Query psy16764
Match_columns 113
No_of_seqs 112 out of 697
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 21:24:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16764.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16764hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07349 NR_LBD_SHP The ligand 100.0 6.1E-32 1.3E-36 196.0 11.1 103 2-109 120-222 (222)
2 cd07069 NR_LBD_Lrh-1 The ligan 100.0 1.8E-31 4E-36 195.5 11.2 107 2-113 134-240 (241)
3 cd07070 NR_LBD_SF-1 The ligand 100.0 3.5E-31 7.6E-36 193.6 11.0 106 2-112 132-237 (237)
4 cd06937 NR_LBD_RAR The ligand 100.0 1.4E-31 3.1E-36 195.0 8.9 105 2-111 127-231 (231)
5 cd07350 NR_LBD_Dax1 The ligand 100.0 1.9E-30 4.2E-35 189.3 10.3 101 2-107 132-232 (232)
6 cd06951 NR_LBD_Dax1_like The l 100.0 2E-30 4.3E-35 188.0 10.0 100 2-107 123-222 (222)
7 cd06944 NR_LBD_Ftz-F1_like The 100.0 1.3E-29 2.8E-34 185.2 10.8 106 2-112 132-237 (237)
8 cd07348 NR_LBD_NGFI-B The liga 100.0 6.7E-30 1.4E-34 187.0 9.2 104 2-111 129-234 (238)
9 cd06949 NR_LBD_ER Ligand bindi 100.0 1.7E-29 3.7E-34 184.5 10.5 105 2-111 122-234 (235)
10 cd07071 NR_LBD_Nurr1 The ligan 100.0 4.7E-29 1E-33 182.6 9.6 104 2-111 129-234 (238)
11 cd06945 NR_LBD_Nurr1_like The 100.0 4.7E-29 1E-33 182.6 9.3 106 2-112 129-236 (239)
12 cd06948 NR_LBD_COUP-TF Ligand 100.0 1.3E-28 2.8E-33 179.8 11.3 107 2-113 121-227 (236)
13 cd06932 NR_LBD_PPAR The ligand 100.0 1E-28 2.2E-33 182.7 8.6 105 2-111 153-258 (259)
14 cd07072 NR_LBD_DHR38_like Liga 100.0 2.1E-28 4.5E-33 179.3 9.9 105 2-112 130-236 (239)
15 cd06935 NR_LBD_TR The ligand b 100.0 2.7E-28 5.9E-33 178.9 7.8 102 2-108 141-243 (243)
16 cd06941 NR_LBD_DmE78_like The 99.9 1.3E-27 2.7E-32 169.9 8.5 104 2-110 91-195 (195)
17 cd06952 NR_LBD_TR2_like The li 99.9 5.8E-27 1.3E-31 169.4 11.4 104 2-110 118-221 (222)
18 cd07076 NR_LBD_GR Ligand bindi 99.9 1.9E-27 4.1E-32 174.8 8.8 102 2-110 119-224 (247)
19 cd06933 NR_LBD_VDR The ligand 99.9 5E-27 1.1E-31 171.7 9.5 106 2-111 128-236 (238)
20 cd06946 NR_LBD_ERR The ligand 99.9 6.9E-27 1.5E-31 168.9 9.8 105 2-111 116-221 (221)
21 cd07073 NR_LBD_AR Ligand bindi 99.9 5.8E-27 1.2E-31 172.3 9.0 103 2-111 119-230 (246)
22 cd07068 NR_LBD_ER_like The lig 99.9 9.5E-27 2.1E-31 168.3 9.5 105 2-111 116-221 (221)
23 cd06939 NR_LBD_ROR_like The li 99.9 5.9E-27 1.3E-31 171.7 8.0 103 2-109 136-241 (241)
24 cd06954 NR_LBD_LXR The ligand 99.9 8.2E-27 1.8E-31 170.0 8.3 103 2-110 133-235 (236)
25 cd06950 NR_LBD_Tlx_PNR_like Th 99.9 3.9E-26 8.4E-31 163.8 9.5 91 2-96 115-205 (206)
26 cd06947 NR_LBD_GR_Like Ligand 99.9 5.4E-26 1.2E-30 167.1 9.8 107 2-112 119-231 (246)
27 cd06936 NR_LBD_Fxr The ligand 99.9 2.4E-26 5.3E-31 166.5 7.3 100 2-107 122-221 (221)
28 cd06934 NR_LBD_PXR_like The li 99.9 4.7E-26 1E-30 165.5 7.9 100 2-108 124-226 (226)
29 cd06940 NR_LBD_REV_ERB The lig 99.9 1.1E-25 2.5E-30 159.6 8.4 88 2-93 101-188 (189)
30 cd06938 NR_LBD_EcR The ligand 99.9 1.7E-24 3.8E-29 157.5 8.1 102 2-110 128-230 (231)
31 cd06943 NR_LBD_RXR_like The li 99.9 3.3E-24 7.1E-29 153.3 8.8 88 2-93 120-207 (207)
32 cd07075 NR_LBD_MR Ligand bindi 99.9 4.4E-24 9.6E-29 157.1 8.6 104 2-109 119-228 (248)
33 cd06931 NR_LBD_HNF4_like The l 99.9 4.5E-23 9.7E-28 148.9 8.8 102 2-108 121-222 (222)
34 cd06953 NR_LBD_DHR4_like The l 99.9 1.5E-22 3.2E-27 145.9 8.2 82 2-87 120-201 (213)
35 KOG4215|consensus 99.9 4.7E-22 1E-26 151.0 7.0 105 3-112 245-352 (432)
36 cd06942 NR_LBD_Sex_1_like The 99.9 1.4E-21 3E-26 138.6 7.3 98 2-104 90-189 (191)
37 cd06929 NR_LBD_F1 Ligand-bindi 99.8 5.6E-21 1.2E-25 132.7 7.8 83 2-88 91-173 (174)
38 cd06930 NR_LBD_F2 Ligand-bindi 99.8 7E-19 1.5E-23 120.8 8.7 76 2-81 90-165 (165)
39 cd07074 NR_LBD_PR Ligand bindi 99.7 1.2E-17 2.6E-22 123.1 10.1 105 2-111 119-230 (248)
40 cd06157 NR_LBD The ligand bind 99.6 5.9E-15 1.3E-19 100.0 8.6 76 2-81 91-168 (168)
41 smart00430 HOLI Ligand binding 99.6 1.1E-14 2.4E-19 98.3 7.6 76 2-81 85-163 (163)
42 PF00104 Hormone_recep: Ligand 99.6 9.1E-15 2E-19 102.0 6.5 89 2-94 110-202 (203)
43 KOG4218|consensus 99.5 2.3E-14 5.1E-19 108.9 4.1 105 3-112 369-473 (475)
44 KOG4217|consensus 99.3 1E-11 2.3E-16 97.5 6.9 104 2-111 496-601 (605)
45 KOG4216|consensus 99.2 3.6E-11 7.9E-16 92.7 6.8 105 2-111 370-476 (479)
46 KOG4846|consensus 88.5 0.25 5.5E-06 39.4 1.5 79 4-92 455-533 (538)
47 PF02020 W2: eIF4-gamma/eIF5/e 50.9 37 0.00079 20.6 3.9 48 44-92 2-49 (84)
48 PF07742 BTG: BTG family; Int 39.8 40 0.00087 22.2 3.0 31 37-67 22-53 (118)
49 smart00526 H15 Domain in histo 38.6 51 0.0011 18.8 3.0 23 50-72 26-48 (66)
50 cd03745 SOCS_WSB2_SWIP2 SOCS ( 38.4 18 0.00039 19.2 0.9 35 75-110 3-37 (39)
51 cd03746 SOCS_WSB1_SWIP1 SOCS ( 37.3 20 0.00042 19.1 1.0 36 75-111 3-38 (40)
52 PF10769 DUF2594: Protein of u 35.8 29 0.00064 21.0 1.6 10 14-23 17-26 (74)
53 PRK10613 hypothetical protein; 33.8 33 0.00072 20.8 1.6 10 14-23 17-26 (74)
54 cd09244 BRO1_Rhophilin Protein 29.4 72 0.0016 24.9 3.3 31 50-80 15-45 (350)
55 PRK11239 hypothetical protein; 28.3 1.3E+02 0.0028 22.1 4.2 66 8-74 92-169 (215)
56 PF05596 Taeniidae_ag: Taeniid 26.7 1.1E+02 0.0024 18.0 3.0 20 40-59 41-60 (64)
57 PF04504 DUF573: Protein of un 25.6 1.2E+02 0.0025 19.1 3.3 21 10-30 7-27 (98)
58 smart00099 btg1 tob/btg1 famil 25.0 1.2E+02 0.0026 19.8 3.2 32 36-67 21-53 (108)
59 PF12427 DUF3665: Branched-cha 24.4 56 0.0012 15.2 1.2 15 58-72 8-22 (23)
60 cd00073 H15 linker histone 1 a 24.2 1.2E+02 0.0025 18.6 3.0 23 50-72 26-48 (88)
61 PF03776 MinE: Septum formatio 22.9 59 0.0013 19.2 1.4 23 37-59 22-44 (70)
62 cd03733 SOCS_WSB_SWIP SOCS (su 21.6 52 0.0011 17.3 0.9 34 76-110 4-37 (39)
63 cd03717 SOCS_SOCS_like SOCS (s 21.4 53 0.0012 17.0 0.9 34 76-110 4-37 (39)
64 COG0851 MinE Septum formation 21.0 1.3E+02 0.0029 18.9 2.8 24 36-59 33-56 (88)
65 PF07146 DUF1389: Protein of u 20.9 3.9E+02 0.0084 20.7 5.8 60 11-77 181-248 (314)
66 TIGR03277 methan_mark_9 putati 20.5 86 0.0019 20.4 1.9 20 3-22 31-50 (109)
67 PF01267 F-actin_cap_A: F-acti 20.3 96 0.0021 23.3 2.4 26 39-64 104-129 (271)
68 PRK09458 pspB phage shock prot 20.1 2.2E+02 0.0048 17.3 4.9 23 40-63 49-71 (75)
No 1
>cd07349 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.
Probab=99.97 E-value=6.1e-32 Score=196.03 Aligned_cols=103 Identities=26% Similarity=0.361 Sum_probs=100.9
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|++||+|||||+||+||+ +|+.+..+|+++||+++.||++|+..+||++|.||+|||++||+||++
T Consensus 120 ~~~~l~~L~ld~~Eya~LkaivLf~pd~----~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~~~r~~kLLl~Lp~LR~i 195 (222)
T cd07349 120 CLNKFWSLDLSPKEYAYLKGTILFNPDV----PGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSI 195 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCc----ccCCCHHHHHHHHHHHHHHHHHHHHHHCCCcccHHHHHHHHhHHHhcC
Confidence 7789999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHHH
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHMY 109 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~eml 109 (113)
+++.+|++||.+.+| +++|++++.||+
T Consensus 196 ~~~~ie~lff~~~~g-~~~i~~Ll~eml 222 (222)
T cd07349 196 PPSLITDLFFRPIIG-DADIAELLGDML 222 (222)
T ss_pred CHHHHHHHhCccccC-CCcHHHHHHHhC
Confidence 999999999999999 999999999996
No 2
>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=1.8e-31 Score=195.53 Aligned_cols=107 Identities=18% Similarity=0.302 Sum_probs=104.3
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|.+||+|||||+|||||+ +|+.+..+|+++||+++.||++|+..+||++|.||++||++||+||++
T Consensus 134 ~~~~lr~L~ld~~E~a~LKaivLfnpd~----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LR~i 209 (241)
T cd07069 134 LVAKLRSLQFDQREFVCLKFLVLFSLDV----KNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAI 209 (241)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHhHHHHHh
Confidence 7889999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHHHhCCC
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHMYKNAG 113 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~~~ 113 (113)
++.++|++||.+.+| .+++++|+.||+.+|.
T Consensus 210 s~~~~e~l~~~~l~g-~~~~~~Ll~Eml~~~~ 240 (241)
T cd07069 210 SMQAEEYLYYKHLNG-DVPYNNLLIEMLHAKR 240 (241)
T ss_pred hHHHHHHHHhccccC-CCcHHHHHHHHHhccc
Confidence 999999999999999 9999999999999874
No 3
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=3.5e-31 Score=193.57 Aligned_cols=106 Identities=15% Similarity=0.225 Sum_probs=103.4
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|.+||+|||||++||||+ +++.++.+|+.+|+++..||.+||..+||..+.||++||++||+||++
T Consensus 132 ~~~kl~~L~ld~~Ey~~LkaIiLfnpd~----~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~kLLl~Lp~LRsi 207 (237)
T cd07070 132 LVLQLHALQLDRQEFVCLKFLILFSLDV----KFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRAL 207 (237)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHhcCCCc----cCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHhHHHHHh
Confidence 7789999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHHHhCC
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHMYKNA 112 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~~ 112 (113)
+++++|++||.+++| .+++++|+.||+.+|
T Consensus 208 s~~~~e~l~~~~l~g-~~~~~~Ll~eml~~~ 237 (237)
T cd07070 208 SMQAKEYLYHKHLGN-EMPRNNLLIEMLQAK 237 (237)
T ss_pred hHHHHHHHHHhcccC-CCcHHHHHHHHhcCC
Confidence 999999999999999 999999999999876
No 4
>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=99.97 E-value=1.4e-31 Score=194.97 Aligned_cols=105 Identities=19% Similarity=0.154 Sum_probs=102.4
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|+.+|++|++|++||+|||||+||+||+ +|+.++.+|+++||+++.||++|+..+||++|.||++||++||+||++
T Consensus 127 ~~~~l~~L~ld~~E~alLkAivLf~pDr----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~Lp~LR~l 202 (231)
T cd06937 127 FANQLLPLEMDDTEIGLLSAICLICGDR----QDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSI 202 (231)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCC----ccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHH
Confidence 7899999999999999999999999999 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHHHhC
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~ 111 (113)
+++++|++||.|.+| ++++++|+.||+++
T Consensus 203 ~~~~~e~l~~~k~~~-~~~~~~Ll~Eml~~ 231 (231)
T cd06937 203 SAKGAERVITLKMEI-PGPMPPLISEMLEN 231 (231)
T ss_pred HHHHHHHHHHHHhcC-CCCCCHHHHHHhcC
Confidence 999999999999999 99999999999963
No 5
>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.
Probab=99.97 E-value=1.9e-30 Score=189.26 Aligned_cols=101 Identities=25% Similarity=0.351 Sum_probs=98.2
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|.+||+|||||+||+||+ +++.+..+|+++|++++.+|++|+..+||++|.||+|||++||+||++
T Consensus 132 ~~~~l~~L~ld~~E~a~LkAivLf~pD~----~~L~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi 207 (232)
T cd07350 132 FLAKCWSLDISTKEYAYLKGTVLFNPDL----PGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAI 207 (232)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCc----ccCCCHHHHHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHhHHHHcc
Confidence 7889999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHH
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWH 107 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~e 107 (113)
+.+.+|++||.+++| +++|++++.|
T Consensus 208 ~~~~iE~lff~~l~g-~v~i~~ll~E 232 (232)
T cd07350 208 NANVIAELFFRPIIG-TVNMDDMLLE 232 (232)
T ss_pred CHHHHHHHhccccCC-CCcHHHHhcC
Confidence 999999999999999 9999999865
No 6
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=99.97 E-value=2e-30 Score=188.03 Aligned_cols=100 Identities=25% Similarity=0.337 Sum_probs=97.1
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|++||||||||+|||||+ +++ +..+|+++|++++.||++|+..+||++|.||+|||++||+||++
T Consensus 123 ~~~~l~~L~ld~~Eya~LkAivLfnpD~----~gl-~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LRsl 197 (222)
T cd06951 123 FLMKCWSLDLDCKEYAYLKGAVLFTPVP----PLL-CPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGI 197 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCC----Ccc-CHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHhhcC
Confidence 7889999999999999999999999998 789 99999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHH
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWH 107 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~e 107 (113)
+++.+|++||.+++| +++|++++.|
T Consensus 198 ~~~~~e~lff~~~~g-~~~i~~ll~~ 222 (222)
T cd06951 198 KTEPVTELFFRPIIG-NVSMDDVLLQ 222 (222)
T ss_pred CHHHHHHHhCccccC-CCcHHHHhcC
Confidence 999999999999999 9999999864
No 7
>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=99.96 E-value=1.3e-29 Score=185.20 Aligned_cols=106 Identities=18% Similarity=0.308 Sum_probs=103.3
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|++||+|||||++||||+ +|+++...|+++|+++..||.+|+..+||+.|.||++||++||+||++
T Consensus 132 ~~~~l~~L~ld~~E~~lLkaIiL~npd~----~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~Lp~Lr~i 207 (237)
T cd06944 132 LVNKLRELQFDRQEFVCLKFLILFNPDV----KGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAI 207 (237)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCc----CCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHhHHHHHH
Confidence 6789999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHHHhCC
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHMYKNA 112 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~~ 112 (113)
++.+++++||.+++| .+|+++|+.||+++|
T Consensus 208 s~~~~e~l~~~~l~g-~~~~~~Ll~eml~~~ 237 (237)
T cd06944 208 SMQAEEYLYYKHLNG-EVPCNNLLIEMLHAK 237 (237)
T ss_pred HHHHHHHHHhcccCC-CCcHHHHHHHHHcCC
Confidence 999999999999999 999999999999886
No 8
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=99.96 E-value=6.7e-30 Score=187.05 Aligned_cols=104 Identities=14% Similarity=0.192 Sum_probs=99.8
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhh--CCCcchHHHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTV--YPSQPTRFCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~--~p~~~~Rf~kLLl~Lp~Lr 79 (113)
|+.+|++|++|.+||+|||||+|| +|+ +|+.++.+|+++||+++.||++|+..+ +|++|.||+|||++||+||
T Consensus 129 f~~~l~~L~ld~~E~a~LkAIvLf-~Dr----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl~Lp~LR 203 (238)
T cd07348 129 FSQSLHRMNLDVSAFSCLAALVII-TDR----HGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELR 203 (238)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHc-CCC----cCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHHHHHHHH
Confidence 789999999999999999999999 687 799999999999999999999999985 4999999999999999999
Q ss_pred cCChhhhhhhhcccccCCCCcHHHHHHHHHhC
Q psy16764 80 SIPSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~ 111 (113)
+++++++|++|+.|++| .+++++|+.||+.+
T Consensus 204 sl~~~~~e~lf~~kl~~-~~~~~pLl~e~~~~ 234 (238)
T cd07348 204 TLCTQGLQRIFYLKLED-LVPPPPIVDKIFMD 234 (238)
T ss_pred HHHHHHHHHHHHHHhCC-CCCCCHHHHHHHhc
Confidence 99999999999999999 99999999999975
No 9
>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=99.96 E-value=1.7e-29 Score=184.49 Aligned_cols=105 Identities=13% Similarity=0.108 Sum_probs=101.8
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccC-----CCChhHHHHHHHHHHHHHHHHHHhhC---CCcchHHHHHHH
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRF-----KTGSKFTAAIQGHTQIFLNKYIHTVY---PSQPTRFCKIQL 73 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~-----l~~~~~Ve~lqe~~~~aL~~~~~~~~---p~~~~Rf~kLLl 73 (113)
|..+|++|++|++||+|||||++||||+ ++ +++..+|+++|++++.||++|+..+| |.+|.||++||+
T Consensus 122 ~~~~l~~L~ld~~EyalLKAIvLfnpd~----~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~~~~Rf~~LLl 197 (235)
T cd06949 122 TASRFRELQLQREEYVCLKAIILLNSSV----YTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLL 197 (235)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHcCCCc----CCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHHH
Confidence 7889999999999999999999999998 68 88999999999999999999999999 999999999999
Q ss_pred hchhhhcCChhhhhhhhcccccCCCCcHHHHHHHHHhC
Q psy16764 74 ILPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 74 ~Lp~Lr~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~ 111 (113)
+||+||+++++++|++++.|.+| .+++++|+.||+++
T Consensus 198 ~Lp~LR~l~~~~~e~l~~~k~~~-~~~~~~Ll~Eml~~ 234 (235)
T cd06949 198 ILSHIRHVSNKGMEHLYSMKCKN-VVPLYDLLLEMLDA 234 (235)
T ss_pred hchHHHHhhHHHHHHHHHHHhCC-CCChHHHHHHHhcC
Confidence 99999999999999999999999 99999999999986
No 10
>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=99.96 E-value=4.7e-29 Score=182.58 Aligned_cols=104 Identities=16% Similarity=0.169 Sum_probs=99.0
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhh--CCCcchHHHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTV--YPSQPTRFCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~--~p~~~~Rf~kLLl~Lp~Lr 79 (113)
|+++|++|++|.+||+|||||+||+ |+ +|+.|+.+|+++||+++.||++|+..+ +|++|.||+|||++||+||
T Consensus 129 f~~~l~~L~ld~~E~alLkAIvLf~-D~----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl~Lp~LR 203 (238)
T cd07071 129 FSSNLQNMNIDISAFSCIAALAMVT-ER----HGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELR 203 (238)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHcC-CC----CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHhHHHH
Confidence 8899999999999999999999995 77 689999999999999999999999977 4689999999999999999
Q ss_pred cCChhhhhhhhcccccCCCCcHHHHHHHHHhC
Q psy16764 80 SIPSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~ 111 (113)
+++++++|++|+.+.+| .+++++|+.||+.+
T Consensus 204 sl~~~~~e~l~~~k~~~-~~p~~~Ll~e~~~~ 234 (238)
T cd07071 204 TLCTQGLQRIFYLKLED-LVPPPAIIDKLFLD 234 (238)
T ss_pred HHHHHHHHHHHHHHcCC-CCCCcHHHHHHHHh
Confidence 99999999999999999 99999999999875
No 11
>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=99.96 E-value=4.7e-29 Score=182.59 Aligned_cols=106 Identities=19% Similarity=0.228 Sum_probs=102.7
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCC--CcchHHHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYP--SQPTRFCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p--~~~~Rf~kLLl~Lp~Lr 79 (113)
|+.+|++|++|++||+|||||++|+||+ +|+.++++|+++|++++.||++|+..+|| ++|.||+|||++||+||
T Consensus 129 f~~~l~~L~ld~~E~~~LkaivL~~pD~----~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl~Lp~LR 204 (239)
T cd06945 129 FSSSLQSLLLDDISAFCCLALLLLITER----HGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELR 204 (239)
T ss_pred HHHHHHHHhCChHHHHHHHHHHHhCCCc----cccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHH
Confidence 7889999999999999999999999999 79999999999999999999999999999 99999999999999999
Q ss_pred cCChhhhhhhhcccccCCCCcHHHHHHHHHhCC
Q psy16764 80 SIPSLVLEELFFRNIIGHNTTIKKTIWHMYKNA 112 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~~ 112 (113)
+++++++|+++|.|.+| ++++++|+.||+...
T Consensus 205 ~ls~~~~e~l~~~k~~~-~~~~~~Ll~e~~~~~ 236 (239)
T cd06945 205 TLSKKGLQRIFFLKLED-LLPPPPLIDKRFLDT 236 (239)
T ss_pred HHHHHHHHHHHHHHccC-CCCCChHHHHHHHhc
Confidence 99999999999999999 999999999999753
No 12
>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=99.96 E-value=1.3e-28 Score=179.82 Aligned_cols=107 Identities=33% Similarity=0.483 Sum_probs=103.0
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
+..+|++|++|++||+|||||++|+||+ +++.+.++|+++|+++.+||.+|+..+||+.|.||++||++||+||++
T Consensus 121 l~~~l~~L~ld~~E~~lLkaiiL~npd~----~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~i 196 (236)
T cd06948 121 QVEKLKALHVDSAEFSCLKAIVLFTSDA----CGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTV 196 (236)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCccc----ccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhc
Confidence 5678999999999999999999999998 789999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHHHhCCC
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHMYKNAG 113 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~~~ 113 (113)
++.++|+++|.+++| ++++++++.||+.+++
T Consensus 197 s~~~~e~l~~~~l~g-~~~~~~ll~e~l~~~~ 227 (236)
T cd06948 197 SSSVIEQLFFVRLVG-KTPIETLIRDMLLSGS 227 (236)
T ss_pred cHHHHHHhhcccccC-CCcHHHHHHHHHhCCC
Confidence 999999999999999 9999999999998763
No 13
>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=99.95 E-value=1e-28 Score=182.73 Aligned_cols=105 Identities=15% Similarity=0.161 Sum_probs=100.2
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|+.+|++|++|++||+|||||+||+||+ +|+.|+.+|+++||+++.||++|+..+||++|.||+|||++||+||++
T Consensus 153 ~~~~l~~L~ld~~E~alLkAivLf~pDr----~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~kLLl~L~~LRsl 228 (259)
T cd06932 153 FAEKFNALELTDSELALFCAVIILSPDR----PGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQL 228 (259)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCc----ccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHHHHHHHHHHHHH
Confidence 7899999999999999999999999999 799999999999999999999999999999999999999999999999
Q ss_pred Chhhhhhhhccc-ccCCCCcHHHHHHHHHhC
Q psy16764 82 PSLVLEELFFRN-IIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 82 ~~~~~e~L~f~~-~~g~~~~i~~Ll~eml~~ 111 (113)
++.++|++++.+ ..| .+++++|+.||+..
T Consensus 229 ~~~~~e~l~~~k~~~~-~~~~~pLl~Ei~~~ 258 (259)
T cd06932 229 VTDHVQMVQQIKKTET-DASLPPLLQEIYKD 258 (259)
T ss_pred HHHHHHHHHHHHccCC-CCCCCcHHHHHhhc
Confidence 999999999766 567 79999999999864
No 14
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.95 E-value=2.1e-28 Score=179.28 Aligned_cols=105 Identities=17% Similarity=0.165 Sum_probs=98.9
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhC--CCcchHHHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVY--PSQPTRFCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~--p~~~~Rf~kLLl~Lp~Lr 79 (113)
|+.+|++|++|++||+|||||+||+ |+ +|+.|+++|+++|++++.||++|+..++ |++|.||+|||++||+||
T Consensus 130 f~~~l~~L~ld~~E~a~LkAivLf~-dr----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kLLl~Lp~LR 204 (239)
T cd07072 130 FSKSLHAMDIDISAFACLCALTLIT-ER----HGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELR 204 (239)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhC-CC----CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHH
Confidence 7899999999999999999999995 66 6899999999999999999999999765 478999999999999999
Q ss_pred cCChhhhhhhhcccccCCCCcHHHHHHHHHhCC
Q psy16764 80 SIPSLVLEELFFRNIIGHNTTIKKTIWHMYKNA 112 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~~ 112 (113)
+++.+++|++||.|.+| .+++++|+.||+.+.
T Consensus 205 sl~~~~~e~lf~~k~~~-~~p~~~Ll~Em~~~~ 236 (239)
T cd07072 205 SLSVQGLQRIFYLKLED-LVPAPPLIENMFVAS 236 (239)
T ss_pred hhHHHHHHHHHHHHcCC-CCCCcHHHHHHHhcc
Confidence 99999999999999999 999999999999763
No 15
>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=99.95 E-value=2.7e-28 Score=178.90 Aligned_cols=102 Identities=13% Similarity=0.104 Sum_probs=98.9
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|+.+|++|++|++||+|||||+||+||+ +|+.+..+|+++||.+..||++|+..++|++|.||+|||++||+||++
T Consensus 141 f~~~l~~L~ld~~E~alLkAivLf~pDr----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~L~~LR~i 216 (243)
T cd06935 141 LGVSLSSFNLDDTEVALLQAVLLMSSDR----PGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMI 216 (243)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHhCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHHHH
Confidence 8899999999999999999999999999 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcH-HHHHHHH
Q psy16764 82 PSLVLEELFFRNIIGHNTTI-KKTIWHM 108 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i-~~Ll~em 108 (113)
++.++|++++.|..| ..++ ++|+.||
T Consensus 217 ~~~~~e~l~~~k~~~-~~~~~~~L~~Em 243 (243)
T cd06935 217 GACHASRFLHMKVEC-PTELFPPLFLEV 243 (243)
T ss_pred HHHHHHHHHHHHhcC-CCCCCChhhhcC
Confidence 999999999999999 8885 9999986
No 16
>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=99.95 E-value=1.3e-27 Score=169.87 Aligned_cols=104 Identities=16% Similarity=0.142 Sum_probs=98.6
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|+++|++|++|++||+|||||++|+||+ +|+.+..+|+++|++++.+|++|+..+||++|.||++|+++||+||++
T Consensus 91 ~~~~l~~L~ld~~E~allkAi~Lf~pd~----~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~Lr~l 166 (195)
T cd06941 91 FSDSFNSLGLSDTEVALFCAVVLLSPDR----IGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPELRSI 166 (195)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHcCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHH
Confidence 7899999999999999999999999998 789999999999999999999999999999999999999999999999
Q ss_pred Chhhhhhhh-cccccCCCCcHHHHHHHHHh
Q psy16764 82 PSLVLEELF-FRNIIGHNTTIKKTIWHMYK 110 (113)
Q Consensus 82 ~~~~~e~L~-f~~~~g~~~~i~~Ll~eml~ 110 (113)
++.++++++ |+...+ .+++++|+.||++
T Consensus 167 ~~~~~e~l~~~~~~~~-~~~~p~L~~E~~~ 195 (195)
T cd06941 167 GAKHQMHLDWYRVNWP-LLRLPPLFAEIYD 195 (195)
T ss_pred HHHHHHHHHHHHhcCC-CCCCCcHHHHhcC
Confidence 999999998 566667 7899999999985
No 17
>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=99.94 E-value=5.8e-27 Score=169.36 Aligned_cols=104 Identities=25% Similarity=0.402 Sum_probs=100.6
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|.+||+|||||++|+||+ +++++.+.|+++|++++.||++|+..++|.++.||+++|++||+||++
T Consensus 118 ~~~~l~~L~ld~~E~~~LkaiiLf~~d~----~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~R~~klLl~Lp~Lr~~ 193 (222)
T cd06952 118 FVNSMQKLDVDDHEYAYLKAIVLFSPDH----PGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSL 193 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCC----cCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHhHHhhhc
Confidence 6789999999999999999999999998 689999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHHHh
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHMYK 110 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~eml~ 110 (113)
+.+++|+++|.+++| ++++++++..++-
T Consensus 194 ~~~~~e~l~~~~~~g-~~~~~~ll~~~~~ 221 (222)
T cd06952 194 SPAITEELFFAGLIG-NVQIDSVIPYILR 221 (222)
T ss_pred CHHHHHHHhcccccC-CCcHHHHHHHHHh
Confidence 999999999999999 9999999999874
No 18
>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=99.94 E-value=1.9e-27 Score=174.83 Aligned_cols=102 Identities=16% Similarity=0.128 Sum_probs=94.5
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcC-CCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcch---HHHHHHHhchh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTS-RRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPT---RFCKIQLILPR 77 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~-~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~---Rf~kLLl~Lp~ 77 (113)
|+.+|++|++|.+||+|||||+||+| |+ +|+.++.+|+++||+++.||.+||..++|++|. ||++||++||+
T Consensus 119 ~~~~~r~L~ld~~EfacLKAIvLfnp~d~----~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~RF~kLLllLp~ 194 (247)
T cd07076 119 VSSELHRLQVSYEEYLCMKTLLLLSTVPK----DGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDS 194 (247)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhCCCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhHHHHHHHHHHH
Confidence 67899999999999999999999998 87 799999999999999999999999999987655 99999999999
Q ss_pred hhcCChhhhhhhhcccccCCCCcHHHHHHHHHh
Q psy16764 78 LKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110 (113)
Q Consensus 78 Lr~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~ 110 (113)
||+++.+.+| ||++.+| +.++..++.||+.
T Consensus 195 Lr~i~~~~~e--f~~~~~~-~~~~~~~~~~ml~ 224 (247)
T cd07076 195 MHEVVENLLN--FCFQTFL-DKTMSIEFPEMLA 224 (247)
T ss_pred HHHHHHHHHH--HHHHHhc-ccchhhhhHHHHH
Confidence 9999999999 9999999 8888777777764
No 19
>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=99.94 E-value=5e-27 Score=171.74 Aligned_cols=106 Identities=20% Similarity=0.197 Sum_probs=94.9
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCC--cchHHHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPS--QPTRFCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~--~~~Rf~kLLl~Lp~Lr 79 (113)
|+++|++|++|++||+|||||+||+||+ +|+.|..+|+++||+++.||++|+..+||. ++.||+|||++||+||
T Consensus 128 ~~~~l~~L~ld~~E~alLkAivLf~pDr----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~~~~f~kLLl~L~~LR 203 (238)
T cd06933 128 FQVGLKKLNLHEEEHVLLMAICILSPDR----PGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYAKMIQKLADLR 203 (238)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHCCCC----CCCcchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHhHHHH
Confidence 7889999999999999999999999999 799999999999999999999999999884 5567999999999999
Q ss_pred cCChhhhhhhhcccccC-CCCcHHHHHHHHHhC
Q psy16764 80 SIPSLVLEELFFRNIIG-HNTTIKKTIWHMYKN 111 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g-~~~~i~~Ll~eml~~ 111 (113)
+++..|.+.+...+..+ ++.+++||+.||++.
T Consensus 204 si~~~h~~~~~~~~~~~~~~~~~~pL~~Ei~~~ 236 (238)
T cd06933 204 SLNEEHSKQYRSLSFQPEHSMKLTPLVLEVFGN 236 (238)
T ss_pred hhhHHHHHHHHHHHhccCCCCCCCcHHHHHhcc
Confidence 99999999876544443 134689999999975
No 20
>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=99.94 E-value=6.9e-27 Score=168.94 Aligned_cols=105 Identities=18% Similarity=0.165 Sum_probs=101.5
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHhchhhhc
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYP-SQPTRFCKIQLILPRLKS 80 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p-~~~~Rf~kLLl~Lp~Lr~ 80 (113)
|..+|++|++|.+||+|||||++++|++ +++.+..+|+++|+++.+||.+||..+|| +.|.||++||+++|+||+
T Consensus 116 ~~~~l~~L~l~~~E~~lLkai~L~npd~----~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~LL~~l~~Lr~ 191 (221)
T cd06946 116 LVRRLQRLRLEKEEYVLLKALALANSDS----VHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQ 191 (221)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHhhchhHHH
Confidence 7789999999999999999999999997 78999999999999999999999999999 799999999999999999
Q ss_pred CChhhhhhhhcccccCCCCcHHHHHHHHHhC
Q psy16764 81 IPSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 81 l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~ 111 (113)
++..+++++++.+.+| .+++++|+.||+.+
T Consensus 192 ~~~~~~e~l~~~~~~~-~~~~~~Ll~eml~~ 221 (221)
T cd06946 192 TDGKARRFFYGVKREG-KVPMHKLFLEMLEA 221 (221)
T ss_pred HHHHHHHHHHHHHhcC-CCCHHHHHHHHhcC
Confidence 9999999999999999 99999999999964
No 21
>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=99.94 E-value=5.8e-27 Score=172.28 Aligned_cols=103 Identities=14% Similarity=0.147 Sum_probs=93.8
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcC-CCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhC---CCcchHHHHHHHhchh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTS-RRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVY---PSQPTRFCKIQLILPR 77 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~-~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~---p~~~~Rf~kLLl~Lp~ 77 (113)
|..+|++|++|.+||+|||||+|||| ++ +|++|+.+|+++||+++.||.+|+..++ |++|.||+|||++||+
T Consensus 119 ~~~~l~~L~ld~~EyacLKAIiLfnp~d~----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp~ 194 (246)
T cd07073 119 LSQEFGWLQITPQEFLCMKALLLFSIIPV----DGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDS 194 (246)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCCc----ccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHHHHHHHHHHH
Confidence 67899999999999999999999998 76 7899999999999999999999998874 3568999999999999
Q ss_pred hhcCChhhhhhhhcccccCCCC-----cHHHHHHHHHhC
Q psy16764 78 LKSIPSLVLEELFFRNIIGHNT-----TIKKTIWHMYKN 111 (113)
Q Consensus 78 Lr~l~~~~~e~L~f~~~~g~~~-----~i~~Ll~eml~~ 111 (113)
||+++++. .+||.+++| +. ++++|+.||+..
T Consensus 195 LRsi~~~~--~~~~~~l~~-~~~~~~~~~~pll~ei~~~ 230 (246)
T cd07073 195 VQPIAREL--HQFTFDLLI-KSHMVSVDFPEMMAEIISV 230 (246)
T ss_pred HHHHHHHH--HHHHHHHhC-ccccCccCccHHHHHHHHh
Confidence 99999998 778888887 54 799999999984
No 22
>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=99.94 E-value=9.5e-27 Score=168.32 Aligned_cols=105 Identities=17% Similarity=0.169 Sum_probs=101.5
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHhchhhhc
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYP-SQPTRFCKIQLILPRLKS 80 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p-~~~~Rf~kLLl~Lp~Lr~ 80 (113)
|..+|++|++|++||+|||||++|+||+ +++.+..+|+..|+++..||.+||..+|| +.|.||++||+++|+||+
T Consensus 116 ~~~~l~~L~ld~~E~~lLkaIil~npd~----~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~LL~~l~~Lr~ 191 (221)
T cd07068 116 LVRRFRELGLQREEYVCLKAIILANSDV----RHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQ 191 (221)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCc----cCccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHHhccHHHH
Confidence 6789999999999999999999999998 68899999999999999999999999999 999999999999999999
Q ss_pred CChhhhhhhhcccccCCCCcHHHHHHHHHhC
Q psy16764 81 IPSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 81 l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~ 111 (113)
+++.+++++++.+.+| .+++++|+.||+++
T Consensus 192 ~~~~~~e~l~~~k~~~-~~~~~~Ll~e~l~~ 221 (221)
T cd07068 192 ASNKGVRHLYSVKCEG-KVPMYKLFLEMLEA 221 (221)
T ss_pred HHHHHHHHHHHHHHcC-CccHHHHHHHHhcC
Confidence 9999999999999999 99999999999974
No 23
>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=99.94 E-value=5.9e-27 Score=171.71 Aligned_cols=103 Identities=15% Similarity=0.145 Sum_probs=97.3
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|+++|++|++|++||+|||||+||+||+ +|+.|+.+|+++|+++..||++|+..+| .+|.||++||++||+||++
T Consensus 136 f~~~l~~L~ld~~E~all~AivL~~pDr----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~kLL~~Lp~LR~l 210 (241)
T cd06939 136 FAKSLCELKLTEDEIALFSALVLISADR----PGLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTKLLAKMPTLRAL 210 (241)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHhcCCC----cCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHHHHHHHHHHHHH
Confidence 7899999999999999999999999999 7999999999999999999999999999 8999999999999999999
Q ss_pred ChhhhhhhhcccccCC---CCcHHHHHHHHH
Q psy16764 82 PSLVLEELFFRNIIGH---NTTIKKTIWHMY 109 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~---~~~i~~Ll~eml 109 (113)
++.++|++++.|...+ ...+++|+.||+
T Consensus 211 ~~~~~e~l~~~k~~~p~~~~~~~ppL~~Elf 241 (241)
T cd06939 211 CSLHMEKLQKFKQSYPDIVHLEFPPLYKELF 241 (241)
T ss_pred HHHHHHHHHHHhccCCCcccCCCCcHHHhhC
Confidence 9999999999999952 236899999985
No 24
>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=99.94 E-value=8.2e-27 Score=170.01 Aligned_cols=103 Identities=17% Similarity=0.242 Sum_probs=99.3
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|+.+|++|++|++||+|||||++|+||+ +++.+.++|+.+|+++..+|++|+..+||++|.||+++|++||+||++
T Consensus 133 ~~~~l~~L~ld~~E~~lL~aivLf~pd~----~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~L~~Lr~l 208 (236)
T cd06954 133 FSKSMRELQLDDAEYALLIAINIFSADR----PNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTL 208 (236)
T ss_pred HHHHHHHcCCCHHHHHHHHHHhhccCCc----ccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHH
Confidence 7899999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHHHh
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHMYK 110 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~eml~ 110 (113)
++.++|++++.+..+ .++++|+.||++
T Consensus 209 ~~~~~e~l~~~k~~~--~~~~~L~~El~~ 235 (236)
T cd06954 209 SSVHSEQVFALRLQD--KKLPPLLSEIWD 235 (236)
T ss_pred HHHHHHHHHHHHhcC--CCCCcHHHHHhc
Confidence 999999999999866 689999999986
No 25
>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=99.93 E-value=3.9e-26 Score=163.81 Aligned_cols=91 Identities=36% Similarity=0.544 Sum_probs=88.7
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|++||+|||||++||||+ +++.+..+|+++|++++.||++|+..+||++|.||++||++||+||++
T Consensus 115 ~~~~~~~L~ld~~EyalLKai~L~npd~----~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf~kLLl~Lp~lr~l 190 (206)
T cd06950 115 TLSRFRQLRVDATEFACLKAIVLFKPET----RGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFI 190 (206)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHhCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhh
Confidence 6789999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccC
Q psy16764 82 PSLVLEELFFRNIIG 96 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g 96 (113)
+++++|++||.+++|
T Consensus 191 s~~~~e~l~~~~~~g 205 (206)
T cd06950 191 SSSTIEELFFKKTIG 205 (206)
T ss_pred hHHHHHHHhccCcCC
Confidence 999999999999998
No 26
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=99.93 E-value=5.4e-26 Score=167.12 Aligned_cols=107 Identities=13% Similarity=0.132 Sum_probs=95.9
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcC-CCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCC---CcchHHHHHHHhchh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTS-RRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYP---SQPTRFCKIQLILPR 77 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~-~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p---~~~~Rf~kLLl~Lp~ 77 (113)
|..+|++|++|.+||+|||||+|||| ++ +|+.++.+|+++||+++.||++|+.+++| +.|.||++||++||.
T Consensus 119 ~~~~l~~L~ld~~E~acLKAIvLfn~~d~----~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~Rf~kLLllLp~ 194 (246)
T cd06947 119 ISQEFVRLQVTYEEFLCMKVLLLLSTIPK----DGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQRFYQLTKLLDS 194 (246)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHcCCCcc----ccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHhhhh
Confidence 67899999999999999999999998 66 68999999999999999999999998874 558999999999999
Q ss_pred hhcCChhhhhhhhcccccCC--CCcHHHHHHHHHhCC
Q psy16764 78 LKSIPSLVLEELFFRNIIGH--NTTIKKTIWHMYKNA 112 (113)
Q Consensus 78 Lr~l~~~~~e~L~f~~~~g~--~~~i~~Ll~eml~~~ 112 (113)
||+++++.+++++......+ .+++++|+.||+.+.
T Consensus 195 Lr~i~~~~~e~~~~~~~~~~~~~v~~~~ll~ei~~~~ 231 (246)
T cd06947 195 MHDLVKNLLQFCFYTFIQSHALSVEFPEMLVEIISDQ 231 (246)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCccccHHHHHHHHHcc
Confidence 99999999999997733331 479999999999853
No 27
>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=99.93 E-value=2.4e-26 Score=166.47 Aligned_cols=100 Identities=16% Similarity=0.201 Sum_probs=95.5
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|+.+|++|++|.+||+|||||++||||+ +++.+...|+.+|+++..||++||..+||++|.||++||++||+||++
T Consensus 122 ~~~kl~~L~l~~~E~~lLkaIvL~npd~----~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~LL~~L~~LR~l 197 (221)
T cd06936 122 FYKSMGELKMTQEEYALLTAITILFPDR----PYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLLGRLTELRTL 197 (221)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhcCCC----cCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHHHHHH
Confidence 7889999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHH
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWH 107 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~e 107 (113)
++.++|++++.|... .+++||+.|
T Consensus 198 ~~~~~e~l~~~k~~~--~~~~pl~~e 221 (221)
T cd06936 198 NHHHAEMLMSWKVND--HKFTPLLCE 221 (221)
T ss_pred HHHHHHHHHHHHccC--CCCCccccC
Confidence 999999999999986 578998865
No 28
>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=99.93 E-value=4.7e-26 Score=165.52 Aligned_cols=100 Identities=19% Similarity=0.280 Sum_probs=91.0
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchH--HHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTR--FCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~R--f~kLLl~Lp~Lr 79 (113)
|+.+|++|++|++||+|||||+||+||+ +|+.|..+|+++|++++.||++|+..+||.++.| |+|||++||+||
T Consensus 124 ~~~~l~~L~ld~~E~alLkAivLf~pDr----~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r~~f~kLLl~L~~LR 199 (226)
T cd06934 124 FHYTLRKLQLQEEEYVLMQAMSLFSPDR----PGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFLYPKILACLTELR 199 (226)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCC----cCCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhHHHh
Confidence 7889999999999999999999999999 7999999999999999999999999999876555 999999999999
Q ss_pred cCChhhhhhhhcccccCCCCcH-HHHHHHH
Q psy16764 80 SIPSLVLEELFFRNIIGHNTTI-KKTIWHM 108 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g~~~~i-~~Ll~em 108 (113)
++++.+++++. +.++ ..++ ++|+.|+
T Consensus 200 sl~~~~~~~~~--~~~~-~~~~~~pl~~Ei 226 (226)
T cd06934 200 TINEEYTKQIL--HIQD-IQPMATPLMQEI 226 (226)
T ss_pred cchHHHHHHHH--HHhc-cCCCCCchhhcC
Confidence 99999999875 4566 5664 9999875
No 29
>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=99.93 E-value=1.1e-25 Score=159.55 Aligned_cols=88 Identities=24% Similarity=0.295 Sum_probs=85.7
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|+.+|++|++|++||+|||||+||+||+ +++.+..+|+++|+++..||++|+..+||++|.||++||++||+||++
T Consensus 101 ~~~~l~~L~ld~~E~a~LkAivLf~pd~----~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL~~L~~LR~l 176 (189)
T cd06940 101 FSEKLNSLQLSDEEMGLFTAVVLVSADR----SGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLPDLRTL 176 (189)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHhCCCC----cCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHH
Confidence 7899999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred Chhhhhhhhccc
Q psy16764 82 PSLVLEELFFRN 93 (113)
Q Consensus 82 ~~~~~e~L~f~~ 93 (113)
++.++|+++|.|
T Consensus 177 ~~~~~e~l~~~~ 188 (189)
T cd06940 177 NNLHSEKLLAFK 188 (189)
T ss_pred HHHHHHHHHHhh
Confidence 999999999976
No 30
>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=99.91 E-value=1.7e-24 Score=157.52 Aligned_cols=102 Identities=18% Similarity=0.191 Sum_probs=96.7
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCC-cchHHHHHHHhchhhhc
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPS-QPTRFCKIQLILPRLKS 80 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~-~~~Rf~kLLl~Lp~Lr~ 80 (113)
|..+|++|++|++||+|||||++|++ + +++.+...|+++|+++..+|++||..+||. .|.||++||++||+||+
T Consensus 128 ~~~~l~~L~ld~~E~~lL~AI~Lf~d-~----~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~~L~~Lr~ 202 (231)
T cd06938 128 FCRAMCSMKVDNAEYALLTAIVIFSD-R----PGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSILTELRT 202 (231)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHccC-C----CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHHHHHHHHH
Confidence 78999999999999999999999984 4 579999999999999999999999999997 89999999999999999
Q ss_pred CChhhhhhhhcccccCCCCcHHHHHHHHHh
Q psy16764 81 IPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110 (113)
Q Consensus 81 l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~ 110 (113)
+++.+++++++.+..+ .++++|+.|+++
T Consensus 203 l~~~~~e~~~~~k~~~--~~~~pl~~Ei~d 230 (231)
T cd06938 203 LGNQNSEMCFSLKLKN--RKLPPFLAEIWD 230 (231)
T ss_pred HHHHHHHHHHHHHHhC--CCCCcHHHHHhC
Confidence 9999999999999996 689999999986
No 31
>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=99.91 E-value=3.3e-24 Score=153.29 Aligned_cols=88 Identities=25% Similarity=0.331 Sum_probs=85.0
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|++||+|||||++|+||+ +++.+.+.|+++|+++..+|++|+..+||+.|.||++||++||+||++
T Consensus 120 ~~~~l~~L~ld~~E~~lLkaI~L~~pd~----~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L~~lr~l 195 (207)
T cd06943 120 LVVKMRDLKMDRTELGCLRAIILFNPDV----KGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSI 195 (207)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhcCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHHHHHHhH
Confidence 6789999999999999999999999998 689999999999999999999999999999999999999999999999
Q ss_pred Chhhhhhhhccc
Q psy16764 82 PSLVLEELFFRN 93 (113)
Q Consensus 82 ~~~~~e~L~f~~ 93 (113)
+++++|++||.+
T Consensus 196 ~~~~~e~l~~~~ 207 (207)
T cd06943 196 GLKCLEHLFFFK 207 (207)
T ss_pred hHHHHHHHhhcC
Confidence 999999999975
No 32
>cd07075 NR_LBD_MR Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR h
Probab=99.90 E-value=4.4e-24 Score=157.10 Aligned_cols=104 Identities=12% Similarity=0.114 Sum_probs=88.9
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCC-CCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCC---CcchHHHHHHHhchh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSR-RGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYP---SQPTRFCKIQLILPR 77 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~-~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p---~~~~Rf~kLLl~Lp~ 77 (113)
|+.+|++|++|.+||+|||||+||||| + +|+.|..+|+++|++++.||++|+..++| +.+.||++|+++||.
T Consensus 119 ~~~~l~~L~Ld~~E~acLKAIvLfn~d~~----~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~~RF~~LLllLp~ 194 (248)
T cd07075 119 ISLQFVRLQLTFEEYTIMKVLLLLSTIPK----DGLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSWQRFYQLTKLLDS 194 (248)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccchhHHHHHHHHHHH
Confidence 678999999999999999999999996 5 68999999999999999999999996665 456999999999999
Q ss_pred hhcCChhhhhhhhcccccCCCCcH--HHHHHHHH
Q psy16764 78 LKSIPSLVLEELFFRNIIGHNTTI--KKTIWHMY 109 (113)
Q Consensus 78 Lr~l~~~~~e~L~f~~~~g~~~~i--~~Ll~eml 109 (113)
||+++++.+|++||.=.-.+.+++ +.++.|++
T Consensus 195 Lr~i~~k~iE~lff~~~~~~~~~~~~~~~~~~~~ 228 (248)
T cd07075 195 MHDLVSDLLEFCFYTFRESQALKVEFPAMLVEII 228 (248)
T ss_pred HHHHHHHHHHHHHHHHccccceeeehHHHHHHHH
Confidence 999999999999986554214444 55555554
No 33
>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=99.89 E-value=4.5e-23 Score=148.89 Aligned_cols=102 Identities=22% Similarity=0.291 Sum_probs=98.2
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|++||+|||||++|+|+. +++.+.++|+.+|++++.||.+|+..++|+.|.||++|++++|.||++
T Consensus 121 ~~~~l~~L~l~~~E~~lLkaiil~~p~~----~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL~~l~~lr~~ 196 (222)
T cd06931 121 LVLPLRDLNIDDNEYACLKAIVFFDPDA----KGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSI 196 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCc----cCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHH
Confidence 5678999999999999999999999997 789999999999999999999999988999999999999999999999
Q ss_pred ChhhhhhhhcccccCCCCcHHHHHHHH
Q psy16764 82 PSLVLEELFFRNIIGHNTTIKKTIWHM 108 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~i~~Ll~em 108 (113)
+...++++++.+++| .+++++|+.||
T Consensus 197 ~~~~~e~l~~~~lf~-~~~~~~L~~e~ 222 (222)
T cd06931 197 TWQMIEQIQFARLFG-VAKIDNLLQEM 222 (222)
T ss_pred HHHHHHHHhhhhhcC-CCcHHHHHhhC
Confidence 999999999999999 99999999986
No 34
>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=99.88 E-value=1.5e-22 Score=145.95 Aligned_cols=82 Identities=21% Similarity=0.330 Sum_probs=79.4
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|++||+|||||++||||+ +++.+.++|+++|+++.++|.+||..+||+.|.||++||++||+||++
T Consensus 120 l~~~l~~L~ld~eEy~lLkAIvLfnpd~----~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf~~LL~~L~~Lr~l 195 (213)
T cd06953 120 LLAKFRQLKVSNEEYVCLKVINFLNQDI----DGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAA 195 (213)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCC----CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHhHHHHHH
Confidence 6789999999999999999999999998 799999999999999999999999999999999999999999999999
Q ss_pred Chhhhh
Q psy16764 82 PSLVLE 87 (113)
Q Consensus 82 ~~~~~e 87 (113)
+++.+|
T Consensus 196 ~~~~~e 201 (213)
T cd06953 196 AGKLLH 201 (213)
T ss_pred HHHHHH
Confidence 999887
No 35
>KOG4215|consensus
Probab=99.86 E-value=4.7e-22 Score=151.00 Aligned_cols=105 Identities=17% Similarity=0.269 Sum_probs=98.3
Q ss_pred HHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChh--HHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHhchhhh
Q psy16764 3 QTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSK--FTAAIQGHTQIFLNKYIHTVYP-SQPTRFCKIQLILPRLK 79 (113)
Q Consensus 3 ~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~--~Ve~lqe~~~~aL~~~~~~~~p-~~~~Rf~kLLl~Lp~Lr 79 (113)
..-|++|++|+.||+|||||++|+|+. .|+.|.. .|++++.+++.+|++||..+.| +.+.||++||++||+|.
T Consensus 245 v~Pmr~L~md~~Ey~cLKAi~FfdP~a----kGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~g~LLLllPsLq 320 (432)
T KOG4215|consen 245 VNPMRRLQMDEIEYVCLKAIAFFDPDA----KGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRFGNLLLLLPSLQ 320 (432)
T ss_pred hhHHHHhccchHHHHHHHHHHhcCccc----cccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccchhhHHHHHHHHH
Confidence 467899999999999999999999987 6888887 9999999999999999999986 45899999999999999
Q ss_pred cCChhhhhhhhcccccCCCCcHHHHHHHHHhCC
Q psy16764 80 SIPSLVLEELFFRNIIGHNTTIKKTIWHMYKNA 112 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~~ 112 (113)
+|++..+|++.+.++|| -+.|++++.|++..+
T Consensus 321 sIt~qliE~iqlaklFG-la~vDsll~e~~l~~ 352 (432)
T KOG4215|consen 321 SITQQLIEQIQLAKLFG-LAKVDSLLQEFLLGG 352 (432)
T ss_pred HHHHHHHHHHHHHHHhh-hhhHhHHHHHhhcCC
Confidence 99999999999999999 999999999998763
No 36
>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.85 E-value=1.4e-21 Score=138.62 Aligned_cols=98 Identities=14% Similarity=0.033 Sum_probs=87.2
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCC--CCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSR--RGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~--~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr 79 (113)
|..+|++|++|++||+||+||++|+|| + +++.+..+|+.+|+.+..+|.+|+..+||+.+.||++||+++|+||
T Consensus 90 ~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~----~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~kLL~~l~~Lr 165 (191)
T cd06942 90 FANKILTLNLTNAELALLCAAELLQPDSLG----IQLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFDILNRLR 165 (191)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCCCC----CCccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHH
Confidence 788999999999999999999999999 7 7899999999999999999999999999999999999999999999
Q ss_pred cCChhhhhhhhcccccCCCCcHHHH
Q psy16764 80 SIPSLVLEELFFRNIIGHNTTIKKT 104 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g~~~~i~~L 104 (113)
+++..+.+.+.. +...++..+|+|
T Consensus 166 ~~~~~~~~~l~~-~~~~~~~~~ppl 189 (191)
T cd06942 166 NMNKEHQNILAD-RDKRSNLQLPPL 189 (191)
T ss_pred HHHHHHHHHHHc-cccCccCCCCCc
Confidence 999999997665 222213445554
No 37
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.84 E-value=5.6e-21 Score=132.68 Aligned_cols=83 Identities=19% Similarity=0.256 Sum_probs=79.7
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|.+||+|||||++|+|++ +++.++..|++.|+++..+|++|+..+||+.|.||++|++++|+||++
T Consensus 91 ~~~~l~~L~l~~~E~~llkai~l~~pd~----~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~Ll~~l~~lr~l 166 (174)
T cd06929 91 FAEKMNKLQLDDNEYALLTAIVLFSPDR----PGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLTELRTL 166 (174)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCCc----ccCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHhHHHHHH
Confidence 6789999999999999999999999998 689999999999999999999999999999999999999999999999
Q ss_pred Chhhhhh
Q psy16764 82 PSLVLEE 88 (113)
Q Consensus 82 ~~~~~e~ 88 (113)
+..++|.
T Consensus 167 ~~~~~e~ 173 (174)
T cd06929 167 NELHAEL 173 (174)
T ss_pred HHHHHhc
Confidence 9998875
No 38
>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=99.79 E-value=7e-19 Score=120.81 Aligned_cols=76 Identities=29% Similarity=0.429 Sum_probs=72.6
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|..+|++|++|++||+|||||++|+|++ +++.+...|+..|+++..||.+|+..++|+.|.||++|++.+|+||++
T Consensus 90 ~~~~l~~L~l~~~E~~lLkai~l~~p~~----~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~ll~~l~~lr~~ 165 (165)
T cd06930 90 LLSKLRSLQLDPKEYACLKAIVLFNPDL----PGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI 165 (165)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCC----CCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHhhccC
Confidence 6788999999999999999999999998 689999999999999999999999999999999999999999999975
No 39
>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=99.75 E-value=1.2e-17 Score=123.06 Aligned_cols=105 Identities=10% Similarity=0.025 Sum_probs=82.5
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcC-CCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhC---CCcchHHHHHHHhchh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTS-RRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVY---PSQPTRFCKIQLILPR 77 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~-~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~---p~~~~Rf~kLLl~Lp~ 77 (113)
|..+|+++++|.+||+|||||+|||| ++ +|+.+..+|+++|+++..||.+||..++ ++.|+||++|+..++.
T Consensus 119 ~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~----~gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~RF~~Ll~ll~~ 194 (248)
T cd07074 119 IPQEFVKLQVSQEEFLCMKALLLLNTIPL----EGLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQRFYQLTKLMDN 194 (248)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHCCCCcC----CCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcHHHHHHHHHHHH
Confidence 57899999999999999999999999 66 6899999999999999999999977664 3679999999999999
Q ss_pred hhcCChhhhhhhh--ccc-ccCCCCcHHHHHHHHHhC
Q psy16764 78 LKSIPSLVLEELF--FRN-IIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 78 Lr~l~~~~~e~L~--f~~-~~g~~~~i~~Ll~eml~~ 111 (113)
|+.+-...-.-.+ |.. ..- ++..+..+.|++.+
T Consensus 195 l~~~~k~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 230 (248)
T cd07074 195 MHDLVKQLHLYCLNTFIQSRAL-SVEFPEMMSEVIAA 230 (248)
T ss_pred HHHHHHHHHHHHHHHHHhhhhh-eeecHHHHHHHHHh
Confidence 9932222111110 111 122 57789999998764
No 40
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.60 E-value=5.9e-15 Score=100.05 Aligned_cols=76 Identities=28% Similarity=0.490 Sum_probs=70.7
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCccc-CCCChhHHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVR-FKTGSKFTAAIQGHTQIFLNKYIHTVYP-SQPTRFCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~-~l~~~~~Ve~lqe~~~~aL~~~~~~~~p-~~~~Rf~kLLl~Lp~Lr 79 (113)
|..+|.+|++|++|+++|+|+++++|+. + +..+...+++.|+++..+|+.|+..+++ +.+.||++|++.+|++|
T Consensus 91 ~~~~~~~L~l~~~E~~~l~ai~l~~~~~----~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~l~ 166 (168)
T cd06157 91 FVNPLRALKLDDEEYALLKAIVLFSPDR----KESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLR 166 (168)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHhCCCC----CCCccCHHHHHHHHHHHHHHHHHHHHHhCCccchhHHHHHHHhchhcc
Confidence 6788999999999999999999999987 4 6788999999999999999999999997 88999999999999998
Q ss_pred cC
Q psy16764 80 SI 81 (113)
Q Consensus 80 ~l 81 (113)
.+
T Consensus 167 ~~ 168 (168)
T cd06157 167 KL 168 (168)
T ss_pred cC
Confidence 64
No 41
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=99.57 E-value=1.1e-14 Score=98.26 Aligned_cols=76 Identities=22% Similarity=0.297 Sum_probs=69.5
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCCh--hHHHHHHHHHHHHHHHHHHhhCC-CcchHHHHHHHhchhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGS--KFTAAIQGHTQIFLNKYIHTVYP-SQPTRFCKIQLILPRL 78 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~--~~Ve~lqe~~~~aL~~~~~~~~p-~~~~Rf~kLLl~Lp~L 78 (113)
+..++++|++|++||++|+|+++++|+. +++.+. +.++++|+.+..+|++|+..++| +.+.||++|++++|++
T Consensus 85 ~~~~l~~L~l~~~E~~~l~ai~l~~~~~----~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~i 160 (163)
T smart00430 85 LVKPLRELKLDDEEYALLKAILLFNPAG----PGLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGRFGELLLILNAI 160 (163)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcChhh----hhhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHHHHh
Confidence 5678999999999999999999999976 577777 89999999999999999999988 6689999999999999
Q ss_pred hcC
Q psy16764 79 KSI 81 (113)
Q Consensus 79 r~l 81 (113)
+.+
T Consensus 161 ~~~ 163 (163)
T smart00430 161 QKI 163 (163)
T ss_pred hcC
Confidence 864
No 42
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=99.56 E-value=9.1e-15 Score=102.01 Aligned_cols=89 Identities=19% Similarity=0.307 Sum_probs=78.2
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCC-ChhH-HHHHHHHHHHHHHHHH-HhhCCCc-chHHHHHHHhchh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKT-GSKF-TAAIQGHTQIFLNKYI-HTVYPSQ-PTRFCKIQLILPR 77 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~-~~~~-Ve~lqe~~~~aL~~~~-~~~~p~~-~~Rf~kLLl~Lp~ 77 (113)
+...|+++++|++||++++|+++++|+. +++. +... ++++|+++..+|..|+ ...++.+ +.||++|+..+|.
T Consensus 110 ~~~~~~~l~l~~~E~~~l~~l~l~~~~~----~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~~~R~~~ll~ll~~ 185 (203)
T PF00104_consen 110 VLRPFRRLKLDEEEFALLKALILFNPDY----PGLSEETREIVEELRDRIIQALHSYYNQSKGPEDYAQRFGKLLLLLPS 185 (203)
T ss_dssp HHHHHHHTT-BHHHHHHHHHHHHSSTTS----TTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTHTTHHHHHHHHHHH
T ss_pred HHHHHHHhhhhhHHHHHHHHHhhhcccc----cccccchhHHHHHHHHHHHHHHHHHHhccCCCccHHHHHHHHHHHHHH
Confidence 4568899999999999999999999977 5666 6655 9999999999999999 7777766 7999999999999
Q ss_pred hhcCChhhhhhhhcccc
Q psy16764 78 LKSIPSLVLEELFFRNI 94 (113)
Q Consensus 78 Lr~l~~~~~e~L~f~~~ 94 (113)
++.++..+.|++++.++
T Consensus 186 l~~~~~~~~e~~~~~~l 202 (203)
T PF00104_consen 186 LRKISEKHIENMFLSDL 202 (203)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhHHhh
Confidence 99999999999887654
No 43
>KOG4218|consensus
Probab=99.48 E-value=2.3e-14 Score=108.85 Aligned_cols=105 Identities=15% Similarity=0.225 Sum_probs=100.2
Q ss_pred HHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcCC
Q psy16764 3 QTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIP 82 (113)
Q Consensus 3 ~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l~ 82 (113)
.-+|+.|++|..||+|||.++||+-|- .++++-..|+++|+++..+|-+|....||+....|++++++|+++|+++
T Consensus 369 V~~Lr~lqfd~~efvclkFl~LFsld~----kfLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF~qllL~L~eiRa~s 444 (475)
T KOG4218|consen 369 VIRLRNLQFDNFEFVCLKFLALFSLDM----KFLENFELVRRLQEDSNAALLDYTSCCYPNWEQKFPQLLLVLEEIRATS 444 (475)
T ss_pred HHHHHhcCCccchhhHHHHHHHHhhhH----HHHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999999999876 6999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhcccccCCCCcHHHHHHHHHhCC
Q psy16764 83 SLVLEELFFRNIIGHNTTIKKTIWHMYKNA 112 (113)
Q Consensus 83 ~~~~e~L~f~~~~g~~~~i~~Ll~eml~~~ 112 (113)
....|.++..++-+ .++-.+++-||+.++
T Consensus 445 mqa~eyly~khl~~-~~p~nnllieml~Ak 473 (475)
T KOG4218|consen 445 MQAAEYLYTKHLQV-PAPQNNLLIEMLTAK 473 (475)
T ss_pred HHHHHHHHHHHhCC-CccccchHHHHhhcc
Confidence 99999999999999 999999999999886
No 44
>KOG4217|consensus
Probab=99.27 E-value=1e-11 Score=97.51 Aligned_cols=104 Identities=16% Similarity=0.176 Sum_probs=94.1
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhh--CCCcchHHHHHHHhchhhh
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTV--YPSQPTRFCKIQLILPRLK 79 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~--~p~~~~Rf~kLLl~Lp~Lr 79 (113)
|.+.+..|++|-.-|+||.|+.+.... .|+.+++.||++|.++..+|.+|+..+ -+..+.++.++|-+||+||
T Consensus 496 FS~~l~~l~idi~AfacL~aLa~iTEr-----hGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr 570 (605)
T KOG4217|consen 496 FSRSLHSLNIDISAFACLSALALITER-----HGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELR 570 (605)
T ss_pred HHHHhhhchhhHHHHHHHHHHHhhhhh-----hcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHH
Confidence 889999999999999999999998865 479999999999999999999999654 4567899999999999999
Q ss_pred cCChhhhhhhhcccccCCCCcHHHHHHHHHhC
Q psy16764 80 SIPSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 80 ~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~ 111 (113)
.++.....+.|+.|+.. -++.+.++..|+..
T Consensus 571 ~l~tqgLqrifyLklEd-lvp~p~iidklf~d 601 (605)
T KOG4217|consen 571 TLCTQGLQRIFYLKLED-LVPPPAIIDKLFLD 601 (605)
T ss_pred HHHHHhhhhhhcccHhh-ccCchhhhhhhhhc
Confidence 99999999999999999 88888888777643
No 45
>KOG4216|consensus
Probab=99.21 E-value=3.6e-11 Score=92.66 Aligned_cols=105 Identities=12% Similarity=0.089 Sum_probs=93.8
Q ss_pred hHHhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcC
Q psy16764 2 FQTELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSI 81 (113)
Q Consensus 2 f~~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l 81 (113)
|...+..|++.+.|+|++.|+||.++++ .|+.+..+|+++|..+..|+++.+.++|-. ..-..+|+-+.|.+|++
T Consensus 370 ~~ksL~~Lq~te~EiAL~~alVL~~~~r----~gl~e~~ki~~lq~~~~~a~qhvl~knh~~-~~~l~kl~~k~~~~r~~ 444 (479)
T KOG4216|consen 370 FGKSLCSLQLTEDEIALFSALVLMSADR----SGLQEKVKIEKLQQKIQLALQHVLQKNHRE-DGILTKLICKVSTLRAL 444 (479)
T ss_pred hhHHHHhhccCcHHHHHHHHHHhhCCcc----ccccchHHHHHHHHHHHHHHHHHHHhcCCh-hhhHHHhhcccchHHHH
Confidence 6788999999999999999999999999 699999999999999999999999888743 34789999999999999
Q ss_pred ChhhhhhhhcccccCCCCc--HHHHHHHHHhC
Q psy16764 82 PSLVLEELFFRNIIGHNTT--IKKTIWHMYKN 111 (113)
Q Consensus 82 ~~~~~e~L~f~~~~g~~~~--i~~Ll~eml~~ 111 (113)
+..|.|.|..++...+++. +++|.-|++.+
T Consensus 445 ~~lH~E~Lq~Fk~~hP~iv~~fP~LYKELFt~ 476 (479)
T KOG4216|consen 445 CGLHTEKLQAFKASHPDIVRHFPPLYKELFTS 476 (479)
T ss_pred HHHHHHHHHHHhhcCchHHhhccHHHHHHhcc
Confidence 9999999999999874444 68888888764
No 46
>KOG4846|consensus
Probab=88.54 E-value=0.25 Score=39.40 Aligned_cols=79 Identities=11% Similarity=0.017 Sum_probs=57.8
Q ss_pred HhhccccCCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcCCh
Q psy16764 4 TELTMLRIVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPS 83 (113)
Q Consensus 4 ~~l~~L~ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l~~ 83 (113)
.++..|+...+|- +.++-+.++ .+++.+..||.+||..+.++ -...+.|....++.+.+...++++++.+
T Consensus 455 ~~ln~L~~~~~~~----~~~l~s~~s----~~~e~~~sVe~lqe~~lr~~--~~~~n~pl~~s~~~~~~~~~~d~~sl~~ 524 (538)
T KOG4846|consen 455 HELNRLNELHKQQ----LNILRSNLS----FLNEPPLSVEMLQESTLRLP--VNHNNQPLNQSLPHVRHQVKRDVQSLEN 524 (538)
T ss_pred cchhhcCchHHHH----HHHHHHhhh----hhccCCchHHHHHhhhhhcc--ccccCCcccccCcchhhccCCcCCcccc
Confidence 3445555554444 445555555 57888999999999999887 3335567777899999999999999999
Q ss_pred hhhhhhhcc
Q psy16764 84 LVLEELFFR 92 (113)
Q Consensus 84 ~~~e~L~f~ 92 (113)
.+.+.+...
T Consensus 525 lhs~kv~~~ 533 (538)
T KOG4846|consen 525 LHSMKVHPV 533 (538)
T ss_pred hhccccccc
Confidence 888766543
No 47
>PF02020 W2: eIF4-gamma/eIF5/eIF2-epsilon; InterPro: IPR003307 This entry represents the W2 domain (two invariant tryptophans) and is a region of ~165 amino acids which is found in the C terminus of the following eIFs [, , , ]: Eukaryotic translation initiation factor 2B epsilon (eIF-2B-epsilon) Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2 Translation initiation is a sophisticated, well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukayrotic initiation factors (eIFs) are included []. The W2 domain has a globular fold and is exclusively composed out of alpha-helices [, , ]. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions. For example, the W2 domain of H. sapiens eIF5 binds eIF2-beta, eIF3 and eIF1 [], and therefore plays an important role in multifactor complex assembly. The entry covers the entire W2 domain.; GO: 0005488 binding; PDB: 3D3M_A 3L6A_A 1PAQ_A 2FUL_D 2IU1_A 1UG3_B 3JUI_A.
Probab=50.86 E-value=37 Score=20.56 Aligned_cols=48 Identities=17% Similarity=0.027 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHhhCCCcchHHHHHHHhchhhhcCChhhhhhhhcc
Q psy16764 44 AIQGHTQIFLNKYIHTVYPSQPTRFCKIQLILPRLKSIPSLVLEELFFR 92 (113)
Q Consensus 44 ~lqe~~~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~l~~~~~e~L~f~ 92 (113)
+-|-.++.+++.|| ...|..-..|+++|..|=..=-++-..|-..+-.
T Consensus 2 ~~Q~~~L~ale~~~-~~~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~ 49 (84)
T PF02020_consen 2 DDQVDLLNALEEFC-AENPNLMPLFPKILQQLYDEDILEEEAILEWYED 49 (84)
T ss_dssp HHHHHHHHHHHHHH-HHTCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC
T ss_pred HHHHHHHHHHHHHH-HhCccHHHHHHHHHHHHhhhhhccHHHHHHHHHc
Confidence 45777889999999 5567777889999999888888888877777655
No 48
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=39.85 E-value=40 Score=22.17 Aligned_cols=31 Identities=13% Similarity=0.245 Sum_probs=25.1
Q ss_pred CChhHHHHHHHHHHHHHHHHHHhh-CCCcchH
Q psy16764 37 TGSKFTAAIQGHTQIFLNKYIHTV-YPSQPTR 67 (113)
Q Consensus 37 ~~~~~Ve~lqe~~~~aL~~~~~~~-~p~~~~R 67 (113)
-+..+|+...++....|.+..+.+ ||+.|.|
T Consensus 22 l~~~~~~~F~~~L~~~L~~ry~~HW~P~~P~k 53 (118)
T PF07742_consen 22 LPRRQVDRFAEELENLLCERYKGHWYPENPSK 53 (118)
T ss_dssp B-HHHHHHHHHHHHHHHHHHHTTS--TTSTTT
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCC
Confidence 457899999999999999977766 6888876
No 49
>smart00526 H15 Domain in histone families 1 and 5.
Probab=38.65 E-value=51 Score=18.83 Aligned_cols=23 Identities=26% Similarity=0.446 Sum_probs=17.7
Q ss_pred HHHHHHHHHhhCCCcchHHHHHH
Q psy16764 50 QIFLNKYIHTVYPSQPTRFCKIQ 72 (113)
Q Consensus 50 ~~aL~~~~~~~~p~~~~Rf~kLL 72 (113)
..++..|+..+|+..+.+|..+|
T Consensus 26 ~~aI~kyi~~~~~~~~~~~~~~l 48 (66)
T smart00526 26 LQAIKKYIEANYKVLPNNFRSLL 48 (66)
T ss_pred HHHHHHHHHHhCCCChHHHHHHH
Confidence 45678899999887777877754
No 50
>cd03745 SOCS_WSB2_SWIP2 SOCS (suppressors of cytokine signaling) box of WSB2/SWiP2-like proteins. This family consists of WSB-2 (SOCS-box-containing WD-40 protein) and SWiP-2 (SOCS box and WD-repeats in Protein). No functional information is available for WSB2 or SWiP-2, but limited information is available for the isoforms WSB-1 and SWiP-1. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=38.35 E-value=18 Score=19.17 Aligned_cols=35 Identities=17% Similarity=0.225 Sum_probs=22.6
Q ss_pred chhhhcCChhhhhhhhcccccCCCCcHHHHHHHHHh
Q psy16764 75 LPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110 (113)
Q Consensus 75 Lp~Lr~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~ 110 (113)
+|+|+.+|-..|....-..... ..|+++-|.|-+.
T Consensus 3 v~SLQHLCR~~I~~~~~~~~~~-~LPLP~~Lk~yL~ 37 (39)
T cd03745 3 LPSLRHLCRKALRHFLTTYQVL-ALPIPKKMKEFLT 37 (39)
T ss_pred cccHHHHHHHHHHHhccccccc-cCCCcHHHHHHHc
Confidence 4777777777776554334445 5777777776554
No 51
>cd03746 SOCS_WSB1_SWIP1 SOCS (suppressors of cytokine signaling) box of WSB1/SWiP1-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2) and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh). The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=37.28 E-value=20 Score=19.07 Aligned_cols=36 Identities=6% Similarity=0.182 Sum_probs=23.2
Q ss_pred chhhhcCChhhhhhhhcccccCCCCcHHHHHHHHHhC
Q psy16764 75 LPRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYKN 111 (113)
Q Consensus 75 Lp~Lr~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~~ 111 (113)
+|+|..+|...|....-.+.++ ..++++-+.+-+..
T Consensus 3 v~sLQhLCR~~Ir~~~~~~~i~-~LpLP~~Lk~YL~y 38 (40)
T cd03746 3 VASLQHLCRMAIRRVMPTQQVK-ELPIPSKLLEFLTY 38 (40)
T ss_pred CcCHHHHHHHHHHHHccccccc-cCCCCHHHHHHHhc
Confidence 4666666666666554445566 67888877776543
No 52
>PF10769 DUF2594: Protein of unknown function (DUF2594); InterPro: IPR019705 This entry represents proteins with unknown function and appear to be restricted to Enterobacteriaceae.
Probab=35.80 E-value=29 Score=20.97 Aligned_cols=10 Identities=20% Similarity=-0.004 Sum_probs=9.1
Q ss_pred HHHHHHHHHH
Q psy16764 14 EENSNLEIRN 23 (113)
Q Consensus 14 ~E~~~Lkai~ 23 (113)
.|.+|||+++
T Consensus 17 ~EV~CLK~~l 26 (74)
T PF10769_consen 17 TEVACLKALL 26 (74)
T ss_pred HHHHHHHHHH
Confidence 6999999987
No 53
>PRK10613 hypothetical protein; Provisional
Probab=33.82 E-value=33 Score=20.76 Aligned_cols=10 Identities=30% Similarity=0.082 Sum_probs=9.0
Q ss_pred HHHHHHHHHH
Q psy16764 14 EENSNLEIRN 23 (113)
Q Consensus 14 ~E~~~Lkai~ 23 (113)
.|..|||+++
T Consensus 17 ~EV~CLK~ll 26 (74)
T PRK10613 17 NEVSCLKAML 26 (74)
T ss_pred HHHHHHHHHH
Confidence 6999999987
No 54
>cd09244 BRO1_Rhophilin Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin and related domains. This family contains the Bro1-like domain of RhoA-binding proteins, Rhophilin-1 and -2, and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-1 and -2 bind both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-1 and -2, contain an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. Their PDZ domains have limited homology. Rhophilin-1 and -2 have different ac
Probab=29.40 E-value=72 Score=24.93 Aligned_cols=31 Identities=13% Similarity=0.204 Sum_probs=27.6
Q ss_pred HHHHHHHHHhhCCCcchHHHHHHHhchhhhc
Q psy16764 50 QIFLNKYIHTVYPSQPTRFCKIQLILPRLKS 80 (113)
Q Consensus 50 ~~aL~~~~~~~~p~~~~Rf~kLLl~Lp~Lr~ 80 (113)
...|.+||..+|.++|..|..=+..+..||.
T Consensus 15 ~~~L~~yI~~~Y~e~~~~y~~~l~~l~~LR~ 45 (350)
T cd09244 15 MEPFKDFILEHYSEDPSLYEDEIADFTDLRQ 45 (350)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 5679999999999999999999999988886
No 55
>PRK11239 hypothetical protein; Provisional
Probab=28.32 E-value=1.3e+02 Score=22.06 Aligned_cols=66 Identities=5% Similarity=-0.041 Sum_probs=36.3
Q ss_pred cccCCHHHHHHHHHHHhhcCCCCCcc-------cCCCChhHHHHHHHHHHHHHH-HHHHhhCCCc----chHHHHHHHh
Q psy16764 8 MLRIVTEENSNLEIRNAYTSRRGSRV-------RFKTGSKFTAAIQGHTQIFLN-KYIHTVYPSQ----PTRFCKIQLI 74 (113)
Q Consensus 8 ~L~ld~~E~~~Lkai~l~~~~~g~~~-------~~l~~~~~Ve~lqe~~~~aL~-~~~~~~~p~~----~~Rf~kLLl~ 74 (113)
.++++..|.+++..+.|=.|-...++ ....|...|+..-++...-=. -++ .+-|.+ .+||.+|+.-
T Consensus 92 ~l~l~~~~~All~~LlLRGPQT~gELRtRs~Rl~~F~dv~~Ve~~L~~L~~r~~~plV-~~LpR~pG~RE~Ry~hLl~g 169 (215)
T PRK11239 92 DLKLSAAEVALITTLLLRGAQTPGELRSRAARMYEFSDMAEVESTLEQLANREDGPFV-VRLAREPGKRESRYMHLFSG 169 (215)
T ss_pred ccCCCHHHHHHHHHHHhcCCCChHHHHHhHhcCCcCCCHHHHHHHHHHHHhccCCcee-eecCCCCCcchHHHHHHhcC
Confidence 49999999999999987665321111 223455666543333221100 011 122333 3799999974
No 56
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=26.74 E-value=1.1e+02 Score=18.01 Aligned_cols=20 Identities=10% Similarity=0.243 Sum_probs=17.0
Q ss_pred hHHHHHHHHHHHHHHHHHHh
Q psy16764 40 KFTAAIQGHTQIFLNKYIHT 59 (113)
Q Consensus 40 ~~Ve~lqe~~~~aL~~~~~~ 59 (113)
..+..+|-++..+|.+||+.
T Consensus 41 ~~~~~~r~KiR~~L~ey~k~ 60 (64)
T PF05596_consen 41 EICQEVRKKIRAALAEYCKG 60 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 66778899999999999974
No 57
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=25.60 E-value=1.2e+02 Score=19.14 Aligned_cols=21 Identities=14% Similarity=0.087 Sum_probs=17.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCC
Q psy16764 10 RIVTEENSNLEIRNAYTSRRG 30 (113)
Q Consensus 10 ~ld~~E~~~Lkai~l~~~~~g 30 (113)
==++.|+++|++++-|....|
T Consensus 7 WS~eDEi~iL~gl~~~~~~~G 27 (98)
T PF04504_consen 7 WSEEDEIVILQGLIDFRAKTG 27 (98)
T ss_pred CCchHHHHHHHHHHHHHHhcC
Confidence 346789999999999987765
No 58
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=24.96 E-value=1.2e+02 Score=19.76 Aligned_cols=32 Identities=16% Similarity=0.291 Sum_probs=25.6
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHhh-CCCcchH
Q psy16764 36 KTGSKFTAAIQGHTQIFLNKYIHTV-YPSQPTR 67 (113)
Q Consensus 36 l~~~~~Ve~lqe~~~~aL~~~~~~~-~p~~~~R 67 (113)
.-+..+|+...+.....|.+..+.. ||+.|.+
T Consensus 21 ~l~~~~v~~F~~~L~~~L~~~y~~HWyP~~P~k 53 (108)
T smart00099 21 KLSKRRVEIFAEKLTRLLKEKYKNHWYPEKPYK 53 (108)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Confidence 3468899999999999999977655 5887765
No 59
>PF12427 DUF3665: Branched-chain amino acid aminotransferase ; InterPro: IPR024614 This uncharacterised domain is found in the N-terminal region of branched-chain amino acid aminotransferase II proteins in Corynebacterium. It is typically between 23 and 35 amino acids in length and contains a conserved TRT sequence motif.
Probab=24.38 E-value=56 Score=15.18 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=11.1
Q ss_pred HhhCCCcchHHHHHH
Q psy16764 58 HTVYPSQPTRFCKIQ 72 (113)
Q Consensus 58 ~~~~p~~~~Rf~kLL 72 (113)
++..|..|.|..++|
T Consensus 8 RT~nPTs~~~L~eIL 22 (23)
T PF12427_consen 8 RTENPTSPERLKEIL 22 (23)
T ss_pred ccCCCCCHHHHHHHh
Confidence 455688888888776
No 60
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=24.25 E-value=1.2e+02 Score=18.56 Aligned_cols=23 Identities=26% Similarity=0.411 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhCCCcchHHHHHH
Q psy16764 50 QIFLNKYIHTVYPSQPTRFCKIQ 72 (113)
Q Consensus 50 ~~aL~~~~~~~~p~~~~Rf~kLL 72 (113)
..++..|+..+|+....+|..++
T Consensus 26 ~~aI~kyI~~~y~~~~~~~~~~l 48 (88)
T cd00073 26 LQAIKKYIEAKYKVDDENFNKLL 48 (88)
T ss_pred HHHHHHHHHHHCCcchHHHHHHH
Confidence 56788999999997766776654
No 61
>PF03776 MinE: Septum formation topological specificity factor MinE; InterPro: IPR005527 Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerisation, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD []. MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for `topological specificity' - that is, the ability of MinE to antagonise MinCD inhibition of Z rings at the midcell position but not at the poles.; GO: 0032955 regulation of barrier septum formation, 0051301 cell division; PDB: 2KXO_A 3MCD_B 3KU7_A 3R9J_C 3R9I_E 1EV0_B.
Probab=22.91 E-value=59 Score=19.21 Aligned_cols=23 Identities=9% Similarity=0.291 Sum_probs=18.6
Q ss_pred CChhHHHHHHHHHHHHHHHHHHh
Q psy16764 37 TGSKFTAAIQGHTQIFLNKYIHT 59 (113)
Q Consensus 37 ~~~~~Ve~lqe~~~~aL~~~~~~ 59 (113)
+.+..++.+++.+..++..|+..
T Consensus 22 ~~~~~l~~lk~eil~viskYv~i 44 (70)
T PF03776_consen 22 PQPDYLEQLKKEILEVISKYVEI 44 (70)
T ss_dssp CTTSSHHHHHHHHHHHHHHHS--
T ss_pred CcHHHHHHHHHHHHHHHHhheec
Confidence 33589999999999999999864
No 62
>cd03733 SOCS_WSB_SWIP SOCS (suppressors of cytokine signaling) box of WSB/SWiP-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2), and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh), as well as, their isoforms WSB-2 and SWiP-2. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=21.56 E-value=52 Score=17.27 Aligned_cols=34 Identities=12% Similarity=0.173 Sum_probs=19.2
Q ss_pred hhhhcCChhhhhhhhcccccCCCCcHHHHHHHHHh
Q psy16764 76 PRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110 (113)
Q Consensus 76 p~Lr~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~ 110 (113)
|+|+.+|-..|....-...++ ..++++-+.+-+.
T Consensus 4 ~sLqhLCR~~Ir~~~~~~~i~-~LpLP~~Lk~YL~ 37 (39)
T cd03733 4 SSLQHLCRMALRRVMTTQQVL-ALPIPKKMKEFLT 37 (39)
T ss_pred CCHHHHHHHHHHHHccccccc-cCCCCHHHHHHHc
Confidence 555666655555444334455 6677777666443
No 63
>cd03717 SOCS_SOCS_like SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. These intracellular proteins regulate the responses of immune cells to cytokines. Identified as negative regulators of the cytokine-JAK-STAT pathway, they seem to play a role in many immunological and pathological processes. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. Related SOCS boxes are also present in Rab40-like proteins and insect proteins of unknown function that also contain a NEUZ (domain in neuralized proteins) domain.
Probab=21.41 E-value=53 Score=17.05 Aligned_cols=34 Identities=15% Similarity=0.274 Sum_probs=17.7
Q ss_pred hhhhcCChhhhhhhhcccccCCCCcHHHHHHHHHh
Q psy16764 76 PRLKSIPSLVLEELFFRNIIGHNTTIKKTIWHMYK 110 (113)
Q Consensus 76 p~Lr~l~~~~~e~L~f~~~~g~~~~i~~Ll~eml~ 110 (113)
++|+.+|-..|.+..-...+. ..++++-+.+-+.
T Consensus 4 ~sLq~LCR~~Ir~~~~~~~i~-~LpLP~~Lk~yL~ 37 (39)
T cd03717 4 RSLQHLCRFVIRQCTRRDLID-QLPLPRRLKDYLK 37 (39)
T ss_pred CCHHHHHHHHHHHHccccccc-cCCCCHHHHHHHH
Confidence 445555555544443334455 5677666665443
No 64
>COG0851 MinE Septum formation topological specificity factor [Cell division and chromosome partitioning]
Probab=20.96 E-value=1.3e+02 Score=18.86 Aligned_cols=24 Identities=8% Similarity=0.256 Sum_probs=20.7
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHh
Q psy16764 36 KTGSKFTAAIQGHTQIFLNKYIHT 59 (113)
Q Consensus 36 l~~~~~Ve~lqe~~~~aL~~~~~~ 59 (113)
-..++.++.+|+.++..+..|+..
T Consensus 33 ~~~pd~l~~Lr~eIl~VI~KYV~i 56 (88)
T COG0851 33 GLQPDYLEQLRKEILEVISKYVQI 56 (88)
T ss_pred CCCcchHHHHHHHHHHHHHHHhee
Confidence 345899999999999999999865
No 65
>PF07146 DUF1389: Protein of unknown function (DUF1389); InterPro: IPR010792 This family consists of several hypothetical bacterial proteins, which seem to be specific to Chlamydia pneumoniae (Chlamydophila pneumoniae). Members of this family are typically around 400 residues in length. The function of this family is unknown.
Probab=20.87 E-value=3.9e+02 Score=20.67 Aligned_cols=60 Identities=17% Similarity=0.242 Sum_probs=38.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCcccCCCChhHHHHHHHHHHHHHHHHHHhhCCCc--------chHHHHHHHhchh
Q psy16764 11 IVTEENSNLEIRNAYTSRRGSRVRFKTGSKFTAAIQGHTQIFLNKYIHTVYPSQ--------PTRFCKIQLILPR 77 (113)
Q Consensus 11 ld~~E~~~Lkai~l~~~~~g~~~~~l~~~~~Ve~lqe~~~~aL~~~~~~~~p~~--------~~Rf~kLLl~Lp~ 77 (113)
++++||.+|+.-.--+ -+..+..-|.++++++..++..|-......+ ..-|.+.|+.|..
T Consensus 181 vS~eey~~L~~hA~n~-------tW~~~~~~V~~i~~rl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~LL~lc~ 248 (314)
T PF07146_consen 181 VSEEEYSTLKNHARNN-------TWDQQQDIVSAIVDRLIACLGNYYQYSFENDKVILLSLTEESISNWLLLLCK 248 (314)
T ss_pred ccHHHHHHHHHHHhhC-------CccchhhHHHHHHHHHHhhhhhhhhhhhccchhHHHHhhhhhHHHHHHHHHH
Confidence 6889999998875433 1344455599999999777777644332211 1236677776654
No 66
>TIGR03277 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Probab=20.51 E-value=86 Score=20.45 Aligned_cols=20 Identities=15% Similarity=0.222 Sum_probs=17.1
Q ss_pred HHhhccccCCHHHHHHHHHH
Q psy16764 3 QTELTMLRIVTEENSNLEIR 22 (113)
Q Consensus 3 ~~~l~~L~ld~~E~~~Lkai 22 (113)
+..|+.++++.+||+-+|-=
T Consensus 31 ~~al~~~~~sp~ef~~~K~e 50 (109)
T TIGR03277 31 HPKLAELGLSPQEFVRIKEE 50 (109)
T ss_pred HHHHHHcCCCHHHHHHHHHH
Confidence 46789999999999998864
No 67
>PF01267 F-actin_cap_A: F-actin capping protein alpha subunit; InterPro: IPR002189 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis [], as well as muscle contraction. The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta (see IPR001698 from INTERPRO). Neither of the subunits shows sequence similarity to other filament-capping proteins []. The alpha subunit is a protein of about 268 to 286 amino acid residues whose sequence is well conserved in eukaryotic species [].; GO: 0003779 actin binding, 0030036 actin cytoskeleton organization, 0008290 F-actin capping protein complex; PDB: 1MQ1_D 1MWN_X 2KBM_Y 2KZ7_A 3AAE_C 3AA6_A 3LK4_G 1IZN_A 3AA7_A 3AAA_A ....
Probab=20.29 E-value=96 Score=23.29 Aligned_cols=26 Identities=23% Similarity=0.347 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhCCCc
Q psy16764 39 SKFTAAIQGHTQIFLNKYIHTVYPSQ 64 (113)
Q Consensus 39 ~~~Ve~lqe~~~~aL~~~~~~~~p~~ 64 (113)
...++..|..+..+|..|+...||..
T Consensus 104 ~~~~e~~R~~l~~~l~~Yv~~hy~~g 129 (271)
T PF01267_consen 104 DEELESYRDALDKALEKYVKEHYPSG 129 (271)
T ss_dssp -TSSHHHHHHHHHHHHHHHHHHSTTE
T ss_pred ccchHHHHHHHHHHHHHHHHHhccCc
Confidence 46788999999999999999999754
No 68
>PRK09458 pspB phage shock protein B; Provisional
Probab=20.12 E-value=2.2e+02 Score=17.31 Aligned_cols=23 Identities=13% Similarity=0.197 Sum_probs=15.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhhCCC
Q psy16764 40 KFTAAIQGHTQIFLNKYIHTVYPS 63 (113)
Q Consensus 40 ~~Ve~lqe~~~~aL~~~~~~~~p~ 63 (113)
...+++|+++. +|+..+...+|+
T Consensus 49 ~~A~rm~~RI~-tLE~ILDae~P~ 71 (75)
T PRK09458 49 EKAERMRERIQ-ALEAILDAEHPN 71 (75)
T ss_pred HHHHHHHHHHH-HHHHHHcccCCC
Confidence 45556666665 577777777774
Done!