Query 014531
Match_columns 423
No_of_seqs 45 out of 47
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 06:03:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014531.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014531hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06941 NR_LBD_DmE78_like The 94.3 0.37 8E-06 43.9 9.5 112 274-398 49-160 (195)
2 smart00430 HOLI Ligand binding 93.7 0.75 1.6E-05 38.2 9.6 77 269-345 34-112 (163)
3 cd06940 NR_LBD_REV_ERB The lig 92.3 0.87 1.9E-05 41.9 8.8 103 286-400 70-172 (189)
4 cd06944 NR_LBD_Ftz-F1_like The 91.6 1.9 4.1E-05 41.0 10.4 115 272-398 83-201 (237)
5 cd06931 NR_LBD_HNF4_like The l 91.5 3.5 7.5E-05 38.2 11.7 115 271-399 76-191 (222)
6 cd07069 NR_LBD_Lrh-1 The ligan 90.8 2.6 5.6E-05 40.5 10.5 115 272-397 85-202 (241)
7 cd06937 NR_LBD_RAR The ligand 90.2 2.4 5.3E-05 40.3 9.7 98 287-399 97-197 (231)
8 cd06945 NR_LBD_Nurr1_like The 89.9 1.7 3.8E-05 41.6 8.5 107 275-398 89-200 (239)
9 cd06943 NR_LBD_RXR_like The li 89.4 5.1 0.00011 36.6 10.9 116 272-399 75-190 (207)
10 cd06938 NR_LBD_EcR The ligand 89.2 4 8.6E-05 38.6 10.3 108 278-398 89-197 (231)
11 cd06930 NR_LBD_F2 Ligand-bindi 89.1 7.3 0.00016 33.6 11.1 117 270-398 42-159 (165)
12 cd07075 NR_LBD_MR Ligand bindi 89.0 4.2 9.2E-05 39.8 10.5 112 279-399 80-193 (248)
13 cd06935 NR_LBD_TR The ligand b 88.3 2.3 4.9E-05 40.8 8.1 98 286-398 110-210 (243)
14 PF00104 Hormone_recep: Ligand 87.9 14 0.00031 31.9 12.1 157 223-399 24-184 (203)
15 cd07076 NR_LBD_GR Ligand bindi 86.1 7.2 0.00016 38.2 10.2 109 279-399 80-193 (247)
16 cd06948 NR_LBD_COUP-TF Ligand 85.8 5.9 0.00013 37.6 9.3 110 272-398 75-190 (236)
17 cd06950 NR_LBD_Tlx_PNR_like Th 84.9 11 0.00024 35.1 10.4 112 274-398 73-184 (206)
18 cd06942 NR_LBD_Sex_1_like The 83.7 7.9 0.00017 35.4 8.9 150 223-398 2-161 (191)
19 cd06929 NR_LBD_F1 Ligand-bindi 82.7 9.3 0.0002 33.5 8.6 115 272-399 47-161 (174)
20 cd07070 NR_LBD_SF-1 The ligand 82.7 13 0.00027 35.7 10.1 113 274-398 85-201 (237)
21 cd06157 NR_LBD The ligand bind 82.2 21 0.00046 29.8 10.2 121 270-399 41-163 (168)
22 cd06932 NR_LBD_PPAR The ligand 81.4 12 0.00027 36.4 9.7 100 284-398 117-222 (259)
23 cd06949 NR_LBD_ER Ligand bindi 81.3 14 0.0003 35.3 9.9 117 274-398 79-199 (235)
24 cd06947 NR_LBD_GR_Like Ligand 80.5 19 0.00042 35.0 10.6 116 274-398 75-192 (246)
25 cd07071 NR_LBD_Nurr1 The ligan 80.1 21 0.00047 34.4 10.7 102 285-398 98-199 (238)
26 cd06954 NR_LBD_LXR The ligand 79.1 9.2 0.0002 36.0 7.8 108 280-398 95-202 (236)
27 cd07068 NR_LBD_ER_like The lig 74.9 27 0.00059 32.7 9.6 73 271-345 71-143 (221)
28 cd07348 NR_LBD_NGFI-B The liga 74.4 25 0.00055 34.0 9.5 112 274-398 88-199 (238)
29 PF09862 DUF2089: Protein of u 73.6 3.9 8.4E-05 36.4 3.5 48 325-400 32-79 (113)
30 cd07074 NR_LBD_PR Ligand bindi 73.6 55 0.0012 32.2 11.7 69 274-343 75-144 (248)
31 cd07072 NR_LBD_DHR38_like Liga 72.4 28 0.00062 33.7 9.3 112 274-398 89-200 (239)
32 cd07073 NR_LBD_AR Ligand bindi 71.3 52 0.0011 32.1 10.8 110 280-399 81-193 (246)
33 cd06933 NR_LBD_VDR The ligand 69.4 32 0.00069 33.0 8.8 78 311-399 121-200 (238)
34 cd06946 NR_LBD_ERR The ligand 63.0 66 0.0014 30.1 9.4 72 272-345 72-143 (221)
35 cd06934 NR_LBD_PXR_like The li 62.7 22 0.00047 33.8 6.3 74 311-398 117-195 (226)
36 cd07349 NR_LBD_SHP The ligand 57.6 35 0.00076 32.6 6.8 71 317-398 119-189 (222)
37 cd07350 NR_LBD_Dax1 The ligand 57.6 52 0.0011 31.7 7.9 75 313-398 127-201 (232)
38 cd06952 NR_LBD_TR2_like The li 53.5 41 0.00089 31.4 6.4 73 315-398 115-187 (222)
39 cd06936 NR_LBD_Fxr The ligand 53.2 54 0.0012 31.0 7.2 80 308-398 112-191 (221)
40 cd06951 NR_LBD_Dax1_like The l 49.5 52 0.0011 31.3 6.5 77 310-398 115-191 (222)
41 cd06939 NR_LBD_ROR_like The li 48.6 43 0.00094 32.3 5.8 47 312-366 130-176 (241)
42 PF04911 ATP-synt_J: ATP synth 48.5 22 0.00049 28.3 3.2 18 99-116 9-26 (54)
43 cd06953 NR_LBD_DHR4_like The l 45.9 84 0.0018 29.5 7.2 74 311-398 113-189 (213)
44 KOG2511 Nicotinic acid phospho 45.8 15 0.00033 38.7 2.5 22 318-339 53-77 (420)
45 smart00054 EFh EF-hand, calciu 44.1 24 0.00051 20.3 2.2 27 225-256 2-28 (29)
46 PRK00523 hypothetical protein; 44.0 31 0.00068 28.9 3.5 26 95-120 1-26 (72)
47 cd08323 CARD_APAF1 Caspase act 41.6 29 0.00063 29.2 3.1 33 215-258 10-42 (86)
48 COG3413 Predicted DNA binding 41.4 1.6E+02 0.0035 27.5 8.3 58 326-404 155-212 (215)
49 PLN00151 potassium transporter 37.3 45 0.00097 38.6 4.6 26 118-144 479-504 (852)
50 COG2981 CysZ Uncharacterized p 36.6 37 0.0008 34.2 3.4 31 96-126 68-107 (250)
51 PF14946 DUF4501: Domain of un 36.4 82 0.0018 30.4 5.5 21 155-175 112-132 (180)
52 PLN00149 potassium transporter 35.4 50 0.0011 37.9 4.6 25 118-143 406-430 (779)
53 cd08785 CARD_CARD9-like Caspas 32.6 50 0.0011 27.9 3.1 33 215-258 12-44 (86)
54 cd08819 CARD_MDA5_2 Caspase ac 32.2 57 0.0012 28.2 3.4 32 215-257 15-46 (88)
55 PRK13511 6-phospho-beta-galact 28.9 77 0.0017 33.6 4.5 64 274-337 189-286 (469)
56 TIGR00794 kup potassium uptake 26.9 99 0.0022 35.1 5.1 26 118-144 373-398 (688)
57 cd04371 DEP DEP domain, named 26.6 32 0.00069 26.8 0.9 31 219-249 29-67 (81)
58 PF15052 TMEM169: TMEM169 prot 25.8 42 0.00091 31.0 1.7 87 51-162 23-109 (133)
59 cd08810 CARD_BCL10 Caspase act 25.5 81 0.0018 26.7 3.2 34 215-259 12-45 (84)
60 PLN00148 potassium transporter 24.1 79 0.0017 36.4 3.7 25 118-143 402-426 (785)
61 PRK10535 macrolide transporter 23.7 55 0.0012 35.7 2.4 25 100-124 609-633 (648)
62 cd08326 CARD_CASP9 Caspase act 23.5 91 0.002 26.0 3.1 33 215-258 12-44 (84)
63 PF14223 UBN2: gag-polypeptide 23.2 1.2E+02 0.0025 25.3 3.8 83 315-402 25-110 (119)
64 COG2928 Uncharacterized conser 23.0 2.3E+02 0.0049 28.3 6.2 63 69-147 1-69 (222)
65 TIGR02978 phageshock_pspC phag 22.1 87 0.0019 28.1 2.9 44 351-394 75-121 (121)
66 PLN00150 potassium ion transpo 22.0 1.2E+02 0.0025 35.1 4.5 25 118-143 419-443 (779)
67 KOG0742 AAA+-type ATPase [Post 22.0 1.3E+02 0.0028 33.3 4.6 221 73-353 307-546 (630)
68 cd01014 nicotinamidase_related 21.7 1.7E+02 0.0038 25.6 4.7 49 245-295 85-134 (155)
69 PF01788 PsbJ: PsbJ; InterPro 21.3 1.1E+02 0.0023 23.4 2.7 26 100-125 10-36 (40)
70 PF14789 THDPS_M: Tetrahydrodi 21.2 34 0.00074 25.8 0.2 33 350-385 5-40 (41)
71 PF01325 Fe_dep_repress: Iron 20.8 89 0.0019 24.3 2.4 18 326-343 1-18 (60)
No 1
>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=94.29 E-value=0.37 Score=43.94 Aligned_cols=112 Identities=16% Similarity=0.220 Sum_probs=72.6
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccC
Q 014531 274 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDN 353 (423)
Q Consensus 274 lL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~ 353 (423)
+|+ +-++...+++++.+.||..++..+-......+ +.+++.-+=++++.++++++|=.||+-++|++.|...
T Consensus 49 ll~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~g------ 120 (195)
T cd06941 49 LVR-ISRLINSKSGSITFDDGISISRQQLDIIYDSD-FVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIG------ 120 (195)
T ss_pred HHH-HHHHHcCCCCeEEecCCeEeeHHHHHhccchH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCC------
Confidence 444 44677778888999999776643321100012 4567777888999999999999999999999977533
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 354 GGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 354 ~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
.-..+.+.+.|= .+..=|+.-+. +++|....||-+++..|
T Consensus 121 --l~~~~~Ve~lq~-~~~~aL~~~i~--~~~p~~~~rf~~Ll~~L 160 (195)
T cd06941 121 --LSEPKKVAILQD-RVLEALKVQVS--RNRPAEAQLFASLLMKI 160 (195)
T ss_pred --CCCHHHHHHHHH-HHHHHHHHHHH--hhCCCcccHHHHHHHHh
Confidence 333445555441 11222333333 46788888999887644
No 2
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=93.71 E-value=0.75 Score=38.24 Aligned_cols=77 Identities=22% Similarity=0.248 Sum_probs=58.7
Q ss_pred cchHHHHHHHHHhhhcCCCceeecCCceecccCCC--CccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCc
Q 014531 269 LPCYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRP--NNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 345 (423)
Q Consensus 269 LPayslL~~LL~SaKa~S~Glll~D~~EiT~~NrP--kd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~ 345 (423)
-+.+.+|...-+|.|.+...++..||+.+...... .......+...+.-+-+.++.+++|++|=.||.-++++..|.
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 45788899899999998887777887766543322 134455566666677888999999999999999999998643
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=92.33 E-value=0.87 Score=41.85 Aligned_cols=103 Identities=18% Similarity=0.263 Sum_probs=69.5
Q ss_pred CCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHH
Q 014531 286 SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAA 365 (423)
Q Consensus 286 S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrA 365 (423)
...+.+.||..++...-+...+-+ +.+++.-+=++++.++++++|=.||+-++|++.|.. |+...+.|++.
T Consensus 70 ~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~--------~L~~~~~Ve~l 140 (189)
T cd06940 70 ERSVTFLSGQKYSVDDLHSMGAGD-LLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRS--------GLENVNLVEAL 140 (189)
T ss_pred CCeEEecCCcEEcHHHHHHcCcHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCc--------CCCCHHHHHHH
Confidence 344777788766543322222323 345566778999999999999999999999998742 35556677777
Q ss_pred HHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHHH
Q 014531 366 QIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALVS 400 (423)
Q Consensus 366 qLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~ 400 (423)
| +.+..-|+..+. .++|.-..||-.++..|-.
T Consensus 141 q-~~~~~aL~~~~~--~~~p~~~~rf~kLL~~L~~ 172 (189)
T cd06940 141 Q-ETLIRALRTLIA--KNHPNEPSIFTKLLLKLPD 172 (189)
T ss_pred H-HHHHHHHHHHHH--HhCCCCccHHHHHHHHHHH
Confidence 7 334444555544 3478888899998776643
No 4
>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=91.64 E-value=1.9 Score=41.00 Aligned_cols=115 Identities=16% Similarity=0.279 Sum_probs=74.0
Q ss_pred HHHHHHHHHhhhcC-CCceeecCCceecccCCCC---ccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccc
Q 014531 272 YSFLQTLLYSIKAG-SGGLLLPDSVEITHLNRPN---NKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 347 (423)
Q Consensus 272 yslL~~LL~SaKa~-S~Glll~D~~EiT~~NrPk---d~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r 347 (423)
+.+|...-+|+..+ ++.+++.||..+....-+. ....+ +.+.+.-+=..++.+++|++|=.||+-++|++.|...
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 7778999998776554222 11223 3455666667899999999999999999999987533
Q ss_pred cccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 348 MEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 348 ~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
+...+.|.+.| +.+..=|+.-+. .++|..--||-+++-.|
T Consensus 162 --------L~~~~~Ve~~q-~~~~~aL~~y~~--~~~~~~~~Rf~~LL~~L 201 (237)
T cd06944 162 --------LENRQLVESVQ-EQVNAALLDYTL--CNYPQQTDKFGQLLLRL 201 (237)
T ss_pred --------CCCHHHHHHHH-HHHHHHHHHHHH--hhCCCCccHHHHHHHHh
Confidence 33334444443 222333443333 45666667888776543
No 5
>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=91.46 E-value=3.5 Score=38.24 Aligned_cols=115 Identities=17% Similarity=0.196 Sum_probs=73.0
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHH-HHHHHHHhccCChhHHHHHHHhhhcCCCccccc
Q 014531 271 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIM-VLKEQISVLKLTEPEVRYLEKVVLFGSTTERME 349 (423)
Q Consensus 271 ayslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~Pll-vlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~ 349 (423)
.+.+|..--+|. .+.+++++.+|.-++..+-+ ..+-.. .++.+ -+-++++.+++|++|=.||+-+++++.|.....
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 45788999999866654433 222222 33332 466789999999999999999999987765433
Q ss_pred cccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 014531 350 AWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 399 (423)
Q Consensus 350 ~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 399 (423)
....+++.|=+ +..=|+..+. .+.|..-.||-+++..|.
T Consensus 153 --------~~~~i~~~r~~-~~~aL~~y~~--~~~~~~~~Rf~~LL~~l~ 191 (222)
T cd06931 153 --------DPQKIKRLRFQ-VQVSLEDYIN--DRQYDSRGRFGELLLLLP 191 (222)
T ss_pred --------CHHHHHHHHHH-HHHHHHHHHH--hcCCchhhHHHHHHHHHH
Confidence 23334333322 2233333443 346888889999887654
No 6
>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=90.80 E-value=2.6 Score=40.50 Aligned_cols=115 Identities=15% Similarity=0.237 Sum_probs=73.1
Q ss_pred HHHHHHHHHhhhcCCCc-eeecCCceecccCC-CCccc-hhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCcccc
Q 014531 272 YSFLQTLLYSIKAGSGG-LLLPDSVEITHLNR-PNNKL-LDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERM 348 (423)
Q Consensus 272 yslL~~LL~SaKa~S~G-lll~D~~EiT~~Nr-Pkd~~-fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 348 (423)
+.+|...-+|+-.+..+ +++.+|+.++.... +.... ++=+.+++.-+-.+++.++++++|=.||+-++|++.|...
T Consensus 85 llvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~g- 163 (241)
T cd07069 85 LLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKN- 163 (241)
T ss_pred HHHHHHHHHhhccCCCCeeEecCCCccCchhhhhhhhhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCC-
Confidence 34555556677665444 67788876654321 11111 3224466777888999999999999999999999987533
Q ss_pred ccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHH
Q 014531 349 EAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKA 397 (423)
Q Consensus 349 ~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~ 397 (423)
.-..+.|++.|= .+..-|+.-++ .++|.-..||-+++=.
T Consensus 164 -------L~~~~~Ve~lQe-~~~~aL~~yi~--~~~p~~~~Rf~kLLl~ 202 (241)
T cd07069 164 -------LENFQLVEGVQE-QVNAALLDYTM--CNYPQQTEKFGQLLLR 202 (241)
T ss_pred -------CCCHHHHHHHHH-HHHHHHHHHHH--hcCCCchhHHHHHHHH
Confidence 334444555442 22234454444 4789999999877543
No 7
>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=90.16 E-value=2.4 Score=40.29 Aligned_cols=98 Identities=12% Similarity=0.239 Sum_probs=68.6
Q ss_pred CceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHH
Q 014531 287 GGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ 366 (423)
Q Consensus 287 ~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq 366 (423)
.-+++.+|..++..+-.+.. +.-+.+++.-+=++++.++++++|=.||+-++|++.|.. |+-..+.|++.|
T Consensus 97 ~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~--------gL~~~~~Ve~lQ 167 (231)
T cd06937 97 DTMTFSDGLTLNRTQMHNAG-FGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQ--------DLEEPDRVEKLQ 167 (231)
T ss_pred CeEEecCCceecHHHHhhcC-hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCc--------cCCCHHHHHHHH
Confidence 33667777665554433322 335678888899999999999999999999999998753 344555666666
Q ss_pred ---HHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 014531 367 ---IQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 399 (423)
Q Consensus 367 ---Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 399 (423)
++|+-+-+. .++|.-..||-.++-.|-
T Consensus 168 e~~~~aL~~yi~------~~~p~~p~rf~kLLl~Lp 197 (231)
T cd06937 168 EPLLEALKIYAR------KRRPDKPHMFPKMLMKIT 197 (231)
T ss_pred HHHHHHHHHHHH------hhCCCcccHHHHHHHHhH
Confidence 455544332 468888899998865543
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=89.94 E-value=1.7 Score=41.55 Aligned_cols=107 Identities=16% Similarity=0.259 Sum_probs=69.6
Q ss_pred HHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCC
Q 014531 275 LQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNG 354 (423)
Q Consensus 275 L~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~ 354 (423)
|..--+|... .+.+++.+|.-++.... ...+-+ +.++++-.=++++.++++++|..||+.++|++.|. .
T Consensus 89 L~~a~r~~~~-~~~l~~~~~~~~~~~~~-~~~~~~-~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~--------~ 157 (239)
T cd06945 89 LRLAYRSNPV-DGKLVFCNGLVLHRLQC-VRGFGE-WLDSILAFSSSLQSLLLDDISAFCCLALLLLITER--------H 157 (239)
T ss_pred HHHHHHhcCC-CCceEeeCCceecHHHH-HHhHHH-HHHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCc--------c
Confidence 3333344443 44477778876665542 223334 46888877789999999999999999999998764 2
Q ss_pred CCCChhHHHHHH---HHHHHHhhhhhhhhcccCc--hhhHhHHHHHHHH
Q 014531 355 GLLPEDALRAAQ---IQGISRRMIGLIRSVSKFP--TYRRRFRQVVKAL 398 (423)
Q Consensus 355 g~pp~d~vrrAq---Lqai~RRLqGI~~s~SR~P--T~RRrf~~lvK~L 398 (423)
|+-..+.|.+.| ++|+-..+ + .++| .-..||-.++-.|
T Consensus 158 gL~~~~~Ve~lQe~~~~aL~~y~----~--~~~p~~~~~~rf~kLLl~L 200 (239)
T cd06945 158 GLKEPKKVEELQNKIISCLRDHV----T--SNYPGQDKPNRLSKLLLKL 200 (239)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHH----H--HhCCCcccccHHHHHHHHh
Confidence 455556666666 44443333 2 3567 7777888775433
No 9
>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=89.43 E-value=5.1 Score=36.64 Aligned_cols=116 Identities=17% Similarity=0.218 Sum_probs=68.6
Q ss_pred HHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccc
Q 014531 272 YSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAW 351 (423)
Q Consensus 272 yslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~w 351 (423)
+.+|..--+|.. ..+|+++++|..++...-.+..+-+.+-..+--+-..++.+++|++|=.+|+-++|++.|...
T Consensus 75 ~~~l~~a~~s~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~---- 149 (207)
T cd06943 75 LLIAAFAHRSIA-VKDGILLATGLHLHRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKG---- 149 (207)
T ss_pred HHHHHHHHHccC-CCCeeEecCCceeccchhhhccchHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCC----
Confidence 445554445554 368899999977764433333333332222224667899999999999999999999976532
Q ss_pred cCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 014531 352 DNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 399 (423)
Q Consensus 352 d~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 399 (423)
+-..+.+.+.|= .+..=|+..+. .+.|.-..||-+++-.|-
T Consensus 150 ----L~~~~~v~~~q~-~~~~aL~~y~~--~~~~~~~~Rf~~LLl~L~ 190 (207)
T cd06943 150 ----LKSRQEVESLRE-KVYASLEEYCR--QKHPEQPGRFAKLLLRLP 190 (207)
T ss_pred ----CCCHHHHHHHHH-HHHHHHHHHHH--hhCCCcccHHHHHHHHHH
Confidence 222333333331 12222333332 346777778888775543
No 10
>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=89.24 E-value=4 Score=38.59 Aligned_cols=108 Identities=15% Similarity=0.214 Sum_probs=70.1
Q ss_pred HHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCC
Q 014531 278 LLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLL 357 (423)
Q Consensus 278 LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~p 357 (423)
+-++...+.++++..||...+..+-....+ .=+.+++.-+-++++.++++++|=.+|+-++|++ | | .|+-
T Consensus 89 ~a~~~~~~~~~~~f~~g~~~~~~~~~~~~~-~~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d--~------~~L~ 158 (231)
T cd06938 89 VARRYDAKTDSIVFANNQPYTRDSYRKAGM-GDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS-D--R------PGLL 158 (231)
T ss_pred HHHHhCCCCCeEEeeCCEEecHHHHhhcCH-HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcc-C--C------CCCC
Confidence 336677888889999998888755333322 2256677778899999999999999999999985 2 1 2343
Q ss_pred ChhHHHHHHHHHHHHhhhhhhhhcccCch-hhHhHHHHHHHH
Q 014531 358 PEDALRAAQIQGISRRMIGLIRSVSKFPT-YRRRFRQVVKAL 398 (423)
Q Consensus 358 p~d~vrrAqLqai~RRLqGI~~s~SR~PT-~RRrf~~lvK~L 398 (423)
..+.|.+.|= .+..-|+..+. .++|. -..||-+++-.|
T Consensus 159 ~~~~Ve~~Q~-~~~~aL~~y~~--~~~~~~~~~rf~kLL~~L 197 (231)
T cd06938 159 QPKKVEKIQE-IYLEALRAYVD--NRRPPSQRVIFAKLLSIL 197 (231)
T ss_pred CHHHHHHHHH-HHHHHHHHHHH--HhCCCCcccHHHHHHHHH
Confidence 4444544442 23334444443 34565 677888775444
No 11
>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=89.14 E-value=7.3 Score=33.57 Aligned_cols=117 Identities=20% Similarity=0.222 Sum_probs=74.1
Q ss_pred chHHHHHHHHHhhhcC-CCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCcccc
Q 014531 270 PCYSFLQTLLYSIKAG-SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERM 348 (423)
Q Consensus 270 PayslL~~LL~SaKa~-S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 348 (423)
+.+.+|..--+|.+.+ +.++..++|..+...+-.+....++ .+.+.-+=.+++.+++|++|=.+|+-+++++.|...
T Consensus 42 ~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~- 119 (165)
T cd06930 42 AELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAEL-VQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPG- 119 (165)
T ss_pred HHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCC-
Confidence 4566777777888885 5678888988777665443333343 466666778899999999999999999999876532
Q ss_pred ccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 349 EAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 349 ~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
....+.+.+.| +.+.+=|+..+.. +.|..--||-+++-.|
T Consensus 120 -------l~~~~~v~~~q-~~~~~aL~~~~~~--~~~~~~~R~~~ll~~l 159 (165)
T cd06930 120 -------LKNQQQVEELQ-EKAQQALQEYIRK--RYPQQPARFAKLLLRL 159 (165)
T ss_pred -------CcCHHHHHHHH-HHHHHHHHHHHHh--hCCCchhHHHHHHHHh
Confidence 22223333322 2233333333332 2366666777776554
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=89.00 E-value=4.2 Score=39.79 Aligned_cols=112 Identities=16% Similarity=0.194 Sum_probs=72.6
Q ss_pred HHhhhc-CCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCC
Q 014531 279 LYSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLL 357 (423)
Q Consensus 279 L~SaKa-~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~p 357 (423)
-+|.-. ++.-+++.+|.-++..+-++..+.| +.+++.-+=.+++.++|+++|=.||+-+||++.|+.+ |+-
T Consensus 80 ~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~~~-~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~-------gL~ 151 (248)
T cd07075 80 WRSYKHTNSQFLYFAPDLVFNEERMHQSAMYE-LCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKD-------GLK 151 (248)
T ss_pred HhccCCCCCceEEecCCccccHHHHhhccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCC-------CCC
Confidence 355544 3455888888888777766667888 5677776777899999999999999999999986421 343
Q ss_pred ChhHHHHHHHHHHHHhhhhhhh-hcccCchhhHhHHHHHHHHH
Q 014531 358 PEDALRAAQIQGISRRMIGLIR-SVSKFPTYRRRFRQVVKALV 399 (423)
Q Consensus 358 p~d~vrrAqLqai~RRLqGI~~-s~SR~PT~RRrf~~lvK~L~ 399 (423)
..+.|.+-|= .+..-|+-.++ .=...|..-.||-.+.+-|-
T Consensus 152 ~~~~Ve~lqe-~~~~aL~~yi~~~~~~~~~~~~RF~~LLllLp 193 (248)
T cd07075 152 SQAAFEEMRT-NYIKELRKMVTKAPNNSGQSWQRFYQLTKLLD 193 (248)
T ss_pred CHHHHHHHHH-HHHHHHHHHHHHcCCCcccchhHHHHHHHHHH
Confidence 4443333321 12222333322 11334566689988877654
No 13
>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=88.30 E-value=2.3 Score=40.79 Aligned_cols=98 Identities=20% Similarity=0.234 Sum_probs=69.6
Q ss_pred CCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHH
Q 014531 286 SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAA 365 (423)
Q Consensus 286 S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrA 365 (423)
...+++++|..++..+-....+-+ +.+++.-+=++++.++|+++|=.||+-+||++.|.. |+-..+.|.+-
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~--------gL~~~~~Ve~l 180 (243)
T cd06935 110 SETLTLSGEMAVTREQLKNGGLGV-VSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRP--------GLACVERIEKL 180 (243)
T ss_pred CCeEEeeCCeEeeHHHHHhcChHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCC--------CCCCHHHHHHH
Confidence 456888888877765433444445 678888899999999999999999999999998753 34445555555
Q ss_pred H---HHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 366 Q---IQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 366 q---Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
| ++|+-+- ++ .+.|.-..||-.++-.|
T Consensus 181 Qe~~~~aL~~y----i~--~~~p~~~~rf~kLL~~L 210 (243)
T cd06935 181 QDSFLLAFEHY----IN--YRKHHVPHFWPKLLMKV 210 (243)
T ss_pred HHHHHHHHHHH----HH--hhCCCCccHHHHHHHHH
Confidence 4 4454332 22 35688888998887655
No 14
>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=87.88 E-value=14 Score=31.88 Aligned_cols=157 Identities=17% Similarity=0.220 Sum_probs=96.7
Q ss_pred HHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcCCCCcceEeeccchHHHHHHHHHhhhcCCCceeecCCceecccCC
Q 014531 223 QIWVNMMRSCETRGRELLDADVITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSVEITHLNR 302 (423)
Q Consensus 223 qiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~~~~~k~l~vgLPayslL~~LL~SaKa~S~Glll~D~~EiT~~Nr 302 (423)
++|+..+..+-.--+.+=.=.-++..|=...++. +.+.+.+|..--+|...+...+.+.+|..+...+.
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 5666666666666666544455677775444443 34667778877777777889999999988755443
Q ss_pred CCc--cchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHH-HHHH-HHHHHhhhhhh
Q 014531 303 PNN--KLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALR-AAQI-QGISRRMIGLI 378 (423)
Q Consensus 303 Pkd--~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vr-rAqL-qai~RRLqGI~ 378 (423)
+.. ..+.=+.+.+.-+=..++.+++|++|=.+|.-+++++.+... +.+ +..+ -.++ +.+++-|+=..
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~--------~~~-~~~~~~~~~r~~~~~~L~~y~ 163 (203)
T PF00104_consen 93 DDFITGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPG--------LSE-ETREIVEELRDRIIQALHSYY 163 (203)
T ss_dssp HHTSTTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTT--------HS--SHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccc--------ccc-chhHHHHHHHHHHHHHHHHHH
Confidence 322 222222234444445999999999999999999999875533 221 2222 1222 23455555555
Q ss_pred hhcccCchhhHhHHHHHHHHH
Q 014531 379 RSVSKFPTYRRRFRQVVKALV 399 (423)
Q Consensus 379 ~s~SR~PT~RRrf~~lvK~L~ 399 (423)
..-...+.+-.||-++++.|-
T Consensus 164 ~~~~~~~~~~~R~~~ll~ll~ 184 (203)
T PF00104_consen 164 NQSKGPEDYAQRFGKLLLLLP 184 (203)
T ss_dssp HHHHSTTTHTTHHHHHHHHHH
T ss_pred hccCCCccHHHHHHHHHHHHH
Confidence 444556667788888876653
No 15
>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=86.14 E-value=7.2 Score=38.20 Aligned_cols=109 Identities=17% Similarity=0.298 Sum_probs=66.6
Q ss_pred HHhhhcCCCc-eeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCC-CccccccccCCCC
Q 014531 279 LYSIKAGSGG-LLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS-TTERMEAWDNGGL 356 (423)
Q Consensus 279 L~SaKa~S~G-lll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~-d~~r~~~wd~~g~ 356 (423)
-+|.+.+..- +++.+|.-++..+--...+.+ +..++.-+=.++++++++++|=.||+-++|++. |.. |+
T Consensus 80 ~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~~~-~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~--------GL 150 (247)
T cd07076 80 WRSYRQSNGNLLCFAPDLIINEQRMTLPCMYD-QCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKD--------GL 150 (247)
T ss_pred HhccCCCCCceEEecCCeeecHHHHhhhhHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCC--------CC
Confidence 4777654433 667777766655432233444 466777888899999999999999999999986 433 33
Q ss_pred CCh---hHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 014531 357 LPE---DALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 399 (423)
Q Consensus 357 pp~---d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 399 (423)
-.. |++|..=+.|+.+-+. +.-...|...+||-++..-|-
T Consensus 151 ~~~~~Ve~lqe~~~~aL~~yi~---~~~p~~~~~~~RF~kLLllLp 193 (247)
T cd07076 151 KSQELFDEIRMTYIKELGKAIV---KREGNSSQNWQRFYQLTKLLD 193 (247)
T ss_pred CCHHHHHHHHHHHHHHHHHHHH---hcCCCcchhhhHHHHHHHHHH
Confidence 333 3333333333333222 111223444669988876653
No 16
>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=85.78 E-value=5.9 Score=37.60 Aligned_cols=110 Identities=17% Similarity=0.304 Sum_probs=67.6
Q ss_pred HHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHH---HHHHHHhccCChhHHHHHHHhhhcCCCcccc
Q 014531 272 YSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMV---LKEQISVLKLTEPEVRYLEKVVLFGSTTERM 348 (423)
Q Consensus 272 yslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~Pllv---lKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 348 (423)
..+|.+--+|...+.+-++..||+.+...+ .+++-+ +.+.+-+ +=.+++.+++|++|=.||+-++|++.|...
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 344555556666666667778887654332 122222 2333322 235789999999999999999999977533
Q ss_pred ccccCCCCCChhHHHHHH---HHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 349 EAWDNGGLLPEDALRAAQ---IQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 349 ~~wd~~g~pp~d~vrrAq---Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
+-..+.+++.| ++|+-+-.+ .++|.-..||-+++-.|
T Consensus 151 -------L~~~~~v~~~q~~~~~aL~~y~~------~~~~~~~~Rf~~LLl~L 190 (236)
T cd06948 151 -------LSDPAHIESLQEKSQCALEEYVR------TQYPNQPTRFGKLLLRL 190 (236)
T ss_pred -------ccCHHHHHHHHHHHHHHHHHHHH------HhCCCcccHHHHHHHHH
Confidence 23334455544 555555443 34677778888876544
No 17
>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=84.86 E-value=11 Score=35.11 Aligned_cols=112 Identities=21% Similarity=0.293 Sum_probs=64.5
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccC
Q 014531 274 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDN 353 (423)
Q Consensus 274 lL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~ 353 (423)
+|..--+|...+..-++-+++......+ +...+.+. ...+.-+-.+++.++|+++|=.||+-++|++.|..
T Consensus 73 iL~~a~~s~~~~~~~ll~~~~~~~~~~~-~~~~~~~~-~~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~------- 143 (206)
T cd06950 73 LLGAAQWSLPLDSCPLLAVPGLSPDNTE-AERTFLSE-VRALQETLSRFRQLRVDATEFACLKAIVLFKPETR------- 143 (206)
T ss_pred HHHHHHHhcCCCcceeecCCcccccccc-hhhHHHHH-HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC-------
Confidence 4444445554444433334443222222 22223332 23444455689999999999999999999997753
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 354 GGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 354 ~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
|+...+.+++.| +.+..=|+--+. .++|.-..||-+++-.|
T Consensus 144 -~L~~~~~Ve~lq-~~~~~aL~~y~~--~~~~~~~~Rf~kLLl~L 184 (206)
T cd06950 144 -GLKDPAQVEALQ-DQAQLMLNKHIR--TRYPTQPARFGKLLLLL 184 (206)
T ss_pred -CCCCHHHHHHHH-HHHHHHHHHHHH--HhCCCcccHHHHHHHHH
Confidence 244445566655 233333443333 45788888998887444
No 18
>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=83.74 E-value=7.9 Score=35.39 Aligned_cols=150 Identities=15% Similarity=0.195 Sum_probs=83.8
Q ss_pred HHHHHHHHHHHhhhhhhhc-------cCCCChhhHHHHHHhcCCCCcceEeeccchHHHHHHHHHhhhcCCCceeecCCc
Q 014531 223 QIWVNMMRSCETRGRELLD-------ADVITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSV 295 (423)
Q Consensus 223 qiwd~lfk~ce~~G~~Ll~-------~gvIt~~Diee~~~~k~~~~~k~l~vgLPayslL~~LL~SaKa~S~Glll~D~~ 295 (423)
++|.++.......-+..++ =.-++.+|=-.-+++. . .+. .+| .+-++.... +.++.||.
T Consensus 2 ~~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~-~---------~e~-~ll-~~~~~~~~~--~~~~~~g~ 67 (191)
T cd06942 2 NAWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGN-M---------FPL-YLL-RLSRDYNNE--GTVLCDFR 67 (191)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHH-H---------HHH-HHH-HHHHHhCcC--CeEEeCCc
Confidence 5677776666554443332 1234445533333332 1 122 223 344565544 88999998
Q ss_pred eecccCC-CCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCC--ccccccccCCCCCChhHHHHHHHHHHHH
Q 014531 296 EITHLNR-PNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGST--TERMEAWDNGGLLPEDALRAAQIQGISR 372 (423)
Q Consensus 296 EiT~~Nr-Pkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d--~~r~~~wd~~g~pp~d~vrrAqLqai~R 372 (423)
.++...- .+....+ +.+++.-+=+.++++++|++|=.||+-+++++.| ... +-....+... .+.+.+
T Consensus 68 ~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~--------l~~~~~v~~~-q~~l~~ 137 (191)
T cd06942 68 PVEFASLLSQLLHGK-LIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLGIQ--------LEETAKSNLQ-LSVLFQ 137 (191)
T ss_pred cccHHHHHHhcchHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCC--------ccchHHHHHH-HHHHHH
Confidence 8865321 0111223 4566667778999999999999999999999987 422 2222222221 123333
Q ss_pred hhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 373 RMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 373 RLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
-|+=-+. .++|.-..||-.++-.|
T Consensus 138 ~L~~~~~--~~~~~~~~rf~kLL~~l 161 (191)
T cd06942 138 FLKSVLF--KDGEDTEQRLQKLFDIL 161 (191)
T ss_pred HHHHHHH--hcCCChHHHHHHHHHHH
Confidence 3432222 36777778887776544
No 19
>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=82.74 E-value=9.3 Score=33.51 Aligned_cols=115 Identities=18% Similarity=0.263 Sum_probs=69.5
Q ss_pred HHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccc
Q 014531 272 YSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAW 351 (423)
Q Consensus 272 yslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~w 351 (423)
+.++..- ++.+.+.+.+..+||+......-+... +.=+.+.+.-+=..++.+++|++|=.+|+-++|++.|...
T Consensus 47 l~~l~~a-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~---- 120 (174)
T cd06929 47 ILLLRSA-TLYDPEKNSLTFGDGKGNSRDVLLNGG-FGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPG---- 120 (174)
T ss_pred HHHHHHH-HHhcccCCeEEecCCceecHHHHHHcc-cHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCccc----
Confidence 4444443 566778888999999763322111111 1123455556668899999999999999999999866432
Q ss_pred cCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 014531 352 DNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 399 (423)
Q Consensus 352 d~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 399 (423)
+-..+.+.+.| +.+..-|+-.+ ..++|....||-+++..|.
T Consensus 121 ----l~~~~~v~~~q-~~~~~aL~~y~--~~~~~~~~~Rf~~Ll~~l~ 161 (174)
T cd06929 121 ----LQDVDTVEKLQ-ERLLEALQRYL--KVNHPDAPQMFAKLLKKLT 161 (174)
T ss_pred ----CcCHHHHHHHH-HHHHHHHHHHH--HhcCCCChhHHHHHHHHhH
Confidence 22233333333 12222333333 2457788889998877654
No 20
>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=82.72 E-value=13 Score=35.68 Aligned_cols=113 Identities=17% Similarity=0.275 Sum_probs=68.6
Q ss_pred HHHHHHHhhhc-CCCceeecCCceecccCCCCccchhhhhhhHHH---HHHHHHhccCChhHHHHHHHhhhcCCCccccc
Q 014531 274 FLQTLLYSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMV---LKEQISVLKLTEPEVRYLEKVVLFGSTTERME 349 (423)
Q Consensus 274 lL~~LL~SaKa-~S~Glll~D~~EiT~~NrPkd~~fDWff~Pllv---lKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~ 349 (423)
+|...-+|.-. +.+-+++.+|++++..+-.. ..-.++-..+.. +=.+++.++++++|=.||+-++|++.|...
T Consensus 85 vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~g-- 161 (237)
T cd07070 85 VFDHIYRQVQHGKEGSILLVTGQEVELSTVAA-QAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKF-- 161 (237)
T ss_pred HHHHHHHhhhcCCCCceeecCCCeechhHHHH-HHhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccC--
Confidence 44445666644 34557788998887555221 111232223322 445788999999999999999999876532
Q ss_pred cccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 350 AWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 350 ~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
+-....|...|=+ +..-|+..++ .++|.-..||-+++-.|
T Consensus 162 ------L~~~~~Ve~lQe~-~~~aL~~y~~--~~~p~~~~Rf~kLLl~L 201 (237)
T cd07070 162 ------LNNHSLVKDAQEK-ANAALLDYTL--CHYPHCGDKFQQLLLRL 201 (237)
T ss_pred ------CCCHHHHHHHHHH-HHHHHHHHHH--hcCCCcchHHHHHHHHh
Confidence 3333344444322 2233444444 47899999999986443
No 21
>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=82.19 E-value=21 Score=29.78 Aligned_cols=121 Identities=18% Similarity=0.204 Sum_probs=78.1
Q ss_pred chHHHHHHHHHhhhcCCCceeecCCceec-ccCCCCccch-hhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccc
Q 014531 270 PCYSFLQTLLYSIKAGSGGLLLPDSVEIT-HLNRPNNKLL-DWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 347 (423)
Q Consensus 270 PayslL~~LL~SaKa~S~Glll~D~~EiT-~~NrPkd~~f-DWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r 347 (423)
..+.+|...-+|.+.+....+..++...+ ..+.+..+.+ .=+-..+.-+-+.++.+++|++|=.+|+-++++..+...
T Consensus 41 ~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~ 120 (168)
T cd06157 41 LELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE 120 (168)
T ss_pred HHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCC
Confidence 46789999999999999888877775431 1222222221 122234455677889999999999999999999865421
Q ss_pred cccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 014531 348 MEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 399 (423)
Q Consensus 348 ~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 399 (423)
+....+-+++ .-+.+.+-|+-.+..-.. |..--||-+++..+.
T Consensus 121 -------s~~~~~~~~~-~~~~~~~~L~~y~~~~~~-~~~~~R~~~ll~~l~ 163 (168)
T cd06157 121 -------SLEDRKIVEE-LQERLLEALQDYLRKNYP-EEAPSRFAKLLLLLP 163 (168)
T ss_pred -------CccCHHHHHH-HHHHHHHHHHHHHHHhCC-ccchhHHHHHHHhch
Confidence 2223333333 335566666666655444 677778888877653
No 22
>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=81.39 E-value=12 Score=36.36 Aligned_cols=100 Identities=18% Similarity=0.356 Sum_probs=67.6
Q ss_pred cCCCceeecCCce-ecccC--CCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChh
Q 014531 284 AGSGGLLLPDSVE-ITHLN--RPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPED 360 (423)
Q Consensus 284 a~S~Glll~D~~E-iT~~N--rPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d 360 (423)
.+.+|+++.+|-. +|... .... -+.=+.+|+.-+=++++.++|+++|=.||+-++|++.|.. |+-..+
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~--------gL~~~~ 187 (259)
T cd06932 117 YNKDGLLFPEGNGYVTREFLESLRK-PFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRP--------GLINRK 187 (259)
T ss_pred cCCCCeEEeCCCEEeeHHHHHHhcc-cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcc--------cCcCHH
Confidence 3566777776532 33321 1111 1233678888889999999999999999999999998743 344555
Q ss_pred HHHHHH---HHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 361 ALRAAQ---IQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 361 ~vrrAq---Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
.|.+.| ++|+-+-+. +++|....||-.++-.|
T Consensus 188 ~Ve~lQe~~~~aL~~~i~------~~~p~~~~rf~kLLl~L 222 (259)
T cd06932 188 PVERIQEHVLQALELQLK------KNHPDSPQLFAKLLQKM 222 (259)
T ss_pred HHHHHHHHHHHHHHHHHh------hhCCCcccHHHHHHHHH
Confidence 666666 555554432 45799999998886544
No 23
>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=81.31 E-value=14 Score=35.30 Aligned_cols=117 Identities=15% Similarity=0.190 Sum_probs=69.6
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCC-CccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCcccccccc
Q 014531 274 FLQTLLYSIKAGSGGLLLPDSVEITHLNRP-NNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWD 352 (423)
Q Consensus 274 lL~~LL~SaKa~S~Glll~D~~EiT~~NrP-kd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd 352 (423)
+|..--+|...+. -+++.+|.-++..... ... +..+++++.-+=++++.++++++|=.||+-++|++.|... -.
T Consensus 79 ~L~~a~rs~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g---~~ 153 (235)
T cd06949 79 MLGLVWRSMEHPG-KLLFAPDLLLDRNQGSCVEG-MVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYT---FL 153 (235)
T ss_pred HHHHHHHhcCCCC-eEEeeCCceecHHHhhhccc-HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCC---cc
Confidence 4444456665533 3666777665543221 333 3445677777777999999999999999999999876421 00
Q ss_pred CCCCCChhHHHHHHHHHHHHhhhhhhhhcccC---chhhHhHHHHHHHH
Q 014531 353 NGGLLPEDALRAAQIQGISRRMIGLIRSVSKF---PTYRRRFRQVVKAL 398 (423)
Q Consensus 353 ~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~---PT~RRrf~~lvK~L 398 (423)
+-+......|++.| +.+..-|+.-+. .+. |.-..||-.++-.|
T Consensus 154 ~~~l~~~~~Ve~lq-~~~~~aL~~y~~--~~~~~~p~~~~Rf~~LLl~L 199 (235)
T cd06949 154 LESLESRRQVQRLL-DKITDALVHACS--KRGLSLQQQSRRLAQLLLIL 199 (235)
T ss_pred cccccCHHHHHHHH-HHHHHHHHHHHH--hcCCCCCCcccHHHHHHHhc
Confidence 00133445566665 233334444433 244 77788888875443
No 24
>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=80.45 E-value=19 Score=34.99 Aligned_cols=116 Identities=15% Similarity=0.169 Sum_probs=65.3
Q ss_pred HHHHHHHhhhcC-CCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCcccccccc
Q 014531 274 FLQTLLYSIKAG-SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWD 352 (423)
Q Consensus 274 lL~~LL~SaKa~-S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd 352 (423)
+|..-.+|.-.+ ++-+++.+|.-++...--...+.+ +.+++.-+=..++.++++++|=.||+-+||++.++ +
T Consensus 75 iL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d-~----- 147 (246)
T cd06947 75 VFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQSAMYS-LCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIP-K----- 147 (246)
T ss_pred HHHHHHhhccCCCCCeEEecCCeeecHHHhhhccHHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCc-c-----
Confidence 344445666544 333667777644433322345666 35666556668999999999999999999999632 1
Q ss_pred CCCCCChhHHHHHHHHHHHHhhhhhhhh-cccCchhhHhHHHHHHHH
Q 014531 353 NGGLLPEDALRAAQIQGISRRMIGLIRS-VSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 353 ~~g~pp~d~vrrAqLqai~RRLqGI~~s-~SR~PT~RRrf~~lvK~L 398 (423)
.|+-..+.|.+-|= .+..-|+.-+.. --..|....||-++..-|
T Consensus 148 -~gL~~~~~Ve~lqe-~i~~AL~~yi~~~~~~~~~~~~Rf~kLLllL 192 (246)
T cd06947 148 -DGLKSQAAFDEMRM-NYIKELRKAIVKREKNSSQSWQRFYQLTKLL 192 (246)
T ss_pred -ccccCHHHHHHHHH-HHHHHHHHHHHHhCCCCcccchHHHHHHHhh
Confidence 23444444444331 111222332221 112445577887776544
No 25
>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=80.07 E-value=21 Score=34.45 Aligned_cols=102 Identities=10% Similarity=0.147 Sum_probs=66.9
Q ss_pred CCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHH
Q 014531 285 GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRA 364 (423)
Q Consensus 285 ~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrr 364 (423)
..+.+++.+|.-.+.... ...+-+ +.+++.-+=.+++.++|+++|=.||+-++|++ |. .|+-..+.|.+
T Consensus 98 ~~~~l~~~~g~~~~~~~~-~~~~~~-~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf~-D~--------~gL~~~~~Ve~ 166 (238)
T cd07071 98 VEGKLIFCNGVVLHRLQC-VRGFGE-WIDSIVEFSSNLQNMNIDISAFSCIAALAMVT-ER--------HGLKEPKRVEE 166 (238)
T ss_pred CCCceEeeCCceechhhh-hhcHHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcC-CC--------CCCCCHHHHHH
Confidence 345588888877766553 333445 57788888899999999999999999999883 32 24444444444
Q ss_pred HHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 365 AQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 365 AqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
-| +.+..-|+..++.-...|.-..||-.++-.|
T Consensus 167 lQ-e~~~~aL~~yi~~~~~~p~~~~rf~kLLl~L 199 (238)
T cd07071 167 LQ-NKIVNCLKDHVTFNNGGLNRPNYLSKLLGKL 199 (238)
T ss_pred HH-HHHHHHHHHHHHHhCCCCCcccHHHHHHHHh
Confidence 33 1223345555554344677888888876543
No 26
>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=79.07 E-value=9.2 Score=36.04 Aligned_cols=108 Identities=17% Similarity=0.216 Sum_probs=66.4
Q ss_pred HhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCCh
Q 014531 280 YSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPE 359 (423)
Q Consensus 280 ~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~ 359 (423)
++.....+.+.+.||..++..+-....+..=+.+++.-+-+.++.+++|++|=.||+-++|++.|... +-..
T Consensus 95 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~g--------L~~~ 166 (236)
T cd06954 95 RRYNPESEAITFLKDFPYSRDDFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPN--------VQDH 166 (236)
T ss_pred HHhcCCCCeEEeeCCccccHHHHHHhcChHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCccc--------CCCH
Confidence 34455567788889977665432212222234566767888999999999999999999999876422 3333
Q ss_pred hHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 360 DALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 360 d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
+.|.+.|= .+..=|+--++ +++|.-+.||-.+.-.|
T Consensus 167 ~~V~~lQ~-~~~~aL~~y~~--~~~p~~~~rf~klL~~L 202 (236)
T cd06954 167 HRVERLQE-TYVEALHSYIK--IKRPSDRLMFPRMLMKL 202 (236)
T ss_pred HHHHHHHH-HHHHHHHHHHH--hcCCCcccHHHHHHHHH
Confidence 34444331 11222333332 46888888886665444
No 27
>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=74.93 E-value=27 Score=32.66 Aligned_cols=73 Identities=18% Similarity=0.231 Sum_probs=46.6
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCc
Q 014531 271 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 345 (423)
Q Consensus 271 ayslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~ 345 (423)
.+.+|.+--+|+..+. ++.+++|.-.+.....+..+-+ +.+++.-+=..++.+++|++|=.+|+-+++++.|.
T Consensus 71 ~~~~l~~a~~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~npd~ 143 (221)
T cd07068 71 EILMLGLVWRSLPHPG-KLVFAPDLLLDREQARVEGLLE-IFDMLLQLVRRFRELGLQREEYVCLKAIILANSDV 143 (221)
T ss_pred HHHHHHHHHhhcCCCC-eEEeCCCceECHHHHhhccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCc
Confidence 4555555556665544 7888888644432211223323 23444445568999999999999999999997554
No 28
>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=74.40 E-value=25 Score=34.03 Aligned_cols=112 Identities=14% Similarity=0.232 Sum_probs=69.9
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccC
Q 014531 274 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDN 353 (423)
Q Consensus 274 lL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~ 353 (423)
+|..--+|... .+-+++.+|..++..+. ...+-+| .+++.-+=.+++.++++++|=.||+-++|+ .|.
T Consensus 88 vL~~a~r~~~~-~~~l~f~~~~~~~r~~~-~~~~~~~-~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr-------- 155 (238)
T cd07348 88 ILRLAYRSNPE-EGKLIFCNGVVLHRTQC-VRGFGDW-IDSILEFSQSLHRMNLDVSAFSCLAALVII-TDR-------- 155 (238)
T ss_pred HHHHHHHcCCC-CCeEEeeCCeeecHHHH-HhhHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCC--------
Confidence 34444455444 44577888887766553 3345565 467777888999999999999999999998 322
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 354 GGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 354 ~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
.|+-..+.|.+-|= .+..-|+.-++.-.+.|.-..||-.++-.|
T Consensus 156 ~gL~~~~~Ve~lQe-~~~~aL~~yi~~~~~~p~~p~rf~kLLl~L 199 (238)
T cd07348 156 HGLKEPKRVEELQN-RLISCLKEHVSGSASEPQRPNCLSRLLGKL 199 (238)
T ss_pred cCCCCHHHHHHHHH-HHHHHHHHHHHhhCCCCccccHHHHHHHHH
Confidence 23444444544441 122334444443334688888898876443
No 29
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=73.62 E-value=3.9 Score=36.38 Aligned_cols=48 Identities=19% Similarity=0.479 Sum_probs=40.3
Q ss_pred ccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHHH
Q 014531 325 LKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALVS 400 (423)
Q Consensus 325 ~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~ 400 (423)
.+|++++-.|++..+.-.||=+.|+ |.-|| -|||.|.|.++++++|-.
T Consensus 32 ~~L~~E~~~Fi~~Fi~~rGnlKe~e-----------------------~~lgi-----SYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 32 ARLSPEQLEFIKLFIKNRGNLKEME-----------------------KELGI-----SYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hcCCHHHHHHHHHHHHhcCCHHHHH-----------------------HHHCC-----CcHHHHHHHHHHHHHhCC
Confidence 5799999999999999999987765 33354 399999999999999876
No 30
>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=73.58 E-value=55 Score=32.23 Aligned_cols=69 Identities=10% Similarity=0.186 Sum_probs=45.5
Q ss_pred HHHHHHHhhhcCCCce-eecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCC
Q 014531 274 FLQTLLYSIKAGSGGL-LLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS 343 (423)
Q Consensus 274 lL~~LL~SaKa~S~Gl-ll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~ 343 (423)
+|..--+|.+.+++.. .+++|.-++........+.| +..++.-+-.+++.++++++|=.||+-++|++.
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 31
>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=72.43 E-value=28 Score=33.71 Aligned_cols=112 Identities=13% Similarity=0.220 Sum_probs=67.8
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccC
Q 014531 274 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDN 353 (423)
Q Consensus 274 lL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~ 353 (423)
+|..--+|... .+-+++.+|..++.....+ .+-+| .+++.-+=.+++.++++++|=.||+-++|+. | |
T Consensus 89 ~L~~a~r~~~~-~~~l~~~~g~~~~~~~~~~-~~~~~-~~~i~ef~~~l~~L~ld~~E~a~LkAivLf~-d--r------ 156 (239)
T cd07072 89 VLRLAYRTAPE-DTKLTFCNGVVLHKQQCQR-SFGDW-LHAILEFSKSLHAMDIDISAFACLCALTLIT-E--R------ 156 (239)
T ss_pred HHHHHHHccCC-CCeEEeeCCeeecHHHHHh-hHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhC-C--C------
Confidence 33433445444 3447788887766654322 45564 5777778889999999999999999999993 2 2
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 014531 354 GGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 398 (423)
Q Consensus 354 ~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 398 (423)
.|+-..+.|++-|=+ +..=|+.-++.-...|.-..||-.++-.|
T Consensus 157 ~gL~~~~~Ve~lQe~-~~~aL~~yi~~~~~~~~~~~rf~kLLl~L 200 (239)
T cd07072 157 HGLKEPHKVEQLQMK-IISSLRDHVTYNAEAQKKPHYFSRLLGKL 200 (239)
T ss_pred CCCCCHHHHHHHHHH-HHHHHHHHHHHhCCCcccccHHHHHHHHh
Confidence 245555555555522 22223333332223455567777765433
No 32
>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=71.32 E-value=52 Score=32.08 Aligned_cols=110 Identities=17% Similarity=0.252 Sum_probs=65.0
Q ss_pred Hhhhc-CCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCC-CccccccccCCCCC
Q 014531 280 YSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS-TTERMEAWDNGGLL 357 (423)
Q Consensus 280 ~SaKa-~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~-d~~r~~~wd~~g~p 357 (423)
+|.-. +...+.+.+|..++..+..+..+.+... .+.-+=.+++.++++++|=.||+-++|++. |.. |+-
T Consensus 81 rs~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~-~l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~--------gL~ 151 (246)
T cd07073 81 RSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCV-RMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVD--------GLK 151 (246)
T ss_pred hccccCCCCeEEecCCeeechhhhccccHHHHHH-HHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcc--------ccc
Confidence 56654 4555888888877766655666666432 333444578889999999999999999995 321 233
Q ss_pred ChhHHHHHHHHHHHHhhhhhhhhcccC-chhhHhHHHHHHHHH
Q 014531 358 PEDALRAAQIQGISRRMIGLIRSVSKF-PTYRRRFRQVVKALV 399 (423)
Q Consensus 358 p~d~vrrAqLqai~RRLqGI~~s~SR~-PT~RRrf~~lvK~L~ 399 (423)
..+.|..-|= .+..-|+--+.+-... |.-..||-.+.-.|-
T Consensus 152 ~~~~Ve~lQe-~~~~aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp 193 (246)
T cd07073 152 NQKFFDELRM-NYIKELDRIIACKRKNPTSCSRRFYQLTKLLD 193 (246)
T ss_pred CHHHHHHHHH-HHHHHHHHHHHhcCCCCcccchHHHHHHHHHH
Confidence 3332222221 1112233333322212 355788988876654
No 33
>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=69.38 E-value=32 Score=32.98 Aligned_cols=78 Identities=19% Similarity=0.372 Sum_probs=53.2
Q ss_pred hhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCc--hhh
Q 014531 311 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFP--TYR 388 (423)
Q Consensus 311 ff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~P--T~R 388 (423)
+.+|+.-+-.+++.++|+++|=.||+-++|++.|.. |+-..+.|.+-| +.+..-|+.-++ +++| ..|
T Consensus 121 ~~~~l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~--------gL~~~~~Ve~lQ-e~~~~aL~~yi~--~~~p~~~~~ 189 (238)
T cd06933 121 LLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRP--------GVQDHALIEAIQ-DRLSDTLQTYIR--CRHPPPGSR 189 (238)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCC--------CCcchHHHHHHH-HHHHHHHHHHHH--hcCCCCCch
Confidence 467888888899999999999999999999987642 233333343333 122333444444 3555 678
Q ss_pred HhHHHHHHHHH
Q 014531 389 RRFRQVVKALV 399 (423)
Q Consensus 389 Rrf~~lvK~L~ 399 (423)
.||-.++-.|-
T Consensus 190 ~~f~kLLl~L~ 200 (238)
T cd06933 190 LLYAKMIQKLA 200 (238)
T ss_pred hHHHHHHHHhH
Confidence 88998876653
No 34
>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=63.01 E-value=66 Score=30.07 Aligned_cols=72 Identities=17% Similarity=0.256 Sum_probs=44.0
Q ss_pred HHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCc
Q 014531 272 YSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 345 (423)
Q Consensus 272 yslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~ 345 (423)
+.+|..--+|...+. -+++.+|.-...........-+ +.+++.-+=..++.+++|++|=.||+-++|++.|.
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 3555555432211111112223 23555555678899999999999999999998774
No 35
>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=62.70 E-value=22 Score=33.82 Aligned_cols=74 Identities=20% Similarity=0.363 Sum_probs=49.5
Q ss_pred hhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHH---HHHHHHhhhhhhhhcccCc--
Q 014531 311 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ---IQGISRRMIGLIRSVSKFP-- 385 (423)
Q Consensus 311 ff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq---Lqai~RRLqGI~~s~SR~P-- 385 (423)
+.+|+.-+=+++++++++++|=.||+-+||++.|.. |+-..+.|.+.| ++|+-+.+ .++.|
T Consensus 117 ~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~--------gL~~~~~Ve~lQe~~~~aL~~yi------~~~~p~~ 182 (226)
T cd06934 117 LLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRP--------GVTQHDVIDQLQEKMALTLKSYI------DSKRPGP 182 (226)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCc--------CCcChHHHHHHHHHHHHHHHHHH------HHcCCCC
Confidence 567887788899999999999999999999998753 333344444443 34444332 12343
Q ss_pred hhhHhHHHHHHHH
Q 014531 386 TYRRRFRQVVKAL 398 (423)
Q Consensus 386 T~RRrf~~lvK~L 398 (423)
.-|.||-.++-.|
T Consensus 183 ~~r~~f~kLLl~L 195 (226)
T cd06934 183 EKRFLYPKILACL 195 (226)
T ss_pred CcccHHHHHHHHh
Confidence 3455688777554
No 36
>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=57.61 E-value=35 Score=32.61 Aligned_cols=71 Identities=18% Similarity=0.306 Sum_probs=49.2
Q ss_pred HHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHH
Q 014531 317 VLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVK 396 (423)
Q Consensus 317 vlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK 396 (423)
-+=.+++.++++++|=.||+-+||++.|.. |+-..+.|.+-|=+ +..-|+..++ +++|.-..||-.++-
T Consensus 119 e~~~~l~~L~ld~~Eya~LkaivLf~pd~~--------gl~~~~~V~~lqe~-~~~aL~~~~~--~~~p~~~~r~~kLLl 187 (222)
T cd07349 119 CCLNKFWSLDLSPKEYAYLKGTILFNPDVP--------GLTASSHVGHLQQE-AQWALCEVLE--PLHPQDQGRFARILL 187 (222)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHcCCCcc--------cCCCHHHHHHHHHH-HHHHHHHHHH--HHCCCcccHHHHHHH
Confidence 345689999999999999999999987643 23344445444422 2244555554 558999999988765
Q ss_pred HH
Q 014531 397 AL 398 (423)
Q Consensus 397 ~L 398 (423)
.|
T Consensus 188 ~L 189 (222)
T cd07349 188 TA 189 (222)
T ss_pred Hh
Confidence 54
No 37
>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=57.55 E-value=52 Score=31.74 Aligned_cols=75 Identities=20% Similarity=0.222 Sum_probs=50.8
Q ss_pred hhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHH
Q 014531 313 NPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFR 392 (423)
Q Consensus 313 ~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~ 392 (423)
.++.-+=.+++.++|+++|=.||+-+||++.|... +-..+.|.+-|=+.. .=|+..++ +++|.-..||-
T Consensus 127 ~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~--------L~~~~~Ve~lQe~~~-~aL~~yi~--~~~p~~~~rf~ 195 (232)
T cd07350 127 RAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPG--------LQCVQYIQGLQWEAQ-QALNEHVR--MIHRGDQARFA 195 (232)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCccc--------CCCHHHHHHHHHHHH-HHHHHHHH--hhCCChhhHHH
Confidence 45556667889999999999999999999987533 333444554443322 33444444 46888888998
Q ss_pred HHHHHH
Q 014531 393 QVVKAL 398 (423)
Q Consensus 393 ~lvK~L 398 (423)
.++-.|
T Consensus 196 kLLl~L 201 (232)
T cd07350 196 KLNIAL 201 (232)
T ss_pred HHHHHh
Confidence 876544
No 38
>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=53.47 E-value=41 Score=31.38 Aligned_cols=73 Identities=15% Similarity=0.272 Sum_probs=48.4
Q ss_pred HHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHH
Q 014531 315 IMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQV 394 (423)
Q Consensus 315 llvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~l 394 (423)
+.-+.++++.++|++.|=.||+-++|++.|-..+ -..+.+++.|=+ +.+=|+..++. +.|...-||-.+
T Consensus 115 l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l--------~~~~~v~~lq~~-i~~aL~~y~~~--~~p~~~~R~~kl 183 (222)
T cd06952 115 LQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQ--------ELRQQIEKLQEK-ALMELRDYVGK--TYPEDEYRLSKL 183 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCC--------cCHHHHHHHHHH-HHHHHHHHHHH--hCCCcccHHHHH
Confidence 4567889999999999999999999999875332 223344433321 11223333332 378888899888
Q ss_pred HHHH
Q 014531 395 VKAL 398 (423)
Q Consensus 395 vK~L 398 (423)
+-.|
T Consensus 184 Ll~L 187 (222)
T cd06952 184 LLRL 187 (222)
T ss_pred HHHh
Confidence 7544
No 39
>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=53.25 E-value=54 Score=31.02 Aligned_cols=80 Identities=18% Similarity=0.243 Sum_probs=52.6
Q ss_pred hhhhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchh
Q 014531 308 LDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTY 387 (423)
Q Consensus 308 fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~ 387 (423)
.+=+.+|+.-+-+.++.+++|++|=.||+-++|++.|... +-..+.|..-|= .+..=|+-.+. .++|..
T Consensus 112 ~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~g--------L~~~~~Ve~~Q~-~~~~aL~~y~~--~~~p~~ 180 (221)
T cd06936 112 SDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPY--------LKDKEAVEKLQE-PLLDLLQKFCK--LYHPED 180 (221)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcC--------CCCHHHHHHHHH-HHHHHHHHHHH--hhCCCc
Confidence 4446677777788899999999999999999999887533 222333333331 11222333332 478888
Q ss_pred hHhHHHHHHHH
Q 014531 388 RRRFRQVVKAL 398 (423)
Q Consensus 388 RRrf~~lvK~L 398 (423)
..||-.++-.|
T Consensus 181 p~rf~~LL~~L 191 (221)
T cd06936 181 PQHFACLLGRL 191 (221)
T ss_pred hhHHHHHHHHh
Confidence 99998876544
No 40
>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=49.50 E-value=52 Score=31.29 Aligned_cols=77 Identities=19% Similarity=0.088 Sum_probs=54.3
Q ss_pred hhhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhH
Q 014531 310 WFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRR 389 (423)
Q Consensus 310 Wff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RR 389 (423)
.+.+++.-+=..++.++|+++|=.||+-+||++.|. .|. ..+.|++.|=+.. .=|+--++ +++|.-..
T Consensus 115 ~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~--------~gl-~~~~Ve~lQe~~~-~aL~~yi~--~~~p~~~~ 182 (222)
T cd06951 115 ADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVP--------PLL-CPHYIEALQKEAQ-QALNEHTM--MTRPLEQL 182 (222)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCC--------Ccc-CHHHHHHHHHHHH-HHHHHHHH--hhCCCccc
Confidence 356788788888999999999999999999999874 234 4455555442222 22333333 57899999
Q ss_pred hHHHHHHHH
Q 014531 390 RFRQVVKAL 398 (423)
Q Consensus 390 rf~~lvK~L 398 (423)
||-.+.=.|
T Consensus 183 Rf~kLLl~L 191 (222)
T cd06951 183 RSARLLLML 191 (222)
T ss_pred HHHHHHHHh
Confidence 998876544
No 41
>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=48.55 E-value=43 Score=32.28 Aligned_cols=47 Identities=23% Similarity=0.389 Sum_probs=37.4
Q ss_pred hhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHH
Q 014531 312 FNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ 366 (423)
Q Consensus 312 f~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq 366 (423)
.+++.-.=+.++.++|+++|=.||+-+||++.|. .|+-..+.|.+-|
T Consensus 130 ~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr--------~gL~~~~~Ve~lQ 176 (241)
T cd06939 130 ISAVFDFAKSLCELKLTEDEIALFSALVLISADR--------PGLQEKRKVEKLQ 176 (241)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCC--------cCCCCHHHHHHHH
Confidence 4677788899999999999999999999999764 2455555666655
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=48.55 E-value=22 Score=28.32 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 014531 99 LLWPIIVIGSIVIAIFSS 116 (423)
Q Consensus 99 lLWPl~Vvgavl~aiisS 116 (423)
-+||+.+.|+|..--|+|
T Consensus 9 P~wPFf~ag~iv~ygv~k 26 (54)
T PF04911_consen 9 PMWPFFAAGAIVYYGVNK 26 (54)
T ss_pred hhhHHHHHHHHHHHHHHH
Confidence 379999999887655544
No 43
>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=45.91 E-value=84 Score=29.53 Aligned_cols=74 Identities=16% Similarity=0.257 Sum_probs=49.9
Q ss_pred hhhhHHHHHHHHHhccCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHH---HHHHHHhhhhhhhhcccCchh
Q 014531 311 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ---IQGISRRMIGLIRSVSKFPTY 387 (423)
Q Consensus 311 ff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq---Lqai~RRLqGI~~s~SR~PT~ 387 (423)
+.+++.-+=.+++.++++++|=.||+-++|++.|... +-..+.+.+-| .+|+-+.. . .++|..
T Consensus 113 ~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~g--------Ls~~~~Ve~lQ~~~~~aL~~y~----~--~~~~~~ 178 (213)
T cd06953 113 VVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDG--------LTNASQLESLQKRYWYVLQDFT----E--LNYPNQ 178 (213)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCC--------CCCHHHHHHHHHHHHHHHHHHH----H--HhCCCc
Confidence 3566666667899999999999999999999887533 33333344433 33444333 2 345888
Q ss_pred hHhHHHHHHHH
Q 014531 388 RRRFRQVVKAL 398 (423)
Q Consensus 388 RRrf~~lvK~L 398 (423)
..||-+++--|
T Consensus 179 p~Rf~~LL~~L 189 (213)
T cd06953 179 PNRFSDLLSCL 189 (213)
T ss_pred chHHHHHHHHh
Confidence 88998876544
No 44
>KOG2511 consensus Nicotinic acid phosphoribosyltransferase [Coenzyme transport and metabolism]
Probab=45.78 E-value=15 Score=38.73 Aligned_cols=22 Identities=55% Similarity=0.780 Sum_probs=19.3
Q ss_pred HHHHHH---hccCChhHHHHHHHhh
Q 014531 318 LKEQIS---VLKLTEPEVRYLEKVV 339 (423)
Q Consensus 318 lKeQIk---~~~L~E~EE~yL~Klv 339 (423)
|+|||| +++||++|+.||+|-.
T Consensus 53 Lee~irfl~N~~lt~eei~~lkk~l 77 (420)
T KOG2511|consen 53 LEEQIRFLANLKLTDEEIDYLKKEL 77 (420)
T ss_pred HHHHHHHHhhcCCCHHHHHHHHHhC
Confidence 689987 6799999999999865
No 45
>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=44.06 E-value=24 Score=20.34 Aligned_cols=27 Identities=30% Similarity=0.373 Sum_probs=20.2
Q ss_pred HHHHHHHHHhhhhhhhccCCCChhhHHHHHHh
Q 014531 225 WVNMMRSCETRGRELLDADVITPADLKDWLKA 256 (423)
Q Consensus 225 wd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~ 256 (423)
|..+|+.|..++ .|.|+..|+..++++
T Consensus 2 ~~~~f~~~d~~~-----~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDG-----DGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCC-----CCcEeHHHHHHHHHh
Confidence 456788887765 678888888877753
No 46
>PRK00523 hypothetical protein; Provisional
Probab=43.98 E-value=31 Score=28.89 Aligned_cols=26 Identities=23% Similarity=0.240 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhh
Q 014531 95 GLTILLWPIIVIGSIVIAIFSSIFIG 120 (423)
Q Consensus 95 GLaIlLWPl~Vvgavl~aiisS~flG 120 (423)
|+++.+|=+.++.+++++.+..||++
T Consensus 1 ~~~~~l~I~l~i~~li~G~~~Gffia 26 (72)
T PRK00523 1 GLAIGLALGLGIPLLIVGGIIGYFVS 26 (72)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777887777777777776666654
No 47
>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=41.65 E-value=29 Score=29.21 Aligned_cols=33 Identities=15% Similarity=0.142 Sum_probs=27.0
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcC
Q 014531 215 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKC 258 (423)
Q Consensus 215 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~ 258 (423)
-+|++++-.|||+| +++|+||.+|.|+-.....
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 7899999999998877653
No 48
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=41.37 E-value=1.6e+02 Score=27.52 Aligned_cols=58 Identities=17% Similarity=0.313 Sum_probs=47.6
Q ss_pred cCChhHHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHHHhHhh
Q 014531 326 KLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALVSYSES 404 (423)
Q Consensus 326 ~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~~~~~ 404 (423)
+|||-|.+.|+...=.+=-+.+ |++.++.||..| ||++| |+-.|-++..+.|...+.+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~P---------------R~~~l~dLA~~l-GISks-----t~~ehLRrAe~Kl~~~~~~ 212 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYP---------------RRVSLKDLAKEL-GISKS-----TLSEHLRRAERKLIEAYFD 212 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCC---------------ccCCHHHHHHHh-CCCHH-----HHHHHHHHHHHHHHHHhhh
Confidence 8999999999987655544422 889999999987 88886 9999999999988887754
No 49
>PLN00151 potassium transporter; Provisional
Probab=37.32 E-value=45 Score=38.59 Aligned_cols=26 Identities=27% Similarity=0.225 Sum_probs=20.8
Q ss_pred hhhhheeeEEeechhhhhhHHHHHHHh
Q 014531 118 FIGLYGSVVVYQERSFRRGVAYVIAMV 144 (423)
Q Consensus 118 flG~yaaVVvYQE~Sf~~GL~Yvva~V 144 (423)
++|+.+-++.||. |-..|=||=+|.+
T Consensus 479 mv~~i~v~l~F~~-s~~l~~AYGiAV~ 504 (852)
T PLN00151 479 LVMCLVVVCSFRS-ITDIGNAYGIAEV 504 (852)
T ss_pred HHHHHhheeeecC-HHHHHHHhhhhhh
Confidence 4788899999997 6688999977643
No 50
>COG2981 CysZ Uncharacterized protein involved in cysteine biosynthesis [Amino acid transport and metabolism]
Probab=36.57 E-value=37 Score=34.17 Aligned_cols=31 Identities=35% Similarity=0.567 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHH---------HHHHHHHHHHhhhhheeeE
Q 014531 96 LTILLWPIIVIG---------SIVIAIFSSIFIGLYGSVV 126 (423)
Q Consensus 96 LaIlLWPl~Vvg---------avl~aiisS~flG~yaaVV 126 (423)
|..++||+++++ |-++++|+|+|.|+.|=+|
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 445666666654 5567888888888887666
No 51
>PF14946 DUF4501: Domain of unknown function (DUF4501)
Probab=36.42 E-value=82 Score=30.38 Aligned_cols=21 Identities=33% Similarity=0.667 Sum_probs=18.3
Q ss_pred ccccCCCcCCCcccccCCCCC
Q 014531 155 LYLREGTILPKPRYRQKKVHS 175 (423)
Q Consensus 155 LyLrEGSc~PRP~YRK~~~~~ 175 (423)
.||+.-+=||+--||+|+...
T Consensus 112 FYLKrs~kLP~vfYrrnKA~a 132 (180)
T PF14946_consen 112 FYLKRSSKLPHVFYRRNKAPA 132 (180)
T ss_pred eeecccccCCccccccccccc
Confidence 699999999999999997633
No 52
>PLN00149 potassium transporter; Provisional
Probab=35.45 E-value=50 Score=37.88 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=20.4
Q ss_pred hhhhheeeEEeechhhhhhHHHHHHH
Q 014531 118 FIGLYGSVVVYQERSFRRGVAYVIAM 143 (423)
Q Consensus 118 flG~yaaVVvYQE~Sf~~GL~Yvva~ 143 (423)
++|+.+-++.||. |-+.|=||=+|.
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 4788899999997 668999997774
No 53
>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=32.55 E-value=50 Score=27.90 Aligned_cols=33 Identities=9% Similarity=0.129 Sum_probs=27.2
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcC
Q 014531 215 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKC 258 (423)
Q Consensus 215 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~ 258 (423)
-.+++++=.+||+| .++|++|..|.|+-.+...
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 45777888888876 7889999999999988654
No 54
>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=32.19 E-value=57 Score=28.19 Aligned_cols=32 Identities=16% Similarity=0.209 Sum_probs=27.0
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhc
Q 014531 215 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAK 257 (423)
Q Consensus 215 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k 257 (423)
-++++++-++||++ ++.|++|.+|+++....+
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 35678888999986 788999999999998853
No 55
>PRK13511 6-phospho-beta-galactosidase; Provisional
Probab=28.86 E-value=77 Score=33.57 Aligned_cols=64 Identities=9% Similarity=0.190 Sum_probs=43.2
Q ss_pred HHHHHHHhhh----------cCCCceeecCCceeccc-CCCCccc---------hhhhhhhHH------HHHHHHH----
Q 014531 274 FLQTLLYSIK----------AGSGGLLLPDSVEITHL-NRPNNKL---------LDWFFNPIM------VLKEQIS---- 323 (423)
Q Consensus 274 lL~~LL~SaK----------a~S~Glll~D~~EiT~~-NrPkd~~---------fDWff~Pll------vlKeQIk---- 323 (423)
.-|.||..|| .+.-|+.+....-.... +.|+|.. ..||++|+. .|+++++
T Consensus 189 ~hn~llAHa~A~~~~~~~~~~g~IGi~~~~~~~~P~~~~~~~d~~aa~~~~~~~~~~f~dp~~~G~Yp~~~~~~~~~~~~ 268 (469)
T PRK13511 189 HHNMMVAHARAVKLFKDKGYKGEIGVVHALPTKYPIDPDNPEDVRAAELEDIIHNKFILDATYLGYYSEETMEGVNHILE 268 (469)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCeEEEEecCceEeeCCCCCHHHHHHHHHHHHHhhhcccchhhCCCCCHHHHHHHHHhhh
Confidence 3355666666 35778888877444444 7788754 479999985 5677664
Q ss_pred ----hccCChhHHHHHHH
Q 014531 324 ----VLKLTEPEVRYLEK 337 (423)
Q Consensus 324 ----~~~L~E~EE~yL~K 337 (423)
.+++|++|...+++
T Consensus 269 ~~~~~l~~t~~d~~~ik~ 286 (469)
T PRK13511 269 ANGGSLDIRDEDFEILKA 286 (469)
T ss_pred hcCCCCCCCHHHHHHHhc
Confidence 24688888887764
No 56
>TIGR00794 kup potassium uptake protein. Proteins of the KUP family include the KUP (TrkD) protein of E. coli, a partially sequenced ORF from Lactococcus lactis, high affinity K+ uptake systems (Hak1) of the yeast Debaryomyces occidentalis as well as the fungus, Neurospora crassa, and several homologues in plants. While the E. coli KUP protein is assumed to be a secondary transporter, and uptake is blocked by protonophores such as CCCP (but not arsenate), the energy coupling mechanism has not been defined. However, the N. crassa protein has been shown to be a K+:H+ symporter, establishing that the KUP family consists of secondary carriers. The plant high affinity (20mM) K+ transporter can complement K+ uptake defects in E. coli.
Probab=26.89 E-value=99 Score=35.09 Aligned_cols=26 Identities=23% Similarity=0.438 Sum_probs=21.1
Q ss_pred hhhhheeeEEeechhhhhhHHHHHHHh
Q 014531 118 FIGLYGSVVVYQERSFRRGVAYVIAMV 144 (423)
Q Consensus 118 flG~yaaVVvYQE~Sf~~GL~Yvva~V 144 (423)
++|+.+-|+.||++ -.+|-||=+|..
T Consensus 373 mv~~i~vvl~F~~S-~~la~AYGiaVt 398 (688)
T TIGR00794 373 MLGVIAVTAGFRDT-NNLGAAYGIAVT 398 (688)
T ss_pred HHHHHheeEEecCh-HHHHHHhhhhhh
Confidence 47888899999985 489999988754
No 57
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=26.60 E-value=32 Score=26.76 Aligned_cols=31 Identities=16% Similarity=0.195 Sum_probs=24.3
Q ss_pred hhhHHHHHHHHHHHH--------hhhhhhhccCCCChhh
Q 014531 219 VKMVQIWVNMMRSCE--------TRGRELLDADVITPAD 249 (423)
Q Consensus 219 ~k~vqiwd~lfk~ce--------~~G~~Ll~~gvIt~~D 249 (423)
+.--+++|||.+.|+ .-|..|++.|+|...+
T Consensus 29 F~G~e~v~WL~~~~~~~~r~ea~~~~~~ll~~g~i~~v~ 67 (81)
T cd04371 29 FTGSELVDWLLDNLEAITREEAVELGQALLKHGLIHHVS 67 (81)
T ss_pred eEcHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 345689999987766 5678899999998765
No 58
>PF15052 TMEM169: TMEM169 protein family
Probab=25.83 E-value=42 Score=30.98 Aligned_cols=87 Identities=24% Similarity=0.500 Sum_probs=55.4
Q ss_pred hhhhhhhhhhhcccchhhhcHHHHHhhhhcCCCCccccccccchhHHHHHHHHHHHHHHHHHHHHHHhhhhheeeEEeec
Q 014531 51 DIPLYTVIAVIKSPYMLFKGWFRLLHDLISREGPFLETACIPIAGLTILLWPIIVIGSIVIAIFSSIFIGLYGSVVVYQE 130 (423)
Q Consensus 51 Dvplit~IAl~KsPyMLfKGW~RLl~DLIgReGPFLET~CVPfAGLaIlLWPl~Vvgavl~aiisS~flG~yaaVVvYQE 130 (423)
=.|.+++++.+-|=||=---|...+-- ...|=-|.-- +-++=|-|++-|+..+ +.++-+|+|||++ .
T Consensus 23 clP~vfv~s~~~sFY~GTlTWYNiF~~-y~Eers~~hK--i~~cPlLIl~YP~lIv-------~~t~~LglYaa~~---Q 89 (133)
T PF15052_consen 23 CLPFVFVLSFIYSFYYGTLTWYNIFLV-YNEERSFWHK--ITVCPLLILFYPFLIV-------LVTLSLGLYAAFV---Q 89 (133)
T ss_pred HhHHHHHHHHHHHhhhhhheeeeehee-eeccceeeee--ehhccHHHHHHHHHHH-------HHHHHHHHHHHhh---h
Confidence 357888888888888866667665421 2333333322 1233467888887765 5567799999987 2
Q ss_pred hhhhhhHHHHHHHhHhhhhcccccccccCCCc
Q 014531 131 RSFRRGVAYVIAMVAEFDEYTNDWLYLREGTI 162 (423)
Q Consensus 131 ~Sf~~GL~Yvva~Va~FDEYtND~LyLrEGSc 162 (423)
-|+ .|.+.-||+=|+..|-|
T Consensus 90 lSw------------~~~~W~~~v~D~EKGF~ 109 (133)
T PF15052_consen 90 LSW------------SFGSWWNEVRDFEKGFY 109 (133)
T ss_pred eee------------eHHHHHHHhhHhhcchh
Confidence 233 25667777777766643
No 59
>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=25.46 E-value=81 Score=26.74 Aligned_cols=34 Identities=6% Similarity=0.020 Sum_probs=27.2
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcCC
Q 014531 215 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKCV 259 (423)
Q Consensus 215 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~~ 259 (423)
-.+++++=.+||+| .++|++|..|.|+-.+...+
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 45677788888876 68899999999998886643
No 60
>PLN00148 potassium transporter; Provisional
Probab=24.11 E-value=79 Score=36.42 Aligned_cols=25 Identities=20% Similarity=0.252 Sum_probs=19.9
Q ss_pred hhhhheeeEEeechhhhhhHHHHHHH
Q 014531 118 FIGLYGSVVVYQERSFRRGVAYVIAM 143 (423)
Q Consensus 118 flG~yaaVVvYQE~Sf~~GL~Yvva~ 143 (423)
++|+.+-++.||. |-..|=||=+|.
T Consensus 402 mv~~i~vv~~F~~-s~~la~AYGiAV 426 (785)
T PLN00148 402 MILTLAVTIGFRD-TTLIGNAYGLAC 426 (785)
T ss_pred HHHHHHhheeecc-chhHHHhhhhhe
Confidence 4788889999997 558888997764
No 61
>PRK10535 macrolide transporter ATP-binding /permease protein; Provisional
Probab=23.67 E-value=55 Score=35.70 Aligned_cols=25 Identities=12% Similarity=0.414 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhee
Q 014531 100 LWPIIVIGSIVIAIFSSIFIGLYGS 124 (423)
Q Consensus 100 LWPl~Vvgavl~aiisS~flG~yaa 124 (423)
+=|..+++|++.|++..+++|+|=|
T Consensus 609 ~~~~~~~~a~~~s~~vGl~~GlyPA 633 (648)
T PRK10535 609 FSPLALLSAFLCSTVTGILFGWLPA 633 (648)
T ss_pred eCHHHHHHHHHHHHHHHHHHhHHHH
Confidence 3456777888888888889998854
No 62
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=23.45 E-value=91 Score=26.03 Aligned_cols=33 Identities=21% Similarity=0.428 Sum_probs=25.9
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcC
Q 014531 215 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKC 258 (423)
Q Consensus 215 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~ 258 (423)
-.+++++=.+||+| +++|++|..++|+-.+.+.
T Consensus 12 Lv~~l~~~~v~~~L-----------~~~~Vlt~~~~e~I~~~~t 44 (84)
T cd08326 12 LVEELQPKYLWDHL-----------LSRGVFTPDMIEEIQAAGS 44 (84)
T ss_pred HHHHCCHHHHHHHH-----------HhcCCCCHHHHHHHHcCCC
Confidence 35667777788876 7899999999998887553
No 63
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=23.22 E-value=1.2e+02 Score=25.31 Aligned_cols=83 Identities=11% Similarity=0.209 Sum_probs=63.4
Q ss_pred HHHHHHHHHhccCChh--HHHHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhh-HhH
Q 014531 315 IMVLKEQISVLKLTEP--EVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYR-RRF 391 (423)
Q Consensus 315 llvlKeQIk~~~L~E~--EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGI~~s~SR~PT~R-Rrf 391 (423)
+.-++.|+..+++.+. =+.|+.++.-+...- ...+...+++.+-.-=|.++-.+...++.++.--|... .-|
T Consensus 25 ~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L-----~~~g~~i~d~~~v~~iL~~Lp~~y~~~~~~i~~~~~~~~~t~ 99 (119)
T PF14223_consen 25 VQQLKSQLENLKMKDGESVDEYISRLKEIVDEL-----RAIGKPISDEDLVSKILRSLPPSYDTFVTAIRNSKDLPKMTL 99 (119)
T ss_pred HHHHHHHHHHHHhcccccHHHHHHHHHHhhhhh-----hhcCCcccchhHHHHHHhcCCchhHHHHHHHHhcCCCCcCCH
Confidence 4668899999997544 488999998777665 34455677788888888888888888888877666555 468
Q ss_pred HHHHHHHHHhH
Q 014531 392 RQVVKALVSYS 402 (423)
Q Consensus 392 ~~lvK~L~~~~ 402 (423)
++++..|..+=
T Consensus 100 ~el~~~L~~~E 110 (119)
T PF14223_consen 100 EELISRLLAEE 110 (119)
T ss_pred HHHHHHHHHHH
Confidence 88888887654
No 64
>COG2928 Uncharacterized conserved protein [Function unknown]
Probab=22.95 E-value=2.3e+02 Score=28.31 Aligned_cols=63 Identities=24% Similarity=0.291 Sum_probs=39.1
Q ss_pred hcHHHHHhhhhcCCCCccccccccchhHHHHHHHHHHHHHHHHHHH---HHHhhhhheeeEEeechhh---hhhHHHHHH
Q 014531 69 KGWFRLLHDLISREGPFLETACIPIAGLTILLWPIIVIGSIVIAIF---SSIFIGLYGSVVVYQERSF---RRGVAYVIA 142 (423)
Q Consensus 69 KGW~RLl~DLIgReGPFLET~CVPfAGLaIlLWPl~Vvgavl~aii---sS~flG~yaaVVvYQE~Sf---~~GL~Yvva 142 (423)
|+|+||-.+.+ |||- +|-|+++--.|+..++ ++++.+ |--=.-++...| .-||.++++
T Consensus 1 k~~~~lk~~fl--------------tGLl-vllPlaiT~~vv~~i~~~l~~~~~~-~lp~~~~~~~~~~~~i~~lg~il~ 64 (222)
T COG2928 1 KGAKRLKKYFL--------------TGLL-VLLPLAITLWVVSWIFGLLDQFVGP-LLPDRLRPAVYFPFNIPGLGVILA 64 (222)
T ss_pred ChHHHHHHHHH--------------HHHH-HHHHHHHHHHHHHHHHHHHHHhhhh-hccchhchhhcCchhhHHHHHHHH
Confidence 67777777775 5664 4558887766665544 344443 222223334333 368999999
Q ss_pred HhHhh
Q 014531 143 MVAEF 147 (423)
Q Consensus 143 ~Va~F 147 (423)
.+.+|
T Consensus 65 iili~ 69 (222)
T COG2928 65 IILIF 69 (222)
T ss_pred HHHHH
Confidence 99988
No 65
>TIGR02978 phageshock_pspC phage shock protein C. All members of this protein family are the phage shock protein PspC. These proteins contain a PspC domain, as do other members of the larger family of proteins described by Pfam model pfam04024. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor, PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin overexpression, ethanol, heat shock, and protein export defects.
Probab=22.08 E-value=87 Score=28.07 Aligned_cols=44 Identities=32% Similarity=0.437 Sum_probs=34.8
Q ss_pred ccCCCCCChhHHHH--HHHHHHHHhhhhhhhhc-ccCchhhHhHHHH
Q 014531 351 WDNGGLLPEDALRA--AQIQGISRRMIGLIRSV-SKFPTYRRRFRQV 394 (423)
Q Consensus 351 wd~~g~pp~d~vrr--AqLqai~RRLqGI~~s~-SR~PT~RRrf~~l 394 (423)
|+..|-+|...+++ ++++++=||||.|=+-+ |+-.+.+|+|+++
T Consensus 75 ~~~~~~~~~~~l~~~~~~~~~~e~Rl~~mE~yVTS~~f~l~ref~~L 121 (121)
T TIGR02978 75 PWQAGQSPRQALREVKREFRDLERRLRNMERYVTSDTFRLRREFRNL 121 (121)
T ss_pred hhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHhcC
Confidence 66667777776664 68999999999997765 6788889999874
No 66
>PLN00150 potassium ion transporter family protein; Provisional
Probab=22.01 E-value=1.2e+02 Score=35.11 Aligned_cols=25 Identities=20% Similarity=0.190 Sum_probs=19.9
Q ss_pred hhhhheeeEEeechhhhhhHHHHHHH
Q 014531 118 FIGLYGSVVVYQERSFRRGVAYVIAM 143 (423)
Q Consensus 118 flG~yaaVVvYQE~Sf~~GL~Yvva~ 143 (423)
++|+.+-++.||. |-..|=||=+|.
T Consensus 419 mv~~i~vv~~F~~-s~~l~~AYGiAV 443 (779)
T PLN00150 419 MVLCLVITAGFRD-TDEIGNAYGIAV 443 (779)
T ss_pred HHHHHhheEEecC-hHHHHHHhhhhe
Confidence 4788888999987 568899997764
No 67
>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=22.01 E-value=1.3e+02 Score=33.27 Aligned_cols=221 Identities=24% Similarity=0.292 Sum_probs=124.5
Q ss_pred HHHhhhhcCCCCcccccc--ccchhH-HHHHHHHHHHHHHHHHHHHHHhhhhheeeEEeechhhhhhHHHHHHHhHh---
Q 014531 73 RLLHDLISREGPFLETAC--IPIAGL-TILLWPIIVIGSIVIAIFSSIFIGLYGSVVVYQERSFRRGVAYVIAMVAE--- 146 (423)
Q Consensus 73 RLl~DLIgReGPFLET~C--VPfAGL-aIlLWPl~Vvgavl~aiisS~flG~yaaVVvYQE~Sf~~GL~Yvva~Va~--- 146 (423)
|.++...|..-=..||-- .|..|- .-+.=|+-+ +...|+=.-+-+.+||.+ .|+..-+--+--+-|-
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 445555565555556644 576664 344556655 334566677778888875 4666655544333321
Q ss_pred -hhhcccccccccCCC---cCCCcccccCCCCCCCCC--CCCCCcccCCcccCCCCCCCccccccccccccHHHhhHhhh
Q 014531 147 -FDEYTNDWLYLREGT---ILPKPRYRQKKVHSSSEL--PVGGNQVAGGKFTSASADAPAMLMPSLAHSRSVREAIQEVK 220 (423)
Q Consensus 147 -FDEYtND~LyLrEGS---c~PRP~YRK~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~p~l~~s~S~k~~iqe~k 220 (423)
=-.|-|=++|=++|| -|-|---|| ||. .--. || ...+-.+ +++ -|
T Consensus 380 h~apfRNilfyGPPGTGKTm~ArelAr~------SGlDYA~mT----GG--DVAPlG~---------------qaV--Tk 430 (630)
T KOG0742|consen 380 HQAPFRNILFYGPPGTGKTMFARELARH------SGLDYAIMT----GG--DVAPLGA---------------QAV--TK 430 (630)
T ss_pred ccchhhheeeeCCCCCCchHHHHHHHhh------cCCceehhc----CC--Cccccch---------------HHH--HH
Confidence 235778888988887 343333333 222 0000 00 0000000 011 14
Q ss_pred hHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcCCCCcceEeeccchHHHHHHHHHhhhcCCCceeecCCceeccc
Q 014531 221 MVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSVEITHL 300 (423)
Q Consensus 221 ~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~~~~~k~l~vgLPayslL~~LL~SaKa~S~Glll~D~~EiT~~ 300 (423)
+-||+||-=|| .+|-.| .|.- -+.++-..+++ .+|= .--|-|++||+-.=.-|.-++| +-..
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 66789987554 333332 1333 34566665542 2332 3457899999998888887766 4578
Q ss_pred CCCCccchhhhhhhHHHHHHHHHhccCChhHHH------HHHHhhhcCCCcc-ccccccC
Q 014531 301 NRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVR------YLEKVVLFGSTTE-RMEAWDN 353 (423)
Q Consensus 301 NrPkd~~fDWff~PllvlKeQIk~~~L~E~EE~------yL~KlvL~~~d~~-r~~~wd~ 353 (423)
|||.| |||-.+-= =+|+-..-|--+||+ ||.|.++...+.. +-+ |++
T Consensus 493 Nrpgd--lDsAV~DR---ide~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~-~~~ 546 (630)
T KOG0742|consen 493 NRPGD--LDSAVNDR---IDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGK-WSH 546 (630)
T ss_pred CCccc--hhHHHHhh---hhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCch-hhH
Confidence 99998 78865421 134445566667775 8999998877765 333 553
No 68
>cd01014 nicotinamidase_related Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia.
Probab=21.67 E-value=1.7e+02 Score=25.63 Aligned_cols=49 Identities=18% Similarity=0.305 Sum_probs=42.6
Q ss_pred CChhhHHHHHHhcCCCCcceEeeccch-HHHHHHHHHhhhcCCCceeecCCc
Q 014531 245 ITPADLKDWLKAKCVNEEAIVGFGLPC-YSFLQTLLYSIKAGSGGLLLPDSV 295 (423)
Q Consensus 245 It~~Diee~~~~k~~~~~k~l~vgLPa-yslL~~LL~SaKa~S~Glll~D~~ 295 (423)
....++++++++.+.. .++=+|+-+ +|++++-+.-.+.+=.=.|++|.+
T Consensus 85 f~~t~l~~~L~~~gi~--~viv~G~~td~CV~~Ta~~a~~~g~~v~vi~Da~ 134 (155)
T cd01014 85 FYGTDLEEWLREAGID--HLVICGAMTEMCVDTTVRSAFDLGYDVTVVADAC 134 (155)
T ss_pred cCCCCHHHHHHHCCCC--EEEEEeeccchhHHHHHHHHHHCCCcEEEecccc
Confidence 3447999999988764 589999987 999999999999999999999975
No 69
>PF01788 PsbJ: PsbJ; InterPro: IPR002682 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbJ found in PSII. PsbJ is one of the most hydrophobic proteins in the thylakoid membrane, and is located in a gene cluster with PsbE, PsbF and PsbL (PsbEFJL). Both PsbJ and PsbL (IPR003372 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbJ cause the light-harvesting antenna to remain detached from the PSII dimers []. In addition, both PsbJ and PsbL are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_J 3ARC_J 3A0B_J 3KZI_J 2AXT_J 3PRQ_J 4FBY_b 3BZ2_J 1S5L_j 3PRR_J ....
Probab=21.28 E-value=1.1e+02 Score=23.36 Aligned_cols=26 Identities=27% Similarity=0.629 Sum_probs=18.0
Q ss_pred HHHHHHHHH-HHHHHHHHHhhhhheee
Q 014531 100 LWPIIVIGS-IVIAIFSSIFIGLYGSV 125 (423)
Q Consensus 100 LWPl~Vvga-vl~aiisS~flG~yaaV 125 (423)
||=.+.++. ...+++.-||-|.|+++
T Consensus 10 LWlVgtv~G~~vi~lvglFfYGsYsGl 36 (40)
T PF01788_consen 10 LWLVGTVAGIAVIGLVGLFFYGSYSGL 36 (40)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCTTTST
T ss_pred chHHHHHHHHHHHHHHHHheecccCCc
Confidence 676655544 34567788899999875
No 70
>PF14789 THDPS_M: Tetrahydrodipicolinate N-succinyltransferase middle; PDB: 3R5A_F 3R5B_A 3R5C_B 3R5D_D 3FSY_C 3FSX_A 2RIJ_A.
Probab=21.18 E-value=34 Score=25.77 Aligned_cols=33 Identities=30% Similarity=0.542 Sum_probs=24.8
Q ss_pred cccCCCCCChhHHHHHHHHHHHHhhhh---hhhhcccCc
Q 014531 350 AWDNGGLLPEDALRAAQIQGISRRMIG---LIRSVSKFP 385 (423)
Q Consensus 350 ~wd~~g~pp~d~vrrAqLqai~RRLqG---I~~s~SR~P 385 (423)
+|.|.|.-..|+++.-|+++= +.| -+.||=|||
T Consensus 5 aWT~~GP~~~~~~~~~r~~lr---~~g~~~~V~~VDKFP 40 (41)
T PF14789_consen 5 AWTNAGPCEPEDFEENRLRLR---ARGRPLTVYSVDKFP 40 (41)
T ss_dssp EEETTEEEEHHHHHHHHHHHH---HTT----EEEEESS-
T ss_pred eecCCCCcCHHHHHHHHHHHH---hCCCCcEEEEEcCCC
Confidence 699999999999999988863 455 456677777
No 71
>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=20.79 E-value=89 Score=24.31 Aligned_cols=18 Identities=33% Similarity=0.462 Sum_probs=15.4
Q ss_pred cCChhHHHHHHHhhhcCC
Q 014531 326 KLTEPEVRYLEKVVLFGS 343 (423)
Q Consensus 326 ~L~E~EE~yL~KlvL~~~ 343 (423)
.||+.+|.||+-+-.+..
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 489999999998877764
Done!