Query 010481
Match_columns 509
No_of_seqs 47 out of 49
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 01:02:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010481.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010481hhsearch_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 95.1 0.16 3.6E-06 47.2 9.6 112 360-484 49-160 (195)
2 smart00430 HOLI Ligand binding 94.2 0.64 1.4E-05 39.5 10.2 77 355-431 34-112 (163)
3 cd06940 NR_LBD_REV_ERB The lig 93.9 0.31 6.8E-06 45.7 8.5 103 372-486 70-172 (189)
4 cd06944 NR_LBD_Ftz-F1_like The 93.1 0.81 1.7E-05 44.4 10.2 115 358-484 83-201 (237)
5 cd06931 NR_LBD_HNF4_like The l 93.0 1.5 3.2E-05 41.6 11.4 115 357-485 76-191 (222)
6 cd07069 NR_LBD_Lrh-1 The ligan 92.8 1.2 2.5E-05 43.8 10.8 116 358-484 85-203 (241)
7 cd06937 NR_LBD_RAR The ligand 92.3 0.96 2.1E-05 43.9 9.4 98 373-485 97-197 (231)
8 cd06945 NR_LBD_Nurr1_like The 92.2 0.75 1.6E-05 45.0 8.6 107 361-484 89-200 (239)
9 cd06943 NR_LBD_RXR_like The li 91.6 2.1 4.6E-05 40.0 10.6 117 357-485 74-190 (207)
10 PF00104 Hormone_recep: Ligand 91.6 1.2 2.6E-05 39.4 8.5 157 309-485 24-184 (203)
11 cd06935 NR_LBD_TR The ligand b 91.2 0.96 2.1E-05 44.2 8.2 98 372-484 110-210 (243)
12 cd06930 NR_LBD_F2 Ligand-bindi 90.9 3.5 7.5E-05 36.4 10.7 117 356-484 42-159 (165)
13 cd07075 NR_LBD_MR Ligand bindi 90.0 2.5 5.4E-05 42.2 10.0 113 365-486 80-194 (248)
14 cd07076 NR_LBD_GR Ligand bindi 89.5 3 6.6E-05 41.7 10.2 109 365-485 80-193 (247)
15 cd06948 NR_LBD_COUP-TF Ligand 89.4 2.3 5E-05 41.2 9.1 110 358-484 75-190 (236)
16 cd06929 NR_LBD_F1 Ligand-bindi 89.3 3.5 7.6E-05 37.0 9.5 116 357-485 46-161 (174)
17 cd06938 NR_LBD_EcR The ligand 89.0 3.8 8.3E-05 39.5 10.2 108 364-484 89-197 (231)
18 cd06950 NR_LBD_Tlx_PNR_like Th 88.4 4.4 9.5E-05 38.6 10.0 113 359-484 72-184 (206)
19 cd06954 NR_LBD_LXR The ligand 88.2 2.6 5.6E-05 40.5 8.4 108 366-484 95-202 (236)
20 cd06942 NR_LBD_Sex_1_like The 87.7 4.5 9.9E-05 37.8 9.5 150 309-484 2-161 (191)
21 cd07070 NR_LBD_SF-1 The ligand 86.9 5.9 0.00013 38.7 10.1 113 360-484 85-201 (237)
22 cd06949 NR_LBD_ER Ligand bindi 86.4 5.2 0.00011 39.0 9.5 117 360-484 79-199 (235)
23 cd06932 NR_LBD_PPAR The ligand 85.5 6.5 0.00014 39.1 9.8 100 370-484 117-222 (259)
24 cd07068 NR_LBD_ER_like The lig 82.2 9.9 0.00022 36.3 9.2 74 357-432 71-144 (221)
25 cd07071 NR_LBD_Nurr1 The ligan 80.7 18 0.00039 35.8 10.6 102 371-484 98-199 (238)
26 cd06157 NR_LBD The ligand bind 80.3 23 0.0005 30.2 10.0 121 356-485 41-163 (168)
27 cd06947 NR_LBD_GR_Like Ligand 79.6 17 0.00038 36.1 10.2 116 360-484 75-192 (246)
28 cd07348 NR_LBD_NGFI-B The liga 79.2 13 0.00028 36.8 9.1 112 360-484 88-199 (238)
29 cd06933 NR_LBD_VDR The ligand 78.7 11 0.00024 36.9 8.4 78 397-485 121-200 (238)
30 cd07072 NR_LBD_DHR38_like Liga 76.6 20 0.00043 35.6 9.5 112 360-484 89-200 (239)
31 cd07073 NR_LBD_AR Ligand bindi 76.5 30 0.00066 34.4 10.8 111 365-485 80-193 (246)
32 cd07074 NR_LBD_PR Ligand bindi 75.6 36 0.00078 34.3 11.1 69 360-429 75-144 (248)
33 cd06946 NR_LBD_ERR The ligand 74.0 24 0.00053 33.7 9.2 72 358-431 72-143 (221)
34 PF09862 DUF2089: Protein of u 73.4 3.8 8.3E-05 37.3 3.4 48 411-486 32-79 (113)
35 cd06936 NR_LBD_Fxr The ligand 72.4 20 0.00043 34.7 8.3 80 394-484 112-191 (221)
36 cd06952 NR_LBD_TR2_like The li 71.8 18 0.00039 34.5 7.7 73 401-484 115-187 (222)
37 cd07349 NR_LBD_SHP The ligand 71.0 13 0.00028 36.3 6.7 71 404-485 120-190 (222)
38 cd06934 NR_LBD_PXR_like The li 70.8 18 0.00038 35.2 7.5 74 397-484 117-195 (226)
39 cd07350 NR_LBD_Dax1 The ligand 69.9 20 0.00044 35.3 7.8 76 399-485 127-202 (232)
40 cd06953 NR_LBD_DHR4_like The l 66.6 29 0.00064 33.3 8.0 74 397-484 113-189 (213)
41 cd06951 NR_LBD_Dax1_like The l 53.6 65 0.0014 31.3 8.0 77 396-484 115-191 (222)
42 cd06939 NR_LBD_ROR_like The li 52.6 57 0.0012 32.2 7.5 47 398-452 130-176 (241)
43 KOG2511 Nicotinic acid phospho 46.5 14 0.00031 39.7 2.5 23 404-426 53-78 (420)
44 COG3413 Predicted DNA binding 45.2 1.3E+02 0.0028 28.8 8.5 58 412-490 155-212 (215)
45 PRK00523 hypothetical protein; 44.3 15 0.00032 31.5 1.7 23 28-51 3-25 (72)
46 PF04911 ATP-synt_J: ATP synth 42.5 31 0.00066 28.2 3.2 18 185-202 9-26 (54)
47 smart00054 EFh EF-hand, calciu 39.7 30 0.00064 20.4 2.2 27 311-342 2-28 (29)
48 cd08323 CARD_APAF1 Caspase act 36.7 37 0.00081 29.2 3.1 33 301-344 10-42 (86)
49 COG3790 Predicted membrane pro 34.9 36 0.00078 30.6 2.7 33 24-56 45-85 (97)
50 cd08819 CARD_MDA5_2 Caspase ac 33.8 93 0.002 27.6 5.0 32 301-343 15-46 (88)
51 PRK00523 hypothetical protein; 32.2 60 0.0013 27.9 3.5 26 181-206 1-26 (72)
52 PF14946 DUF4501: Domain of un 31.7 1E+02 0.0022 30.4 5.5 22 241-262 112-133 (180)
53 PRK01844 hypothetical protein; 29.5 35 0.00076 29.3 1.7 22 29-51 3-24 (72)
54 PLN00151 potassium transporter 29.3 70 0.0015 37.9 4.6 26 204-230 479-504 (852)
55 cd08785 CARD_CARD9-like Caspas 28.2 63 0.0014 28.0 3.1 33 301-344 12-44 (86)
56 PLN00149 potassium transporter 27.8 78 0.0017 37.2 4.6 25 204-229 406-430 (779)
57 PRK13511 6-phospho-beta-galact 27.5 83 0.0018 34.1 4.5 54 370-423 209-286 (469)
58 COG2981 CysZ Uncharacterized p 27.4 64 0.0014 33.3 3.4 31 182-212 68-107 (250)
59 PF01325 Fe_dep_repress: Iron 23.2 71 0.0015 25.5 2.3 18 412-429 1-18 (60)
60 cd01014 nicotinamidase_related 21.8 1.7E+02 0.0037 26.3 4.8 49 331-381 85-134 (155)
61 TIGR02978 phageshock_pspC phag 21.7 87 0.0019 28.7 2.9 44 437-480 75-121 (121)
62 cd04371 DEP DEP domain, named 21.6 44 0.00096 26.6 0.9 31 305-335 29-67 (81)
63 cd08810 CARD_BCL10 Caspase act 21.4 1E+02 0.0023 26.7 3.2 34 301-345 12-45 (84)
64 TIGR00794 kup potassium uptake 20.9 1.5E+02 0.0032 34.5 5.0 26 204-230 373-398 (688)
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=95.14 E-value=0.16 Score=47.21 Aligned_cols=112 Identities=15% Similarity=0.223 Sum_probs=73.1
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccC
Q 010481 360 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDN 439 (509)
Q Consensus 360 lL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~ 439 (509)
+++ +-++...+++++.+.||..++..+-......+ +.+++.-+=++++.++++++|=.||+-++|++.|.....
T Consensus 49 ll~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl~---- 122 (195)
T cd06941 49 LVR-ISRLINSKSGSITFDDGISISRQQLDIIYDSD-FVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLS---- 122 (195)
T ss_pred HHH-HHHHHcCCCCeEEecCCeEeeHHHHHhccchH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCCC----
Confidence 444 44677778888999998776643321100012 456777788899999999999999999999997754433
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 440 GGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 440 ~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
..+.+++.|= .+..=|+.-+. +++|....||-+++..|
T Consensus 123 ----~~~~Ve~lq~-~~~~aL~~~i~--~~~p~~~~rf~~Ll~~L 160 (195)
T cd06941 123 ----EPKKVAILQD-RVLEALKVQVS--RNRPAEAQLFASLLMKI 160 (195)
T ss_pred ----CHHHHHHHHH-HHHHHHHHHHH--hhCCCcccHHHHHHHHh
Confidence 4445555541 11222333333 46788888999887654
No 2
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=94.15 E-value=0.64 Score=39.53 Aligned_cols=77 Identities=22% Similarity=0.248 Sum_probs=58.7
Q ss_pred cchHHHHHHHHHhhhcCCCceeecCCceecccCCC--CccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCc
Q 010481 355 LPCYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRP--NNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 431 (509)
Q Consensus 355 LPayslL~~LL~SaKa~S~Glll~D~~EiT~~NrP--kdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~ 431 (509)
-+.+.+|...-+|.|.+...++..||+.+...... .......+...+.-+-+.++.+++|++|=.||.-++++..|.
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 45688899999999998887777887666543322 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=93.90 E-value=0.31 Score=45.72 Aligned_cols=103 Identities=17% Similarity=0.238 Sum_probs=69.7
Q ss_pred CCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHH
Q 010481 372 SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAA 451 (509)
Q Consensus 372 S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrA 451 (509)
...+.+.||..++...-+...+-+ +.+++.-+=++++.++++++|=.||+-++|++.|... +-..+.|++.
T Consensus 70 ~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~--------L~~~~~Ve~l 140 (189)
T cd06940 70 ERSVTFLSGQKYSVDDLHSMGAGD-LLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSG--------LENVNLVEAL 140 (189)
T ss_pred CCeEEecCCcEEcHHHHHHcCcHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcC--------CCCHHHHHHH
Confidence 344777788766543322222323 3455667789999999999999999999999987543 3356677777
Q ss_pred HHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHHH
Q 010481 452 QIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALVS 486 (509)
Q Consensus 452 qLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~~ 486 (509)
| +.+..-|+..++ .++|....||-+++..|-.
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 344445555544 3578888899998876643
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=93.13 E-value=0.81 Score=44.44 Aligned_cols=115 Identities=16% Similarity=0.294 Sum_probs=74.6
Q ss_pred HHHHHHHHHhhhcC-CCceeecCCceecccCCCC---ccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 010481 358 YSFLQTLLYSIKAG-SGGLLLPDSVEITHLNRPN---NKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 433 (509)
Q Consensus 358 yslL~~LL~SaKa~-S~Glll~D~~EiT~~NrPk---dr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r 433 (509)
+.+|...-+|+..+ ++.+++.||..+...+-+. ....+ +.+.+.-+=..++.++++++|=.||+-++|++.|...
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 45677777888887 7778999998876554222 11223 3455666667899999999999999999999987543
Q ss_pred cccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 434 MEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 434 ~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
.. ..+.+.+.| +.+..-|+.-+. .++|..-.||-+++-.|
T Consensus 162 L~--------~~~~Ve~~q-~~~~~aL~~y~~--~~~~~~~~Rf~~LL~~L 201 (237)
T cd06944 162 LE--------NRQLVESVQ-EQVNAALLDYTL--CNYPQQTDKFGQLLLRL 201 (237)
T ss_pred CC--------CHHHHHHHH-HHHHHHHHHHHH--hhCCCCccHHHHHHHHh
Confidence 32 334444443 222333443333 45666677888776543
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=92.97 E-value=1.5 Score=41.56 Aligned_cols=115 Identities=17% Similarity=0.196 Sum_probs=73.7
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHH-HHHHHHHhccCChhHHhHHHHhhhcCCCccccc
Q 010481 357 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIM-VLKEQISVLKLTEPEVRYLEKVVLFGSTTERME 435 (509)
Q Consensus 357 ayslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~Pll-vlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~ 435 (509)
.+.+|..--+|. .+.+++++.||..++..+-+ ..+-+. .++.+ -+-++++.+++|++|=.||+-+++++.|..+..
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 566676667776 45788999999866654433 222222 33332 466789999999999999999999998765543
Q ss_pred cccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 010481 436 AWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 485 (509)
Q Consensus 436 ~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~ 485 (509)
....+++.|=+ +..=|+..++ .+.|..-.||-+++..|.
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 346888899999887654
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=92.76 E-value=1.2 Score=43.76 Aligned_cols=116 Identities=16% Similarity=0.261 Sum_probs=74.4
Q ss_pred HHHHHHHHHhhhcCCCc-eeecCCceecccCC-CCccc-hhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccc
Q 010481 358 YSFLQTLLYSIKAGSGG-LLLPDSVEITHLNR-PNNKL-LDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERM 434 (509)
Q Consensus 358 yslL~~LL~SaKa~S~G-lll~D~~EiT~~Nr-Pkdr~-fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 434 (509)
+.+|...-+|+..+..+ +++.+|+.++.... +.... ++=+.+++.-+-++++.++++++|=.||+-++|++.|....
T Consensus 85 llvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~gL 164 (241)
T cd07069 85 LLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNL 164 (241)
T ss_pred HHHHHHHHHhhccCCCCeeEecCCCccCchhhhhhhhhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCC
Confidence 44555556677665444 77788876654331 11111 32234667678889999999999999999999999876443
Q ss_pred ccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 435 EAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 435 ~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
. ..+.|++.|= .+..-|+.-++ .++|.-..||-+++=.|
T Consensus 165 ~--------~~~~Ve~lQe-~~~~aL~~yi~--~~~p~~~~Rf~kLLl~L 203 (241)
T cd07069 165 E--------NFQLVEGVQE-QVNAALLDYTM--CNYPQQTEKFGQLLLRL 203 (241)
T ss_pred C--------CHHHHHHHHH-HHHHHHHHHHH--hcCCCchhHHHHHHHHh
Confidence 3 4445555442 22334555444 47899999998776433
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=92.29 E-value=0.96 Score=43.93 Aligned_cols=98 Identities=12% Similarity=0.256 Sum_probs=68.7
Q ss_pred CceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHH
Q 010481 373 GGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ 452 (509)
Q Consensus 373 ~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq 452 (509)
.-+.+.+|..++..+-.+.. +.-+.+++.-+=++++.++++++|=.||+-++|++.|..... ..+.|++.|
T Consensus 97 ~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~--------~~~~Ve~lQ 167 (231)
T cd06937 97 DTMTFSDGLTLNRTQMHNAG-FGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLE--------EPDRVEKLQ 167 (231)
T ss_pred CeEEecCCceecHHHHhhcC-hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccCC--------CHHHHHHHH
Confidence 33667777665554433322 335678888899999999999999999999999998754333 555666666
Q ss_pred ---HHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 010481 453 ---IQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 485 (509)
Q Consensus 453 ---Lqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~ 485 (509)
++|+-+-+. .++|.-..||-.++-.|-
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 445544332 468998899998875553
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=92.22 E-value=0.75 Score=44.97 Aligned_cols=107 Identities=15% Similarity=0.241 Sum_probs=69.7
Q ss_pred HHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCC
Q 010481 361 LQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNG 440 (509)
Q Consensus 361 L~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~ 440 (509)
|..--+|... .+.+++.+|.-++.... +..+-+ +.++++-.=++++.++++++|..||+.++|++.|...
T Consensus 89 L~~a~r~~~~-~~~l~~~~~~~~~~~~~-~~~~~~-~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~g------- 158 (239)
T cd06945 89 LRLAYRSNPV-DGKLVFCNGLVLHRLQC-VRGFGE-WLDSILAFSSSLQSLLLDDISAFCCLALLLLITERHG------- 158 (239)
T ss_pred HHHHHHhcCC-CCceEeeCCceecHHHH-HHhHHH-HHHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCccc-------
Confidence 3333445443 34477778876665543 223334 4688887778999999999999999999999876533
Q ss_pred CCCChhHHHHHH---HHHHHHhhhhhhhhcccCc--hhhHhHHHHHHHH
Q 010481 441 GLLPEDALRAAQ---IQGISRRMIGLIRSVSKFP--TYRRRFRQVVKAL 484 (509)
Q Consensus 441 g~pp~d~vrrAq---Lqai~RRLqGi~~s~SR~P--T~RRrf~~lvK~L 484 (509)
+-..+.|.+.| ++|+-+.+ + .++| .-..||-+++-.|
T Consensus 159 -L~~~~~Ve~lQe~~~~aL~~y~----~--~~~p~~~~~~rf~kLLl~L 200 (239)
T cd06945 159 -LKEPKKVEELQNKIISCLRDHV----T--SNYPGQDKPNRLSKLLLKL 200 (239)
T ss_pred -cCCHHHHHHHHHHHHHHHHHHH----H--HhCCCcccccHHHHHHHHh
Confidence 33555666665 44443333 2 3567 7777888876443
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=91.64 E-value=2.1 Score=40.02 Aligned_cols=117 Identities=16% Similarity=0.226 Sum_probs=69.5
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccccc
Q 010481 357 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEA 436 (509)
Q Consensus 357 ayslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~ 436 (509)
.+.+|..--+|.. ..+|+++++|..++...-.+..+-+.+-..+--+-..++.+++|++|=.+|+-++|++.|.....
T Consensus 74 e~~~l~~a~~s~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L~- 151 (207)
T cd06943 74 ELLIAAFAHRSIA-VKDGILLATGLHLHRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLK- 151 (207)
T ss_pred HHHHHHHHHHccC-CCCeeEecCCceeccchhhhccchHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCCC-
Confidence 3455555455554 36889999997776543333333333222222466789999999999999999999997654322
Q ss_pred ccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 010481 437 WDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 485 (509)
Q Consensus 437 wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~ 485 (509)
..+.+.+.| +.+..=|+..+. .++|.-..||-+++-.|-
T Consensus 152 -------~~~~v~~~q-~~~~~aL~~y~~--~~~~~~~~Rf~~LLl~L~ 190 (207)
T cd06943 152 -------SRQEVESLR-EKVYASLEEYCR--QKHPEQPGRFAKLLLRLP 190 (207)
T ss_pred -------CHHHHHHHH-HHHHHHHHHHHH--hhCCCcccHHHHHHHHHH
Confidence 233333333 112222333332 346777778888875543
No 10
>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=91.63 E-value=1.2 Score=39.39 Aligned_cols=157 Identities=16% Similarity=0.222 Sum_probs=97.8
Q ss_pred HHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcCCCCceeEeeccchHHHHHHHHHhhhcCCCceeecCCceecccCC
Q 010481 309 QIWVNMMRSCETRGRELLDADVITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSVEITHLNR 388 (509)
Q Consensus 309 qiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~~~~~~~i~vgLPayslL~~LL~SaKa~S~Glll~D~~EiT~~Nr 388 (509)
++|+..+..+-.--+.+=.=.-++..|=...++. +.+.+.+|..--+|...+.+.+.+.+|..+...+-
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 6666666666666666544455677774444443 35677888888888777889999999988755443
Q ss_pred CCc--cchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHH-HHHH-HHHHHhhhhhh
Q 010481 389 PNN--KLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALR-AAQI-QGISRRMIGLI 464 (509)
Q Consensus 389 Pkd--r~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vr-rAqL-qai~RRLqGi~ 464 (509)
+.. ..+.=+.+.+.-+=..++.+++|++|=.+|.-+++++.+..... + +..+ -.++ +.+++-|+=..
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~--------~-~~~~~~~~~r~~~~~~L~~y~ 163 (203)
T PF00104_consen 93 DDFITGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGLS--------E-ETREIVEELRDRIIQALHSYY 163 (203)
T ss_dssp HHTSTTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTHS----------SHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhcccccccc--------c-chhHHHHHHHHHHHHHHHHHH
Confidence 322 22222223444444499999999999999999999987554422 1 2222 1222 23555565555
Q ss_pred hhcccCchhhHhHHHHHHHHH
Q 010481 465 RSVSKFPTYRRRFRQVVKALV 485 (509)
Q Consensus 465 ~s~SR~PT~RRrf~~lvK~L~ 485 (509)
..-...+.+-.||-++++.|-
T Consensus 164 ~~~~~~~~~~~R~~~ll~ll~ 184 (203)
T PF00104_consen 164 NQSKGPEDYAQRFGKLLLLLP 184 (203)
T ss_dssp HHHHSTTTHTTHHHHHHHHHH
T ss_pred hccCCCccHHHHHHHHHHHHH
Confidence 444566667888888877653
No 11
>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=91.20 E-value=0.96 Score=44.25 Aligned_cols=98 Identities=18% Similarity=0.208 Sum_probs=70.1
Q ss_pred CCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHH
Q 010481 372 SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAA 451 (509)
Q Consensus 372 S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrA 451 (509)
.+-+++++|..++..+-....+-+ +.+++.-+=+++++++|+++|=.||+-++|++.|..... ..+.|.+-
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL~--------~~~~Ve~l 180 (243)
T cd06935 110 SETLTLSGEMAVTREQLKNGGLGV-VSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLA--------CVERIEKL 180 (243)
T ss_pred CCeEEeeCCeEeeHHHHHhcChHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCCC--------CHHHHHHH
Confidence 456888888877665433444445 678888899999999999999999999999998764433 45555555
Q ss_pred H---HHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 452 Q---IQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 452 q---Lqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
| ++|+-+- ++ .+.|....||-.++-.|
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 4444332 22 35688888999887665
No 12
>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=90.92 E-value=3.5 Score=36.38 Aligned_cols=117 Identities=19% Similarity=0.228 Sum_probs=74.4
Q ss_pred chHHHHHHHHHhhhcC-CCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccc
Q 010481 356 PCYSFLQTLLYSIKAG-SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERM 434 (509)
Q Consensus 356 PayslL~~LL~SaKa~-S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 434 (509)
+.+.+|..--+|.+.+ ++++..++|..+...+-.+....++ .+.+.-+=++++.+++|++|=.+|+-+++++.|....
T Consensus 42 ~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~~l 120 (165)
T cd06930 42 AELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAEL-VQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGL 120 (165)
T ss_pred HHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCC
Confidence 4566777777888885 5678888988777665443333343 4566667788999999999999999999998765332
Q ss_pred ccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 435 EAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 435 ~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
. ..+.+.+.| +.+.+=|+..+.. +.|..--||-+++-.|
T Consensus 121 ~--------~~~~v~~~q-~~~~~aL~~~~~~--~~~~~~~R~~~ll~~l 159 (165)
T cd06930 121 K--------NQQQVEELQ-EKAQQALQEYIRK--RYPQQPARFAKLLLRL 159 (165)
T ss_pred c--------CHHHHHHHH-HHHHHHHHHHHHh--hCCCchhHHHHHHHHh
Confidence 2 223333322 2233333333332 2366667777776554
No 13
>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=89.98 E-value=2.5 Score=42.23 Aligned_cols=113 Identities=17% Similarity=0.199 Sum_probs=72.8
Q ss_pred HHhhhc-CCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCC
Q 010481 365 LYSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLL 443 (509)
Q Consensus 365 L~SaKa-~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~p 443 (509)
-||.-. +++-+++.+|.-++..+-++..+.| +.+++.-+=.+++.++|+++|=.||+-++|++.|+.+ |+-
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 355554 3555888888888777766667888 5677776777899999999999999999999987422 222
Q ss_pred ChhHHHHHHHHHHHHhhhhhhh-hcccCchhhHhHHHHHHHHHH
Q 010481 444 PEDALRAAQIQGISRRMIGLIR-SVSKFPTYRRRFRQVVKALVS 486 (509)
Q Consensus 444 p~d~vrrAqLqai~RRLqGi~~-s~SR~PT~RRrf~~lvK~L~~ 486 (509)
..+.+.+-|= .+.+-|+-.++ .=...|..-.||-++.+-|-.
T Consensus 152 ~~~~Ve~lqe-~~~~aL~~yi~~~~~~~~~~~~RF~~LLllLp~ 194 (248)
T cd07075 152 SQAAFEEMRT-NYIKELRKMVTKAPNNSGQSWQRFYQLTKLLDS 194 (248)
T ss_pred CHHHHHHHHH-HHHHHHHHHHHHcCCCcccchhHHHHHHHHHHH
Confidence 3333333321 12222333322 113345666899988876543
No 14
>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=89.55 E-value=3 Score=41.65 Aligned_cols=109 Identities=14% Similarity=0.276 Sum_probs=66.6
Q ss_pred HHhhhcCCCc-eeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCC-CccccccccCCCC
Q 010481 365 LYSIKAGSGG-LLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS-TTERMEAWDNGGL 442 (509)
Q Consensus 365 L~SaKa~S~G-lll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~-d~~r~~~wd~~g~ 442 (509)
-||.+.+..- +++.+|.-++..+--...+.+ +..++.-+=.++++++++++|=.||+-++|++. |....+
T Consensus 80 ~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~~~-~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~------- 151 (247)
T cd07076 80 WRSYRQSNGNLLCFAPDLIINEQRMTLPCMYD-QCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLK------- 151 (247)
T ss_pred HhccCCCCCceEEecCCeeecHHHHhhhhHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCC-------
Confidence 4777654433 667777766655432233444 466777888899999999999999999999986 543333
Q ss_pred CChh---HHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 010481 443 LPED---ALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 485 (509)
Q Consensus 443 pp~d---~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~ 485 (509)
..+ ++|..=+.|+-+-+. +.-...|...+||-++..-|-
T Consensus 152 -~~~~Ve~lqe~~~~aL~~yi~---~~~p~~~~~~~RF~kLLllLp 193 (247)
T cd07076 152 -SQELFDEIRMTYIKELGKAIV---KREGNSSQNWQRFYQLTKLLD 193 (247)
T ss_pred -CHHHHHHHHHHHHHHHHHHHH---hcCCCcchhhhHHHHHHHHHH
Confidence 333 333333333333221 111223444669998876653
No 15
>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=89.45 E-value=2.3 Score=41.25 Aligned_cols=110 Identities=16% Similarity=0.308 Sum_probs=68.5
Q ss_pred HHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHH---HHHHHHhccCChhHHhHHHHhhhcCCCcccc
Q 010481 358 YSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMV---LKEQISVLKLTEPEVRYLEKVVLFGSTTERM 434 (509)
Q Consensus 358 yslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~Pllv---lKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 434 (509)
.-+|.+--+|...+.+-++..||..+...+ .+++-+ +.+.+-+ +=.+++.+++|++|=.||+-++|++.|....
T Consensus 75 l~lL~~a~~s~~~~~~~~~~~~g~~~~~~~--~~~~~~-~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L 151 (236)
T cd06948 75 LFVLNAAQCCMPLHVAPLLAAAGLHASPMS--ADRVVA-FMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGL 151 (236)
T ss_pred HHHHHHHHHcccccchhhhhccccccCccc--hhhHhH-HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCcccccc
Confidence 345555556666666667778887654332 122222 2333322 2357899999999999999999999775443
Q ss_pred ccccCCCCCChhHHHHHH---HHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 435 EAWDNGGLLPEDALRAAQ---IQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 435 ~~wd~~g~pp~d~vrrAq---Lqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
. ..+.+++.| ++|+-+-.+ .++|....||-+++-.|
T Consensus 152 ~--------~~~~v~~~q~~~~~aL~~y~~------~~~~~~~~Rf~~LLl~L 190 (236)
T cd06948 152 S--------DPAHIESLQEKSQCALEEYVR------TQYPNQPTRFGKLLLRL 190 (236)
T ss_pred c--------CHHHHHHHHHHHHHHHHHHHH------HhCCCcccHHHHHHHHH
Confidence 2 334455544 555555443 34677778898876544
No 16
>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=89.26 E-value=3.5 Score=36.96 Aligned_cols=116 Identities=17% Similarity=0.258 Sum_probs=70.5
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccccc
Q 010481 357 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEA 436 (509)
Q Consensus 357 ayslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~ 436 (509)
.+.++..- ++.+.+.+.+..+||+......-+.... .=+.+.+.-+=..++.+++|++|=.+|+-+++++.|.....
T Consensus 46 ~l~~l~~a-~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l~- 122 (174)
T cd06929 46 EILLLRSA-TLYDPEKNSLTFGDGKGNSRDVLLNGGF-GEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQ- 122 (174)
T ss_pred HHHHHHHH-HHhcccCCeEEecCCceecHHHHHHccc-HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCc-
Confidence 34444443 5677888889999997633221111111 12345555566889999999999999999999987654322
Q ss_pred ccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 010481 437 WDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 485 (509)
Q Consensus 437 wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~ 485 (509)
..+.+.+.| +.+..-|+-.+ ..++|....||-+++..|.
T Consensus 123 -------~~~~v~~~q-~~~~~aL~~y~--~~~~~~~~~Rf~~Ll~~l~ 161 (174)
T cd06929 123 -------DVDTVEKLQ-ERLLEALQRYL--KVNHPDAPQMFAKLLKKLT 161 (174)
T ss_pred -------CHHHHHHHH-HHHHHHHHHHH--HhcCCCChhHHHHHHHHhH
Confidence 233333333 12223333333 2457788889998877654
No 17
>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=88.98 E-value=3.8 Score=39.53 Aligned_cols=108 Identities=15% Similarity=0.214 Sum_probs=70.1
Q ss_pred HHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCC
Q 010481 364 LLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLL 443 (509)
Q Consensus 364 LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~p 443 (509)
+-++...+.+.++..||...+..+-....+ .=+.+++.-+-++++.++++++|=.+|+-+++++ | | .|+-
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 2246677777889999999999999999999985 2 1 1332
Q ss_pred ChhHHHHHHHHHHHHhhhhhhhhcccCch-hhHhHHHHHHHH
Q 010481 444 PEDALRAAQIQGISRRMIGLIRSVSKFPT-YRRRFRQVVKAL 484 (509)
Q Consensus 444 p~d~vrrAqLqai~RRLqGi~~s~SR~PT-~RRrf~~lvK~L 484 (509)
..+.+.+.|= .+..-|+-.+. .++|. -..||-+++-.|
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 3444444442 23334444444 34565 677888876544
No 18
>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=88.42 E-value=4.4 Score=38.58 Aligned_cols=113 Identities=19% Similarity=0.257 Sum_probs=65.2
Q ss_pred HHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccccccc
Q 010481 359 SFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWD 438 (509)
Q Consensus 359 slL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd 438 (509)
.+|..--+|...+..-++-+++......+ +.....+. ...+.-+-.+++.++++++|=.||+-++|++.|....
T Consensus 72 ~iL~~a~~s~~~~~~~ll~~~~~~~~~~~-~~~~~~~~-~~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L---- 145 (206)
T cd06950 72 FLLGAAQWSLPLDSCPLLAVPGLSPDNTE-AERTFLSE-VRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGL---- 145 (206)
T ss_pred HHHHHHHHhcCCCcceeecCCcccccccc-hhhHHHHH-HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCC----
Confidence 34444455655444433333443222222 22223332 2334445568999999999999999999999875433
Q ss_pred CCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 439 NGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 439 ~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
-..+.+++.| +.+..-|+--+. .++|.-..||-+++-.|
T Consensus 146 ----~~~~~Ve~lq-~~~~~aL~~y~~--~~~~~~~~Rf~kLLl~L 184 (206)
T cd06950 146 ----KDPAQVEALQ-DQAQLMLNKHIR--TRYPTQPARFGKLLLLL 184 (206)
T ss_pred ----CCHHHHHHHH-HHHHHHHHHHHH--HhCCCcccHHHHHHHHH
Confidence 2445566655 333333444333 45788888999887544
No 19
>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=88.18 E-value=2.6 Score=40.55 Aligned_cols=108 Identities=17% Similarity=0.226 Sum_probs=66.8
Q ss_pred HhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCCh
Q 010481 366 YSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPE 445 (509)
Q Consensus 366 ~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~ 445 (509)
++.....+.+.+.||..++..+-....+..=+.+++.-+-+.++.++++++|=.||+-++|++.|..... ..
T Consensus 95 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL~--------~~ 166 (236)
T cd06954 95 RRYNPESEAITFLKDFPYSRDDFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQ--------DH 166 (236)
T ss_pred HHhcCCCCeEEeeCCccccHHHHHHhcChHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccCC--------CH
Confidence 3445556778888987766543221222223456666788899999999999999999999997743322 33
Q ss_pred hHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 446 DALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 446 d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
+.|.+.|= .+..=|+--++ +++|.-+.||-.+.-.|
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 20
>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=87.73 E-value=4.5 Score=37.79 Aligned_cols=150 Identities=15% Similarity=0.196 Sum_probs=84.7
Q ss_pred HHHHHHHHHHHhhhhhhhc-------cCCCChhhHHHHHHhcCCCCceeEeeccchHHHHHHHHHhhhcCCCceeecCCc
Q 010481 309 QIWVNMMRSCETRGRELLD-------ADVITPADLKDWLKAKCVNEEAIVGFGLPCYSFLQTLLYSIKAGSGGLLLPDSV 381 (509)
Q Consensus 309 qiwd~lfk~ce~~G~~Ll~-------~gvIt~~Diee~~~~k~~~~~~~i~vgLPayslL~~LL~SaKa~S~Glll~D~~ 381 (509)
++|.++.+.....-+..++ =.-++.+|=-.-+++.-. +. .+| .+-++.... +.++.||.
T Consensus 2 ~~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~----------e~-~ll-~~~~~~~~~--~~~~~~g~ 67 (191)
T cd06942 2 NAWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMF----------PL-YLL-RLSRDYNNE--GTVLCDFR 67 (191)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHH----------HH-HHH-HHHHHhCcC--CeEEeCCc
Confidence 5677776666654444332 122444453333333211 12 223 344665544 88999998
Q ss_pred eecccCC-CCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCC--ccccccccCCCCCChhHHHHHHHHHHHH
Q 010481 382 EITHLNR-PNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGST--TERMEAWDNGGLLPEDALRAAQIQGISR 458 (509)
Q Consensus 382 EiT~~Nr-Pkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d--~~r~~~wd~~g~pp~d~vrrAqLqai~R 458 (509)
.++...- .+....+ +.+++.-+=+.++++++|++|=.||+-+++++.| ..... ....+... .+.+.+
T Consensus 68 ~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~--------~~~~v~~~-q~~l~~ 137 (191)
T cd06942 68 PVEFASLLSQLLHGK-LIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLGIQLE--------ETAKSNLQ-LSVLFQ 137 (191)
T ss_pred cccHHHHHHhcchHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCcc--------chHHHHHH-HHHHHH
Confidence 8865321 0111223 4566677778999999999999999999999987 43322 22222221 123344
Q ss_pred hhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 459 RMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 459 RLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
-|+=-+. .++|.-..||-.++-.|
T Consensus 138 ~L~~~~~--~~~~~~~~rf~kLL~~l 161 (191)
T cd06942 138 FLKSVLF--KDGEDTEQRLQKLFDIL 161 (191)
T ss_pred HHHHHHH--hcCCChHHHHHHHHHHH
Confidence 4432222 36787778888776544
No 21
>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=86.92 E-value=5.9 Score=38.73 Aligned_cols=113 Identities=16% Similarity=0.283 Sum_probs=69.0
Q ss_pred HHHHHHHhhhc-CCCceeecCCceecccCCCCccchhhhhhhHHH---HHHHHHhccCChhHHhHHHHhhhcCCCccccc
Q 010481 360 FLQTLLYSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMV---LKEQISVLKLTEPEVRYLEKVVLFGSTTERME 435 (509)
Q Consensus 360 lL~~LL~SaKa-~S~Glll~D~~EiT~~NrPkdr~fDWff~Pllv---lKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~ 435 (509)
+|...-+|.-. +.+-+++.+|++++..+-.. ..-.++-..... +=.+++.++++++|=.||+-++|++.|.....
T Consensus 85 vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~-~~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~ 163 (237)
T cd07070 85 VFDHIYRQVQHGKEGSILLVTGQEVELSTVAA-QAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLN 163 (237)
T ss_pred HHHHHHHhhhcCCCCceeecCCCeechhHHHH-HHhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCCC
Confidence 44555666644 34557788999887555221 111232223322 44578899999999999999999987653322
Q ss_pred cccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 436 AWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 436 ~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
....|+..|=+ +..-|+..++ .++|.-..||-+++-.|
T Consensus 164 --------~~~~Ve~lQe~-~~~aL~~y~~--~~~p~~~~Rf~kLLl~L 201 (237)
T cd07070 164 --------NHSLVKDAQEK-ANAALLDYTL--CHYPHCGDKFQQLLLRL 201 (237)
T ss_pred --------CHHHHHHHHHH-HHHHHHHHHH--hcCCCcchHHHHHHHHh
Confidence 33344444322 2233444444 47899999999986544
No 22
>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=86.44 E-value=5.2 Score=39.02 Aligned_cols=117 Identities=15% Similarity=0.174 Sum_probs=70.1
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCC-CCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccccccc
Q 010481 360 FLQTLLYSIKAGSGGLLLPDSVEITHLNR-PNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWD 438 (509)
Q Consensus 360 lL~~LL~SaKa~S~Glll~D~~EiT~~Nr-Pkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd 438 (509)
+|..--+|...+. -+++.+|..++.... ++.. +..+++++.-+=++++.++++++|=.||+-++|++.|.... .
T Consensus 79 ~L~~a~rs~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~---~ 153 (235)
T cd06949 79 MLGLVWRSMEHPG-KLLFAPDLLLDRNQGSCVEG-MVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTF---L 153 (235)
T ss_pred HHHHHHHhcCCCC-eEEeeCCceecHHHhhhccc-HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCc---c
Confidence 4444456665543 366677766554322 1333 33456777777779999999999999999999998764220 0
Q ss_pred CCCCCChhHHHHHHHHHHHHhhhhhhhhcccC---chhhHhHHHHHHHH
Q 010481 439 NGGLLPEDALRAAQIQGISRRMIGLIRSVSKF---PTYRRRFRQVVKAL 484 (509)
Q Consensus 439 ~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~---PT~RRrf~~lvK~L 484 (509)
+-+......+++.| +.+..-|+--+. .++ |.-..||-+++-.|
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 00123455566666 333344444443 244 78888888876443
No 23
>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=85.51 E-value=6.5 Score=39.11 Aligned_cols=100 Identities=17% Similarity=0.336 Sum_probs=67.5
Q ss_pred cCCCceeecCCce-ecccC--CCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChh
Q 010481 370 AGSGGLLLPDSVE-ITHLN--RPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPED 446 (509)
Q Consensus 370 a~S~Glll~D~~E-iT~~N--rPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d 446 (509)
.+.+++++.+|-. +|... ..... +.=+.+|+.-+=++++.++|+++|=.||+-++|++.|... +-..+
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~g--------L~~~~ 187 (259)
T cd06932 117 YNKDGLLFPEGNGYVTREFLESLRKP-FCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPG--------LINRK 187 (259)
T ss_pred cCCCCeEEeCCCEEeeHHHHHHhccc-HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCccc--------CcCHH
Confidence 3566777776532 33321 11111 2336788888899999999999999999999999987543 33555
Q ss_pred HHHHHH---HHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 447 ALRAAQ---IQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 447 ~vrrAq---Lqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
.|++.| ++|+-+-+. +++|....||-.++-.|
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 455554432 45799999998886544
No 24
>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=82.24 E-value=9.9 Score=36.35 Aligned_cols=74 Identities=18% Similarity=0.230 Sum_probs=47.2
Q ss_pred hHHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcc
Q 010481 357 CYSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTE 432 (509)
Q Consensus 357 ayslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~ 432 (509)
.+.+|.+--+|+..+. ++.+++|.-.+.....+..+-+ +.+++.-+=..++.++++++|=.+|+-+++++.|..
T Consensus 71 ~~~~l~~a~~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~ 144 (221)
T cd07068 71 EILMLGLVWRSLPHPG-KLVFAPDLLLDREQARVEGLLE-IFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVR 144 (221)
T ss_pred HHHHHHHHHhhcCCCC-eEEeCCCceECHHHHhhccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcc
Confidence 4555666566665544 7888888644432211223323 234444455689999999999999999999975543
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=80.70 E-value=18 Score=35.75 Aligned_cols=102 Identities=10% Similarity=0.147 Sum_probs=66.7
Q ss_pred CCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHH
Q 010481 371 GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRA 450 (509)
Q Consensus 371 ~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrr 450 (509)
..+.+++.+|.-.+..+. ...+-+ +.+++.-+=++++.++|+++|=.||+-++|++ |. .|+-..+.|.+
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 334445 57788888899999999999999999999883 32 23334444444
Q ss_pred HHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 451 AQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 451 AqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
-| +.+..-|+..++.=...|.-..||-.+.-.|
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 1223445555554344678888998876544
No 26
>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=80.35 E-value=23 Score=30.24 Aligned_cols=121 Identities=18% Similarity=0.204 Sum_probs=78.3
Q ss_pred chHHHHHHHHHhhhcCCCceeecCCceec-ccCCCCccch-hhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccc
Q 010481 356 PCYSFLQTLLYSIKAGSGGLLLPDSVEIT-HLNRPNNKLL-DWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTER 433 (509)
Q Consensus 356 PayslL~~LL~SaKa~S~Glll~D~~EiT-~~NrPkdr~f-DWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r 433 (509)
..+.+|...-+|.+.+....+..++...+ ..+.+..+.+ .=+-..+.-+-+.++.+++|++|=.+|+-++++..+..+
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 122234455667889999999999999999999866421
Q ss_pred cccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHH
Q 010481 434 MEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALV 485 (509)
Q Consensus 434 ~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~ 485 (509)
+.-..+-+++ .-+.+.+-|+-.+..-.. |..--||-+++..+.
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 1223333333 335566666666655444 677778888887654
No 27
>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=79.60 E-value=17 Score=36.10 Aligned_cols=116 Identities=15% Similarity=0.159 Sum_probs=65.2
Q ss_pred HHHHHHHhhhcC-CCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCcccccccc
Q 010481 360 FLQTLLYSIKAG-SGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWD 438 (509)
Q Consensus 360 lL~~LL~SaKa~-S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd 438 (509)
+|..-.+|.-.+ ++-+++.+|.-++...--+..+.| +.+++.-+=.+++.++++++|=.||+-++|++.++ +
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 45666556668999999999999999999999632 1
Q ss_pred CCCCCChhHHHHHHHHHHHHhhhhhhhh-cccCchhhHhHHHHHHHH
Q 010481 439 NGGLLPEDALRAAQIQGISRRMIGLIRS-VSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 439 ~~g~pp~d~vrrAqLqai~RRLqGi~~s-~SR~PT~RRrf~~lvK~L 484 (509)
.|+-..+.|.+-| |.+..-|+.-++. --..|...+||-++..-|
T Consensus 148 -~gL~~~~~Ve~lq-e~i~~AL~~yi~~~~~~~~~~~~Rf~kLLllL 192 (246)
T cd06947 148 -DGLKSQAAFDEMR-MNYIKELRKAIVKREKNSSQSWQRFYQLTKLL 192 (246)
T ss_pred -ccccCHHHHHHHH-HHHHHHHHHHHHHhCCCCcccchHHHHHHHhh
Confidence 2333433344333 1111223332221 112455678888876554
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=79.19 E-value=13 Score=36.83 Aligned_cols=112 Identities=14% Similarity=0.237 Sum_probs=70.0
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccC
Q 010481 360 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDN 439 (509)
Q Consensus 360 lL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~ 439 (509)
+|..--+|... .+-+++.+|..++..+. ...+-+| .+++.-+=.+++.++++++|=.||+-++|+ .|..
T Consensus 88 vL~~a~r~~~~-~~~l~f~~~~~~~r~~~-~~~~~~~-~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~------- 156 (238)
T cd07348 88 ILRLAYRSNPE-EGKLIFCNGVVLHRTQC-VRGFGDW-IDSILEFSQSLHRMNLDVSAFSCLAALVII-TDRH------- 156 (238)
T ss_pred HHHHHHHcCCC-CCeEEeeCCeeecHHHH-HhhHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCc-------
Confidence 34444455444 34577888887766553 3345565 467777788999999999999999999998 3332
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 440 GGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 440 ~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
|+-..+.|.+-|= .+..-|+.-++.-.+.|.-..||-+++-.|
T Consensus 157 -gL~~~~~Ve~lQe-~~~~aL~~yi~~~~~~p~~p~rf~kLLl~L 199 (238)
T cd07348 157 -GLKEPKRVEELQN-RLISCLKEHVSGSASEPQRPNCLSRLLGKL 199 (238)
T ss_pred -CCCCHHHHHHHHH-HHHHHHHHHHHhhCCCCccccHHHHHHHHH
Confidence 3334444444441 122334444443334688888998876443
No 29
>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=78.72 E-value=11 Score=36.85 Aligned_cols=78 Identities=18% Similarity=0.353 Sum_probs=53.3
Q ss_pred hhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCc--hhh
Q 010481 397 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFP--TYR 474 (509)
Q Consensus 397 ff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~P--T~R 474 (509)
+.+|+.-+-++++.++|+++|=.||+-++|++.|..... ..+.|.+-| +.+..-|+.-++ +++| ..|
T Consensus 121 ~~~~l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~--------~~~~Ve~lQ-e~~~~aL~~yi~--~~~p~~~~~ 189 (238)
T cd06933 121 LLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQ--------DHALIEAIQ-DRLSDTLQTYIR--CRHPPPGSR 189 (238)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCCCCc--------chHHHHHHH-HHHHHHHHHHHH--hcCCCCCch
Confidence 467888888899999999999999999999987643322 333343333 222333444444 3555 678
Q ss_pred HhHHHHHHHHH
Q 010481 475 RRFRQVVKALV 485 (509)
Q Consensus 475 Rrf~~lvK~L~ 485 (509)
.||-.++-.|-
T Consensus 190 ~~f~kLLl~L~ 200 (238)
T cd06933 190 LLYAKMIQKLA 200 (238)
T ss_pred hHHHHHHHHhH
Confidence 88998876653
No 30
>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=76.65 E-value=20 Score=35.57 Aligned_cols=112 Identities=13% Similarity=0.220 Sum_probs=67.6
Q ss_pred HHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccC
Q 010481 360 FLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDN 439 (509)
Q Consensus 360 lL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~ 439 (509)
+|..--+|... .+-+++.+|..++.....+ .+-+| .+++.-+=++++.++++++|=.||+-++|+. | |
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 34444455444 3447788887766654322 45564 5777778889999999999999999999993 2 2
Q ss_pred CCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHH
Q 010481 440 GGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKAL 484 (509)
Q Consensus 440 ~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L 484 (509)
.|+-..+.|++-|=+ +..=|+.-++.-...|.-..||-.++-.|
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 234345555555422 22233333332223455667787775443
No 31
>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=76.45 E-value=30 Score=34.41 Aligned_cols=111 Identities=17% Similarity=0.240 Sum_probs=65.4
Q ss_pred HHhhhc-CCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCC-CccccccccCCCC
Q 010481 365 LYSIKA-GSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS-TTERMEAWDNGGL 442 (509)
Q Consensus 365 L~SaKa-~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~-d~~r~~~wd~~g~ 442 (509)
-+|.-. +.+.+.+.+|..++..+..+..+.+.. ..+.-+=++.+.++++++|=.||+-++|++. |.. |+
T Consensus 80 ~rs~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~-~~l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~--------gL 150 (246)
T cd07073 80 WRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQC-VRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVD--------GL 150 (246)
T ss_pred HhccccCCCCeEEecCCeeechhhhccccHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcc--------cc
Confidence 366654 455588888887776665566666643 2333444578889999999999999999996 422 22
Q ss_pred CChhHHHHHHHHHHHHhhhhhhhhcccC-chhhHhHHHHHHHHH
Q 010481 443 LPEDALRAAQIQGISRRMIGLIRSVSKF-PTYRRRFRQVVKALV 485 (509)
Q Consensus 443 pp~d~vrrAqLqai~RRLqGi~~s~SR~-PT~RRrf~~lvK~L~ 485 (509)
-..+.|.+-|= .+..-|+--+.+-... |.-..||-++.-.|-
T Consensus 151 ~~~~~Ve~lQe-~~~~aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp 193 (246)
T cd07073 151 KNQKFFDELRM-NYIKELDRIIACKRKNPTSCSRRFYQLTKLLD 193 (246)
T ss_pred cCHHHHHHHHH-HHHHHHHHHHHhcCCCCcccchHHHHHHHHHH
Confidence 23332222221 1112233333322212 355788988876654
No 32
>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=75.62 E-value=36 Score=34.28 Aligned_cols=69 Identities=10% Similarity=0.186 Sum_probs=45.7
Q ss_pred HHHHHHHhhhcCCCce-eecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCC
Q 010481 360 FLQTLLYSIKAGSGGL-LLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGS 429 (509)
Q Consensus 360 lL~~LL~SaKa~S~Gl-ll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~ 429 (509)
+|..--+|.+.+++.. .+++|.-++.....+..+.| +..++.-+-.+++.++++++|=.||+-++|++.
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 4444458888776654 45555544433322334555 334443345688999999999999999999997
No 33
>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=73.99 E-value=24 Score=33.66 Aligned_cols=72 Identities=17% Similarity=0.256 Sum_probs=44.2
Q ss_pred HHHHHHHHHhhhcCCCceeecCCceecccCCCCccchhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCc
Q 010481 358 YSFLQTLLYSIKAGSGGLLLPDSVEITHLNRPNNKLLDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTT 431 (509)
Q Consensus 358 yslL~~LL~SaKa~S~Glll~D~~EiT~~NrPkdr~fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~ 431 (509)
+.+|..--+|...+. -+++.+|.-...........-+ +.+++.-+=..++.+++|++|=.||+-++|++.|.
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 456666667776653 3555555432211111112223 23455555578899999999999999999998874
No 34
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=73.44 E-value=3.8 Score=37.25 Aligned_cols=48 Identities=19% Similarity=0.479 Sum_probs=40.5
Q ss_pred ccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHHH
Q 010481 411 LKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALVS 486 (509)
Q Consensus 411 ~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~~ 486 (509)
.+|++++-.|++..+.-.||=+.|+ |.-|| -|||.|.|.++++++|-.
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 33344 399999999999999876
No 35
>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=72.38 E-value=20 Score=34.68 Aligned_cols=80 Identities=16% Similarity=0.252 Sum_probs=53.0
Q ss_pred hhhhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchh
Q 010481 394 LDWFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTY 473 (509)
Q Consensus 394 fDWff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~ 473 (509)
.+=+.+|+.-+-+.++.+++|++|=.||+-++|++.|..... ..+.|.+-|= .+..=|+-.+. .++|..
T Consensus 112 ~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL~--------~~~~Ve~~Q~-~~~~aL~~y~~--~~~p~~ 180 (221)
T cd06936 112 SDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLK--------DKEAVEKLQE-PLLDLLQKFCK--LYHPED 180 (221)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCCC--------CHHHHHHHHH-HHHHHHHHHHH--hhCCCc
Confidence 444667777778889999999999999999999988754332 2333333331 11222333332 478999
Q ss_pred hHhHHHHHHHH
Q 010481 474 RRRFRQVVKAL 484 (509)
Q Consensus 474 RRrf~~lvK~L 484 (509)
..||-.++-.|
T Consensus 181 p~rf~~LL~~L 191 (221)
T cd06936 181 PQHFACLLGRL 191 (221)
T ss_pred hhHHHHHHHHh
Confidence 99999876554
No 36
>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=71.82 E-value=18 Score=34.51 Aligned_cols=73 Identities=16% Similarity=0.301 Sum_probs=49.7
Q ss_pred HHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHH
Q 010481 401 IMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQV 480 (509)
Q Consensus 401 llvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~l 480 (509)
+.-+.++++.+++++.|=.||+-++|++.|-..++ ..+.+++.|=+ +.+=|+..++. +.|....||-++
T Consensus 115 l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~--------~~~~v~~lq~~-i~~aL~~y~~~--~~p~~~~R~~kl 183 (222)
T cd06952 115 LQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQE--------LRQQIEKLQEK-ALMELRDYVGK--TYPEDEYRLSKL 183 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCc--------CHHHHHHHHHH-HHHHHHHHHHH--hCCCcccHHHHH
Confidence 35678899999999999999999999998754433 33444444322 12233333332 378888999988
Q ss_pred HHHH
Q 010481 481 VKAL 484 (509)
Q Consensus 481 vK~L 484 (509)
+-.|
T Consensus 184 Ll~L 187 (222)
T cd06952 184 LLRL 187 (222)
T ss_pred HHHh
Confidence 7554
No 37
>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=71.01 E-value=13 Score=36.33 Aligned_cols=71 Identities=15% Similarity=0.265 Sum_probs=49.7
Q ss_pred HHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHH
Q 010481 404 LKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKA 483 (509)
Q Consensus 404 lKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~ 483 (509)
+=.+++.++++++|=.||+-+||++.|....+ ..+.|++-|=+ +..-|+..++ +++|.-..||-.++-.
T Consensus 120 ~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~--------~~~~V~~lqe~-~~~aL~~~~~--~~~p~~~~r~~kLLl~ 188 (222)
T cd07349 120 CLNKFWSLDLSPKEYAYLKGTILFNPDVPGLT--------ASSHVGHLQQE-AQWALCEVLE--PLHPQDQGRFARILLT 188 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCcccCC--------CHHHHHHHHHH-HHHHHHHHHH--HHCCCcccHHHHHHHH
Confidence 45689999999999999999999987654333 44445444422 2344555554 5689999999888755
Q ss_pred HH
Q 010481 484 LV 485 (509)
Q Consensus 484 L~ 485 (509)
|-
T Consensus 189 Lp 190 (222)
T cd07349 189 AS 190 (222)
T ss_pred hH
Confidence 43
No 38
>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=70.82 E-value=18 Score=35.23 Aligned_cols=74 Identities=19% Similarity=0.333 Sum_probs=49.8
Q ss_pred hhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHH---HHHHHHhhhhhhhhcccCc--
Q 010481 397 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ---IQGISRRMIGLIRSVSKFP-- 471 (509)
Q Consensus 397 ff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq---Lqai~RRLqGi~~s~SR~P-- 471 (509)
+.+|+.-+=+++++++++++|=.||+-.+|++.|..... ..+.|.+-| ++|+-+.+ .+++|
T Consensus 117 ~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~--------~~~~Ve~lQe~~~~aL~~yi------~~~~p~~ 182 (226)
T cd06934 117 LLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVT--------QHDVIDQLQEKMALTLKSYI------DSKRPGP 182 (226)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCc--------ChHHHHHHHHHHHHHHHHHH------HHcCCCC
Confidence 567887788899999999999999999999998754332 344444443 34444332 12344
Q ss_pred hhhHhHHHHHHHH
Q 010481 472 TYRRRFRQVVKAL 484 (509)
Q Consensus 472 T~RRrf~~lvK~L 484 (509)
.-|.||-.++-.|
T Consensus 183 ~~r~~f~kLLl~L 195 (226)
T cd06934 183 EKRFLYPKILACL 195 (226)
T ss_pred CcccHHHHHHHHh
Confidence 3555688877554
No 39
>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.
Probab=69.89 E-value=20 Score=35.27 Aligned_cols=76 Identities=18% Similarity=0.224 Sum_probs=51.9
Q ss_pred hhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHH
Q 010481 399 NPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFR 478 (509)
Q Consensus 399 ~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~ 478 (509)
.++.-+=++++.++|+++|=.||+-+||++.|....+ ..+.|.+-|=+.. .-|+..++ +++|....||-
T Consensus 127 ~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~--------~~~~Ve~lQe~~~-~aL~~yi~--~~~p~~~~rf~ 195 (232)
T cd07350 127 RAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQ--------CVQYIQGLQWEAQ-QALNEHVR--MIHRGDQARFA 195 (232)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCC--------CHHHHHHHHHHHH-HHHHHHHH--hhCCChhhHHH
Confidence 4555666788999999999999999999998754433 3445555443322 33444444 47888888998
Q ss_pred HHHHHHH
Q 010481 479 QVVKALV 485 (509)
Q Consensus 479 ~lvK~L~ 485 (509)
.++-.|-
T Consensus 196 kLLl~Lp 202 (232)
T cd07350 196 KLNIALS 202 (232)
T ss_pred HHHHHhH
Confidence 8765443
No 40
>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=66.59 E-value=29 Score=33.29 Aligned_cols=74 Identities=15% Similarity=0.257 Sum_probs=50.3
Q ss_pred hhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHH---HHHHHHhhhhhhhhcccCchh
Q 010481 397 FFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ---IQGISRRMIGLIRSVSKFPTY 473 (509)
Q Consensus 397 ff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq---Lqai~RRLqGi~~s~SR~PT~ 473 (509)
+.+++.-+=.+++.++++++|=.||+-++|++.|..... ..+.+++-| .+|+-+.. . .++|..
T Consensus 113 ~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs--------~~~~Ve~lQ~~~~~aL~~y~----~--~~~~~~ 178 (213)
T cd06953 113 VVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLT--------NASQLESLQKRYWYVLQDFT----E--LNYPNQ 178 (213)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCC--------CHHHHHHHHHHHHHHHHHHH----H--HhCCCc
Confidence 356666666789999999999999999999998754332 333344443 33444333 2 345888
Q ss_pred hHhHHHHHHHH
Q 010481 474 RRRFRQVVKAL 484 (509)
Q Consensus 474 RRrf~~lvK~L 484 (509)
..||-++.-.|
T Consensus 179 p~Rf~~LL~~L 189 (213)
T cd06953 179 PNRFSDLLSCL 189 (213)
T ss_pred chHHHHHHHHh
Confidence 88998876554
No 41
>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=53.61 E-value=65 Score=31.34 Aligned_cols=77 Identities=19% Similarity=0.088 Sum_probs=53.9
Q ss_pred hhhhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhH
Q 010481 396 WFFNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRR 475 (509)
Q Consensus 396 Wff~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RR 475 (509)
.+.+++.-+=..+++++++++|=.||+-+||++.|. .|+ ..+.|++.|=+.. .=|+--++ +++|.-..
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 346778788888999999999999999999999764 234 4445554442221 22333333 57899999
Q ss_pred hHHHHHHHH
Q 010481 476 RFRQVVKAL 484 (509)
Q Consensus 476 rf~~lvK~L 484 (509)
||-.+.=.|
T Consensus 183 Rf~kLLl~L 191 (222)
T cd06951 183 RSARLLLML 191 (222)
T ss_pred HHHHHHHHh
Confidence 998886554
No 42
>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=52.65 E-value=57 Score=32.21 Aligned_cols=47 Identities=23% Similarity=0.397 Sum_probs=37.1
Q ss_pred hhhHHHHHHHHHhccCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHH
Q 010481 398 FNPIMVLKEQISVLKLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQ 452 (509)
Q Consensus 398 f~PllvlKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAq 452 (509)
.+++.-.=++++.++|+++|=.||+-+||++.|.. |+-..+.|.+-|
T Consensus 130 ~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~--------gL~~~~~Ve~lQ 176 (241)
T cd06939 130 ISAVFDFAKSLCELKLTEDEIALFSALVLISADRP--------GLQEKRKVEKLQ 176 (241)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCc--------CCCCHHHHHHHH
Confidence 46777888999999999999999999999997643 333555666555
No 43
>KOG2511 consensus Nicotinic acid phosphoribosyltransferase [Coenzyme transport and metabolism]
Probab=46.53 E-value=14 Score=39.72 Aligned_cols=23 Identities=52% Similarity=0.713 Sum_probs=19.7
Q ss_pred HHHHHH---hccCChhHHhHHHHhhh
Q 010481 404 LKEQIS---VLKLTEPEVRYLEKVVL 426 (509)
Q Consensus 404 lKeQIk---~~~L~E~EE~yL~KlvL 426 (509)
|+|||| +++||+||+.||+|-.=
T Consensus 53 Lee~irfl~N~~lt~eei~~lkk~lP 78 (420)
T KOG2511|consen 53 LEEQIRFLANLKLTDEEIDYLKKELP 78 (420)
T ss_pred HHHHHHHHhhcCCCHHHHHHHHHhCC
Confidence 689987 67999999999998653
No 44
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=45.24 E-value=1.3e+02 Score=28.81 Aligned_cols=58 Identities=17% Similarity=0.313 Sum_probs=47.9
Q ss_pred cCChhHHhHHHHhhhcCCCccccccccCCCCCChhHHHHHHHHHHHHhhhhhhhhcccCchhhHhHHHHHHHHHHhhhh
Q 010481 412 KLTEPEVRYLEKVVLFGSTTERMEAWDNGGLLPEDALRAAQIQGISRRMIGLIRSVSKFPTYRRRFRQVVKALVSYSES 490 (509)
Q Consensus 412 ~L~E~EE~yL~KlvL~~~d~~r~~~wd~~g~pp~d~vrrAqLqai~RRLqGi~~s~SR~PT~RRrf~~lvK~L~~~~~~ 490 (509)
+|||-|.+.|+...=.+=-+.+ |++.++.||..| ||++| |+-.|-++..+.|...+.+
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 8999999999987665544433 889999999987 88886 9999999999988887754
No 45
>PRK00523 hypothetical protein; Provisional
Probab=44.28 E-value=15 Score=31.52 Aligned_cols=23 Identities=43% Similarity=0.674 Sum_probs=19.0
Q ss_pred HHHHHHHHHHhhhhhhhhcccchh
Q 010481 28 LFGLWLGLSIAGSVLVGVGYGFFT 51 (509)
Q Consensus 28 ~l~LW~vlgI~GSvl~G~gYGff~ 51 (509)
-+.||.+++|++ +++|+.-|||.
T Consensus 3 ~~~l~I~l~i~~-li~G~~~Gffi 25 (72)
T PRK00523 3 AIGLALGLGIPL-LIVGGIIGYFV 25 (72)
T ss_pred hHHHHHHHHHHH-HHHHHHHHHHH
Confidence 367888999988 88888889885
No 46
>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=42.53 E-value=31 Score=28.25 Aligned_cols=18 Identities=28% Similarity=0.600 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 010481 185 LLWPIIVIGSIVIAIFSS 202 (509)
Q Consensus 185 lLWPl~Vvgavl~aiisS 202 (509)
-+||+.+-|+|..--|+|
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 47
>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=39.66 E-value=30 Score=20.42 Aligned_cols=27 Identities=30% Similarity=0.373 Sum_probs=20.2
Q ss_pred HHHHHHHHHhhhhhhhccCCCChhhHHHHHHh
Q 010481 311 WVNMMRSCETRGRELLDADVITPADLKDWLKA 342 (509)
Q Consensus 311 wd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~ 342 (509)
|..+|+.+..++ .|.|+..|+..++++
T Consensus 2 ~~~~f~~~d~~~-----~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDG-----DGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCC-----CCcEeHHHHHHHHHh
Confidence 456888887764 678888888887753
No 48
>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=36.69 E-value=37 Score=29.24 Aligned_cols=33 Identities=15% Similarity=0.142 Sum_probs=27.0
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcC
Q 010481 301 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKC 344 (509)
Q Consensus 301 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~ 344 (509)
-+|++++-.|||+| +++|+||.+|.|+-.+...
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 7899999999998887653
No 49
>COG3790 Predicted membrane protein [Function unknown]
Probab=34.93 E-value=36 Score=30.63 Aligned_cols=33 Identities=33% Similarity=0.708 Sum_probs=29.0
Q ss_pred hhhHHHHHHHHHHHhhhhhhhhcc--------cchhhHHhH
Q 010481 24 PLPALFGLWLGLSIAGSVLVGVGY--------GFFTPWVSA 56 (509)
Q Consensus 24 ~lP~~l~LW~vlgI~GSvl~G~gY--------Gff~P~~aT 56 (509)
.+|++.++..+-++.-+++-|+|+ |+|+|+.|-
T Consensus 45 s~~a~~~llmiWavca~~IhGVGFrpr~~~wqg~FsPlla~ 85 (97)
T COG3790 45 SLEAWHGLLMIWAVCAGVIHGVGFRPRSVLWQGIFSPLLAD 85 (97)
T ss_pred CchHHHHHHHHHHHHHHHHhcccCchHHHHHHHHhhhHHHH
Confidence 468888888889999999999997 899999874
No 50
>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=33.79 E-value=93 Score=27.58 Aligned_cols=32 Identities=16% Similarity=0.209 Sum_probs=27.0
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhc
Q 010481 301 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAK 343 (509)
Q Consensus 301 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k 343 (509)
-++++++-++||++ ++.|++|.+|+|+-...+
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 678999999999998864
No 51
>PRK00523 hypothetical protein; Provisional
Probab=32.21 E-value=60 Score=27.88 Aligned_cols=26 Identities=23% Similarity=0.240 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhh
Q 010481 181 GLTILLWPIIVIGSIVIAIFSSIFIG 206 (509)
Q Consensus 181 GLaIlLWPl~Vvgavl~aiisS~flG 206 (509)
|+++-+|=+.++.+++++.+..||++
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 52
>PF14946 DUF4501: Domain of unknown function (DUF4501)
Probab=31.68 E-value=1e+02 Score=30.37 Aligned_cols=22 Identities=32% Similarity=0.605 Sum_probs=18.7
Q ss_pred ccccCCCcCCCcccccCCCCCC
Q 010481 241 LYLREGTILPKPRYRQKKVHSS 262 (509)
Q Consensus 241 LyLrEGSc~PRP~YRk~~~~~~ 262 (509)
.||+.-+=||+--||+|+....
T Consensus 112 FYLKrs~kLP~vfYrrnKA~al 133 (180)
T PF14946_consen 112 FYLKRSSKLPHVFYRRNKAPAL 133 (180)
T ss_pred eeecccccCCcccccccccccc
Confidence 6999999999999999976433
No 53
>PRK01844 hypothetical protein; Provisional
Probab=29.45 E-value=35 Score=29.28 Aligned_cols=22 Identities=27% Similarity=0.547 Sum_probs=16.1
Q ss_pred HHHHHHHHHhhhhhhhhcccchh
Q 010481 29 FGLWLGLSIAGSVLVGVGYGFFT 51 (509)
Q Consensus 29 l~LW~vlgI~GSvl~G~gYGff~ 51 (509)
+.+|.+++|+ .+++|+.-|||.
T Consensus 3 ~~~~I~l~I~-~li~G~~~Gff~ 24 (72)
T PRK01844 3 IWLGILVGVV-ALVAGVALGFFI 24 (72)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHH
Confidence 4677777776 677777778875
No 54
>PLN00151 potassium transporter; Provisional
Probab=29.31 E-value=70 Score=37.89 Aligned_cols=26 Identities=27% Similarity=0.225 Sum_probs=20.7
Q ss_pred hhhhheeEEEeechhhhhhHHHHHHHh
Q 010481 204 FIGLYGSVVVYQERSFRRGVAYVIAMV 230 (509)
Q Consensus 204 flG~yaaVVvYQE~Sf~~GL~Yvva~V 230 (509)
++++.+-++.||. |-..|=||=+|.+
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 55
>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=28.24 E-value=63 Score=27.96 Aligned_cols=33 Identities=9% Similarity=0.129 Sum_probs=27.2
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcC
Q 010481 301 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKC 344 (509)
Q Consensus 301 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~ 344 (509)
-.+++++=.+||+| .++|++|..|.||-.+...
T Consensus 12 L~~~l~~~~l~d~L-----------~q~~VLt~~d~EeI~~~~t 44 (86)
T cd08785 12 LTRKINPSRLTPYL-----------RQCKVLDEQDEEEVLSSPR 44 (86)
T ss_pred HHHHhhHHHHHHHH-----------HhcCCCCHHHHHHHhCCCc
Confidence 45778888888876 7789999999999988654
No 56
>PLN00149 potassium transporter; Provisional
Probab=27.83 E-value=78 Score=37.18 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=20.3
Q ss_pred hhhhheeEEEeechhhhhhHHHHHHH
Q 010481 204 FIGLYGSVVVYQERSFRRGVAYVIAM 229 (509)
Q Consensus 204 flG~yaaVVvYQE~Sf~~GL~Yvva~ 229 (509)
++|+.+-++.||. |-+.|=||=+|.
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 57
>PRK13511 6-phospho-beta-galactosidase; Provisional
Probab=27.54 E-value=83 Score=34.11 Aligned_cols=54 Identities=11% Similarity=0.212 Sum_probs=37.0
Q ss_pred cCCCceeecCCceeccc-CCCCccc---------hhhhhhhHH------HHHHHHH--------hccCChhHHhHHHH
Q 010481 370 AGSGGLLLPDSVEITHL-NRPNNKL---------LDWFFNPIM------VLKEQIS--------VLKLTEPEVRYLEK 423 (509)
Q Consensus 370 a~S~Glll~D~~EiT~~-NrPkdr~---------fDWff~Pll------vlKeQIk--------~~~L~E~EE~yL~K 423 (509)
.+.-|+.+....-.... +.|+|.. ..||++|+. .|+++++ .+++|++|.+.+++
T Consensus 209 ~g~IGi~~~~~~~~P~~~~~~~d~~aa~~~~~~~~~~f~dp~~~G~Yp~~~~~~~~~~~~~~~~~l~~t~~d~~~ik~ 286 (469)
T PRK13511 209 KGEIGVVHALPTKYPIDPDNPEDVRAAELEDIIHNKFILDATYLGYYSEETMEGVNHILEANGGSLDIRDEDFEILKA 286 (469)
T ss_pred CCeEEEEecCceEeeCCCCCHHHHHHHHHHHHHhhhcccchhhCCCCCHHHHHHHHHhhhhcCCCCCCCHHHHHHHhc
Confidence 34678888776444444 6787754 479999985 5677664 24688888887764
No 58
>COG2981 CysZ Uncharacterized protein involved in cysteine biosynthesis [Amino acid transport and metabolism]
Probab=27.37 E-value=64 Score=33.27 Aligned_cols=31 Identities=35% Similarity=0.567 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHH---------HHHHHHHHHHhhhhheeEE
Q 010481 182 LTILLWPIIVIG---------SIVIAIFSSIFIGLYGSVV 212 (509)
Q Consensus 182 LaIlLWPl~Vvg---------avl~aiisS~flG~yaaVV 212 (509)
|..++||+++++ |-++++|+|+|.|+.|=+|
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 59
>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=23.15 E-value=71 Score=25.46 Aligned_cols=18 Identities=33% Similarity=0.462 Sum_probs=15.4
Q ss_pred cCChhHHhHHHHhhhcCC
Q 010481 412 KLTEPEVRYLEKVVLFGS 429 (509)
Q Consensus 412 ~L~E~EE~yL~KlvL~~~ 429 (509)
.||+.+|.||+-+-.+..
T Consensus 1 ~Lt~~~e~YL~~Iy~l~~ 18 (60)
T PF01325_consen 1 MLTESEEDYLKAIYELSE 18 (60)
T ss_dssp TCSCHHHHHHHHHHHHHH
T ss_pred CCCcHHHHHHHHHHHHHc
Confidence 489999999998887775
No 60
>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=21.76 E-value=1.7e+02 Score=26.32 Aligned_cols=49 Identities=18% Similarity=0.313 Sum_probs=42.6
Q ss_pred CChhhHHHHHHhcCCCCceeEeeccch-HHHHHHHHHhhhcCCCceeecCCc
Q 010481 331 ITPADLKDWLKAKCVNEEAIVGFGLPC-YSFLQTLLYSIKAGSGGLLLPDSV 381 (509)
Q Consensus 331 It~~Diee~~~~k~~~~~~~i~vgLPa-yslL~~LL~SaKa~S~Glll~D~~ 381 (509)
....++++++++.+..+ ++=+|+-+ +|++++-+.-.+.+=.=.+++|.+
T Consensus 85 f~~t~l~~~L~~~gi~~--viv~G~~td~CV~~Ta~~a~~~g~~v~vi~Da~ 134 (155)
T cd01014 85 FYGTDLEEWLREAGIDH--LVICGAMTEMCVDTTVRSAFDLGYDVTVVADAC 134 (155)
T ss_pred cCCCCHHHHHHHCCCCE--EEEEeeccchhHHHHHHHHHHCCCcEEEecccc
Confidence 34479999999988745 99999987 999999999999999999999975
No 61
>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=21.74 E-value=87 Score=28.73 Aligned_cols=44 Identities=32% Similarity=0.437 Sum_probs=34.6
Q ss_pred ccCCCCCChhHHHH--HHHHHHHHhhhhhhhhc-ccCchhhHhHHHH
Q 010481 437 WDNGGLLPEDALRA--AQIQGISRRMIGLIRSV-SKFPTYRRRFRQV 480 (509)
Q Consensus 437 wd~~g~pp~d~vrr--AqLqai~RRLqGi~~s~-SR~PT~RRrf~~l 480 (509)
|+..|.+|...+++ +|++++-||||.|=+-+ |+-.+.+|+|+++
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 66667777766664 68999999999997765 6778889999874
No 62
>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=21.62 E-value=44 Score=26.58 Aligned_cols=31 Identities=16% Similarity=0.195 Sum_probs=24.2
Q ss_pred hhhHHHHHHHHHHHH--------hhhhhhhccCCCChhh
Q 010481 305 VKMVQIWVNMMRSCE--------TRGRELLDADVITPAD 335 (509)
Q Consensus 305 ~k~vqiwd~lfk~ce--------~~G~~Ll~~gvIt~~D 335 (509)
+.--+++|||.+.|+ .-|..|++.|+|..-+
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 346689999987766 5677899999998765
No 63
>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=21.42 E-value=1e+02 Score=26.71 Aligned_cols=34 Identities=6% Similarity=0.020 Sum_probs=27.3
Q ss_pred hhHhhhhHHHHHHHHHHHHhhhhhhhccCCCChhhHHHHHHhcCC
Q 010481 301 AIQEVKMVQIWVNMMRSCETRGRELLDADVITPADLKDWLKAKCV 345 (509)
Q Consensus 301 ~iqe~k~vqiwd~lfk~ce~~G~~Ll~~gvIt~~Diee~~~~k~~ 345 (509)
-.+++++=.+||+| .++|++|..|.||-.+...+
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 64
>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=20.93 E-value=1.5e+02 Score=34.54 Aligned_cols=26 Identities=23% Similarity=0.438 Sum_probs=21.1
Q ss_pred hhhhheeEEEeechhhhhhHHHHHHHh
Q 010481 204 FIGLYGSVVVYQERSFRRGVAYVIAMV 230 (509)
Q Consensus 204 flG~yaaVVvYQE~Sf~~GL~Yvva~V 230 (509)
++|+.+-|+.||++ -.+|-||=+|..
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
Done!