Query 009289
Match_columns 538
No_of_seqs 48 out of 50
Neff 2.9
Searched_HMMs 46136
Date Thu Mar 28 22:44:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009289.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009289hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06944 NR_LBD_Ftz-F1_like The 90.3 1.8 4E-05 42.3 9.2 75 416-491 83-161 (237)
2 smart00430 HOLI Ligand binding 90.2 1.9 4.1E-05 36.9 8.2 77 413-489 34-112 (163)
3 cd06940 NR_LBD_REV_ERB The lig 89.4 1.3 2.9E-05 41.8 7.2 82 430-521 70-151 (189)
4 cd06941 NR_LBD_DmE78_like The 88.9 1.2 2.6E-05 41.8 6.5 73 418-492 49-121 (195)
5 cd06930 NR_LBD_F2 Ligand-bindi 87.8 4.7 0.0001 35.8 9.2 76 414-490 42-118 (165)
6 cd06943 NR_LBD_RXR_like The li 87.4 4.4 9.4E-05 38.1 9.2 76 415-491 74-149 (207)
7 cd07069 NR_LBD_Lrh-1 The ligan 86.0 4.6 0.0001 39.9 9.0 78 416-493 85-165 (241)
8 cd06945 NR_LBD_Nurr1_like The 85.6 2.7 5.8E-05 41.4 7.1 81 419-510 89-169 (239)
9 cd06931 NR_LBD_HNF4_like The l 84.5 7.8 0.00017 36.9 9.5 76 415-493 76-152 (222)
10 cd06942 NR_LBD_Sex_1_like The 82.9 5.1 0.00011 37.7 7.4 107 367-488 2-116 (191)
11 cd06929 NR_LBD_F1 Ligand-bindi 82.2 6.9 0.00015 35.3 7.8 75 415-491 46-120 (174)
12 cd07075 NR_LBD_MR Ligand bindi 82.1 6.3 0.00014 39.7 8.1 66 423-489 80-146 (248)
13 cd06938 NR_LBD_EcR The ligand 81.5 9 0.0002 37.2 8.8 64 422-486 89-152 (231)
14 cd06937 NR_LBD_RAR The ligand 80.3 7.1 0.00015 38.2 7.7 71 431-510 97-167 (231)
15 cd06950 NR_LBD_Tlx_PNR_like Th 80.0 11 0.00024 36.1 8.7 83 418-510 73-155 (206)
16 cd06935 NR_LBD_TR The ligand b 79.2 3.2 7E-05 40.9 5.0 63 430-493 110-172 (243)
17 cd06949 NR_LBD_ER Ligand bindi 77.7 14 0.00031 36.3 8.9 70 418-489 79-149 (235)
18 PF00104 Hormone_recep: Ligand 77.0 37 0.00079 30.2 10.5 114 367-491 24-139 (203)
19 cd06948 NR_LBD_COUP-TF Ligand 75.3 12 0.00027 36.5 7.7 73 416-491 75-150 (236)
20 cd06954 NR_LBD_LXR The ligand 72.4 6.8 0.00015 37.9 5.1 68 424-491 95-162 (236)
21 cd07076 NR_LBD_GR Ligand bindi 72.1 18 0.0004 36.4 8.2 68 423-491 80-149 (247)
22 cd07068 NR_LBD_ER_like The lig 70.4 27 0.00058 33.7 8.6 88 389-489 56-143 (221)
23 cd07348 NR_LBD_NGFI-B The liga 66.5 24 0.00052 35.2 7.6 65 418-485 88-152 (238)
24 cd07070 NR_LBD_SF-1 The ligand 66.1 35 0.00076 33.6 8.6 73 418-491 85-161 (237)
25 cd07072 NR_LBD_DHR38_like Liga 65.2 30 0.00065 34.5 8.0 66 418-486 89-154 (239)
26 cd06947 NR_LBD_GR_Like Ligand 63.7 38 0.00083 33.9 8.5 70 418-488 75-145 (246)
27 cd06157 NR_LBD The ligand bind 61.9 68 0.0015 27.5 8.7 102 414-523 41-144 (168)
28 cd07074 NR_LBD_PR Ligand bindi 61.7 61 0.0013 32.8 9.5 69 418-487 75-144 (248)
29 cd06946 NR_LBD_ERR The ligand 60.4 52 0.0011 31.6 8.5 72 416-489 72-143 (221)
30 cd07071 NR_LBD_Nurr1 The ligan 60.0 57 0.0012 32.5 8.9 56 429-486 98-153 (238)
31 cd06932 NR_LBD_PPAR The ligand 57.5 47 0.001 33.4 7.9 74 428-510 117-193 (259)
32 cd06934 NR_LBD_PXR_like The li 56.6 26 0.00056 34.3 5.8 37 455-491 117-153 (226)
33 cd07073 NR_LBD_AR Ligand bindi 55.7 53 0.0011 32.9 7.9 63 424-487 81-144 (246)
34 cd06933 NR_LBD_VDR The ligand 52.2 42 0.00091 33.1 6.5 36 455-490 121-156 (238)
35 KOG2511 Nicotinic acid phospho 49.5 12 0.00026 40.5 2.4 23 462-484 53-78 (420)
36 cd06939 NR_LBD_ROR_like The li 49.4 39 0.00085 33.5 5.8 47 456-510 130-176 (241)
37 PF14333 DUF4389: Domain of un 44.5 44 0.00096 28.4 4.6 41 6-46 2-42 (80)
38 cd06936 NR_LBD_Fxr The ligand 43.9 72 0.0016 31.1 6.6 40 452-491 112-151 (221)
39 cd07350 NR_LBD_Dax1 The ligand 40.5 85 0.0018 31.2 6.6 36 457-492 127-162 (232)
40 cd07349 NR_LBD_SHP The ligand 40.5 67 0.0015 31.6 5.9 30 462-491 120-149 (222)
41 cd06952 NR_LBD_TR2_like The li 38.9 70 0.0015 30.7 5.6 34 459-492 115-148 (222)
42 PF04911 ATP-synt_J: ATP synth 38.8 37 0.00079 28.0 3.1 18 243-260 9-26 (54)
43 smart00054 EFh EF-hand, calciu 38.1 33 0.00071 20.3 2.2 27 369-400 2-28 (29)
44 cd08323 CARD_APAF1 Caspase act 37.3 36 0.00078 29.5 3.1 33 359-402 10-42 (86)
45 PF01325 Fe_dep_repress: Iron 32.1 40 0.00087 27.1 2.4 18 470-487 1-18 (60)
46 PRK00523 hypothetical protein; 31.2 31 0.00066 29.8 1.7 23 86-109 3-25 (72)
47 cd06953 NR_LBD_DHR4_like The l 29.9 1.4E+02 0.0031 28.8 6.2 37 455-491 113-149 (213)
48 PRK13511 6-phospho-beta-galact 29.7 71 0.0015 34.8 4.5 54 428-481 209-286 (469)
49 cd08785 CARD_CARD9-like Caspas 29.7 57 0.0012 28.4 3.1 33 359-402 12-44 (86)
50 PRK13735 conjugal transfer mat 28.6 90 0.002 37.6 5.4 68 51-120 367-453 (942)
51 PF14946 DUF4501: Domain of un 27.6 1.3E+02 0.0029 29.8 5.4 21 299-319 112-132 (180)
52 cd08819 CARD_MDA5_2 Caspase ac 27.5 73 0.0016 28.4 3.4 32 359-401 15-46 (88)
53 PF15452 NYAP_C: Neuronal tyro 25.4 20 0.00043 37.9 -0.5 21 518-538 240-260 (308)
54 COG3790 Predicted membrane pro 25.0 66 0.0014 29.2 2.7 35 80-114 43-85 (97)
55 PF07127 Nodulin_late: Late no 24.0 65 0.0014 25.4 2.2 21 8-28 2-22 (54)
56 cd06951 NR_LBD_Dax1_like The l 22.9 2.1E+02 0.0045 28.1 5.9 36 454-489 115-150 (222)
57 cd08810 CARD_BCL10 Caspase act 22.6 95 0.0021 27.1 3.2 34 359-403 12-45 (84)
58 PRK10907 intramembrane serine 22.5 51 0.0011 33.9 1.8 48 42-97 196-243 (276)
59 KOG0742 AAA+-type ATPase [Post 22.4 1.2E+02 0.0026 34.4 4.5 215 217-490 307-539 (630)
60 PRK00523 hypothetical protein; 22.0 1.2E+02 0.0026 26.4 3.5 26 239-264 1-26 (72)
61 COG2981 CysZ Uncharacterized p 21.8 93 0.002 32.3 3.4 31 240-270 68-107 (250)
62 PLN00151 potassium transporter 21.1 1.2E+02 0.0026 36.2 4.5 25 262-287 479-503 (852)
63 PLN00149 potassium transporter 20.3 1.3E+02 0.0028 35.6 4.6 25 262-287 406-430 (779)
64 PHA03385 IX capsid protein IX, 20.0 1.1E+02 0.0023 29.3 3.1 23 508-530 106-128 (135)
No 1
>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=90.30 E-value=1.8 Score=42.25 Aligned_cols=75 Identities=16% Similarity=0.247 Sum_probs=55.0
Q ss_pred HHHHHHHHHhhhcC-CCceeecCCceecccCCCC---ccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 416 YSFLQTLLYSIKAG-SGGLLLPDSVEITHLNRPN---NKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 416 yslL~~LL~SaKan-S~GlllsD~~EiT~~NrPk---dr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
..+|...-||+..+ ++-+++.||..+...+-+. ....+ +.+.+.-+=.+++.++++++|=.||+-++|++.|...
T Consensus 83 l~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~-~~~~i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~g 161 (237)
T cd06944 83 LLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLASQAGLGLSS-LVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKG 161 (237)
T ss_pred HHHHHHHHHhcccCCCCceeecCCCccchhhhhhhccccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcCC
Confidence 45667777888887 7778999998876554222 11223 3455666667899999999999999999999988543
No 2
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=90.21 E-value=1.9 Score=36.89 Aligned_cols=77 Identities=22% Similarity=0.248 Sum_probs=58.8
Q ss_pred cchHHHHHHHHHhhhcCCCceeecCCceecccCCC--CccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCc
Q 009289 413 LPCYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRP--NNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 489 (538)
Q Consensus 413 LPAyslL~~LL~SaKanS~GlllsD~~EiT~~NrP--kdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~ 489 (538)
-+.+.+|...-+|.|.+...++.+||+.+...... .......+...+.-+-+.++.+++|++|=.||+-++++..|.
T Consensus 34 ~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~ 112 (163)
T smart00430 34 WFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRILQELVKPLRELKLDDEEYALLKAILLFNPAG 112 (163)
T ss_pred HHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcChhh
Confidence 45678899999999998887777887766543322 134455566666677888999999999999999999998654
No 3
>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=89.35 E-value=1.3 Score=41.82 Aligned_cols=82 Identities=16% Similarity=0.229 Sum_probs=53.5
Q ss_pred CCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHH
Q 009289 430 SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAA 509 (538)
Q Consensus 430 S~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrA 509 (538)
...+.+.||..++...-+...+-+ +.+++.-+=++++.++++++|=.||+-++|++.|....+ ..+.|++.
T Consensus 70 ~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L~--------~~~~Ve~l 140 (189)
T cd06940 70 ERSVTFLSGQKYSVDDLHSMGAGD-LLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLE--------NVNLVEAL 140 (189)
T ss_pred CCeEEecCCcEEcHHHHHHcCcHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCCC--------CHHHHHHH
Confidence 344777788766543322222323 345566788999999999999999999999998754333 55667766
Q ss_pred HHHHHHHHHhhH
Q 009289 510 QIQGISRRYELY 521 (538)
Q Consensus 510 qLqai~RRLqg~ 521 (538)
| +.+..-||.+
T Consensus 141 q-~~~~~aL~~~ 151 (189)
T cd06940 141 Q-ETLIRALRTL 151 (189)
T ss_pred H-HHHHHHHHHH
Confidence 6 3333344443
No 4
>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=88.94 E-value=1.2 Score=41.82 Aligned_cols=73 Identities=19% Similarity=0.302 Sum_probs=52.1
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccc
Q 009289 418 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERM 492 (538)
Q Consensus 418 lL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 492 (538)
+++ +-++...+++++.+.||..++..+-......+ +.+++.-+=++++.++++++|=.||+-++|++.|....
T Consensus 49 ll~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl 121 (195)
T cd06941 49 LVR-ISRLINSKSGSITFDDGISISRQQLDIIYDSD-FVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGL 121 (195)
T ss_pred HHH-HHHHHcCCCCeEEecCCeEeeHHHHHhccchH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCC
Confidence 444 44677778888999999776654321100112 45677778889999999999999999999999875443
No 5
>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=87.83 E-value=4.7 Score=35.76 Aligned_cols=76 Identities=20% Similarity=0.141 Sum_probs=56.9
Q ss_pred chHHHHHHHHHhhhcC-CCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcc
Q 009289 414 PCYSFLQTLLYSIKAG-SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTE 490 (538)
Q Consensus 414 PAyslL~~LL~SaKan-S~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~ 490 (538)
+.+.+|..--+|.+.+ ++.+..++|..+...+-.+....++ .+++.-+=++++.+|+|++|=.+|+-+++++.|..
T Consensus 42 ~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~ 118 (165)
T cd06930 42 AELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAEL-VQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLP 118 (165)
T ss_pred HHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC
Confidence 4566777777888885 6678888998777665443333343 45666677889999999999999999999987654
No 6
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=87.39 E-value=4.4 Score=38.14 Aligned_cols=76 Identities=17% Similarity=0.189 Sum_probs=50.3
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 415 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 415 AyslL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
.+.+|..--+|.. ..+|+++++|..++..+-.+..+-+.+-..+--+-++++.+++|++|=.+|+-+++++.|...
T Consensus 74 e~~~l~~a~~s~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~ 149 (207)
T cd06943 74 ELLIAAFAHRSIA-VKDGILLATGLHLHRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKG 149 (207)
T ss_pred HHHHHHHHHHccC-CCCeeEecCCceeccchhhhccchHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCC
Confidence 3445554455554 368899999987765443333333332222224667899999999999999999999977543
No 7
>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=86.04 E-value=4.6 Score=39.91 Aligned_cols=78 Identities=17% Similarity=0.254 Sum_probs=52.4
Q ss_pred HHHHHHHHHhhhcCCCc-eeecCCceecccCC-CCccc-hhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccc
Q 009289 416 YSFLQTLLYSIKAGSGG-LLLPDSVEITHLNR-PNNKL-LDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERM 492 (538)
Q Consensus 416 yslL~~LL~SaKanS~G-lllsD~~EiT~~Nr-Pkdr~-fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 492 (538)
+.+|...-+|...++.+ +++.+|+.++.... +.... ++=+.+++.-+-++++.++++++|=.||+-++|++.|....
T Consensus 85 llvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL 164 (241)
T cd07069 85 LLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNL 164 (241)
T ss_pred HHHHHHHHHhhccCCCCeeEecCCCccCchhhhhhhhhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCC
Confidence 44555556677665444 77788876654331 11111 22234667778889999999999999999999999876544
Q ss_pred c
Q 009289 493 E 493 (538)
Q Consensus 493 ~ 493 (538)
.
T Consensus 165 ~ 165 (241)
T cd07069 165 E 165 (241)
T ss_pred C
Confidence 3
No 8
>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=85.59 E-value=2.7 Score=41.42 Aligned_cols=81 Identities=12% Similarity=0.192 Sum_probs=54.3
Q ss_pred HHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCC
Q 009289 419 LQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNG 498 (538)
Q Consensus 419 L~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~ 498 (538)
|..--||... .+.+++.+|.-++..+. +..+-+ +.++++-.=++++.++++++|..||+..+|++.|.....
T Consensus 89 L~~a~r~~~~-~~~l~~~~~~~~~~~~~-~~~~~~-~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~gL~----- 160 (239)
T cd06945 89 LRLAYRSNPV-DGKLVFCNGLVLHRLQC-VRGFGE-WLDSILAFSSSLQSLLLDDISAFCCLALLLLITERHGLK----- 160 (239)
T ss_pred HHHHHHhcCC-CCceEeeCCceecHHHH-HHhHHH-HHHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCccccC-----
Confidence 3333445443 34477778877665543 223434 468888777899999999999999999999987654332
Q ss_pred CCCChhHHHHHH
Q 009289 499 GLLPEDALRAAQ 510 (538)
Q Consensus 499 g~pp~d~vrrAq 510 (538)
..+.|.+-|
T Consensus 161 ---~~~~Ve~lQ 169 (239)
T cd06945 161 ---EPKKVEELQ 169 (239)
T ss_pred ---CHHHHHHHH
Confidence 445555554
No 9
>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=84.46 E-value=7.8 Score=36.95 Aligned_cols=76 Identities=18% Similarity=0.173 Sum_probs=53.2
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHH-HHHHHHHhccCChhHHhHHHHhhhcCCCccccc
Q 009289 415 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIM-VLKEQISVLKLTEPEVRYLEKVVLFGSTTERME 493 (538)
Q Consensus 415 AyslL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~Pll-viKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~~ 493 (538)
.+.++..--+|. .+.+.+++.||..++..+-+ ..+-+. .++.+ -+-++++.+++|++|=.+|+-+++++.|..+..
T Consensus 76 ~~~~l~~a~~s~-~~~~~l~~~~g~~~~~~~~~-~~~~~~-~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~ls 152 (222)
T cd06931 76 EHLLLGVARRSM-PYKDILLLGNDLIIPRHCPE-PEISRV-ANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLS 152 (222)
T ss_pred HHHHHHHHHhcc-CCCCeeeeCCCccccccccc-chHHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCCC
Confidence 566666666776 45788999999866655433 222222 33332 466789999999999999999999998766543
No 10
>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=82.89 E-value=5.1 Score=37.67 Aligned_cols=107 Identities=18% Similarity=0.242 Sum_probs=65.5
Q ss_pred HHHHHHHHHHhhhhhhhhc-------cCCCChhhHHHHHHhcCCCCcceEeeccchHHHHHHHHHhhhcCCCceeecCCc
Q 009289 367 QIWVNMMRSCETRGRELLD-------ADVITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSV 439 (538)
Q Consensus 367 qiwd~lfk~ce~~G~~Ll~-------~gvIt~~Diee~~~~k~~~~~k~i~vgLPAyslL~~LL~SaKanS~GlllsD~~ 439 (538)
++|.++.+.....-+..++ =.-++.+|=-.-+++.-. +. .++ .+-++...+ +.++.||.
T Consensus 2 ~~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~----------e~-~ll-~~~~~~~~~--~~~~~~g~ 67 (191)
T cd06942 2 NAWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMF----------PL-YLL-RLSRDYNNE--GTVLCDFR 67 (191)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHH----------HH-HHH-HHHHHhCcC--CeEEeCCc
Confidence 5677776666654444332 122444554333333311 22 223 344665544 88999998
Q ss_pred eecccCC-CCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCC
Q 009289 440 EITHLNR-PNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGST 488 (538)
Q Consensus 440 EiT~~Nr-Pkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d 488 (538)
.++.... .+....+ +.+++.-+=+.++++++|++|=.||+-+++++.|
T Consensus 68 ~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd 116 (191)
T cd06942 68 PVEFASLLSQLLHGK-LIDEMLQFANKILTLNLTNAELALLCAAELLQPD 116 (191)
T ss_pred cccHHHHHHhcchHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCC
Confidence 8865321 0111223 4566677778999999999999999999999988
No 11
>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=82.25 E-value=6.9 Score=35.27 Aligned_cols=75 Identities=19% Similarity=0.242 Sum_probs=50.0
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 415 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 415 AyslL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
.+.++..- ++.+.+.+.+..+||+......-+.... .=+.+.+.-.=..++.+++|++|=.+|+-+++++.|...
T Consensus 46 ~l~~l~~a-~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~ 120 (174)
T cd06929 46 EILLLRSA-TLYDPEKNSLTFGDGKGNSRDVLLNGGF-GEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPG 120 (174)
T ss_pred HHHHHHHH-HHhcccCCeEEecCCceecHHHHHHccc-HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCccc
Confidence 34444443 5677788889999997633221111111 123455555668899999999999999999999876543
No 12
>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=82.07 E-value=6.3 Score=39.68 Aligned_cols=66 Identities=15% Similarity=0.155 Sum_probs=52.4
Q ss_pred HHhhhc-CCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCc
Q 009289 423 LYSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 489 (538)
Q Consensus 423 L~SaKa-nS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~ 489 (538)
-||... +++-+++.+|.-++..+-++..+.| +.+++.-+=.+++.++++++|=.||+-++|++.|+
T Consensus 80 ~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~~~-~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~ 146 (248)
T cd07075 80 WRSYKHTNSQFLYFAPDLVFNEERMHQSAMYE-LCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIP 146 (248)
T ss_pred HhccCCCCCceEEecCCccccHHHHhhccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCC
Confidence 355544 4555888888888777766677888 56777777779999999999999999999999874
No 13
>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=81.54 E-value=9 Score=37.23 Aligned_cols=64 Identities=11% Similarity=0.174 Sum_probs=49.3
Q ss_pred HHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcC
Q 009289 422 LLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFG 486 (538)
Q Consensus 422 LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~ 486 (538)
+-++...+.+.++.+||.+.+..+-....+ .=+.+++.-+-++++.++++++|=.+|+-.++++
T Consensus 89 ~a~~~~~~~~~~~f~~g~~~~~~~~~~~~~-~~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf~ 152 (231)
T cd06938 89 VARRYDAKTDSIVFANNQPYTRDSYRKAGM-GDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS 152 (231)
T ss_pred HHHHhCCCCCeEEeeCCEEecHHHHhhcCH-HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcc
Confidence 336677888889999998888765333322 2246677777899999999999999999999985
No 14
>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=80.29 E-value=7.1 Score=38.23 Aligned_cols=71 Identities=14% Similarity=0.279 Sum_probs=50.9
Q ss_pred CceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHH
Q 009289 431 GGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ 510 (538)
Q Consensus 431 ~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq 510 (538)
.-+.+++|..++..+-.+.. +.-+.+++.-+=++++.++++++|=.||+-++|++.|..... ..+.|++.|
T Consensus 97 ~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~--------~~~~Ve~lQ 167 (231)
T cd06937 97 DTMTFSDGLTLNRTQMHNAG-FGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLE--------EPDRVEKLQ 167 (231)
T ss_pred CeEEecCCceecHHHHhhcC-hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCC--------CHHHHHHHH
Confidence 33667777666554433323 334678888899999999999999999999999998754433 455566665
No 15
>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=79.95 E-value=11 Score=36.07 Aligned_cols=83 Identities=18% Similarity=0.238 Sum_probs=47.4
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccC
Q 009289 418 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDN 497 (538)
Q Consensus 418 lL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~ 497 (538)
+|..--+|...++.-++-+++......+ +.....+. ...+.-+-.+++.++++++|=.||+-++|++.|.....
T Consensus 73 iL~~a~~s~~~~~~~ll~~~~~~~~~~~-~~~~~~~~-~~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L~---- 146 (206)
T cd06950 73 LLGAAQWSLPLDSCPLLAVPGLSPDNTE-AERTFLSE-VRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLK---- 146 (206)
T ss_pred HHHHHHHhcCCCcceeecCCcccccccc-hhhHHHHH-HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCC----
Confidence 4444445655444433333443222222 22223332 23344455689999999999999999999998764333
Q ss_pred CCCCChhHHHHHH
Q 009289 498 GGLLPEDALRAAQ 510 (538)
Q Consensus 498 ~g~pp~d~vrrAq 510 (538)
..+.+++.|
T Consensus 147 ----~~~~Ve~lq 155 (206)
T cd06950 147 ----DPAQVEALQ 155 (206)
T ss_pred ----CHHHHHHHH
Confidence 445565555
No 16
>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=79.21 E-value=3.2 Score=40.85 Aligned_cols=63 Identities=25% Similarity=0.287 Sum_probs=49.2
Q ss_pred CCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccc
Q 009289 430 SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERME 493 (538)
Q Consensus 430 S~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~~ 493 (538)
.+-+.+++|..++..+-....+-+ +.+++.-+=+++++++++++|=.||+-++|++.|....+
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~ 172 (243)
T cd06935 110 SETLTLSGEMAVTREQLKNGGLGV-VSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLA 172 (243)
T ss_pred CCeEEeeCCeEeeHHHHHhcChHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCCC
Confidence 456888888877765444444545 678888899999999999999999999999998864433
No 17
>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=77.73 E-value=14 Score=36.29 Aligned_cols=70 Identities=16% Similarity=0.228 Sum_probs=47.4
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCC-CCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCc
Q 009289 418 FLQTLLYSIKAGSGGLLLPDSVEITHLNR-PNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 489 (538)
Q Consensus 418 lL~~LL~SaKanS~GlllsD~~EiT~~Nr-Pkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~ 489 (538)
+|..--||...+. -+++.+|..++.... +++.+ .-+++++.-+=++++.++++++|=.||+-++|++.|.
T Consensus 79 ~L~~a~rs~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~ 149 (235)
T cd06949 79 MLGLVWRSMEHPG-KLLFAPDLLLDRNQGSCVEGM-VEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSV 149 (235)
T ss_pred HHHHHHHhcCCCC-eEEeeCCceecHHHhhhcccH-HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCc
Confidence 4444456665543 366677766554322 13333 3456777777779999999999999999999998764
No 18
>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=76.99 E-value=37 Score=30.24 Aligned_cols=114 Identities=18% Similarity=0.219 Sum_probs=75.6
Q ss_pred HHHHHHHHHHhhhhhhhhccCCCChhhHHHHHHhcCCCCcceEeeccchHHHHHHHHHhhhcCCCceeecCCceecccCC
Q 009289 367 QIWVNMMRSCETRGRELLDADVITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSVEITHLNR 446 (538)
Q Consensus 367 qiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~~~~~k~i~vgLPAyslL~~LL~SaKanS~GlllsD~~EiT~~Nr 446 (538)
++|+..+..+-.--+.+=.=.-++.+|=...++. +.+.+.+|..--+|...+.+.+.+.+|..+...+-
T Consensus 24 ~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~-----------~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~ 92 (203)
T PF00104_consen 24 EIWRRELRLIVDWAKSFPEFSELSMEDKIALLKS-----------SWFELFILELAYRSYQCNQDQLMFPNGTFIDKDSF 92 (203)
T ss_dssp HHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHH-----------HHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHHH
T ss_pred HHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhh-----------hcccccchhhhhhhccccccccccccccccccccc
Confidence 6666666666666666544455677775544443 34567788877777777889999999988755443
Q ss_pred CCc--cchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 447 PNN--KLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 447 Pkd--r~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
+.. ..+.=+.+.+.-+=.+++.+++|++|=.+|.-+++++.|...
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~ 139 (203)
T PF00104_consen 93 DDFITGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPG 139 (203)
T ss_dssp HHTSTTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTT
T ss_pred ccccccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccc
Confidence 322 222222234444445999999999999999999999875544
No 19
>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=75.25 E-value=12 Score=36.47 Aligned_cols=73 Identities=18% Similarity=0.307 Sum_probs=47.3
Q ss_pred HHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHH---HHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 416 YSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMV---LKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 416 yslL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~Pllv---iKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
.-+|..--+|...+.+-++..||..+...+ .+++-+ +.+.+-. +=++++.+++|++|=.||+-+++++.|...
T Consensus 75 l~lL~~a~~s~~~~~~~~~~~~g~~~~~~~--~~~~~~-~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~ 150 (236)
T cd06948 75 LFVLNAAQCCMPLHVAPLLAAAGLHASPMS--ADRVVA-FMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACG 150 (236)
T ss_pred HHHHHHHHHcccccchhhhhccccccCccc--hhhHhH-HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCccccc
Confidence 345555556666666667778887654332 122222 2333322 235789999999999999999999987644
No 20
>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=72.39 E-value=6.8 Score=37.94 Aligned_cols=68 Identities=16% Similarity=0.228 Sum_probs=48.1
Q ss_pred HhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 424 YSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 424 ~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
++.....+.+...||..++..+-.+..+..=+.+++.-+-+.++.+++|++|=.||+-++|++.|...
T Consensus 95 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~g 162 (236)
T cd06954 95 RRYNPESEAITFLKDFPYSRDDFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPN 162 (236)
T ss_pred HHhcCCCCeEEeeCCccccHHHHHHhcChHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCccc
Confidence 44455567788889977665432212222234566767888999999999999999999999977533
No 21
>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=72.05 E-value=18 Score=36.43 Aligned_cols=68 Identities=12% Similarity=0.218 Sum_probs=48.5
Q ss_pred HHhhhcCCCc-eeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCC-Cccc
Q 009289 423 LYSIKAGSGG-LLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS-TTER 491 (538)
Q Consensus 423 L~SaKanS~G-lllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~-d~~r 491 (538)
-||.+.+..- ++..+|.-++..+--...+.+ +.+++.-+=.++++++++++|=.||+-++|++. |...
T Consensus 80 ~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~~~-~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~G 149 (247)
T cd07076 80 WRSYRQSNGNLLCFAPDLIINEQRMTLPCMYD-QCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDG 149 (247)
T ss_pred HhccCCCCCceEEecCCeeecHHHHhhhhHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCC
Confidence 4777654433 667777766655432333444 466777888899999999999999999999986 5433
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=70.42 E-value=27 Score=33.67 Aligned_cols=88 Identities=17% Similarity=0.215 Sum_probs=54.5
Q ss_pred CChhhHHHHHHhcCCCCcceEeeccchHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHh
Q 009289 389 ITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISV 468 (538)
Q Consensus 389 It~~Diee~~~~k~~~~~k~i~vgLPAyslL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~ 468 (538)
++.+|-..-+++.- ..+.+|..--+|+..+. ++.+++|.-.+.....+..+-+ +.+++.-+=..++.
T Consensus 56 L~~~DQi~LLk~~~-----------~~~~~l~~a~~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~ 122 (221)
T cd07068 56 LSLNDQMHLLQSAW-----------LEILMLGLVWRSLPHPG-KLVFAPDLLLDREQARVEGLLE-IFDMLLQLVRRFRE 122 (221)
T ss_pred CCHHHHHHHHHHhh-----------HHHHHHHHHHhhcCCCC-eEEeCCCceECHHHHhhccHHH-HHHHHHHHHHHHHH
Confidence 56666555444442 34555666566665544 7888888644432222223323 23444445568999
Q ss_pred ccCChhHHhHHHHhhhcCCCc
Q 009289 469 LKLTEPEVRYLEKVVLFGSTT 489 (538)
Q Consensus 469 ~~L~E~EE~yL~KlvL~~~d~ 489 (538)
+++|++|=.+|+-+++++.|.
T Consensus 123 L~ld~~E~~lLkaIil~npd~ 143 (221)
T cd07068 123 LGLQREEYVCLKAIILANSDV 143 (221)
T ss_pred cCCCHHHHHHHHHHHHcCCCc
Confidence 999999999999999997554
No 23
>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=66.49 E-value=24 Score=35.16 Aligned_cols=65 Identities=17% Similarity=0.317 Sum_probs=46.8
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhc
Q 009289 418 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLF 485 (538)
Q Consensus 418 lL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~ 485 (538)
+|..--+|... .+-+++.+|..++..+. ...+-+| .+++.-.=.+++.++++++|=.||+-++|+
T Consensus 88 vL~~a~r~~~~-~~~l~f~~~~~~~r~~~-~~~~~~~-~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf 152 (238)
T cd07348 88 ILRLAYRSNPE-EGKLIFCNGVVLHRTQC-VRGFGDW-IDSILEFSQSLHRMNLDVSAFSCLAALVII 152 (238)
T ss_pred HHHHHHHcCCC-CCeEEeeCCeeecHHHH-HhhHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHc
Confidence 34444455444 34477888887776553 3345565 467777888999999999999999999998
No 24
>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=66.07 E-value=35 Score=33.63 Aligned_cols=73 Identities=16% Similarity=0.239 Sum_probs=47.3
Q ss_pred HHHHHHHhhhc-CCCceeecCCceecccCCCCccchhhhchhHHH---HHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 418 FLQTLLYSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMV---LKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 418 lL~~LL~SaKa-nS~GlllsD~~EiT~~NrPkdr~fDWff~Pllv---iKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
+|...-||.-. +.+-+++.+|++++..+-... .-.++-..... +=.+++.++++++|=.||+-++|++.|...
T Consensus 85 vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~-~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~g 161 (237)
T cd07070 85 VFDHIYRQVQHGKEGSILLVTGQEVELSTVAAQ-AGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKF 161 (237)
T ss_pred HHHHHHHhhhcCCCCceeecCCCeechhHHHHH-HhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccC
Confidence 44555667644 345577889998876553211 11232223322 445788999999999999999999877543
No 25
>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=65.19 E-value=30 Score=34.50 Aligned_cols=66 Identities=12% Similarity=0.233 Sum_probs=47.0
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcC
Q 009289 418 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFG 486 (538)
Q Consensus 418 lL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~ 486 (538)
+|..--+|... .+-+++++|..++.....+ .+-+| .+++.-+=++++.++++++|=.||+-++|+.
T Consensus 89 ~L~~a~r~~~~-~~~l~~~~g~~~~~~~~~~-~~~~~-~~~i~ef~~~l~~L~ld~~E~a~LkAivLf~ 154 (239)
T cd07072 89 VLRLAYRTAPE-DTKLTFCNGVVLHKQQCQR-SFGDW-LHAILEFSKSLHAMDIDISAFACLCALTLIT 154 (239)
T ss_pred HHHHHHHccCC-CCeEEeeCCeeecHHHHHh-hHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhC
Confidence 34444455544 3447788887766654322 45564 5777778889999999999999999999993
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=63.65 E-value=38 Score=33.91 Aligned_cols=70 Identities=11% Similarity=0.104 Sum_probs=46.5
Q ss_pred HHHHHHHhhhcC-CCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCC
Q 009289 418 FLQTLLYSIKAG-SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGST 488 (538)
Q Consensus 418 lL~~LL~SaKan-S~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d 488 (538)
+|..--||...+ ++-+++++|.-++...--+..+.| +.+++.-+=.++++++++++|=.||+-++|++.+
T Consensus 75 iL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~ 145 (246)
T cd06947 75 VFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQSAMYS-LCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTI 145 (246)
T ss_pred HHHHHHhhccCCCCCeEEecCCeeecHHHhhhccHHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCC
Confidence 344445666544 333667777644433322345666 4566655666899999999999999999999973
No 27
>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=61.87 E-value=68 Score=27.53 Aligned_cols=102 Identities=20% Similarity=0.225 Sum_probs=64.7
Q ss_pred chHHHHHHHHHhhhcCCCceeecCCceec-ccCCCCccch-hhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 414 PCYSFLQTLLYSIKAGSGGLLLPDSVEIT-HLNRPNNKLL-DWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 414 PAyslL~~LL~SaKanS~GlllsD~~EiT-~~NrPkdr~f-DWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
..+.+|...-+|.+.+....+..++...+ ..+.+..+.+ .=+-..+.-+-+.++.+++|++|=.+|+-++++..+..+
T Consensus 41 ~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~ 120 (168)
T cd06157 41 LELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE 120 (168)
T ss_pred HHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCC
Confidence 46789999999999999888877776431 1222222221 122234455677889999999999999999999866431
Q ss_pred cccccCCCCCChhHHHHHHHHHHHHHHhhHHH
Q 009289 492 MEAWDNGGLLPEDALRAAQIQGISRRYELYLH 523 (538)
Q Consensus 492 ~~~wd~~g~pp~d~vrrAqLqai~RRLqg~~~ 523 (538)
+....+-+++ .-+.+.+-|+.+++
T Consensus 121 -------s~~~~~~~~~-~~~~~~~~L~~y~~ 144 (168)
T cd06157 121 -------SLEDRKIVEE-LQERLLEALQDYLR 144 (168)
T ss_pred -------CccCHHHHHH-HHHHHHHHHHHHHH
Confidence 1223333333 33556666666553
No 28
>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=61.69 E-value=61 Score=32.85 Aligned_cols=69 Identities=10% Similarity=0.186 Sum_probs=45.7
Q ss_pred HHHHHHHhhhcCCCce-eecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCC
Q 009289 418 FLQTLLYSIKAGSGGL-LLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS 487 (538)
Q Consensus 418 lL~~LL~SaKanS~Gl-llsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~ 487 (538)
+|..--||.+.+++.. .+++|.-++..+..+..+.| +..++.-+-.+++.++++++|=.||+-++|++.
T Consensus 75 vL~~a~rS~~~~~~~~l~fa~d~~~~~~~~~~~~~~~-~~~~m~e~~~~~~~L~ld~~Ey~cLKAIvLfnp 144 (248)
T cd07074 75 VFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYS-LCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNT 144 (248)
T ss_pred HHHHHHhhhccCCCCeEEecCCcccchhhhhhccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHCCC
Confidence 3444458888776654 45555544433322334555 334443345688999999999999999999997
No 29
>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=60.38 E-value=52 Score=31.62 Aligned_cols=72 Identities=17% Similarity=0.256 Sum_probs=44.0
Q ss_pred HHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCc
Q 009289 416 YSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 489 (538)
Q Consensus 416 yslL~~LL~SaKanS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~ 489 (538)
+.+|..--+|...+. -++..+|.-...........-+ +.+++.-+=+.++.+++|++|=.||+-+++++.|.
T Consensus 72 l~lL~~a~~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~ 143 (221)
T cd06946 72 ILTLGVVFRSLPFNG-ELVFAEDFILDEELAREAGLLE-LYSACLQLVRRLQRLRLEKEEYVLLKALALANSDS 143 (221)
T ss_pred HHHHHHHHHccCCCC-ceeecCCeEEcHHHHhhcCHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCC
Confidence 455666667776653 3555454432211111111222 23455555578899999999999999999998874
No 30
>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=60.00 E-value=57 Score=32.49 Aligned_cols=56 Identities=9% Similarity=0.236 Sum_probs=43.2
Q ss_pred CCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcC
Q 009289 429 GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFG 486 (538)
Q Consensus 429 nS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~ 486 (538)
..+.+++.+|.-.+..+. ...+-+ +.+++.-+=++++.++++++|=.||+-++|++
T Consensus 98 ~~~~l~~~~g~~~~~~~~-~~~~~~-~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf~ 153 (238)
T cd07071 98 VEGKLIFCNGVVLHRLQC-VRGFGE-WIDSIVEFSSNLQNMNIDISAFSCIAALAMVT 153 (238)
T ss_pred CCCceEeeCCceechhhh-hhcHHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcC
Confidence 345588888877766553 334445 57788888899999999999999999999883
No 31
>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=57.47 E-value=47 Score=33.36 Aligned_cols=74 Identities=18% Similarity=0.292 Sum_probs=49.4
Q ss_pred cCCCceeecCCce-ecccC--CCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChh
Q 009289 428 AGSGGLLLPDSVE-ITHLN--RPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPED 504 (538)
Q Consensus 428 anS~GlllsD~~E-iT~~N--rPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d 504 (538)
.|.+++++.+|-. +|... ..+.. +.=+.+|+.-+=++++.++|+++|=.+|+-++|++.|..... ..+
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~--------~~~ 187 (259)
T cd06932 117 YNKDGLLFPEGNGYVTREFLESLRKP-FCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGLI--------NRK 187 (259)
T ss_pred cCCCCeEEeCCCEEeeHHHHHHhccc-HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCc--------CHH
Confidence 3566777776532 33321 11111 223678888889999999999999999999999998754332 445
Q ss_pred HHHHHH
Q 009289 505 ALRAAQ 510 (538)
Q Consensus 505 ~vrrAq 510 (538)
.|++.|
T Consensus 188 ~Ve~lQ 193 (259)
T cd06932 188 PVERIQ 193 (259)
T ss_pred HHHHHH
Confidence 555555
No 32
>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=56.65 E-value=26 Score=34.29 Aligned_cols=37 Identities=19% Similarity=0.405 Sum_probs=32.5
Q ss_pred hchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 455 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 455 ff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
+.+|+.-+=+++++++++++|=.||+-.+|++.|...
T Consensus 117 ~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~g 153 (226)
T cd06934 117 LLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPG 153 (226)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcC
Confidence 5678877888999999999999999999999987544
No 33
>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=55.65 E-value=53 Score=32.94 Aligned_cols=63 Identities=14% Similarity=0.207 Sum_probs=46.0
Q ss_pred Hhhhc-CCCceeecCCceecccCCCCccchhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCC
Q 009289 424 YSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS 487 (538)
Q Consensus 424 ~SaKa-nS~GlllsD~~EiT~~NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~ 487 (538)
||.-. +.+.+.+.+|..++..+..+..+.+.. ..+.-+=++.++++++++|=.||+-++|++.
T Consensus 81 rs~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~-~~l~~~~~~l~~L~ld~~EyacLKAIiLfnp 144 (246)
T cd07073 81 RSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQC-VRMRHLSQEFGWLQITPQEFLCMKALLLFSI 144 (246)
T ss_pred hccccCCCCeEEecCCeeechhhhccccHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHcCC
Confidence 66654 455588888887776665666666642 2333445578889999999999999999996
No 34
>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=52.22 E-value=42 Score=33.10 Aligned_cols=36 Identities=17% Similarity=0.351 Sum_probs=31.9
Q ss_pred hchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcc
Q 009289 455 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTE 490 (538)
Q Consensus 455 ff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~ 490 (538)
+.+|+.-+-++++.++++++|=.||+-++|++.|..
T Consensus 121 ~~~~l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~ 156 (238)
T cd06933 121 LLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRP 156 (238)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCC
Confidence 467888888899999999999999999999997643
No 35
>KOG2511 consensus Nicotinic acid phosphoribosyltransferase [Coenzyme transport and metabolism]
Probab=49.49 E-value=12 Score=40.52 Aligned_cols=23 Identities=52% Similarity=0.713 Sum_probs=19.7
Q ss_pred HHHHHH---hccCChhHHhHHHHhhh
Q 009289 462 LKEQIS---VLKLTEPEVRYLEKVVL 484 (538)
Q Consensus 462 iKEQIk---~~~L~E~EE~yL~KlvL 484 (538)
|+|||| +++||+||++||+|-.=
T Consensus 53 Lee~irfl~N~~lt~eei~~lkk~lP 78 (420)
T KOG2511|consen 53 LEEQIRFLANLKLTDEEIDYLKKELP 78 (420)
T ss_pred HHHHHHHHhhcCCCHHHHHHHHHhCC
Confidence 689987 67999999999998653
No 36
>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=49.44 E-value=39 Score=33.50 Aligned_cols=47 Identities=23% Similarity=0.397 Sum_probs=36.6
Q ss_pred chhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHH
Q 009289 456 FNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ 510 (538)
Q Consensus 456 f~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq 510 (538)
.+++.-.=++++.++|+++|=.||+-+||++.|.. |+-..+.|.+-|
T Consensus 130 ~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~--------gL~~~~~Ve~lQ 176 (241)
T cd06939 130 ISAVFDFAKSLCELKLTEDEIALFSALVLISADRP--------GLQEKRKVEKLQ 176 (241)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCc--------CCCCHHHHHHHH
Confidence 47777888999999999999999999999997753 333455555555
No 37
>PF14333 DUF4389: Domain of unknown function (DUF4389)
Probab=44.53 E-value=44 Score=28.36 Aligned_cols=41 Identities=20% Similarity=0.177 Sum_probs=31.4
Q ss_pred cchhhhHHHHHHHHHHHHHHHhhhhhhhHhHHHHHhhhccc
Q 009289 6 NLQGWLKIIYVGFAFCLAFFLGALKGLLVCPVAGLILIIGN 46 (538)
Q Consensus 6 ~~~~~~~~~y~~f~F~~l~~LG~iKg~ligP~a~lIi~iGn 46 (538)
+.+-|+|..|.+++.+.+.+++++=+++.-=-...+++.|.
T Consensus 2 r~~~~~R~l~mi~~~ivl~~~~~~~~~~~~~q~~~~L~tg~ 42 (80)
T PF14333_consen 2 REAVWLRLLLMIPFAIVLSLASIVLGVLVLIQWFAILFTGR 42 (80)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 56789999999999999999998877766555555555553
No 38
>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=43.88 E-value=72 Score=31.11 Aligned_cols=40 Identities=20% Similarity=0.321 Sum_probs=33.2
Q ss_pred hhhhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 452 LDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 452 fDWff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
.+=+.+|+.-+-+.++.+++|++|=.+|+-+++++.|...
T Consensus 112 ~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~g 151 (221)
T cd06936 112 SDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPY 151 (221)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcC
Confidence 4446677777788899999999999999999999887543
No 39
>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=40.54 E-value=85 Score=31.19 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccc
Q 009289 457 NPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERM 492 (538)
Q Consensus 457 ~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 492 (538)
+++.-+=++++.++++++|=.||+-+||++.|....
T Consensus 127 ~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L 162 (232)
T cd07350 127 RAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGL 162 (232)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccC
Confidence 455566678899999999999999999999875443
No 40
>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=40.47 E-value=67 Score=31.64 Aligned_cols=30 Identities=23% Similarity=0.352 Sum_probs=25.9
Q ss_pred HHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 462 LKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 462 iKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
+=.++++++++++|=.||+-++|++.|...
T Consensus 120 ~~~~l~~L~ld~~Eya~LkaivLf~pd~~g 149 (222)
T cd07349 120 CLNKFWSLDLSPKEYAYLKGTILFNPDVPG 149 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCccc
Confidence 456899999999999999999999877543
No 41
>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=38.92 E-value=70 Score=30.74 Aligned_cols=34 Identities=21% Similarity=0.395 Sum_probs=29.3
Q ss_pred HHHHHHHHHhccCChhHHhHHHHhhhcCCCcccc
Q 009289 459 IMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERM 492 (538)
Q Consensus 459 llviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 492 (538)
+.-+.++++++++++.|=.||+-++|++.|-..+
T Consensus 115 l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l 148 (222)
T cd06952 115 LQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQ 148 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCC
Confidence 3567899999999999999999999999885444
No 42
>PF04911 ATP-synt_J: ATP synthase j chain; InterPro: IPR006995 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o)
Probab=38.80 E-value=37 Score=28.00 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 009289 243 LLWPIIVIGSIVIAIFSS 260 (538)
Q Consensus 243 lLWPl~Vvgavl~aiisS 260 (538)
-+||+.+.|+|..--++|
T Consensus 9 P~wPFf~ag~iv~ygv~k 26 (54)
T PF04911_consen 9 PMWPFFAAGAIVYYGVNK 26 (54)
T ss_pred hhhHHHHHHHHHHHHHHH
Confidence 379999999987655544
No 43
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=38.12 E-value=33 Score=20.35 Aligned_cols=27 Identities=30% Similarity=0.373 Sum_probs=20.1
Q ss_pred HHHHHHHHhhhhhhhhccCCCChhhHHHHHHh
Q 009289 369 WVNMMRSCETRGRELLDADVITPADLKDWLKA 400 (538)
Q Consensus 369 wd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~ 400 (538)
|+.+|+.+..++ .|.|+..|+..++++
T Consensus 2 ~~~~f~~~d~~~-----~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDG-----DGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCC-----CCcEeHHHHHHHHHh
Confidence 456788887764 678888888887653
No 44
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=37.29 E-value=36 Score=29.53 Aligned_cols=33 Identities=15% Similarity=0.142 Sum_probs=27.2
Q ss_pred hhhhhhhHHHHHHHHHHHhhhhhhhhccCCCChhhHHHHHHhcC
Q 009289 359 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKC 402 (538)
Q Consensus 359 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~ 402 (538)
-+|++++-.|||+| +++|+||.+|.|+-.+...
T Consensus 10 L~~dL~v~~ild~L-----------~~~gvlt~~~~e~I~~~~t 42 (86)
T cd08323 10 LEKDIKTSYIMDHM-----------ISDGVLTLDEEEKVKSKAT 42 (86)
T ss_pred HHHHccHHHHHHHH-----------HhcCCCCHHHHHHHHcCCC
Confidence 56888866699986 7899999999999887653
No 45
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=32.11 E-value=40 Score=27.06 Aligned_cols=18 Identities=33% Similarity=0.462 Sum_probs=15.5
Q ss_pred cCChhHHhHHHHhhhcCC
Q 009289 470 KLTEPEVRYLEKVVLFGS 487 (538)
Q Consensus 470 ~L~E~EE~yL~KlvL~~~ 487 (538)
.||+.+|.||+-.-.+..
T Consensus 1 ~Lt~~~e~YL~~Iy~l~~ 18 (60)
T PF01325_consen 1 MLTESEEDYLKAIYELSE 18 (60)
T ss_dssp TCSCHHHHHHHHHHHHHH
T ss_pred CCCcHHHHHHHHHHHHHc
Confidence 489999999998887775
No 46
>PRK00523 hypothetical protein; Provisional
Probab=31.21 E-value=31 Score=29.82 Aligned_cols=23 Identities=43% Similarity=0.674 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhhhhhhhhcccchh
Q 009289 86 LFGLWLGLSIAGSVLVGVGYGFFT 109 (538)
Q Consensus 86 ~l~LW~vlgI~GSvl~G~gYGFf~ 109 (538)
-+.||.+++|++ +++|+.-|||.
T Consensus 3 ~~~l~I~l~i~~-li~G~~~Gffi 25 (72)
T PRK00523 3 AIGLALGLGIPL-LIVGGIIGYFV 25 (72)
T ss_pred hHHHHHHHHHHH-HHHHHHHHHHH
Confidence 357888888888 88888888885
No 47
>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=29.90 E-value=1.4e+02 Score=28.83 Aligned_cols=37 Identities=14% Similarity=0.227 Sum_probs=30.6
Q ss_pred hchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 009289 455 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 491 (538)
Q Consensus 455 ff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~~r 491 (538)
+.+++.-+=.++++++++++|=.||+-+++++.|...
T Consensus 113 ~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~g 149 (213)
T cd06953 113 VVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDG 149 (213)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCC
Confidence 3566666667899999999999999999999987543
No 48
>PRK13511 6-phospho-beta-galactosidase; Provisional
Probab=29.70 E-value=71 Score=34.80 Aligned_cols=54 Identities=11% Similarity=0.212 Sum_probs=37.6
Q ss_pred cCCCceeecCCceeccc-CCCCccc---------hhhhchhHH------HHHHHHH--------hccCChhHHhHHHH
Q 009289 428 AGSGGLLLPDSVEITHL-NRPNNKL---------LDWFFNPIM------VLKEQIS--------VLKLTEPEVRYLEK 481 (538)
Q Consensus 428 anS~GlllsD~~EiT~~-NrPkdr~---------fDWff~Pll------viKEQIk--------~~~L~E~EE~yL~K 481 (538)
.+..|+.+....-.... +.|+|.. ..||.+|+. .|+++++ .+++|++|.+.+++
T Consensus 209 ~g~IGi~~~~~~~~P~~~~~~~d~~aa~~~~~~~~~~f~dp~~~G~Yp~~~~~~~~~~~~~~~~~l~~t~~d~~~ik~ 286 (469)
T PRK13511 209 KGEIGVVHALPTKYPIDPDNPEDVRAAELEDIIHNKFILDATYLGYYSEETMEGVNHILEANGGSLDIRDEDFEILKA 286 (469)
T ss_pred CCeEEEEecCceEeeCCCCCHHHHHHHHHHHHHhhhcccchhhCCCCCHHHHHHHHHhhhhcCCCCCCCHHHHHHHhc
Confidence 35778888877444545 7787754 479999985 5677664 24688888887764
No 49
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=29.67 E-value=57 Score=28.41 Aligned_cols=33 Identities=9% Similarity=0.129 Sum_probs=27.4
Q ss_pred hhhhhhhHHHHHHHHHHHhhhhhhhhccCCCChhhHHHHHHhcC
Q 009289 359 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKC 402 (538)
Q Consensus 359 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~ 402 (538)
-.+++++=.+||+| .++|++|.+|.||-.+...
T Consensus 12 L~~~l~~~~l~d~L-----------~q~~VLt~~d~EeI~~~~t 44 (86)
T cd08785 12 LTRKINPSRLTPYL-----------RQCKVLDEQDEEEVLSSPR 44 (86)
T ss_pred HHHHhhHHHHHHHH-----------HhcCCCCHHHHHHHhCCCc
Confidence 45778888888876 7889999999999988664
No 50
>PRK13735 conjugal transfer mating pair stabilization protein TraG; Provisional
Probab=28.61 E-value=90 Score=37.56 Aligned_cols=68 Identities=19% Similarity=0.167 Sum_probs=46.4
Q ss_pred Eeeccc-----ceeeheeeehccccCChhhH--------------HHHhhhhhHHHHHHHHHHHhhhhhhhhcccchhhH
Q 009289 51 IGLFPA-----HVAWTVYTLVKTNRLDIPLK--------------VAIFFPLPALFGLWLGLSIAGSVLVGVGYGFFTPW 111 (538)
Q Consensus 51 lgLwP~-----Hv~WTyY~i~rtkr~g~~lK--------------~~~li~lP~~l~LW~vlgI~GSvl~G~gYGFf~P~ 111 (538)
|.|||. |.+-++| .++.=.+.+|= ++-.+++-+|++=|-++=-.++++..++++|-.+.
T Consensus 367 LqlWppLfAIIN~~m~~~--~~~~G~~~tLs~~~~i~~~~sdia~~aGyL~msIP~LA~~ivkG~~~~~ssl~~~l~~~~ 444 (942)
T PRK13735 367 LQSWPLLYAILNSAMTFY--AKQNGAPVVLSELSQIQLKYSDLASTAGYLSMMIPPLSWGMVKGLGAGFSSVYSHFASSA 444 (942)
T ss_pred HHHHHHHHHHHHHHHHHH--HhhcCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 567875 6667888 34433322221 23345667888889888889999999999998877
Q ss_pred HhHhhhhcc
Q 009289 112 VSAFEAFRN 120 (538)
Q Consensus 112 ~aTFeAvge 120 (538)
.++=++.+.
T Consensus 445 ~saa~~aAs 453 (942)
T PRK13735 445 ISPTASAAS 453 (942)
T ss_pred hhHHHHHHH
Confidence 776655543
No 51
>PF14946 DUF4501: Domain of unknown function (DUF4501)
Probab=27.55 E-value=1.3e+02 Score=29.85 Aligned_cols=21 Identities=33% Similarity=0.667 Sum_probs=18.3
Q ss_pred ccccCCCcCCCcccccCCCCC
Q 009289 299 LYLREGTILPKPRYRQKKVHS 319 (538)
Q Consensus 299 LyLrEGScfPRP~YRK~~~~~ 319 (538)
.||+.-+=+|+--||+|+...
T Consensus 112 FYLKrs~kLP~vfYrrnKA~a 132 (180)
T PF14946_consen 112 FYLKRSSKLPHVFYRRNKAPA 132 (180)
T ss_pred eeecccccCCccccccccccc
Confidence 699999999999999997633
No 52
>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei
Probab=27.50 E-value=73 Score=28.39 Aligned_cols=32 Identities=16% Similarity=0.209 Sum_probs=27.0
Q ss_pred hhhhhhhHHHHHHHHHHHhhhhhhhhccCCCChhhHHHHHHhc
Q 009289 359 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAK 401 (538)
Q Consensus 359 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k 401 (538)
-++++++-++||++ ++.|++|.+|+|+-...+
T Consensus 15 LV~~L~~~~v~d~l-----------l~~~ilT~~d~e~I~aa~ 46 (88)
T cd08819 15 LVDKMKTRDVCDKC-----------LEQGLLTEEDRNRIEAAT 46 (88)
T ss_pred HHHHhhHHHHHHHH-----------HhcCCCCHHHHHHHHHhc
Confidence 35678889999986 678999999999998863
No 53
>PF15452 NYAP_C: Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter
Probab=25.39 E-value=20 Score=37.94 Aligned_cols=21 Identities=48% Similarity=0.638 Sum_probs=18.7
Q ss_pred HhhHHHHHHHHhcCccccccC
Q 009289 518 YELYLHLIEVIERGKTLCTRI 538 (538)
Q Consensus 518 Lqg~~~~~~~~~~~~~~~~~~ 538 (538)
+|+=.||+|||||-.+||..|
T Consensus 240 ~~rD~klLEvIERKRclCkEI 260 (308)
T PF15452_consen 240 RERDGKLLEVIERKRCLCKEI 260 (308)
T ss_pred ccccchHHHHHHHHHHHHHHH
Confidence 678899999999999999765
No 54
>COG3790 Predicted membrane protein [Function unknown]
Probab=25.02 E-value=66 Score=29.22 Aligned_cols=35 Identities=31% Similarity=0.620 Sum_probs=29.9
Q ss_pred hhhhhHHHHHHHHHHHhhhhhhhhcc--------cchhhHHhH
Q 009289 80 FFPLPALFGLWLGLSIAGSVLVGVGY--------GFFTPWVSA 114 (538)
Q Consensus 80 li~lP~~l~LW~vlgI~GSvl~G~gY--------GFf~P~~aT 114 (538)
.=.+|++..+..+-++.-+++-|+|+ |+|+|+.|-
T Consensus 43 ~~s~~a~~~llmiWavca~~IhGVGFrpr~~~wqg~FsPlla~ 85 (97)
T COG3790 43 TSSLEAWHGLLMIWAVCAGVIHGVGFRPRSVLWQGIFSPLLAD 85 (97)
T ss_pred hcCchHHHHHHHHHHHHHHHHhcccCchHHHHHHHHhhhHHHH
Confidence 34578888888888999999999997 899999874
No 55
>PF07127 Nodulin_late: Late nodulin protein; InterPro: IPR009810 This family consists of several plant specific late nodulin sequences which are homologous to the Pisum sativum (Garden pea) ENOD3 protein. ENOD3 is expressed in the late stages of root nodule formation and contains two pairs of cysteine residues toward the proteins C terminus which may be involved in metal-binding [].; GO: 0046872 metal ion binding, 0009878 nodule morphogenesis
Probab=24.01 E-value=65 Score=25.36 Aligned_cols=21 Identities=24% Similarity=0.368 Sum_probs=17.2
Q ss_pred hhhhHHHHHHHHHHHHHHHhh
Q 009289 8 QGWLKIIYVGFAFCLAFFLGA 28 (538)
Q Consensus 8 ~~~~~~~y~~f~F~~l~~LG~ 28 (538)
..-+|+.|++..|++||+...
T Consensus 2 a~ilKFvY~mIiflslflv~~ 22 (54)
T PF07127_consen 2 AKILKFVYAMIIFLSLFLVVT 22 (54)
T ss_pred ccchhhHHHHHHHHHHHHhhc
Confidence 345899999999999988754
No 56
>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=22.86 E-value=2.1e+02 Score=28.12 Aligned_cols=36 Identities=25% Similarity=0.188 Sum_probs=31.5
Q ss_pred hhchhHHHHHHHHHhccCChhHHhHHHHhhhcCCCc
Q 009289 454 WFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 489 (538)
Q Consensus 454 Wff~PllviKEQIk~~~L~E~EE~yL~KlvL~~~d~ 489 (538)
.+.+++.-+=.++++++++++|=.||+-++|++.|.
T Consensus 115 ~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~ 150 (222)
T cd06951 115 ADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVP 150 (222)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCC
Confidence 346778778888999999999999999999999874
No 57
>cd08810 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by asso
Probab=22.58 E-value=95 Score=27.14 Aligned_cols=34 Identities=6% Similarity=0.020 Sum_probs=27.5
Q ss_pred hhhhhhhHHHHHHHHHHHhhhhhhhhccCCCChhhHHHHHHhcCC
Q 009289 359 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKCV 403 (538)
Q Consensus 359 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~~ 403 (538)
-.+++++=.+||+| .++|++|.+|.||-.+...+
T Consensus 12 L~~~L~~~~l~d~L-----------~s~~ILt~~d~EeI~~~~t~ 45 (84)
T cd08810 12 LCDKIIADRHFDYL-----------RSKRILTRDDCEEISCRTTS 45 (84)
T ss_pred HHHHhcHHHHHHHH-----------HHcCCCCHHHHHHHhccCCc
Confidence 45777888888876 68899999999999886643
No 58
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=22.55 E-value=51 Score=33.91 Aligned_cols=48 Identities=25% Similarity=0.223 Sum_probs=25.9
Q ss_pred hhccceeeEEeecccceeeheeeehccccCChhhHHHHhhhhhHHHHHHHHHHHhh
Q 009289 42 LIIGNVGVIIGLFPAHVAWTVYTLVKTNRLDIPLKVAIFFPLPALFGLWLGLSIAG 97 (538)
Q Consensus 42 i~iGnsaVIlgLwP~Hv~WTyY~i~rtkr~g~~lK~~~li~lP~~l~LW~vlgI~G 97 (538)
.+.|-|+|+-||.=. .|.+.. |.+..+..+ --.+-+..++|+++|..+
T Consensus 196 ~~gGaSGvVygL~g~--~~~~~~--~~p~~~~~l----p~~~~~f~llwl~~g~~~ 243 (276)
T PRK10907 196 WFGGLSGVVYALMGY--VWLRGE--RDPQSGIYL----PRGLIAFALLWLVAGYFD 243 (276)
T ss_pred hhhHHHHHHHHHHHH--HHHHhc--cccccchhh----hHHHHHHHHHHHHHHHHH
Confidence 357999999998763 343331 222222221 112234567788866654
No 59
>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=22.37 E-value=1.2e+02 Score=34.45 Aligned_cols=215 Identities=24% Similarity=0.285 Sum_probs=115.4
Q ss_pred HHHhhhhcCCCCcccccc--ccchhH-HHHHHHHHHHHHHHHHHHHHHhhhhheeEEEeechhhhhhHHHHHHHhh----
Q 009289 217 RLLHDLISREGPFLETAC--IPIAGL-TILLWPIIVIGSIVIAIFSSIFIGLYGSVVVYQERSFRRGVAYVIAMVA---- 289 (538)
Q Consensus 217 RLl~DLIgREGPFLET~C--VPfAGL-aIlLWPl~Vvgavl~aiisS~flG~yaaVVvYQE~Sf~~GL~Yvva~Va---- 289 (538)
|.++...|..-=..||-- .|..|- .-+.=|+-+ +...|+=.-+-+.+||.+ .|+..-+--+--+-|
T Consensus 307 ~yi~r~LGqPSLiREsSrg~~pw~gsls~~k~~i~~-----~~~~s~~gk~pl~~ViL~--psLe~Rie~lA~aTaNTK~ 379 (630)
T KOG0742|consen 307 RYIERRLGQPSLIRESSRGRFPWIGSLSALKHPIQG-----SRSASSRGKDPLEGVILH--PSLEKRIEDLAIATANTKK 379 (630)
T ss_pred HHHHHHcCCchhhhhhccccCCCcccHHHHhchhhh-----hHhhhhcCCCCcCCeecC--HHHHHHHHHHHHHhccccc
Confidence 344555555444445543 465553 334445544 233455566667777765 455554444332222
Q ss_pred hhhhcccccccccCCC---cCCCcccccCCCCCCCCC--CCCCCcccCCcccCCCCCCcccccccccccccHHHhhhhhh
Q 009289 290 EFDEYTNDWLYLREGT---ILPKPRYRQKKVHSSSEL--PVGGNQVAGGKFTSASADAPAMLMPSLAHSRSVREAIQEVK 364 (538)
Q Consensus 290 ~FDEYtND~LyLrEGS---cfPRP~YRK~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~p~l~~s~S~k~~iqe~k 364 (538)
-=-.|-|=++|=++|| -|-|---|| |+. .-- .||.- .+-.+ +.. -|
T Consensus 380 h~apfRNilfyGPPGTGKTm~ArelAr~------SGlDYA~m----TGGDV--APlG~---------------qaV--Tk 430 (630)
T KOG0742|consen 380 HQAPFRNILFYGPPGTGKTMFARELARH------SGLDYAIM----TGGDV--APLGA---------------QAV--TK 430 (630)
T ss_pred ccchhhheeeeCCCCCCchHHHHHHHhh------cCCceehh----cCCCc--cccch---------------HHH--HH
Confidence 1235677888888886 333333333 222 000 01110 00000 011 14
Q ss_pred hHHHHHHHHHHHhhhhhhhhccCCCChhhHHHHHHhcCCCCcceEeeccchHHHHHHHHHhhhcCCCceeecCCceeccc
Q 009289 365 MVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSVEITHL 444 (538)
Q Consensus 365 ~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~~~~~k~i~vgLPAyslL~~LL~SaKanS~GlllsD~~EiT~~ 444 (538)
+-||+||-=|| .+|-.| .|.- -+.++-..+++ .+|= ---|-|++||.-.-..|.-++| +-..
T Consensus 431 iH~lFDWakkS--~rGLll----FIDE--ADAFLceRnkt---ymSE--aqRsaLNAlLfRTGdqSrdivL-----vlAt 492 (630)
T KOG0742|consen 431 IHKLFDWAKKS--RRGLLL----FIDE--ADAFLCERNKT---YMSE--AQRSALNALLFRTGDQSRDIVL-----VLAT 492 (630)
T ss_pred HHHHHHHHhhc--ccceEE----Eehh--hHHHHHHhchh---hhcH--HHHHHHHHHHHHhcccccceEE-----Eecc
Confidence 56788887554 233322 1333 34555555542 2332 3457899999998888877766 4578
Q ss_pred CCCCccchhhhchhHHHHHHHHHhccCChhHHh------HHHHhhhcCCCcc
Q 009289 445 NRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVR------YLEKVVLFGSTTE 490 (538)
Q Consensus 445 NrPkdr~fDWff~PllviKEQIk~~~L~E~EE~------yL~KlvL~~~d~~ 490 (538)
|||.| |||-.+-= =||+-.--|--+||+ ||.|.++...+..
T Consensus 493 Nrpgd--lDsAV~DR---ide~veFpLPGeEERfkll~lYlnkyi~~~~~~~ 539 (630)
T KOG0742|consen 493 NRPGD--LDSAVNDR---IDEVVEFPLPGEEERFKLLNLYLNKYILKPATSG 539 (630)
T ss_pred CCccc--hhHHHHhh---hhheeecCCCChHHHHHHHHHHHHHHhcCcCCCC
Confidence 99998 78865421 134445566667775 8999998877765
No 60
>PRK00523 hypothetical protein; Provisional
Probab=22.04 E-value=1.2e+02 Score=26.35 Aligned_cols=26 Identities=23% Similarity=0.240 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhh
Q 009289 239 GLTILLWPIIVIGSIVIAIFSSIFIG 264 (538)
Q Consensus 239 GLaIlLWPl~Vvgavl~aiisS~flG 264 (538)
|+++-+|=+.++.+.+++.+..||++
T Consensus 1 ~~~~~l~I~l~i~~li~G~~~Gffia 26 (72)
T PRK00523 1 GLAIGLALGLGIPLLIVGGIIGYFVS 26 (72)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777777777777777666666654
No 61
>COG2981 CysZ Uncharacterized protein involved in cysteine biosynthesis [Amino acid transport and metabolism]
Probab=21.83 E-value=93 Score=32.33 Aligned_cols=31 Identities=35% Similarity=0.567 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHH---------HHHHHHHHHHhhhhheeEE
Q 009289 240 LTILLWPIIVIG---------SIVIAIFSSIFIGLYGSVV 270 (538)
Q Consensus 240 LaIlLWPl~Vvg---------avl~aiisS~flG~yaaVV 270 (538)
|..++||+++++ |-++++++|+|.|+.|=+|
T Consensus 68 Ls~v~~~la~L~lll~~~~lfs~v~~~IAapFng~lAEkv 107 (250)
T COG2981 68 LSYLLWILAVLLLLLVFAFLFSTVANLIAAPFNGLLAEKV 107 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHH
Confidence 455677776655 5567788888888877665
No 62
>PLN00151 potassium transporter; Provisional
Probab=21.14 E-value=1.2e+02 Score=36.23 Aligned_cols=25 Identities=24% Similarity=0.189 Sum_probs=19.9
Q ss_pred hhhhheeEEEeechhhhhhHHHHHHH
Q 009289 262 FIGLYGSVVVYQERSFRRGVAYVIAM 287 (538)
Q Consensus 262 flG~yaaVVvYQE~Sf~~GL~Yvva~ 287 (538)
.+++.+-++.||. |-..|=||=+|.
T Consensus 479 mv~~i~v~l~F~~-s~~l~~AYGiAV 503 (852)
T PLN00151 479 LVMCLVVVCSFRS-ITDIGNAYGIAE 503 (852)
T ss_pred HHHHHhheeeecC-HHHHHHHhhhhh
Confidence 4788899999997 568888987664
No 63
>PLN00149 potassium transporter; Provisional
Probab=20.28 E-value=1.3e+02 Score=35.61 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=20.1
Q ss_pred hhhhheeEEEeechhhhhhHHHHHHH
Q 009289 262 FIGLYGSVVVYQERSFRRGVAYVIAM 287 (538)
Q Consensus 262 flG~yaaVVvYQE~Sf~~GL~Yvva~ 287 (538)
++|+.+-++.||. |-+.|=||=+|.
T Consensus 406 mv~~i~vv~~F~~-s~~l~~AYGiAV 430 (779)
T PLN00149 406 MLLCLAVTVGFRD-TKRLGNASGLAV 430 (779)
T ss_pred HHHHHhheeEecC-hHHHHHHhhhhh
Confidence 4788889999997 568899997764
No 64
>PHA03385 IX capsid protein IX,hexon associated protein IX; Provisional
Probab=20.00 E-value=1.1e+02 Score=29.26 Aligned_cols=23 Identities=13% Similarity=0.270 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHhhHHHHHHHHhc
Q 009289 508 AAQIQGISRRYELYLHLIEVIER 530 (538)
Q Consensus 508 rAqLqai~RRLqg~~~~~~~~~~ 530 (538)
-|||++++||||...+-++-+.+
T Consensus 106 laqLealsqqL~~ls~qv~~L~~ 128 (135)
T PHA03385 106 LAQLEALSQQLQELSQQVAQLRE 128 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Confidence 58999999999999988776654
Done!