen 292 CKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRR-GRLPSKPKSR--QP----- 363 (605)
T ss_pred chHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecccccccc-CCCCCCCCCC--CC-----
Confidence 999999999999999999999999999999999999999999999999998865433321 1111111111 00
Q ss_pred CCCCCCCCCCCCCCCCcccCcchhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhH
Q psy7884 82 PSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQR 161 (240)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (240)
++++++ ..++..+..+|.-.-.-+.. +....+ .+..+.. ....
T Consensus 364 ----------------sppSpP----i~LltalvrAh~Dstp~~~~----ldys~~-----q~~~~~~--------~~td 406 (605)
T KOG4217|consen 364 ----------------SPPSPP----ISLLTALVRAHVDSTPSTMT----LDYSRF-----QELVPHF--------SGTD 406 (605)
T ss_pred ----------------CCCCCc----hHHHHHHHHHhhcCCCCcch----hhHHHh-----ccccccc--------cccH
Confidence 011111 34555666666432211110 000000 0000000 0011
Q ss_pred HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecH
Q psy7884 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTR 232 (240)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~ 232 (240)
..-.+.|.++.+-.+..+-.||..+|+|.+|..+||-+||..+++|+++|+.||+ ...++++|.+|..+-+
T Consensus 407 A~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~e~kliFcsG~vlhr 479 (605)
T KOG4217|consen 407 ALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPSEDKLIFCSGLVLHR 479 (605)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEecchhhhH
Confidence 1125677778888999999999999999999999999999999999999999999 7889999999988765
No 4
>KOG4218|consensus
Probab=100.00 E-value=9.5e-34 Score=215.61 Aligned_cols=62 Identities=37% Similarity=0.850 Sum_probs=59.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~ 63 (240)
|||||+|||+++++|+|..+.+|.||+.-|++|++||||||+.|||+.+||+-+|++.++.+
T Consensus 38 CKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMRGGRNK 99 (475)
T KOG4218|consen 38 CKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMRGGRNK 99 (475)
T ss_pred hhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhcccccc
Confidence 99999999999999999999999999999999999999999999999999999988876544
No 5
>KOG4846|consensus
Probab=99.97 E-value=2.5e-31 Score=206.92 Aligned_cols=209 Identities=33% Similarity=0.595 Sum_probs=154.8
Q ss_pred CcchhhhhhccCCee-EeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccccccCCCcccCCCCC
Q psy7884 2 FQGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAE 80 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~-~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~~~~~~~~~~~~~~~ 80 (240)
|||||||+|+.+..| .|-+..+|.|.+.+|++||+|||+|||+|||++++|++++++.+.+.++......+.+.++.
T Consensus 155 CKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~rnka~M~~~~~p~~V~sp~-- 232 (538)
T KOG4846|consen 155 CKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKFRNKAAMRDDKSPDSVFSPE-- 232 (538)
T ss_pred chHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhcccccccccccCCCCCCCCCCChh--
Confidence 999999999999999 79999999999999999999999999999999999999999888755443332222221111
Q ss_pred CCCCCCCCCCCCCCCCCcccCcchhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhh
Q psy7884 81 PPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQ 160 (240)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (240)
.++.......+.+++..+.++|.+...|++.+++++...++.+...... ++ -.
T Consensus 233 ----------------~sq~~~Q~env~~V~~~V~rAh~t~~~y~~~k~gsi~~~~fnv~~n~~s-~P----------~~ 285 (538)
T KOG4846|consen 233 ----------------ISQLERQEENVDAVYEAVLRAHTTFSFYTDIKIGSIVARPFNVRINEDS-KP----------MN 285 (538)
T ss_pred ----------------hhhhhhhhccHHHHHHHHHHhhcchhheehhhcCcccCCCcccccccCC-cc----------cc
Confidence 1122222333788999999999999999999999887776644322111 11 12
Q ss_pred HHHHHHHHHHHHhHHHH-HHHhhhcCCcCcCC---CChhHHHHHHHhhhHHHHhhhhhcccC-CCceEecCCeeec--HH
Q psy7884 161 RLWLWQQFAAHVTPSVQ-RVVEFAKRVPGFCD---LSQDDQLILIKMGFFELWIGYVSRLTT-DSSLTFSDGMYVT--RQ 233 (240)
Q Consensus 161 ~~~~~~~~~~~~~~~l~-~~iefak~~p~F~~---L~~~Dq~~Llk~~~~~~~~l~~a~~~~-~~~l~~~~G~~i~--~~ 233 (240)
+...|+..+--+..++. .++.|.+..|.|.. .+-.++..+.+...+-.++++.+.... ..+++.-+|..|. ++
T Consensus 286 ~~~~w~n~~~pa~~di~qe~~n~l~q~pvfd~~~~~~g~a~~s~h~~n~~pty~~~~~~g~~Pn~~~~~rsgR~~qlp~~ 365 (538)
T KOG4846|consen 286 RLNAWQNYAHPADVDIKQEVVNFLKQIPVFDKFNFINGNAKASLHRKNAFPTYLLRIVRGMSPNRGLMLRSGRLIQLPFK 365 (538)
T ss_pred chhHHhhcCCCCcccchHHHHHHHHhCccccccccCCCccchhhhcCCCcchhhhhhcccCCcccccccccccccccCcc
Confidence 33457776433333443 68889999996665 466899999998888888888888755 5888999999876 67
Q ss_pred HHhhhc
Q psy7884 234 QLEVMY 239 (240)
Q Consensus 234 ~~~~~~ 239 (240)
.+.++|
T Consensus 366 ~~~ll~ 371 (538)
T KOG4846|consen 366 SLQLLY 371 (538)
T ss_pred hhhhhh
Confidence 776665
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=99.91 E-value=2.7e-25 Score=141.55 Aligned_cols=61 Identities=49% Similarity=0.980 Sum_probs=58.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~ 62 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|++.+++
T Consensus 22 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~ 82 (85)
T cd06961 22 CKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKR 82 (85)
T ss_pred hhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCccccc
Confidence 8999999999999999999999999999999999999999999999999999999987654
No 7
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=99.90 E-value=1.7e-24 Score=140.55 Aligned_cols=61 Identities=43% Similarity=0.862 Sum_probs=56.8
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~ 62 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+|||+|||++++||.+|......
T Consensus 27 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~~~~ 87 (97)
T cd07170 27 CKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQ 87 (97)
T ss_pred hhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCCCCC
Confidence 8999999999999999999999999999999999999999999999999999998765543
No 8
>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=99.89 E-value=8.8e-25 Score=138.34 Aligned_cols=60 Identities=43% Similarity=0.948 Sum_probs=56.4
Q ss_pred CcchhhhhhccCCeeEec-cCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccc
Q psy7884 2 FQGFFRRSIQKQIEYRCL-RDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~-~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~ 61 (240)
||+||||+|..+..|.|. .+++|.++...|..|++|||+||+++||++++||.+|+|.+.
T Consensus 21 Ck~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~~ 81 (82)
T cd06957 21 CSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRKL 81 (82)
T ss_pred eeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCCC
Confidence 899999999999999999 578999999999999999999999999999999999988764
No 9
>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=99.89 E-value=1e-24 Score=138.68 Aligned_cols=58 Identities=57% Similarity=1.134 Sum_probs=55.4
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK 59 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~ 59 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+|||++||++++||.+|+++
T Consensus 27 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~~ 84 (85)
T cd06964 27 CKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK 84 (85)
T ss_pred eeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccCC
Confidence 8999999999999999999999999999999999999999999999999999999874
No 10
>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=99.89 E-value=1.2e-24 Score=136.12 Aligned_cols=55 Identities=47% Similarity=1.102 Sum_probs=53.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r 56 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++||.+|
T Consensus 23 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 23 CKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred HHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 8999999999999999999999999999999999999999999999999999876
No 11
>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=99.89 E-value=1.6e-24 Score=134.99 Aligned_cols=55 Identities=42% Similarity=0.884 Sum_probs=53.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r 56 (240)
||+||||+|..+..|.|+.+++|.|++..|..|++|||+||+++||++++||.+|
T Consensus 21 Ck~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 21 CKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred hHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 8999999999999999999999999999999999999999999999999999876
No 12
>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=99.89 E-value=2e-24 Score=135.71 Aligned_cols=58 Identities=50% Similarity=1.036 Sum_probs=55.4
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK 59 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~ 59 (240)
||+||||++..+..|+|..+++|.|+...|..|++|||+||++|||++++||.+|++.
T Consensus 21 C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~ 78 (78)
T cd07164 21 CRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAPR 78 (78)
T ss_pred hhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCCC
Confidence 8999999999999999999999999999999999999999999999999999999863
No 13
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=99.89 E-value=1.6e-24 Score=138.43 Aligned_cols=59 Identities=49% Similarity=1.020 Sum_probs=56.4
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~ 60 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++||.+|++..
T Consensus 26 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~~ 84 (87)
T cd06967 26 CKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPID 84 (87)
T ss_pred eeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCCC
Confidence 89999999999999999999999999999999999999999999999999999998854
No 14
>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=99.89 E-value=1.9e-24 Score=141.21 Aligned_cols=59 Identities=37% Similarity=0.715 Sum_probs=56.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~ 60 (240)
||+||||+|..+..|.|..+++|.|+...|..|++|||+||+++||++++||.+|+...
T Consensus 41 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~~~ 99 (101)
T cd07160 41 CKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQIRL 99 (101)
T ss_pred hhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhhhh
Confidence 89999999999999999999999999999999999999999999999999999987654
No 15
>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=99.89 E-value=2.5e-24 Score=138.59 Aligned_cols=62 Identities=39% Similarity=0.927 Sum_probs=57.7
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~ 63 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|.+....+
T Consensus 21 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~~~ 82 (93)
T cd07167 21 CKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNK 82 (93)
T ss_pred HHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCccc
Confidence 89999999999999999999999999999999999999999999999999999997665443
No 16
>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=99.89 E-value=1.9e-24 Score=138.73 Aligned_cols=61 Identities=67% Similarity=1.392 Sum_probs=57.5
Q ss_pred CcchhhhhhccCCee-EeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884 2 FQGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~-~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~ 62 (240)
||+||||+|..+..| .|..+++|.|+...|..|++|||+||+++||++++||.+|++++.+
T Consensus 26 Ck~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~~ 87 (89)
T cd07166 26 CKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKREK 87 (89)
T ss_pred HhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCCCCccc
Confidence 899999999999999 5999999999999999999999999999999999999999987754
No 17
>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=99.89 E-value=2.9e-24 Score=138.25 Aligned_cols=59 Identities=46% Similarity=0.993 Sum_probs=55.8
Q ss_pred CcchhhhhhccCCeeEeccC-CccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRD-GKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~-~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~ 60 (240)
||+||||+|..+..|.|..+ ++|.++...|..|++|||+||+++||++++||.+|+++.
T Consensus 29 Ck~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~ 88 (92)
T cd06970 29 CSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPRN 88 (92)
T ss_pred eeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCccc
Confidence 89999999999999999975 899999999999999999999999999999999998765
No 18
>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=99.89 E-value=3.4e-24 Score=137.82 Aligned_cols=59 Identities=46% Similarity=1.033 Sum_probs=56.6
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~ 60 (240)
||+||||++..+..|.|..+++|.|+...|..|++|||+||+++||++++||.+|++..
T Consensus 29 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~ 87 (90)
T cd07168 29 CKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGG 87 (90)
T ss_pred hhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCCC
Confidence 99999999999999999999999999999999999999999999999999999998865
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=99.89 E-value=3.2e-24 Score=135.58 Aligned_cols=59 Identities=86% Similarity=1.565 Sum_probs=56.6
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~ 60 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+|||++||++++||.+|++++
T Consensus 21 C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~ 79 (81)
T cd07165 21 CKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR 79 (81)
T ss_pred HHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence 89999999999999999999999999999999999999999999999999999999865
No 20
>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=99.89 E-value=2.4e-24 Score=139.08 Aligned_cols=59 Identities=44% Similarity=0.943 Sum_probs=55.5
Q ss_pred CcchhhhhhccCCeeEecc--CCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884 2 FQGFFRRSIQKQIEYRCLR--DGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~ 60 (240)
||+||||+|..+..|.|.. +++|.+++..|..|++|||+||+++||++++||.+|++.+
T Consensus 29 Ck~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~~ 89 (92)
T cd07163 29 CSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPRN 89 (92)
T ss_pred eeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcCC
Confidence 8999999999999999986 4799999999999999999999999999999999998865
No 21
>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=99.88 E-value=4.9e-24 Score=136.93 Aligned_cols=60 Identities=48% Similarity=0.991 Sum_probs=56.8
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~ 61 (240)
||+||||+|..+..|.|..+++|.|+...|..|++|||+||+++||++++||.+|.+.+.
T Consensus 29 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~ 88 (90)
T cd07169 29 CKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGR 88 (90)
T ss_pred hHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccCCCCC
Confidence 899999999999999999999999999999999999999999999999999999987653
No 22
>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=99.88 E-value=4e-24 Score=138.59 Aligned_cols=62 Identities=56% Similarity=1.138 Sum_probs=58.4
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~ 63 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++|+.+|.+++.+.
T Consensus 28 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~~~~~ 89 (95)
T cd06968 28 CKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRD 89 (95)
T ss_pred hHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCChhhhh
Confidence 89999999999999999999999999999999999999999999999999999998887644
No 23
>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=99.88 E-value=5.2e-24 Score=133.37 Aligned_cols=56 Identities=50% Similarity=1.002 Sum_probs=53.7
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 57 (240)
||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|+
T Consensus 21 C~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 21 CKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred ehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 89999999999999999999999999999999999999999999999999999875
No 24
>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=99.88 E-value=4.2e-24 Score=134.77 Aligned_cols=55 Identities=38% Similarity=0.823 Sum_probs=52.8
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r 56 (240)
||+||||+|..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|
T Consensus 26 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~ 80 (82)
T cd07171 26 CKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER 80 (82)
T ss_pred hHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhh
Confidence 8999999999999999999999999999999999999999999999999999876
No 25
>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=99.88 E-value=4.2e-24 Score=135.41 Aligned_cols=58 Identities=38% Similarity=0.729 Sum_probs=54.3
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK 59 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~ 59 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++|+.++.-+
T Consensus 24 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~ 81 (84)
T cd06962 24 CKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCK 81 (84)
T ss_pred ceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHHh
Confidence 9999999999999999999999999999999999999999999999999999877543
No 26
>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=99.88 E-value=6.2e-24 Score=136.59 Aligned_cols=59 Identities=39% Similarity=0.680 Sum_probs=55.4
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~ 60 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++||.+++-..
T Consensus 24 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~~ 82 (91)
T cd07161 24 CKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCAI 82 (91)
T ss_pred hHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhhH
Confidence 89999999999999999999999999999999999999999999999999999876544
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=99.88 E-value=1.5e-23 Score=130.25 Aligned_cols=53 Identities=42% Similarity=0.872 Sum_probs=50.9
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCcccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRY 54 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 54 (240)
||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++|+.
T Consensus 21 C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 73 (74)
T cd07179 21 CKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73 (74)
T ss_pred HHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence 89999999999999999999999999999999999999999999999999975
No 28
>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=99.87 E-value=1.1e-23 Score=131.11 Aligned_cols=53 Identities=53% Similarity=1.098 Sum_probs=50.6
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCcccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRY 54 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 54 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++||.
T Consensus 23 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~ 75 (75)
T cd06969 23 CKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75 (75)
T ss_pred eeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence 89999999999999999999999999999999999999999999999999873
No 29
>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=99.87 E-value=1.9e-23 Score=129.18 Aligned_cols=52 Identities=40% Similarity=0.967 Sum_probs=49.7
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 53 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++|+
T Consensus 21 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd07156 21 CKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL 72 (72)
T ss_pred hhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence 8999999999999999999999999999999999999999999999999874
No 30
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=99.87 E-value=2.6e-23 Score=128.90 Aligned_cols=52 Identities=44% Similarity=1.036 Sum_probs=50.3
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 53 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++||
T Consensus 21 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (73)
T cd06958 21 CKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred hhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 8999999999999999999999999999999999999999999999999987
No 31
>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=99.87 E-value=1e-23 Score=136.54 Aligned_cols=62 Identities=31% Similarity=0.665 Sum_probs=57.6
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~ 63 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+|||++||++++||.+|+..+++.
T Consensus 23 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~~r~ 84 (94)
T cd06966 23 CKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSEKRQ 84 (94)
T ss_pred ehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhHHHH
Confidence 99999999999999999999999999999999999999999999999999999988766543
No 32
>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=99.87 E-value=2.8e-23 Score=128.73 Aligned_cols=52 Identities=42% Similarity=0.798 Sum_probs=49.7
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 53 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||+++.|+
T Consensus 22 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (73)
T cd06959 22 CKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73 (73)
T ss_pred hHHHHHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence 8999999999999999999999999999999999999999999999999874
No 33
>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=99.87 E-value=2.1e-23 Score=129.09 Aligned_cols=52 Identities=56% Similarity=1.180 Sum_probs=50.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 53 (240)
||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||
T Consensus 21 C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 21 CKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred eeeeEeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 8999999999999999999999999999999999999999999999999886
No 34
>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=99.87 E-value=4.1e-23 Score=127.72 Aligned_cols=52 Identities=29% Similarity=0.760 Sum_probs=49.5
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 53 (240)
||+||||++..+..|.|..+++|.|++..|..|++|||+||+++||+++++.
T Consensus 21 Ck~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 21 CKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred hhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 8999999999999999999999999999999999999999999999999863
No 35
>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=99.87 E-value=2.5e-23 Score=129.09 Aligned_cols=52 Identities=48% Similarity=1.041 Sum_probs=49.7
Q ss_pred CcchhhhhhccCCeeEec-cCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCL-RDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~-~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 53 (240)
||+||||+|..+..|.|. .+++|.++...|..|++|||+||+++||++++||
T Consensus 21 C~~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 21 CSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred eeeEeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 899999999999999999 7889999999999999999999999999999986
No 36
>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=99.87 E-value=2.4e-23 Score=132.28 Aligned_cols=59 Identities=47% Similarity=1.127 Sum_probs=54.2
Q ss_pred CcchhhhhhccCCeeE-eccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884 2 FQGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~-C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~ 62 (240)
||+||||+|..+..|. |..+ |.+++..|..|++|||+||+++||++++||.+|+++..+
T Consensus 22 Ck~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~~ 81 (84)
T cd06965 22 CKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRVEK 81 (84)
T ss_pred hhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCchhh
Confidence 8999999999999995 9854 999999999999999999999999999999999987654
No 37
>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=99.87 E-value=3.9e-23 Score=128.38 Aligned_cols=52 Identities=69% Similarity=1.382 Sum_probs=49.9
Q ss_pred CcchhhhhhccCCee-EeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~-~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 53 (240)
||+||||+|..+..| .|..+++|.+++..|..|++|||+||+++||++++|+
T Consensus 21 C~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 73 (73)
T cd07158 21 CKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred HHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence 899999999999999 8999999999999999999999999999999999885
No 38
>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=99.86 E-value=2.2e-23 Score=133.47 Aligned_cols=56 Identities=32% Similarity=0.822 Sum_probs=53.1
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 57 (240)
||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++|+.++.
T Consensus 22 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~ 77 (87)
T cd07162 22 CKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA 77 (87)
T ss_pred hHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence 89999999999999999999999999999999999999999999999999998754
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=99.86 E-value=2.1e-23 Score=137.54 Aligned_cols=54 Identities=35% Similarity=0.870 Sum_probs=51.7
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYG 55 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~ 55 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+|||++||++++|+.+
T Consensus 29 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 82 (107)
T cd06955 29 CKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82 (107)
T ss_pred ecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence 999999999999999999999999999999999999999999999999988876
No 40
>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=99.86 E-value=8.3e-23 Score=130.23 Aligned_cols=57 Identities=44% Similarity=0.843 Sum_probs=52.5
Q ss_pred CcchhhhhhccCC--eeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCC
Q psy7884 2 FQGFFRRSIQKQI--EYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58 (240)
Q Consensus 2 Ck~FFRRsv~~~~--~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~ 58 (240)
||+||||+++.+. .|.|..+++|.++...|..|++|||+||++|||++++++.+|..
T Consensus 23 Ck~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~ 81 (86)
T cd07157 23 CKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS 81 (86)
T ss_pred eeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence 9999999998764 89999999999999999999999999999999999999887754
No 41
>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=99.86 E-value=1.8e-22 Score=126.30 Aligned_cols=52 Identities=31% Similarity=0.806 Sum_probs=49.5
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 53 (240)
||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++.++.
T Consensus 25 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 25 CKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred hHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence 8999999999999999999999999999999999999999999999998764
No 42
>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=99.85 E-value=2.8e-22 Score=126.33 Aligned_cols=54 Identities=26% Similarity=0.711 Sum_probs=50.0
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccC
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYG 55 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~ 55 (240)
||+||||+|..+..|.|..+++|.|++..|..|++|||+||+++||+++....+
T Consensus 26 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~ 79 (82)
T cd07173 26 CKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK 79 (82)
T ss_pred HHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence 899999999999999999999999999999999999999999999998865443
No 43
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.83 E-value=1.3e-21 Score=120.69 Aligned_cols=49 Identities=43% Similarity=0.956 Sum_probs=46.8
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCcc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 50 (240)
||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||+++
T Consensus 22 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 22 CKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred hhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 8999999999999999999999999999999999999999999999974
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=99.77 E-value=5.3e-20 Score=113.91 Aligned_cols=48 Identities=46% Similarity=1.056 Sum_probs=41.9
Q ss_pred CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCc
Q psy7884 2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR 49 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~ 49 (240)
||+||||++..+..|.|..+++|.+++..|..|++|||+||+++||++
T Consensus 23 C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 23 CKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp HHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred ceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence 899999999999999999999999999999999999999999999974
No 45
>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=99.76 E-value=8.7e-18 Score=129.03 Aligned_cols=121 Identities=31% Similarity=0.498 Sum_probs=94.5
Q ss_pred hHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCC
Q psy7884 107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV 186 (240)
Q Consensus 107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~ 186 (240)
...+++.+.++|.+++.++.++++.+...++...... ......+...|.++++.++..|+.+|+|||.+
T Consensus 3 ~~~l~~~v~~ah~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~t~~i~~vVefAK~I 71 (241)
T cd06939 3 LEHLAQNICKAHLETCQYLREELQQLRWKTFSQEEIL-----------AYQNKSREEMWQLCAEKITEAIQYVVEFAKRI 71 (241)
T ss_pred HHHHHHHHHHHHHHHccCcHHHHHHHhcCcCCccccc-----------ccccccHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4678899999999999999999888754443211110 01122355789999999999999999999999
Q ss_pred cCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeeecHHHHhhh
Q psy7884 187 PGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYVTRQQLEVM 238 (240)
Q Consensus 187 p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i~~~~~~~~ 238 (240)
|+|.+|+.+||++|||++|+|+++++.++. ...+..++.+|.+++++.++..
T Consensus 72 PgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~~~~~~~~~~~~~~~~ 124 (241)
T cd06939 72 PGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFDGKYAPIDLFKSL 124 (241)
T ss_pred CCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCEEEECCccccHHHHHHc
Confidence 999999999999999999999999999987 3333444457778888776653
No 46
>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=99.70 E-value=2.4e-16 Score=122.23 Aligned_cols=130 Identities=24% Similarity=0.379 Sum_probs=96.7
Q ss_pred hHHHHHHHHHhhhccCCCCHHHhhhhcCCC------CCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHH
Q psy7884 107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKP------VSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVV 180 (240)
Q Consensus 107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i 180 (240)
...++..+..+|.+++.++.++...+.... +..+..... .............+...|.++...++..|..+|
T Consensus 3 l~~l~~~~~~a~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vV 80 (259)
T cd06932 3 LRALAKHLYVAYLKQFPLTKAKARKILTGKTTDHAPFVIYDIESL--KLNKDGQPQEKTIRIRLFQRCQVRSVETIRELT 80 (259)
T ss_pred HHHHHHHHHHHHHHhccccHHHHHHhccCCCCCCCceeeecchhh--hccCCCCCCcchhHHHHHHHHHHHHHHHHHHHH
Confidence 356788999999999999999987763322 111100000 000111122244566789999999999999999
Q ss_pred hhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCC-eeecHHHHhhh
Q psy7884 181 EFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDG-MYVTRQQLEVM 238 (240)
Q Consensus 181 efak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G-~~i~~~~~~~~ 238 (240)
||||.+|+|.+|+.+||++|||++|+|+++++.++....+++.+++| .+++++.++..
T Consensus 81 ewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~~~~~~~~~~~~~~~~~~~~~~ 139 (259)
T cd06932 81 EFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYNKDGLLFPEGNGYVTREFLESL 139 (259)
T ss_pred HHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcCCCCeEEeCCCEEeeHHHHHHh
Confidence 99999999999999999999999999999999998877777888765 66777765543
No 47
>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=99.66 E-value=1.1e-15 Score=117.85 Aligned_cols=78 Identities=36% Similarity=0.512 Sum_probs=71.6
Q ss_pred hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884 160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV 237 (240)
Q Consensus 160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~ 237 (240)
.....|.++++.++..|..+|+|||.+|+|.+|+.+||+.|||++|+|+++++.+++ ...+.+.|++|..++++.++.
T Consensus 49 ~~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (243)
T cd06935 49 VDLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKN 128 (243)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCeEeeHHHHHh
Confidence 356789999999999999999999999999999999999999999999999999998 567889999999999887654
No 48
>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=99.65 E-value=1.6e-15 Score=116.08 Aligned_cols=77 Identities=31% Similarity=0.502 Sum_probs=69.8
Q ss_pred hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884 160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE 236 (240)
Q Consensus 160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~ 236 (240)
.....|.++.+.++..+..+|+|||.+|+|.+|+.+||+.|||++|+|+++|+.+|+ ..++.++|.+|..+++++..
T Consensus 39 ~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~~g~~~~~~~~~ 117 (239)
T cd07072 39 SEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQ 117 (239)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEeeCCeeecHHHHH
Confidence 344669999999999999999999999999999999999999999999999999998 56778999999988887643
No 49
>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=99.63 E-value=2.6e-15 Score=115.64 Aligned_cols=114 Identities=23% Similarity=0.362 Sum_probs=90.1
Q ss_pred HHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCCcC
Q psy7884 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPG 188 (240)
Q Consensus 109 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~p~ 188 (240)
++|..+..++...+........++...+. .... . .+......|.++.+++...+..+|+|||.+|+
T Consensus 3 ~li~~l~~a~~~~~~~~~~~~~~~~~~~~----~~~~-------~---~~~~~~~~~~~~~~~~~~~i~~~VefaK~lP~ 68 (236)
T cd06954 3 EMIEQLVAAQQQCNKRSFEDVPKVTPWPE----GQDP-------Q---SREARQQRFAHFTELAILSVQEIVDFAKQLPG 68 (236)
T ss_pred HHHHHHHHHHHhhcCCChHHHhccCCCcc----cccc-------c---cchHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 57888999998888777776655443221 0000 0 01112356999999999999999999999999
Q ss_pred cCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884 189 FCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE 236 (240)
Q Consensus 189 F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~ 236 (240)
|..|+.+||+.|||++|+++++++.+++ ...+.+.|++|..++++.+.
T Consensus 69 F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~~~~~~~~~g~~~~~~~~~ 118 (236)
T cd06954 69 FLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFA 118 (236)
T ss_pred cccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCccccHHHHH
Confidence 9999999999999999999999999987 66788999999998887654
No 50
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=99.63 E-value=3.8e-15 Score=113.91 Aligned_cols=72 Identities=29% Similarity=0.525 Sum_probs=67.2
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ 234 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~ 234 (240)
..|.++.++++..+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.+|+ ..++.++|.+|..+.+.+
T Consensus 41 ~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~ 114 (238)
T cd07348 41 SDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQ 114 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHH
Confidence 559999999999999999999999999999999999999999999999999998 567889999999987754
No 51
>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=99.63 E-value=1.8e-15 Score=112.37 Aligned_cols=78 Identities=41% Similarity=0.682 Sum_probs=71.1
Q ss_pred hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884 160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV 237 (240)
Q Consensus 160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~ 237 (240)
.+..+|.++++.++..|..+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++ ...+++.+++|..++++.++.
T Consensus 9 ~~~~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~ 88 (189)
T cd06940 9 SGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLHS 88 (189)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCcEEcHHHHHH
Confidence 345779999999999999999999999999999999999999999999999999987 566789999999999887654
No 52
>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=99.61 E-value=7.6e-15 Score=112.33 Aligned_cols=73 Identities=30% Similarity=0.495 Sum_probs=67.5
Q ss_pred HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ 234 (240)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~ 234 (240)
...|.++++.++..|+.+|+|||++|+|.+|+.+||++|||++|+|+++++.+++ ..++.++|++|..+.+.+
T Consensus 40 ~~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~ 114 (238)
T cd07071 40 TQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQ 114 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhh
Confidence 3569999999999999999999999999999999999999999999999999998 667889999998887654
No 53
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=99.61 E-value=2.6e-15 Score=112.41 Aligned_cols=74 Identities=68% Similarity=1.233 Sum_probs=68.1
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE 236 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~ 236 (240)
.+|.++++.++.+++.+|+|||.+|+|.+|+.+||+.|||++|+++++++.++. ...+++.|++|..++.+.++
T Consensus 2 ~~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (195)
T cd06941 2 WLWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLD 77 (195)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCeEEecCCeEeeHHHHH
Confidence 369999999999999999999999999999999999999999999999999988 55678999999999887654
No 54
>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=99.60 E-value=1.1e-14 Score=111.77 Aligned_cols=74 Identities=32% Similarity=0.467 Sum_probs=68.4
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE 236 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~ 236 (240)
..|.++++++...+..+|+|||++|+|.+|+.+||+.|||++|+++++++.++. ...+++.|+||..++++.+.
T Consensus 39 ~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~~~~~~f~~g~~~~~~~~~ 114 (231)
T cd06938 39 MRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYR 114 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEeeCCEEecHHHHh
Confidence 459999999999999999999999999999999999999999999999999987 67788999999998887653
No 55
>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=99.58 E-value=1.9e-14 Score=110.10 Aligned_cols=78 Identities=35% Similarity=0.630 Sum_probs=70.7
Q ss_pred hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884 160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV 237 (240)
Q Consensus 160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~ 237 (240)
.+...|.++.+.+...+..+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++ ...+.+.|.+|..++++....
T Consensus 35 ~~~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~ 114 (231)
T cd06937 35 LDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHN 114 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhh
Confidence 356789999999999999999999999999999999999999999999999999987 567889999999888876543
No 56
>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=99.56 E-value=4.3e-14 Score=107.79 Aligned_cols=101 Identities=20% Similarity=0.229 Sum_probs=78.2
Q ss_pred hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884 106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR 185 (240)
Q Consensus 106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~ 185 (240)
+...++..+..+|..++.++......... ....|.++++.+...++.+|+|||+
T Consensus 4 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~l~~iV~wAK~ 57 (226)
T cd06934 4 EQEELIRELVGAHTKTFDTTFSQFKQFRP--------------------------PFSLLPHFADLTTYMIKQIIKFAKD 57 (226)
T ss_pred HHHHHHHHHHHHHHhhcCccHHHHHhcCc--------------------------HhhHHHHHHHHHHHHHHHHHHHhcC
Confidence 35678889999999887776655443210 0246999999999999999999999
Q ss_pred CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeeecH
Q psy7884 186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYVTR 232 (240)
Q Consensus 186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i~~ 232 (240)
+|+|.+|+.+||++|||++|+|+++++.+++ .......+.+|..+..
T Consensus 58 iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~~~~~~~~~~~~~~ 105 (226)
T cd06934 58 LPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWECGPLTYCI 105 (226)
T ss_pred CcccccCCcchHHHHHHHhHHHHHHHHHHHHhcccCCeEeeCCEeecH
Confidence 9999999999999999999999999998876 2233334445544443
No 57
>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=99.54 E-value=7.3e-14 Score=107.36 Aligned_cols=72 Identities=33% Similarity=0.550 Sum_probs=67.0
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ 234 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~ 234 (240)
..|.++.+.++.++..+|+|||++|+|.+|+.+||+.|||++|+|+++|+.+++ ...+.+.|++|..+.+++
T Consensus 41 ~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~ 114 (239)
T cd06945 41 QQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQ 114 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHH
Confidence 459999999999999999999999999999999999999999999999999998 567889999999988765
No 58
>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=99.53 E-value=1.3e-13 Score=105.94 Aligned_cols=97 Identities=28% Similarity=0.367 Sum_probs=76.9
Q ss_pred hHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCC
Q psy7884 107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV 186 (240)
Q Consensus 107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~ 186 (240)
...++..+..+|.+++.++........ ...+...|.++++.++..|+.+|+|||.+
T Consensus 5 q~~li~~l~~a~~~~~~~~~~~~~~~~------------------------~~~~~~l~~~l~~l~~~~l~~iI~wAK~i 60 (238)
T cd06933 5 QQKIIDILLEAHHKTYDTTYSDFNKFR------------------------PPVRLSMLPHLADLVSYSIQKVIGFAKMI 60 (238)
T ss_pred HHHHHHHHHHHHHHhcccchhHHhccC------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 467889999999987766655443321 00235679999999999999999999999
Q ss_pred cCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCC--ceEecCC
Q psy7884 187 PGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS--SLTFSDG 227 (240)
Q Consensus 187 p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~--~l~~~~G 227 (240)
|+|.+|+.+||+.|||++|+|+++++.++....+ .+.+.++
T Consensus 61 PgF~~L~~~DQi~LLk~~~~ElliL~~~~~~~~~~~~~~~~~~ 103 (238)
T cd06933 61 PGFRDLTAEDQIALLKSSAIEVIMLRSNQSFSLDDMSWTCGSP 103 (238)
T ss_pred CccccCChHHHHHHHHHhHHHHHHHHHHHhcCcCCCeeEecCC
Confidence 9999999999999999999999999988873333 3455544
No 59
>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=99.52 E-value=3.7e-14 Score=105.73 Aligned_cols=72 Identities=31% Similarity=0.482 Sum_probs=66.4
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCCeeecHHHH
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQL 235 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G~~i~~~~~ 235 (240)
.|.++.+.++.++..+|+|||.+|+|.+|+.+||+.|||++|+++++++.++.....++.+++|..+.++.+
T Consensus 3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~~~~~~~g~~~~~~~~ 74 (191)
T cd06942 3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNEGTVLCDFRPVEFASL 74 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcCCeEEeCCccccHHHH
Confidence 599999999999999999999999999999999999999999999999998886555889999999887643
No 60
>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=99.52 E-value=4.6e-14 Score=108.12 Aligned_cols=74 Identities=23% Similarity=0.321 Sum_probs=65.6
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c---CCCceEecCCeeecHHHHh
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T---TDSSLTFSDGMYVTRQQLE 236 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~---~~~~l~~~~G~~i~~~~~~ 236 (240)
..+.++.+++..++..+|+|||++|+|.+|+.+||++|||++|+|+++++.+++ . ..+.+.|++|..++.+.+.
T Consensus 28 ~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~~ 105 (248)
T cd07075 28 NLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMH 105 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHHh
Confidence 458999999999999999999999999999999999999999999999998877 2 2344889999988887754
No 61
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.51 E-value=5.7e-14 Score=103.48 Aligned_cols=74 Identities=43% Similarity=0.660 Sum_probs=67.7
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV 237 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~ 237 (240)
.|.++.+.+..++..+|+|||++|+|..|+.+||++|||++|+++++++.++. ...+.+.+++|.+.+.+.+..
T Consensus 3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (174)
T cd06929 3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSRDVLLN 78 (174)
T ss_pred HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcccCCeEEecCCceecHHHHHH
Confidence 49999999999999999999999999999999999999999999999999988 677889999999977765543
No 62
>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=99.49 E-value=1.5e-13 Score=105.30 Aligned_cols=75 Identities=21% Similarity=0.327 Sum_probs=65.5
Q ss_pred HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cC-CC--ceEecCCeeecHHHHh
Q psy7884 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TT-DS--SLTFSDGMYVTRQQLE 236 (240)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~-~~--~l~~~~G~~i~~~~~~ 236 (240)
...+..+.+++..++..+|+|||++|+|.+|+.+||++|||++|+|+++++.+++ .. .+ .+.|++|..++.+..+
T Consensus 27 ~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~~ 105 (247)
T cd07076 27 WRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMT 105 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHHh
Confidence 3558899999999999999999999999999999999999999999999999887 32 22 3789999999887653
No 63
>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=99.48 E-value=2e-13 Score=105.02 Aligned_cols=73 Identities=25% Similarity=0.379 Sum_probs=63.9
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c---CCCceEecCCeeecHHHH
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T---TDSSLTFSDGMYVTRQQL 235 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~---~~~~l~~~~G~~i~~~~~ 235 (240)
..+.++.++++.++..+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++ . +.+.+.|.+|..++.+..
T Consensus 28 ~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~~ 104 (246)
T cd06947 28 RLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRM 104 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHHh
Confidence 358899999999999999999999999999999999999999999999999876 2 233477888888887764
No 64
>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=99.45 E-value=3e-13 Score=103.55 Aligned_cols=72 Identities=24% Similarity=0.399 Sum_probs=62.3
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c--C-CCceEecCCeeecHHHH
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T--T-DSSLTFSDGMYVTRQQL 235 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~--~-~~~l~~~~G~~i~~~~~ 235 (240)
.+..+.++...++..+|||||++|+|.+|+.+||++|||++|+++++++.+|+ . + ++.+.|++|..++.+..
T Consensus 29 ~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~ 104 (248)
T cd07074 29 LLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM 104 (248)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhh
Confidence 47888999999999999999999999999999999999999999999999987 2 2 34577877777776654
No 65
>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=99.45 E-value=4.2e-13 Score=103.19 Aligned_cols=72 Identities=22% Similarity=0.329 Sum_probs=64.4
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c---CCCceEecCCeeecHHH
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T---TDSSLTFSDGMYVTRQQ 234 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~---~~~~l~~~~G~~i~~~~ 234 (240)
..+.++.+++..++..+|+|||++|+|.+|+.+||+.|||++|.|+++|+.+++ . +.+.+.|++|..++.+.
T Consensus 28 ~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~ 103 (246)
T cd07073 28 ALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYR 103 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhh
Confidence 458899999999999999999999999999999999999999999999999987 2 34568999998877654
No 66
>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=99.44 E-value=4.7e-13 Score=102.70 Aligned_cols=74 Identities=24% Similarity=0.378 Sum_probs=66.0
Q ss_pred HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL 235 (240)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~ 235 (240)
...+.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|+++++++.+++ ...+.+.+.+|..++.+..
T Consensus 31 ~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~~~~~~~~~~~~~ 106 (235)
T cd06949 31 ASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQG 106 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCceecHHHh
Confidence 3458999999999999999999999999999999999999999999999999887 5567788888888776654
No 67
>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=99.41 E-value=7.7e-13 Score=101.64 Aligned_cols=71 Identities=18% Similarity=0.230 Sum_probs=64.9
Q ss_pred HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHH
Q psy7884 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQL 235 (240)
Q Consensus 165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~ 235 (240)
+.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|+++++|..+++ .+.+.+++++|..++++.+
T Consensus 40 ~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~ 114 (237)
T cd07070 40 FGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTV 114 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHH
Confidence 7789999999999999999999999999999999999999999999999887 3467899999999887654
No 68
>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=99.40 E-value=7.6e-13 Score=101.79 Aligned_cols=73 Identities=21% Similarity=0.229 Sum_probs=65.4
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---c-CCCceEecCCeeecHHHHh
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---T-TDSSLTFSDGMYVTRQQLE 236 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~-~~~~l~~~~G~~i~~~~~~ 236 (240)
.+..+.+++...+..+|+|||++|+|.+|+.+||+.|||++|++++++..+++ . ..+.+.+++|..++++.+.
T Consensus 39 ~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~ 115 (237)
T cd06944 39 TFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLA 115 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhh
Confidence 47788899999999999999999999999999999999999999999998887 2 2678999999998877653
No 69
>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=99.40 E-value=1.1e-12 Score=99.96 Aligned_cols=74 Identities=23% Similarity=0.435 Sum_probs=66.8
Q ss_pred HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL 235 (240)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~ 235 (240)
...|.++.+++...+..+|||||++|+|.+|+.+||++|+|++|++++++..|++ ...+.+.+++|.+++++..
T Consensus 26 ~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~ 101 (221)
T cd07068 26 VSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQA 101 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCCeEEeCCCceECHHHH
Confidence 3569999999999999999999999999999999999999999999999999998 4556789999988887654
No 70
>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=99.39 E-value=1.8e-12 Score=98.90 Aligned_cols=72 Identities=19% Similarity=0.342 Sum_probs=63.9
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ 234 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~ 234 (240)
..|.++.++...++..+|+|||++|+|..|+.+||++|||++|++++++..+++ ...+.+.+++|.+++++.
T Consensus 27 ~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~ 100 (221)
T cd06946 27 KALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEEL 100 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCceeecCCeEEcHHH
Confidence 459999999999999999999999999999999999999999999999999998 344667787887776544
No 71
>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=99.39 E-value=3.2e-12 Score=97.28 Aligned_cols=97 Identities=23% Similarity=0.282 Sum_probs=72.3
Q ss_pred hHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCC
Q psy7884 107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV 186 (240)
Q Consensus 107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~ 186 (240)
...++..++.+|+... .+.+....+..... . ....|.++.+++...+..+|+|||.+
T Consensus 3 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~--------~--------------~~~~~~~~~e~a~~~l~~~IefaK~i 59 (221)
T cd06936 3 QQTLLDYIVDAYQKQR-IPQEITKKLLQEEF--------S--------------PEENFLILTEMATSHVQVLVEFTKGL 59 (221)
T ss_pred HHHHHHHHHHHHHHhc-CChHHHHHHcccCC--------C--------------HhHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4678888888888743 33333333221110 0 01459999999999999999999999
Q ss_pred cCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCCee
Q psy7884 187 PGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMY 229 (240)
Q Consensus 187 p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G~~ 229 (240)
|+|.+|+.+||++|||++|+++++++.++.... .+++|..
T Consensus 60 P~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~---~~~~~~~ 99 (221)
T cd06936 60 PGFETLDHEDQIALLKGSAVEAMFLRSAQIYNK---KLPAGHA 99 (221)
T ss_pred CchhhCChhHHHHHHHHhHHHHHHHHHHHHhcc---cccCCCc
Confidence 999999999999999999999999998866322 1556653
No 72
>cd06930 NR_LBD_F2 Ligand-binding domain of nuclear receptor family 2. Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.38 E-value=1.3e-12 Score=95.39 Aligned_cols=70 Identities=21% Similarity=0.287 Sum_probs=61.8
Q ss_pred HHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHHh
Q psy7884 167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQLE 236 (240)
Q Consensus 167 ~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~~ 236 (240)
.+.+++...+..+|||||++|+|.+|+.+||+.|||++|+++++++.||+ ...+.+.+++|.+++.+.+.
T Consensus 3 ~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~ 76 (165)
T cd06930 3 SLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREA 76 (165)
T ss_pred hHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhh
Confidence 46677888999999999999999999999999999999999999999998 23668999999998877543
No 73
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=99.37 E-value=1.4e-12 Score=98.59 Aligned_cols=71 Identities=27% Similarity=0.499 Sum_probs=64.1
Q ss_pred HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL 235 (240)
Q Consensus 165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~ 235 (240)
..++.+++...+..+|+|||++|+|.+|+.+||+.|+|++|++++++..+++ ...+++++++|.++.++..
T Consensus 32 ~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~ 104 (207)
T cd06943 32 VSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSA 104 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCceeccchh
Confidence 5678888899999999999999999999999999999999999999999988 4568899999988876654
No 74
>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=2.5e-12 Score=98.96 Aligned_cols=70 Identities=21% Similarity=0.224 Sum_probs=62.5
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c---CCCceEecCCeeecHH
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T---TDSSLTFSDGMYVTRQ 233 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~---~~~~l~~~~G~~i~~~ 233 (240)
.|.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|.++++|+.+++ . ..+.+.+++|..++..
T Consensus 41 ~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~ 114 (241)
T cd07069 41 TFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYS 114 (241)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCch
Confidence 48899999999999999999999999999999999999999999999998887 2 3567889999876643
No 75
>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal lig
Probab=99.33 E-value=2.1e-12 Score=98.74 Aligned_cols=72 Identities=24% Similarity=0.348 Sum_probs=64.9
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ 234 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~ 234 (240)
..+.++...+..++..+|+|||.||+|.+|+.+||++|+|++|++++++..+++ ...+.+++++|.+++.+.
T Consensus 32 ~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~l~~~~g~~~~~~~ 105 (222)
T cd06931 32 ASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHC 105 (222)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCCeeeeCCCccccccc
Confidence 347888889999999999999999999999999999999999999999999997 557889999998877653
No 76
>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=99.28 E-value=1.4e-11 Score=92.79 Aligned_cols=53 Identities=25% Similarity=0.342 Sum_probs=50.5
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~ 216 (240)
.+.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|++++++..+++
T Consensus 27 ~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~ 79 (206)
T cd06950 27 SPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQW 79 (206)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 37788999999999999999999999999999999999999999999999987
No 77
>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=99.27 E-value=7.6e-12 Score=96.28 Aligned_cols=68 Identities=21% Similarity=0.311 Sum_probs=60.4
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCeeec
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYVT 231 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~i~ 231 (240)
.+.++.+++...+..+|+|||.+|+|.+|+.+||+.|||++|+++++|..+++ ...+.+.+++|..+.
T Consensus 31 ~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~ 101 (236)
T cd06948 31 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHAS 101 (236)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccC
Confidence 37889999999999999999999999999999999999999999999998887 345557778887654
No 78
>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=99.21 E-value=1.2e-11 Score=94.39 Aligned_cols=56 Identities=25% Similarity=0.304 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216 (240)
Q Consensus 161 ~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~ 216 (240)
+++.|.++.+.+...|..+|+|||++|+|.+|+.+||++|||++|.|+++|..+++
T Consensus 17 ~l~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~ 72 (232)
T cd07350 17 TLKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQD 72 (232)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHH
Confidence 44569999999999999999999999999999999999999999999999999997
No 79
>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=99.18 E-value=4.3e-11 Score=90.63 Aligned_cols=54 Identities=20% Similarity=0.262 Sum_probs=51.9
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~ 216 (240)
..|..+.+.+...+..+|+|||.+|+|.+|+.+||++|||++|++++++..+++
T Consensus 27 ~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~ 80 (213)
T cd06953 27 ELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITV 80 (213)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 458999999999999999999999999999999999999999999999999988
No 80
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=99.18 E-value=9.9e-11 Score=88.19 Aligned_cols=77 Identities=23% Similarity=0.493 Sum_probs=69.3
Q ss_pred HHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCeeecHHHHhh
Q psy7884 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYVTRQQLEV 237 (240)
Q Consensus 161 ~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~i~~~~~~~ 237 (240)
+...|.++..++...+..+++|||.+|+|..|+.+||+.|+|++|+++++|+.++. ...+.+.+++|.+++.+.+..
T Consensus 15 ~~~~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~ 94 (203)
T PF00104_consen 15 RPATFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDSFDD 94 (203)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHHHHH
T ss_pred cHhhHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhccccccccccccccccccccccc
Confidence 34569999999999999999999999999999999999999999999999999998 369999999999998877654
No 81
>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=99.16 E-value=5.1e-11 Score=90.63 Aligned_cols=53 Identities=21% Similarity=0.302 Sum_probs=50.6
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~ 216 (240)
.+..+.+.+...+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.+++
T Consensus 20 ~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~ 72 (222)
T cd06951 20 APQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQD 72 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHH
Confidence 37788999999999999999999999999999999999999999999999987
No 82
>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=99.12 E-value=1e-10 Score=88.82 Aligned_cols=53 Identities=19% Similarity=0.319 Sum_probs=50.4
Q ss_pred HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216 (240)
Q Consensus 164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~ 216 (240)
.+..+.+.+...|..+|+|||.+|+|.+|+.+||++|||++|.|+++|..+++
T Consensus 20 ~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~ 72 (222)
T cd07349 20 TPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQD 72 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHH
Confidence 37788889999999999999999999999999999999999999999999997
No 83
>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=99.02 E-value=3.1e-10 Score=86.74 Aligned_cols=52 Identities=15% Similarity=0.250 Sum_probs=48.7
Q ss_pred HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216 (240)
Q Consensus 165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~ 216 (240)
+..+.+.+..++..+|+|||++|+|.+|+.+||++|+|++|.+++++..+++
T Consensus 23 ~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~ 74 (222)
T cd06952 23 VHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQC 74 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHH
Confidence 6778889999999999999999999999999999999999999999987754
No 84
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=98.94 E-value=2.8e-09 Score=77.72 Aligned_cols=63 Identities=29% Similarity=0.382 Sum_probs=53.5
Q ss_pred HHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCee
Q psy7884 167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMY 229 (240)
Q Consensus 167 ~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~ 229 (240)
++..++..++..+++|++++|+|..|+.+||+.|+|++|+++++|+.++. ........++|..
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~ 67 (168)
T cd06157 2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGH 67 (168)
T ss_pred cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccc
Confidence 35567778899999999999999999999999999999999999999998 4455555666653
No 85
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=98.88 E-value=2.2e-09 Score=77.88 Aligned_cols=60 Identities=33% Similarity=0.461 Sum_probs=51.7
Q ss_pred HHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCeeecHH
Q psy7884 174 PSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYVTRQ 233 (240)
Q Consensus 174 ~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~i~~~ 233 (240)
.++..+++|++++|+|.+|+.+||+.|+|++|+++++++.++. ...+.+.++||.++..+
T Consensus 3 ~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~ 65 (163)
T smart00430 3 RDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDND 65 (163)
T ss_pred hHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcc
Confidence 4567799999999999999999999999999999999999987 34446778888887654
No 86
>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=91.35 E-value=0.07 Score=24.34 Aligned_cols=20 Identities=25% Similarity=0.669 Sum_probs=14.7
Q ss_pred eeEeccCCccccccCCcccc
Q psy7884 15 EYRCLRDGKCLVIRLNRNRC 34 (240)
Q Consensus 15 ~~~C~~~~~C~i~~~~r~~C 34 (240)
.|.|+.++.|.+|..++..|
T Consensus 3 n~~Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 3 NFHCKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp T---BTTEEEEEETTTCEEE
T ss_pred CcccCCCCEeeeCCCCCcCC
Confidence 46899999999999888776
No 87
>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=79.78 E-value=0.73 Score=18.88 Aligned_cols=7 Identities=57% Similarity=1.227 Sum_probs=5.5
Q ss_pred chhhhhh
Q psy7884 4 GFFRRSI 10 (240)
Q Consensus 4 ~FFRRsv 10 (240)
|||+|.-
T Consensus 3 GFFKR~~ 9 (15)
T PF00357_consen 3 GFFKRQR 9 (15)
T ss_dssp CHHHHHH
T ss_pred ccccccC
Confidence 7998864
No 88
>KOG4846|consensus
Probab=75.28 E-value=4.6 Score=33.49 Aligned_cols=48 Identities=8% Similarity=0.012 Sum_probs=39.8
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCC-hhHHHHHHHhhhHHHHh
Q psy7884 163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLS-QDDQLILIKMGFFELWI 210 (240)
Q Consensus 163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~-~~Dq~~Llk~~~~~~~~ 210 (240)
-.|+.+..+....+..+++||+++++|..++ .-+++++|+.+-.+...
T Consensus 362 lp~~~~~ll~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~ 410 (538)
T KOG4846|consen 362 LPFKSLQLLYGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTE 410 (538)
T ss_pred cCcchhhhhhhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHH
Confidence 3488888888888999999999999999999 77999999876444433
No 89
>smart00274 FOLN Follistatin-N-terminal domain-like. Follistatin-N-terminal domain-like, EGF-like. Region distinct from the kazal-like sequence
Probab=74.13 E-value=2 Score=20.59 Aligned_cols=20 Identities=25% Similarity=0.541 Sum_probs=16.4
Q ss_pred eeEeccCCccccccCCcccc
Q psy7884 15 EYRCLRDGKCLVIRLNRNRC 34 (240)
Q Consensus 15 ~~~C~~~~~C~i~~~~r~~C 34 (240)
.++|..+..|.+|+..+.+|
T Consensus 4 ~v~C~~G~~C~~d~~g~p~C 23 (26)
T smart00274 4 NVQCPFGKVCVVDKGGNARC 23 (26)
T ss_pred CEECCCCCEEEeCCCCCEEE
Confidence 46799999999987777666
No 90
>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=67.52 E-value=2 Score=23.73 Aligned_cols=38 Identities=16% Similarity=0.354 Sum_probs=21.2
Q ss_pred CcchhhhhhccCCeeEec---cCCccccccCCcccchhcchh
Q psy7884 2 FQGFFRRSIQKQIEYRCL---RDGKCLVIRLNRNRCQYCRFK 40 (240)
Q Consensus 2 Ck~FFRRsv~~~~~~~C~---~~~~C~i~~~~r~~C~~CR~~ 40 (240)
|..||+..-..+ -+.|. ......+....+.+|+.||.|
T Consensus 6 c~~~l~~~RW~~-g~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 6 CREYLEEIRWPD-GFVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred HHHHHHHhcCCC-CCCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 455666543333 35564 222334444467789999875
No 91
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=58.63 E-value=9.4 Score=23.89 Aligned_cols=22 Identities=27% Similarity=0.416 Sum_probs=17.6
Q ss_pred hhcCCcCcCCCChhHHHHHHHh
Q psy7884 182 FAKRVPGFCDLSQDDQLILIKM 203 (240)
Q Consensus 182 fak~~p~F~~L~~~Dq~~Llk~ 203 (240)
-+..|++|..|..+||..+.+.
T Consensus 59 ~~~~i~G~~~L~~~Dq~~i~~~ 80 (82)
T PF00645_consen 59 DIEEIKGFDELKPEDQEKIRKL 80 (82)
T ss_dssp CGGGCETCCCS-HHHHHHHHHH
T ss_pred CHHHCCChHHCCHHHHHHHHHH
Confidence 3567999999999999988763
No 92
>PF09150 Carot_N: Orange carotenoid protein, N-terminal ; InterPro: IPR015233 Carotenoids such as beta-carotene, lycopene, lutein and beta-cryptoxanthine are produced in plants and certain bacteria, algae and fungi, where they function as accessory photosynthetic pigments and as scavengers of oxygen radicals for photoprotection. They are also essential dietary nutrients in animals. Orange carotenoid-binding proteins (OCP) were first identified in cyanobacterial species, where they occur associated with phycobilisome in the cellular thylakoid membrane. These proteins function in photoprotection, and are essential for inhibiting white and blue-green light non-photochemical quenching (NPQ) [, ]. Carotenoids improve the photoprotectant activity by broadening OCP's absorption spectrum and facilitating the dissipation of absorbed energy. OCP acts as a homodimer, and binds one molecule of carotenoid (3'-hydroxyechinenone) and one chloride ion per subunit, where the carotenoid binding site is lined with a striking number of methionine residues. The carotenoid 3'-hydroxyechinenone is not found in higher plants. OCP has two domains: an N-terminal helical domain and a C-terminal domain that resembles a NTF2 (nuclear transport factor 2) domain. OCP can be proteolytically cleaved into a red form (RCP), which lacks 15 residues from the N terminus and approximately 150 residues from the C terminus []. This entry represents the N-terminal domain found predominantly in prokaryotic orange carotenoid proteins and related carotenoid-binding proteins. It adopts an alpha-helical structure consisting of two four-helix bundles [].; GO: 0031404 chloride ion binding, 0016037 light absorption, 0030089 phycobilisome; PDB: 3MG3_B 3MG1_A 3MG2_A 1M98_A.
Probab=56.37 E-value=11 Score=27.01 Aligned_cols=23 Identities=43% Similarity=0.631 Sum_probs=17.8
Q ss_pred CcCcCCCChhHHHHHHHhhhHHH
Q psy7884 186 VPGFCDLSQDDQLILIKMGFFEL 208 (240)
Q Consensus 186 ~p~F~~L~~~Dq~~Llk~~~~~~ 208 (240)
+..|+.|+.+||+.||-....++
T Consensus 19 ~~~F~~Ls~DdqLAlLWf~Y~em 41 (159)
T PF09150_consen 19 VARFNQLSVDDQLALLWFAYTEM 41 (159)
T ss_dssp HHHHCCS-HHHHHHHHHHHHHHH
T ss_pred HHHHHcCCHHHHHHHHHHHHHHh
Confidence 45688999999999998766655
No 93
>KOG4033|consensus
Probab=42.85 E-value=15 Score=28.26 Aligned_cols=57 Identities=23% Similarity=0.391 Sum_probs=36.8
Q ss_pred HHHHHHHhhhcC--CcCcCCCChhHHHHHHHh--hhHHHHhhhhhcccCCCceEecCCeeec
Q psy7884 174 PSVQRVVEFAKR--VPGFCDLSQDDQLILIKM--GFFELWIGYVSRLTTDSSLTFSDGMYVT 231 (240)
Q Consensus 174 ~~l~~~iefak~--~p~F~~L~~~Dq~~Llk~--~~~~~~~l~~a~~~~~~~l~~~~G~~i~ 231 (240)
..+...|||+++ +.+++-|..+.+..+-+. .|++.+-...+.. -.+++..+||.+|-
T Consensus 130 ~~i~~~Vd~t~~~l~~fy~~lg~~~~~~irqtll~ffQd~~~kVSmf-ikd~~Q~~nGrFVl 190 (314)
T KOG4033|consen 130 AKIHMLVDFTKNTLLDFYNALGEDAQLSIRQTLLAFFQDFNTKVSMF-IKDGFQAMNGRFVL 190 (314)
T ss_pred hHHHHHHHHHHHHHHHHHcccChhHHHHHHHHHHHHHHHhhHHHHHH-HHHhhhcCCCcEEe
Confidence 456778999887 667777887777665553 4555555555553 34556667777653
No 94
>KOG4004|consensus
Probab=41.66 E-value=10 Score=28.24 Aligned_cols=28 Identities=36% Similarity=0.702 Sum_probs=24.3
Q ss_pred eEeccCCccccccCCcccchhcchhhhHH
Q psy7884 16 YRCLRDGKCLVIRLNRNRCQYCRFKKCLA 44 (240)
Q Consensus 16 ~~C~~~~~C~i~~~~r~~C~~CR~~KCl~ 44 (240)
.+|.-+++|.++..+...|-.|| -||-.
T Consensus 56 h~Cg~gk~C~vd~~~~P~Cvc~~-~kCP~ 83 (259)
T KOG4004|consen 56 HKCGPGKNCLVDLQTQPRCVCCR-YKCPR 83 (259)
T ss_pred ccCCCCceeeecCCCCceeEEec-CCCCc
Confidence 47889999999999888999999 67766
No 95
>PF06594 HCBP_related: Haemolysin-type calcium binding protein related domain; InterPro: IPR010566 This family consists of a number of bacteria specific domains, which are found in haemolysin-type calcium binding proteins. This family is found in conjunction with IPR001343 from INTERPRO and is often found in multiple copies.
Probab=40.55 E-value=18 Score=19.40 Aligned_cols=19 Identities=32% Similarity=0.436 Sum_probs=14.5
Q ss_pred cCCCceEecCCeeecHHHH
Q psy7884 217 TTDSSLTFSDGMYVTRQQL 235 (240)
Q Consensus 217 ~~~~~l~~~~G~~i~~~~~ 235 (240)
..-+.+.|.||+.++.+++
T Consensus 25 ~~Ie~i~FaDGt~w~~~~I 43 (43)
T PF06594_consen 25 YRIEQIEFADGTVWTRAQI 43 (43)
T ss_pred CcEeEEEEcCCCEecHHHC
Confidence 3457889999999887653
No 96
>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=40.09 E-value=9.3 Score=16.29 Aligned_cols=8 Identities=25% Similarity=0.738 Sum_probs=5.3
Q ss_pred Ccchhhhh
Q psy7884 2 FQGFFRRS 9 (240)
Q Consensus 2 Ck~FFRRs 9 (240)
||-||-.+
T Consensus 7 CknffWK~ 14 (18)
T PF03002_consen 7 CKNFFWKT 14 (18)
T ss_pred ccceeecc
Confidence 77777554
No 97
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=37.83 E-value=66 Score=20.69 Aligned_cols=28 Identities=39% Similarity=0.615 Sum_probs=21.3
Q ss_pred HHhh-hcCCcCcCCCChhHHHHHHHhhhHH
Q psy7884 179 VVEF-AKRVPGFCDLSQDDQLILIKMGFFE 207 (240)
Q Consensus 179 ~ief-ak~~p~F~~L~~~Dq~~Llk~~~~~ 207 (240)
+..+ +..+|+|..|+...|--|+-. ++|
T Consensus 26 I~~~Lt~~vPgF~~ls~sKqRRLi~~-ALE 54 (92)
T PF10330_consen 26 ITGYLTTSVPGFSDLSPSKQRRLIMA-ALE 54 (92)
T ss_pred HHHHHhccCCCcccCCHHHHHHHHHH-HHh
Confidence 3444 467999999999999988875 444
No 98
>PF05528 Coronavirus_5: Coronavirus gene 5 protein; InterPro: IPR008458 Infectious bronchitis virus, a member of Coronaviridae family, has a single-stranded positive-sense RNA genome, which is 27 kb in length. Gene 5 contains two (5a and 5b) open reading frames. The function of the 5a and 5b proteins is unknown [].
Probab=33.54 E-value=35 Score=20.66 Aligned_cols=32 Identities=19% Similarity=0.481 Sum_probs=22.8
Q ss_pred hhhhhccCCeeEeccCCccc--cccCCc-ccchhc
Q psy7884 6 FRRSIQKQIEYRCLRDGKCL--VIRLNR-NRCQYC 37 (240)
Q Consensus 6 FRRsv~~~~~~~C~~~~~C~--i~~~~r-~~C~~C 37 (240)
|||.+..+.++.=+.+-+|. +++... .-|++|
T Consensus 9 fr~aiARKaRiyLr~GldcvyflN~aGqaE~Cp~C 43 (82)
T PF05528_consen 9 FRGAIARKARIYLREGLDCVYFLNKAGQAEPCPAC 43 (82)
T ss_pred hhhhhhhheeeeeecCCceEEeecccCccccCcch
Confidence 89999888887777788884 444433 357777
No 99
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=32.17 E-value=27 Score=15.48 Aligned_cols=11 Identities=18% Similarity=0.800 Sum_probs=7.6
Q ss_pred hhhhHHhCCCc
Q psy7884 39 FKKCLAVGMSR 49 (240)
Q Consensus 39 ~~KCl~vGM~~ 49 (240)
|++|+...|-+
T Consensus 6 L~~CI~sAmPk 16 (20)
T PF05924_consen 6 LQECIGSAMPK 16 (20)
T ss_dssp HHHHHHCTS--
T ss_pred HHHHHHHhccc
Confidence 67899988854
No 100
>KOG3116|consensus
Probab=31.96 E-value=21 Score=25.20 Aligned_cols=10 Identities=50% Similarity=0.976 Sum_probs=8.7
Q ss_pred chhhhHHhCC
Q psy7884 38 RFKKCLAVGM 47 (240)
Q Consensus 38 R~~KCl~vGM 47 (240)
|-||||++|=
T Consensus 29 rCQKClq~GH 38 (177)
T KOG3116|consen 29 RCQKCLQAGH 38 (177)
T ss_pred hHHHHHhhcc
Confidence 6689999996
No 101
>PF08723 Gag_p15: Gag protein p15; InterPro: IPR014834 Gag p15 is a viral membrane-binding matrix protein which is alpha helical in structure. ; PDB: 1HEK_B.
Probab=31.51 E-value=22 Score=23.77 Aligned_cols=16 Identities=13% Similarity=0.424 Sum_probs=10.6
Q ss_pred hHHhCCCccccccCCC
Q psy7884 42 CLAVGMSRDSVRYGRV 57 (240)
Q Consensus 42 Cl~vGM~~~~v~~~r~ 57 (240)
|+++||.++.|+..+.
T Consensus 83 aVkmGlQi~~v~D~~A 98 (123)
T PF08723_consen 83 AVKMGLQIETVQDAKA 98 (123)
T ss_dssp HHHTT---SCCCCCHH
T ss_pred HHHhcCCccchhhhHH
Confidence 8999999999986653
No 102
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=30.82 E-value=21 Score=20.05 Aligned_cols=12 Identities=33% Similarity=0.855 Sum_probs=9.6
Q ss_pred Ccccchhcchhh
Q psy7884 30 NRNRCQYCRFKK 41 (240)
Q Consensus 30 ~r~~C~~CR~~K 41 (240)
...+|+.||-.+
T Consensus 32 ~p~RC~~CR~~r 43 (49)
T PF13451_consen 32 EPKRCPSCRQAR 43 (49)
T ss_pred CCccCHHHHHHH
Confidence 456899999776
No 103
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=29.55 E-value=17 Score=18.47 Aligned_cols=9 Identities=33% Similarity=0.892 Sum_probs=5.5
Q ss_pred hhhhHHhCC
Q psy7884 39 FKKCLAVGM 47 (240)
Q Consensus 39 ~~KCl~vGM 47 (240)
|+||+..|=
T Consensus 23 LekCmg~g~ 31 (33)
T PF08209_consen 23 LEKCMGRGR 31 (33)
T ss_dssp HHHHTCH--
T ss_pred HHHHHccCC
Confidence 578887763
No 104
>PHA03124 dUTPase; Provisional
Probab=25.10 E-value=24 Score=29.17 Aligned_cols=9 Identities=33% Similarity=0.800 Sum_probs=8.1
Q ss_pred Ccchhhhhh
Q psy7884 2 FQGFFRRSI 10 (240)
Q Consensus 2 Ck~FFRRsv 10 (240)
||+|+||+.
T Consensus 196 ~~~~~~~~~ 204 (418)
T PHA03124 196 CKAFYRRLF 204 (418)
T ss_pred hHHHHHHHH
Confidence 999999975
No 105
>PF15612 WHIM1: WSTF, HB1, Itc1p, MBD9 motif 1; PDB: 2Y9Z_B 2Y9Y_B.
Probab=24.36 E-value=72 Score=17.57 Aligned_cols=20 Identities=15% Similarity=0.285 Sum_probs=15.1
Q ss_pred cCcCCCChhHHHHHHHhhhH
Q psy7884 187 PGFCDLSQDDQLILIKMGFF 206 (240)
Q Consensus 187 p~F~~L~~~Dq~~Llk~~~~ 206 (240)
-+|..|+.++++.+|+.-+-
T Consensus 12 ~~y~~L~~~~kl~iL~~L~~ 31 (50)
T PF15612_consen 12 GEYYELSPEEKLEILRALCD 31 (50)
T ss_dssp STCCCS-HHHHHHHHHHHHH
T ss_pred CCcccCCHHHHHHHHHHHHH
Confidence 46789999999999996433
No 106
>PF15472 DUF4638: Domain of unknown function (DUF4638)
Probab=21.73 E-value=46 Score=25.45 Aligned_cols=18 Identities=44% Similarity=0.970 Sum_probs=15.1
Q ss_pred cchhcchhh---------hHHhCCCcc
Q psy7884 33 RCQYCRFKK---------CLAVGMSRD 50 (240)
Q Consensus 33 ~C~~CR~~K---------Cl~vGM~~~ 50 (240)
.|++-|+-| |-++||+.+
T Consensus 219 ~crylrl~~nNi~Tl~~lCkdaG~~vd 245 (268)
T PF15472_consen 219 SCRYLRLSKNNIRTLLKLCKDAGMDVD 245 (268)
T ss_pred ccceeeechhhHHHHHHHHHHcCCCcc
Confidence 788888755 999999987
No 107
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=20.88 E-value=35 Score=17.71 Aligned_cols=8 Identities=63% Similarity=1.431 Sum_probs=5.9
Q ss_pred cccchhcc
Q psy7884 31 RNRCQYCR 38 (240)
Q Consensus 31 r~~C~~CR 38 (240)
|-+|+.||
T Consensus 29 ryrC~~C~ 36 (36)
T PF03811_consen 29 RYRCKDCR 36 (36)
T ss_pred eEecCcCC
Confidence 55788886
No 108
>cd00435 ACBP Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Probab=20.42 E-value=1.6e+02 Score=18.69 Aligned_cols=25 Identities=20% Similarity=0.286 Sum_probs=19.8
Q ss_pred HHHHHhhhcCCcCcCCCChhHHHHHHH
Q psy7884 176 VQRVVEFAKRVPGFCDLSQDDQLILIK 202 (240)
Q Consensus 176 l~~~iefak~~p~F~~L~~~Dq~~Llk 202 (240)
+..++++++.++. .++.+|++.|.-
T Consensus 5 F~~A~~~v~~~~~--~~~~~~~L~lYa 29 (85)
T cd00435 5 FEAAAEKVKKLKT--KPSNEEKLQLYS 29 (85)
T ss_pred HHHHHHHHHhCCC--CcCHHHHHHHHH
Confidence 4558888999994 799999887765
No 109
>PF08483 IstB_IS21_ATP: IstB-like ATP binding N-terminal; InterPro: IPR013690 This bacterial domain is found to the N terminus of the IPR002611 from INTERPRO-like ATP binding domain in proteins which are putative transposase subunits [].
Probab=20.04 E-value=91 Score=15.46 Aligned_cols=17 Identities=29% Similarity=0.382 Sum_probs=13.7
Q ss_pred CcCcCCCChhHHHHHHH
Q psy7884 186 VPGFCDLSQDDQLILIK 202 (240)
Q Consensus 186 ~p~F~~L~~~Dq~~Llk 202 (240)
-|.+..|+.++...||-
T Consensus 6 ~p~~~~LsFeERl~LLv 22 (30)
T PF08483_consen 6 QPDTQELSFEERLGLLV 22 (30)
T ss_pred CcchhhcCHHHHHHHHH
Confidence 47778899999988875
Done!