Query 007965
Match_columns 583
No_of_seqs 46 out of 48
Neff 2.9
Searched_HMMs 46136
Date Thu Mar 28 17:41:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007965.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007965hhsearch_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 93.8 0.51 1.1E-05 44.7 9.7 113 399-523 49-161 (195)
2 smart00430 HOLI Ligand binding 92.0 1.7 3.6E-05 37.6 9.7 78 393-471 33-112 (163)
3 cd06940 NR_LBD_REV_ERB The lig 90.5 1.3 2.8E-05 42.4 8.1 103 411-524 70-172 (189)
4 cd06931 NR_LBD_HNF4_like The l 90.2 2.6 5.6E-05 40.6 9.9 115 396-523 76-191 (222)
5 cd06945 NR_LBD_Nurr1_like The 89.0 1.9 4.1E-05 42.8 8.4 107 400-522 89-200 (239)
6 cd06944 NR_LBD_Ftz-F1_like The 88.4 3.5 7.6E-05 40.8 9.7 115 397-522 83-201 (237)
7 cd06943 NR_LBD_RXR_like The li 88.2 5.1 0.00011 38.1 10.3 116 397-523 75-190 (207)
8 cd06937 NR_LBD_RAR The ligand 87.9 3.1 6.6E-05 41.2 8.9 99 412-524 97-198 (231)
9 cd07075 NR_LBD_MR Ligand bindi 87.8 2.2 4.8E-05 43.3 8.1 113 404-524 80-194 (248)
10 cd06938 NR_LBD_EcR The ligand 86.3 6.5 0.00014 38.6 10.1 108 403-522 89-197 (231)
11 PF00104 Hormone_recep: Ligand 86.2 7.9 0.00017 34.8 9.9 156 351-522 24-183 (203)
12 cd06935 NR_LBD_TR The ligand b 86.1 3.5 7.6E-05 41.0 8.3 99 411-523 110-211 (243)
13 cd06930 NR_LBD_F2 Ligand-bindi 86.1 9.4 0.0002 34.2 10.3 77 394-472 41-118 (165)
14 cd06942 NR_LBD_Sex_1_like The 84.9 6.7 0.00015 37.3 9.2 151 351-523 2-162 (191)
15 cd07069 NR_LBD_Lrh-1 The ligan 83.7 9.6 0.00021 38.1 10.1 117 396-522 84-203 (241)
16 cd07076 NR_LBD_GR Ligand bindi 82.9 5.9 0.00013 40.2 8.4 112 404-523 80-193 (247)
17 cd06949 NR_LBD_ER Ligand bindi 81.7 10 0.00023 37.6 9.4 117 399-522 79-199 (235)
18 cd06954 NR_LBD_LXR The ligand 80.2 6 0.00013 38.7 7.1 109 405-523 95-203 (236)
19 cd06929 NR_LBD_F1 Ligand-bindi 80.1 10 0.00022 34.6 8.1 117 396-524 46-162 (174)
20 cd06950 NR_LBD_Tlx_PNR_like Th 80.1 13 0.00028 36.0 9.3 74 440-522 111-184 (206)
21 cd07070 NR_LBD_SF-1 The ligand 78.6 11 0.00023 37.6 8.3 114 399-523 85-202 (237)
22 cd07073 NR_LBD_AR Ligand bindi 77.5 23 0.0005 35.8 10.5 111 405-524 81-194 (246)
23 cd07071 NR_LBD_Nurr1 The ligan 75.4 26 0.00056 35.3 10.1 103 410-523 98-200 (238)
24 cd06947 NR_LBD_GR_Like Ligand 73.3 30 0.00065 35.0 10.0 114 399-523 75-193 (246)
25 cd06157 NR_LBD The ligand bind 73.2 41 0.0009 29.2 9.7 122 394-523 40-163 (168)
26 cd06948 NR_LBD_COUP-TF Ligand 73.1 16 0.00034 36.2 7.9 108 399-522 77-190 (236)
27 cd06932 NR_LBD_PPAR The ligand 72.7 30 0.00064 35.1 9.9 102 409-523 117-223 (259)
28 cd07348 NR_LBD_NGFI-B The liga 70.8 32 0.00069 34.7 9.5 113 399-523 88-200 (238)
29 cd07072 NR_LBD_DHR38_like Liga 66.3 39 0.00085 34.1 9.1 113 399-523 89-201 (239)
30 cd06946 NR_LBD_ERR The ligand 64.6 45 0.00098 32.4 9.0 73 396-471 71-143 (221)
31 cd07349 NR_LBD_SHP The ligand 63.6 23 0.00051 35.1 6.9 71 444-523 120-190 (222)
32 cd07074 NR_LBD_PR Ligand bindi 62.6 85 0.0018 32.2 10.8 69 399-469 75-144 (248)
33 PF09862 DUF2089: Protein of u 62.2 7.7 0.00017 35.9 3.1 48 451-524 32-79 (113)
34 cd07068 NR_LBD_ER_like The lig 61.0 45 0.00098 32.5 8.3 111 350-471 26-143 (221)
35 cd06934 NR_LBD_PXR_like The li 60.5 27 0.00059 34.5 6.8 74 437-522 117-195 (226)
36 cd06933 NR_LBD_VDR The ligand 59.7 43 0.00092 33.4 8.0 79 437-524 121-201 (238)
37 PF06161 DUF975: Protein of un 55.6 39 0.00084 32.9 6.8 41 82-122 142-188 (243)
38 cd06936 NR_LBD_Fxr The ligand 55.2 55 0.0012 32.2 7.8 81 434-523 112-192 (221)
39 cd06953 NR_LBD_DHR4_like The l 50.7 44 0.00096 32.6 6.4 77 437-522 113-189 (213)
40 cd07350 NR_LBD_Dax1 The ligand 48.5 53 0.0011 33.0 6.6 76 439-523 127-202 (232)
41 cd06952 NR_LBD_TR2_like The li 48.4 51 0.0011 32.0 6.4 73 441-522 115-187 (222)
42 KOG2511 Nicotinic acid phospho 46.5 15 0.00031 40.3 2.5 23 444-466 53-78 (420)
43 cd06951 NR_LBD_Dax1_like The l 43.4 61 0.0013 32.1 6.1 77 437-523 116-192 (222)
44 PF04911 ATP-synt_J: ATP synth 40.0 35 0.00077 28.4 3.2 32 244-298 9-40 (54)
45 PRK00523 hypothetical protein; 36.1 29 0.00063 30.3 2.3 23 87-110 3-25 (72)
46 PRK10907 intramembrane serine 34.4 43 0.00093 34.8 3.6 48 43-98 196-243 (276)
47 smart00054 EFh EF-hand, calciu 32.5 35 0.00076 20.5 1.7 27 353-384 2-28 (29)
48 PRK10110 bifunctional PTS syst 31.2 1.4E+02 0.0031 33.8 7.2 51 66-116 164-237 (530)
49 PRK13735 conjugal transfer mat 28.5 1.8E+02 0.0039 35.5 7.8 70 50-121 365-453 (942)
50 COG3790 Predicted membrane pro 26.1 63 0.0014 29.6 2.8 33 83-115 45-85 (97)
51 cd06939 NR_LBD_ROR_like The li 26.1 1.1E+02 0.0024 30.7 4.8 35 438-472 130-164 (241)
52 PRK13511 6-phospho-beta-galact 24.5 1.1E+02 0.0025 33.6 5.0 54 409-463 209-286 (469)
53 PRK09695 glycolate transporter 24.3 1.3E+02 0.0028 34.4 5.4 73 12-84 17-112 (560)
54 PRK06814 acylglycerophosphoeth 24.0 2.7E+02 0.0059 32.8 8.1 19 97-115 113-131 (1140)
55 KOG2632 Rhomboid family protei 23.7 98 0.0021 32.5 4.0 98 26-125 99-215 (258)
56 PRK01844 hypothetical protein; 23.0 68 0.0015 28.0 2.3 22 88-110 3-24 (72)
57 PRK00523 hypothetical protein; 21.9 1.1E+02 0.0025 26.7 3.4 26 240-265 1-26 (72)
58 PRK09598 lipid A phosphoethano 21.7 2.6E+02 0.0057 31.5 7.1 55 31-92 70-141 (522)
59 cd01570 NAPRTase_A Nicotinate 21.5 84 0.0018 33.1 3.1 44 421-467 27-72 (327)
60 COG3413 Predicted DNA binding 20.2 4.2E+02 0.0092 25.8 7.4 58 452-528 155-212 (215)
61 PLN00151 potassium transporter 20.0 1.2E+02 0.0026 36.5 4.3 26 263-289 479-504 (852)
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=93.79 E-value=0.51 Score=44.68 Aligned_cols=113 Identities=15% Similarity=0.182 Sum_probs=72.4
Q ss_pred HHHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCC
Q 007965 399 LLQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLN 478 (583)
Q Consensus 399 lL~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~ 478 (583)
+++ +-++...++.++.+.|| ..++..+-......+ +.+++.-+=++++.++++++|=.||+-++|++.|....
T Consensus 49 ll~-~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~gl---- 121 (195)
T cd06941 49 LVR-ISRLINSKSGSITFDDG-ISISRQQLDIIYDSD-FVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGL---- 121 (195)
T ss_pred HHH-HHHHHcCCCCeEEecCC-eEeeHHHHHhccchH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCCC----
Confidence 444 34667777888999998 666543321100012 45677778889999999999999999999999775443
Q ss_pred CCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 479 VSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 479 g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
-..+.+++.| +.+..-|+.-+. +++|....||-+++..|-
T Consensus 122 --~~~~~Ve~lq-~~~~~aL~~~i~--~~~p~~~~rf~~Ll~~Lp 161 (195)
T cd06941 122 --SEPKKVAILQ-DRVLEALKVQVS--RNRPAEAQLFASLLMKIP 161 (195)
T ss_pred --CCHHHHHHHH-HHHHHHHHHHHH--hhCCCcccHHHHHHHHhH
Confidence 1123344433 111222333333 468888899999887664
No 2
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=92.04 E-value=1.7 Score=37.64 Aligned_cols=78 Identities=21% Similarity=0.232 Sum_probs=57.5
Q ss_pred ccchHHHHHHHHHhhhcCCCceEeeCCceeecccCCC--ccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCC
Q 007965 393 GLPAYCLLQALLRSAMANSPGILLSDSVTEITSSNRP--KDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGN 470 (583)
Q Consensus 393 gLPAyslL~~LL~SaKanS~GlllsD~~~EiT~~NrP--kd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d 470 (583)
.-+.+.+|...-+|.|.+...++..|+ +.+...... .......+...+.-+-+.++.+++|++|=.||.-++++..|
T Consensus 33 ~~~~~~~l~~~~~s~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~ 111 (163)
T smart00430 33 FWFEWLLLESAYRSAKMKKSLLLLPDG-TFIDNDKVDLLRKLFSPFLDRILQELVKPLRELKLDDEEYALLKAILLFNPA 111 (163)
T ss_pred HHHHHHHHHHHHHHHHhcCCEEEeCCC-cccCcchhHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcChh
Confidence 456778888888999988887777777 544433221 13445556666667778899999999999999999999865
Q ss_pred c
Q 007965 471 I 471 (583)
Q Consensus 471 ~ 471 (583)
.
T Consensus 112 ~ 112 (163)
T smart00430 112 G 112 (163)
T ss_pred h
Confidence 4
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=90.50 E-value=1.3 Score=42.35 Aligned_cols=103 Identities=15% Similarity=0.200 Sum_probs=67.4
Q ss_pred CCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHH
Q 007965 411 SPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAE 490 (583)
Q Consensus 411 S~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAq 490 (583)
...+.+.|| ..++...-+...+-+ +.+++.-+=++++.++++++|=.||+-++|++.|.... ...+.+++.|
T Consensus 70 ~~~l~~~~~-~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~~L------~~~~~Ve~lq 141 (189)
T cd06940 70 ERSVTFLSG-QKYSVDDLHSMGAGD-LLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGL------ENVNLVEALQ 141 (189)
T ss_pred CCeEEecCC-cEEcHHHHHHcCcHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCcCC------CCHHHHHHHH
Confidence 344777788 655433322222323 34556677899999999999999999999999874332 2244566666
Q ss_pred HHHHHHHhhhhhhcccCCchhhhhHHHHHHHHHH
Q 007965 491 LGALARRLQGITKSVSRYPTFRRQFDDLVKTLTE 524 (583)
Q Consensus 491 Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~ 524 (583)
+.+..-|+.-++ .++|.-..||-+++..|..
T Consensus 142 -~~~~~aL~~~~~--~~~p~~~~rf~kLL~~L~~ 172 (189)
T cd06940 142 -ETLIRALRTLIA--KNHPNEPSIFTKLLLKLPD 172 (189)
T ss_pred -HHHHHHHHHHHH--HhCCCCccHHHHHHHHHHH
Confidence 333344554444 3478888899998877654
No 4
>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=90.16 E-value=2.6 Score=40.60 Aligned_cols=115 Identities=19% Similarity=0.139 Sum_probs=70.5
Q ss_pred hHHHHHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHH-HHHHHHHhccCChhHHHHhHhhhhccCCcccc
Q 007965 396 AYCLLQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFL-IIKEQIKAENLTEAEEDYLSKLVLFCGNIGRL 474 (583)
Q Consensus 396 AyslL~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~Pll-viKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 474 (583)
.+.+|..--+|. .+.+++++.|| ..++..+-+ ..+-+. .++.+ -+-++++.+++|++|=.+|+-+++++.|..+.
T Consensus 76 ~~~~l~~a~~s~-~~~~~l~~~~g-~~~~~~~~~-~~~~~~-~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~~l 151 (222)
T cd06931 76 EHLLLGVARRSM-PYKDILLLGND-LIIPRHCPE-PEISRV-ANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGL 151 (222)
T ss_pred HHHHHHHHHhcc-CCCCeeeeCCC-ccccccccc-chHHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCccCC
Confidence 556666666776 45788999999 655554433 122222 23322 46678999999999999999999998776554
Q ss_pred cCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 475 KDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 475 ~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
.+ .+. .+++|.--++|+. ..++ .+.|....||-+++..|.
T Consensus 152 s~-~~~--i~~~r~~~~~aL~----~y~~--~~~~~~~~Rf~~LL~~l~ 191 (222)
T cd06931 152 SD-PQK--IKRLRFQVQVSLE----DYIN--DRQYDSRGRFGELLLLLP 191 (222)
T ss_pred CC-HHH--HHHHHHHHHHHHH----HHHH--hcCCchhhHHHHHHHHHH
Confidence 22 110 1222222233333 3332 246788889988877654
No 5
>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as
Probab=89.04 E-value=1.9 Score=42.84 Aligned_cols=107 Identities=15% Similarity=0.237 Sum_probs=67.6
Q ss_pred HHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCC
Q 007965 400 LQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNV 479 (583)
Q Consensus 400 L~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g 479 (583)
|..--||... .+.+++.+| .-++..+. +..+-+| .++++-.=++++.++++++|..||+.++|++.|....
T Consensus 89 L~~a~r~~~~-~~~l~~~~~-~~~~~~~~-~~~~~~~-~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~gL----- 159 (239)
T cd06945 89 LRLAYRSNPV-DGKLVFCNG-LVLHRLQC-VRGFGEW-LDSILAFSSSLQSLLLDDISAFCCLALLLLITERHGL----- 159 (239)
T ss_pred HHHHHHhcCC-CCceEeeCC-ceecHHHH-HHhHHHH-HHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCcccc-----
Confidence 3333344443 344777888 65555442 2234344 6888877789999999999999999999998765333
Q ss_pred CCCchhhhHHH---HHHHHHHhhhhhhcccCCc--hhhhhHHHHHHHH
Q 007965 480 SPPESERKRAE---LGALARRLQGITKSVSRYP--TFRRQFDDLVKTL 522 (583)
Q Consensus 480 ~pp~d~~rrAq---Lqai~RRLqGI~~s~SR~P--T~RRrf~~lvK~L 522 (583)
-..+.|.+.| ++|+-+.+. .++| .-..||-+++-.|
T Consensus 160 -~~~~~Ve~lQe~~~~aL~~y~~------~~~p~~~~~~rf~kLLl~L 200 (239)
T cd06945 160 -KEPKKVEELQNKIISCLRDHVT------SNYPGQDKPNRLSKLLLKL 200 (239)
T ss_pred -CCHHHHHHHHHHHHHHHHHHHH------HhCCCcccccHHHHHHHHh
Confidence 2234454444 344433332 3567 7778888876544
No 6
>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=88.43 E-value=3.5 Score=40.75 Aligned_cols=115 Identities=17% Similarity=0.213 Sum_probs=71.1
Q ss_pred HHHHHHHHHhhhcC-CCceEeeCCceeecccCCCc---cccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcc
Q 007965 397 YCLLQALLRSAMAN-SPGILLSDSVTEITSSNRPK---DVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIG 472 (583)
Q Consensus 397 yslL~~LL~SaKan-S~GlllsD~~~EiT~~NrPk---d~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~ 472 (583)
+.+|...-||+..+ ++.+++.|| ..+...+-+. ....+ +.+.+.-+=..++.++++++|=.||+-++|++.|..
T Consensus 83 l~~L~~a~rs~~~~~~~~l~~~~g-~~~~~~~~~~~~~~~~~~-~~~~i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~ 160 (237)
T cd06944 83 LLVLDHIYRQVHHGKEDSILLVTG-QEVDLSTLASQAGLGLSS-LVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVK 160 (237)
T ss_pred HHHHHHHHHhcccCCCCceeecCC-CccchhhhhhhccccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcC
Confidence 44666777888887 677889999 7665554221 11222 345555666788999999999999999999998754
Q ss_pred cccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHH
Q 007965 473 RLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTL 522 (583)
Q Consensus 473 r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 522 (583)
.. ...+.+.+.| +.+..-|+.-+. .++|..-.||-+++-.|
T Consensus 161 gL------~~~~~Ve~~q-~~~~~aL~~y~~--~~~~~~~~Rf~~LL~~L 201 (237)
T cd06944 161 GL------ENRQLVESVQ-EQVNAALLDYTL--CNYPQQTDKFGQLLLRL 201 (237)
T ss_pred CC------CCHHHHHHHH-HHHHHHHHHHHH--hhCCCCccHHHHHHHHh
Confidence 33 1122333332 122222333332 45666667777776543
No 7
>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=88.21 E-value=5.1 Score=38.08 Aligned_cols=116 Identities=16% Similarity=0.187 Sum_probs=66.3
Q ss_pred HHHHHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccC
Q 007965 397 YCLLQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKD 476 (583)
Q Consensus 397 yslL~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d 476 (583)
+.+|..--+|.. ..+|+++++| ..++..+-.+..+-+.+-..+--+-+.++.+++|++|=.+|+-+++++.|.... .
T Consensus 75 ~~~l~~a~~s~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~~L-~ 151 (207)
T cd06943 75 LLIAAFAHRSIA-VKDGILLATG-LHLHRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGL-K 151 (207)
T ss_pred HHHHHHHHHccC-CCCeeEecCC-ceeccchhhhccchHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCCC-C
Confidence 344444445544 3688999999 777654433333333322222245668999999999999999999999765433 1
Q ss_pred CCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 477 LNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 477 ~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
+ .+.+.+.| +.+..=|+..+. .++|.-..||-+++-.|.
T Consensus 152 ~-----~~~v~~~q-~~~~~aL~~y~~--~~~~~~~~Rf~~LLl~L~ 190 (207)
T cd06943 152 S-----RQEVESLR-EKVYASLEEYCR--QKHPEQPGRFAKLLLRLP 190 (207)
T ss_pred C-----HHHHHHHH-HHHHHHHHHHHH--hhCCCcccHHHHHHHHHH
Confidence 1 12222222 112222333332 345666677777765443
No 8
>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=87.89 E-value=3.1 Score=41.16 Aligned_cols=99 Identities=18% Similarity=0.291 Sum_probs=67.7
Q ss_pred CceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHH-
Q 007965 412 PGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAE- 490 (583)
Q Consensus 412 ~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAq- 490 (583)
.-+.+++| ..++..+-.+.. +.-+.+++.-+=++++.++++++|=.||+-++|++.|.... -..+.+++.|
T Consensus 97 ~~l~~~~~-~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL------~~~~~Ve~lQe 168 (231)
T cd06937 97 DTMTFSDG-LTLNRTQMHNAG-FGPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDL------EEPDRVEKLQE 168 (231)
T ss_pred CeEEecCC-ceecHHHHhhcC-hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCccC------CCHHHHHHHHH
Confidence 33667777 555544432222 33467888889999999999999999999999999875433 2234455555
Q ss_pred --HHHHHHHhhhhhhcccCCchhhhhHHHHHHHHHH
Q 007965 491 --LGALARRLQGITKSVSRYPTFRRQFDDLVKTLTE 524 (583)
Q Consensus 491 --Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~ 524 (583)
++|+-+-+. .++|.-.+||-+++-.|.+
T Consensus 169 ~~~~aL~~yi~------~~~p~~p~rf~kLLl~Lp~ 198 (231)
T cd06937 169 PLLEALKIYAR------KRRPDKPHMFPKMLMKITD 198 (231)
T ss_pred HHHHHHHHHHH------hhCCCcccHHHHHHHHhHH
Confidence 445544332 4689999999998766643
No 9
>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=87.84 E-value=2.2 Score=43.26 Aligned_cols=113 Identities=18% Similarity=0.144 Sum_probs=71.8
Q ss_pred HHhhhc-CCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCccc-ccCCCCCC
Q 007965 404 LRSAMA-NSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGR-LKDLNVSP 481 (583)
Q Consensus 404 L~SaKa-nS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r-~~d~~g~p 481 (583)
-||.-. +++-+++++| .-++..+-++..+.| +.+++.-+=.+++.++++++|=.||+-++|++.|+.+ .++..
T Consensus 80 ~rs~~~~~~~~l~fa~~-~~~~~~~~~~~~~~~-~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~--- 154 (248)
T cd07075 80 WRSYKHTNSQFLYFAPD-LVFNEERMHQSAMYE-LCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQA--- 154 (248)
T ss_pred HhccCCCCCceEEecCC-ccccHHHHhhccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCCHH---
Confidence 355544 3455888888 777766656667778 4677776777999999999999999999999987422 31100
Q ss_pred CchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHHH
Q 007965 482 PESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLTE 524 (583)
Q Consensus 482 p~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~ 524 (583)
.-+++|..=+.|+-+-+. +.=...|..-.||-++.+-|-.
T Consensus 155 ~Ve~lqe~~~~aL~~yi~---~~~~~~~~~~~RF~~LLllLp~ 194 (248)
T cd07075 155 AFEEMRTNYIKELRKMVT---KAPNNSGQSWQRFYQLTKLLDS 194 (248)
T ss_pred HHHHHHHHHHHHHHHHHH---HcCCCcccchhHHHHHHHHHHH
Confidence 123333222333333332 2223345666899988876643
No 10
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=86.26 E-value=6.5 Score=38.59 Aligned_cols=108 Identities=17% Similarity=0.197 Sum_probs=68.3
Q ss_pred HHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCC
Q 007965 403 LLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPP 482 (583)
Q Consensus 403 LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp 482 (583)
+-++...+.+.++..|| .+.+..+-....+ .=+.+++.-+-++++.++++++|=.+|+-+++++ | |. |+-.
T Consensus 89 ~a~~~~~~~~~~~f~~g-~~~~~~~~~~~~~-~~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d--~~----~L~~ 159 (231)
T cd06938 89 VARRYDAKTDSIVFANN-QPYTRDSYRKAGM-GDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS-D--RP----GLLQ 159 (231)
T ss_pred HHHHhCCCCCeEEeeCC-EEecHHHHhhcCH-HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcc-C--CC----CCCC
Confidence 33667788888999999 8887765333322 2245667677889999999999999999999985 2 21 2212
Q ss_pred chhhhHHHHHHHHHHhhhhhhcccCCch-hhhhHHHHHHHH
Q 007965 483 ESERKRAELGALARRLQGITKSVSRYPT-FRRQFDDLVKTL 522 (583)
Q Consensus 483 ~d~~rrAqLqai~RRLqGI~~s~SR~PT-~RRrf~~lvK~L 522 (583)
.+.+.+.| +....-|+-.+. .++|. -..||-+++-.|
T Consensus 160 ~~~Ve~~Q-~~~~~aL~~y~~--~~~~~~~~~rf~kLL~~L 197 (231)
T cd06938 160 PKKVEKIQ-EIYLEALRAYVD--NRRPPSQRVIFAKLLSIL 197 (231)
T ss_pred HHHHHHHH-HHHHHHHHHHHH--HhCCCCcccHHHHHHHHH
Confidence 23343333 122333444443 34565 677888876554
No 11
>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=86.21 E-value=7.9 Score=34.81 Aligned_cols=156 Identities=17% Similarity=0.193 Sum_probs=90.8
Q ss_pred HHHHHHHHHHHhhhhhhHhcCCCChhchHHHHhcCCCcEEEeccchHHHHHHHHHhhhcCCCceEeeCCceeecccCCCc
Q 007965 351 ELLERLFKECQRHGEIWVSEGLITAKDIEDAKSNSGSQVVSIGLPAYCLLQALLRSAMANSPGILLSDSVTEITSSNRPK 430 (583)
Q Consensus 351 qiwd~lFk~ce~~G~~Ll~~G~It~~Diee~~~~k~~kvi~vgLPAyslL~~LL~SaKanS~GlllsD~~~EiT~~NrPk 430 (583)
++|+..+..+-.--+.+=.=.-++.+|=...++. +.+.+.+|..--+|...+...+.+.+| +.+...+-+.
T Consensus 24 ~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~--------~~~~~~~l~~~~~s~~~~~~~~~~~~~-~~~~~~~~~~ 94 (203)
T PF00104_consen 24 EIWRRELRLIVDWAKSFPEFSELSMEDKIALLKS--------SWFELFILELAYRSYQCNQDQLMFPNG-TFIDKDSFDD 94 (203)
T ss_dssp HHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHH--------HHHHHHHHHHHHHEEHTTTTEEEETTT-EEEEHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhh--------hcccccchhhhhhhccccccccccccc-cccccccccc
Confidence 4555555555554454433344566665444443 366777777777777777899999999 7764433322
Q ss_pred c--ccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhh-HHHH-HHHHHHhhhhhhccc
Q 007965 431 D--VFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERK-RAEL-GALARRLQGITKSVS 506 (583)
Q Consensus 431 d--~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~r-rAqL-qai~RRLqGI~~s~S 506 (583)
. ..+.=+.+.+.-+=.+++.+++|++|=.+|.-+++++.+.... . ++..+ -.++ +.+++-|+=..+.-.
T Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~~~------~-~~~~~~~~~~r~~~~~~L~~y~~~~~ 167 (203)
T PF00104_consen 95 FITGIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYPGL------S-EETREIVEELRDRIIQALHSYYNQSK 167 (203)
T ss_dssp TSTTTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTSTTH------S--SHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhccccccc------c-cchhHHHHHHHHHHHHHHHHHHhccC
Confidence 2 1222222233334449999999999999999999998865443 1 12112 1122 224555555444444
Q ss_pred CCchhhhhHHHHHHHH
Q 007965 507 RYPTFRRQFDDLVKTL 522 (583)
Q Consensus 507 R~PT~RRrf~~lvK~L 522 (583)
..+.+-.||-++++.+
T Consensus 168 ~~~~~~~R~~~ll~ll 183 (203)
T PF00104_consen 168 GPEDYAQRFGKLLLLL 183 (203)
T ss_dssp STTTHTTHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHH
Confidence 5556677777776654
No 12
>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=86.13 E-value=3.5 Score=41.04 Aligned_cols=99 Identities=15% Similarity=0.133 Sum_probs=69.1
Q ss_pred CCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHH
Q 007965 411 SPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAE 490 (583)
Q Consensus 411 S~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAq 490 (583)
..-+.+++| ..++..+-....+-+ +.+++.-+=+++++++++++|=.||+-++|++.|.... -..+.+.+-|
T Consensus 110 ~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~gL------~~~~~Ve~lQ 181 (243)
T cd06935 110 SETLTLSGE-MAVTREQLKNGGLGV-VSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGL------ACVERIEKLQ 181 (243)
T ss_pred CCeEEeeCC-eEeeHHHHHhcChHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCC------CCHHHHHHHH
Confidence 456888888 666665434444445 57888889999999999999999999999999876443 1233444433
Q ss_pred ---HHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 491 ---LGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 491 ---Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
++|+-+- ++ .+.|.-..||-.++-.|-
T Consensus 182 e~~~~aL~~y----i~--~~~p~~~~rf~kLL~~L~ 211 (243)
T cd06935 182 DSFLLAFEHY----IN--YRKHHVPHFWPKLLMKVT 211 (243)
T ss_pred HHHHHHHHHH----HH--hhCCCCccHHHHHHHHHH
Confidence 4444332 22 357888899998887764
No 13
>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=86.07 E-value=9.4 Score=34.22 Aligned_cols=77 Identities=18% Similarity=0.131 Sum_probs=56.0
Q ss_pred cchHHHHHHHHHhhhcC-CCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcc
Q 007965 394 LPAYCLLQALLRSAMAN-SPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIG 472 (583)
Q Consensus 394 LPAyslL~~LL~SaKan-S~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~ 472 (583)
-+.+.+|..--+|.+.+ +.++..++| ..+...+-.+....++ .+.+.-+=++++.+|+|++|=.+|+-+++++.|..
T Consensus 41 ~~~~~~l~~a~~s~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~ 118 (165)
T cd06930 41 WAELLLLGLAQRSVHFELSELLLPSPL-LVILTEREALLGLAEL-VQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLP 118 (165)
T ss_pred HHHHHHHHHHHHHhccCCCcceeecCC-cccchhhhhhhhHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC
Confidence 45566777777788885 567888888 7776555433333333 45666677889999999999999999999986653
No 14
>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=84.89 E-value=6.7 Score=37.27 Aligned_cols=151 Identities=18% Similarity=0.168 Sum_probs=87.0
Q ss_pred HHHHHHHHHHHhhhhhhHh-------cCCCChhchHHHHhcCCCcEEEeccchHHHHHHHHHhhhcCCCceEeeCCceee
Q 007965 351 ELLERLFKECQRHGEIWVS-------EGLITAKDIEDAKSNSGSQVVSIGLPAYCLLQALLRSAMANSPGILLSDSVTEI 423 (583)
Q Consensus 351 qiwd~lFk~ce~~G~~Ll~-------~G~It~~Diee~~~~k~~kvi~vgLPAyslL~~LL~SaKanS~GlllsD~~~Ei 423 (583)
++|.++.+.....-+..++ =.-++.+|=-.-+++.- .+. .+| .+-++...+ +.++.|| ..+
T Consensus 2 ~~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~-------~e~-~ll-~~~~~~~~~--~~~~~~g-~~~ 69 (191)
T cd06942 2 NAWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNM-------FPL-YLL-RLSRDYNNE--GTVLCDF-RPV 69 (191)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHH-------HHH-HHH-HHHHHhCcC--CeEEeCC-ccc
Confidence 6788888888766555543 12233444333333220 111 223 344555444 8899999 777
Q ss_pred cccCC-CccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCC--cccccCCCCCCCchhhhHHHHHHHHHHhhh
Q 007965 424 TSSNR-PKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGN--IGRLKDLNVSPPESERKRAELGALARRLQG 500 (583)
Q Consensus 424 T~~Nr-Pkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d--~~r~~d~~g~pp~d~~rrAqLqai~RRLqG 500 (583)
+.... .+....+ +.+++.-+=+.++++++|++|=.||+-+++++.| .... .+.+ .+.+ ..+.+.+-|+=
T Consensus 70 ~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~~l-~~~~-----~v~~-~q~~l~~~L~~ 141 (191)
T cd06942 70 EFASLLSQLLHGK-LIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLGIQL-EETA-----KSNL-QLSVLFQFLKS 141 (191)
T ss_pred cHHHHHHhcchHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCc-cchH-----HHHH-HHHHHHHHHHH
Confidence 55321 0111223 4566677778999999999999999999999988 4333 1111 1211 12234444442
Q ss_pred hhhcccCCchhhhhHHHHHHHHH
Q 007965 501 ITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 501 I~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
-++ .++|.-..||-.++-.+.
T Consensus 142 ~~~--~~~~~~~~rf~kLL~~l~ 162 (191)
T cd06942 142 VLF--KDGEDTEQRLQKLFDILN 162 (191)
T ss_pred HHH--hcCCChHHHHHHHHHHHH
Confidence 222 367888889988876554
No 15
>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=83.75 E-value=9.6 Score=38.11 Aligned_cols=117 Identities=17% Similarity=0.218 Sum_probs=72.8
Q ss_pred hHHHHHHHHHhhhcCCCc-eEeeCCceeecccCC-Ccccc-chhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcc
Q 007965 396 AYCLLQALLRSAMANSPG-ILLSDSVTEITSSNR-PKDVF-FDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIG 472 (583)
Q Consensus 396 AyslL~~LL~SaKanS~G-lllsD~~~EiT~~Nr-Pkd~~-fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~ 472 (583)
.+.+|...-+|+..+..+ +++.+| +.++.... +.... ++=+.+++.-+-++++.++++++|=.||+-++|++.|..
T Consensus 84 EllvL~~a~~s~~~~~~~~~ll~~~-~~~~~~~~~~~~~~~~~~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~ 162 (241)
T cd07069 84 ELLILDHIYRQVVHGKEGSIFLVTG-QQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK 162 (241)
T ss_pred HHHHHHHHHHhhccCCCCeeEecCC-CccCchhhhhhhhhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC
Confidence 344555556677665444 777788 66554321 11111 222336666788899999999999999999999998764
Q ss_pred cccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHH
Q 007965 473 RLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTL 522 (583)
Q Consensus 473 r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 522 (583)
.. -..+.|++.|= .+..-|+.-++ .++|.-..||-+++-.|
T Consensus 163 gL------~~~~~Ve~lQe-~~~~aL~~yi~--~~~p~~~~Rf~kLLl~L 203 (241)
T cd07069 163 NL------ENFQLVEGVQE-QVNAALLDYTM--CNYPQQTEKFGQLLLRL 203 (241)
T ss_pred CC------CCHHHHHHHHH-HHHHHHHHHHH--hcCCCchhHHHHHHHHh
Confidence 43 11233444331 22334554444 47899999998876544
No 16
>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=82.91 E-value=5.9 Score=40.25 Aligned_cols=112 Identities=15% Similarity=0.162 Sum_probs=67.0
Q ss_pred HHhhhcCCCc-eEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccC-CcccccCCCCCC
Q 007965 404 LRSAMANSPG-ILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCG-NIGRLKDLNVSP 481 (583)
Q Consensus 404 L~SaKanS~G-lllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~-d~~r~~d~~g~p 481 (583)
-||.+.+..- ++..+| .-++..+--...+.+ +.+++.-+=.++++++++++|=.||+-++|++. |...+++..
T Consensus 80 ~rs~~~~~~~~l~fa~~-~~~~~~~~~~~~~~~-~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~--- 154 (247)
T cd07076 80 WRSYRQSNGNLLCFAPD-LIINEQRMTLPCMYD-QCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQE--- 154 (247)
T ss_pred HhccCCCCCceEEecCC-eeecHHHHhhhhHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCCCCCCHH---
Confidence 4777654433 667787 666554422233344 466777888899999999999999999999986 543331100
Q ss_pred CchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 482 PESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 482 p~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
-.|++|..=+.|+-+-+. +.-...|...+||-++..-|-
T Consensus 155 ~Ve~lqe~~~~aL~~yi~---~~~p~~~~~~~RF~kLLllLp 193 (247)
T cd07076 155 LFDEIRMTYIKELGKAIV---KREGNSSQNWQRFYQLTKLLD 193 (247)
T ss_pred HHHHHHHHHHHHHHHHHH---hcCCCcchhhhHHHHHHHHHH
Confidence 134444433344433332 111223444569998877654
No 17
>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal doma
Probab=81.70 E-value=10 Score=37.58 Aligned_cols=117 Identities=15% Similarity=0.156 Sum_probs=68.4
Q ss_pred HHHHHHHhhhcCCCceEeeCCceeecccCC-CccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCC
Q 007965 399 LLQALLRSAMANSPGILLSDSVTEITSSNR-PKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDL 477 (583)
Q Consensus 399 lL~~LL~SaKanS~GlllsD~~~EiT~~Nr-Pkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~ 477 (583)
+|..--||...+. -+++++| ..++.... +++.+ ..+++++.-+=++++.++++++|=.||+-++|++.|.... .+
T Consensus 79 ~L~~a~rs~~~~~-~~~~~~~-~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~-~~ 154 (235)
T cd06949 79 MLGLVWRSMEHPG-KLLFAPD-LLLDRNQGSCVEGM-VEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTF-LL 154 (235)
T ss_pred HHHHHHHhcCCCC-eEEeeCC-ceecHHHhhhcccH-HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCc-cc
Confidence 3444456665543 3667777 55543322 23333 3456677777779999999999999999999998764321 11
Q ss_pred CCCCCchhhhHHHHHHHHHHhhhhhhcccCC---chhhhhHHHHHHHH
Q 007965 478 NVSPPESERKRAELGALARRLQGITKSVSRY---PTFRRQFDDLVKTL 522 (583)
Q Consensus 478 ~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~---PT~RRrf~~lvK~L 522 (583)
.+......+++.| +.+..-|+.-+. .++ |.-..||-+++-.|
T Consensus 155 ~~l~~~~~Ve~lq-~~~~~aL~~y~~--~~~~~~p~~~~Rf~~LLl~L 199 (235)
T cd06949 155 ESLESRRQVQRLL-DKITDALVHACS--KRGLSLQQQSRRLAQLLLIL 199 (235)
T ss_pred ccccCHHHHHHHH-HHHHHHHHHHHH--hcCCCCCCcccHHHHHHHhc
Confidence 1122344455555 223333444333 244 77778888776544
No 18
>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=80.22 E-value=6 Score=38.74 Aligned_cols=109 Identities=17% Similarity=0.221 Sum_probs=66.7
Q ss_pred HhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCch
Q 007965 405 RSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPES 484 (583)
Q Consensus 405 ~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d 484 (583)
++.....+.+...|| ..++..+-.+..+..=+.+++.-+-+.++.+++|++|=.||+-++|++.|.... .+ .+
T Consensus 95 ~~~~~~~~~~~~~~g-~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~gL-~~-----~~ 167 (236)
T cd06954 95 RRYNPESEAITFLKD-FPYSRDDFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNV-QD-----HH 167 (236)
T ss_pred HHhcCCCCeEEeeCC-ccccHHHHHHhcChHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCcccC-CC-----HH
Confidence 334455667888898 666544322122222345667678889999999999999999999999775333 11 12
Q ss_pred hhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 485 ERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 485 ~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
.+.+.| +.+..=|+--++ +++|.-+.||-.+.-.|.
T Consensus 168 ~V~~lQ-~~~~~aL~~y~~--~~~p~~~~rf~klL~~L~ 203 (236)
T cd06954 168 RVERLQ-ETYVEALHSYIK--IKRPSDRLMFPRMLMKLV 203 (236)
T ss_pred HHHHHH-HHHHHHHHHHHH--hcCCCcccHHHHHHHHHH
Confidence 333332 111222333332 468888888877766554
No 19
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=80.14 E-value=10 Score=34.64 Aligned_cols=117 Identities=21% Similarity=0.246 Sum_probs=68.5
Q ss_pred hHHHHHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCccccc
Q 007965 396 AYCLLQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLK 475 (583)
Q Consensus 396 AyslL~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~ 475 (583)
.+.++..- ++.+.+.+.+...|| +......-+... +.=+.+.+.-.=..++.+++|++|=.+|+-+++++.|...+
T Consensus 46 ~l~~l~~a-~~~~~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~~l- 121 (174)
T cd06929 46 EILLLRSA-TLYDPEKNSLTFGDG-KGNSRDVLLNGG-FGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGL- 121 (174)
T ss_pred HHHHHHHH-HHhcccCCeEEecCC-ceecHHHHHHcc-cHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccC-
Confidence 34444443 566778888999999 552222111111 11234555556688999999999999999999998665333
Q ss_pred CCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHHH
Q 007965 476 DLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLTE 524 (583)
Q Consensus 476 d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~ 524 (583)
. +..-.++.|..=++|+-+ .+ ..++|....||-+++..+..
T Consensus 122 ~--~~~~v~~~q~~~~~aL~~----y~--~~~~~~~~~Rf~~Ll~~l~~ 162 (174)
T cd06929 122 Q--DVDTVEKLQERLLEALQR----YL--KVNHPDAPQMFAKLLKKLTE 162 (174)
T ss_pred c--CHHHHHHHHHHHHHHHHH----HH--HhcCCCChhHHHHHHHHhHH
Confidence 1 111122222222334333 33 24577778889888776543
No 20
>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=80.06 E-value=13 Score=36.01 Aligned_cols=74 Identities=19% Similarity=0.235 Sum_probs=49.1
Q ss_pred hHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHH
Q 007965 440 PFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLV 519 (583)
Q Consensus 440 PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lv 519 (583)
.+.-+-.+++.++++++|=.||+-++|++.|.... ...+.+++.| +.+..-|+--+. .++|.-..||-+++
T Consensus 111 ~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~~L------~~~~~Ve~lq-~~~~~aL~~y~~--~~~~~~~~Rf~kLL 181 (206)
T cd06950 111 ALQETLSRFRQLRVDATEFACLKAIVLFKPETRGL------KDPAQVEALQ-DQAQLMLNKHIR--TRYPTQPARFGKLL 181 (206)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCC------CCHHHHHHHH-HHHHHHHHHHHH--HhCCCcccHHHHHH
Confidence 34445568999999999999999999999775433 1234455544 233333443333 45788888998887
Q ss_pred HHH
Q 007965 520 KTL 522 (583)
Q Consensus 520 K~L 522 (583)
-.|
T Consensus 182 l~L 184 (206)
T cd06950 182 LLL 184 (206)
T ss_pred HHH
Confidence 544
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=78.60 E-value=11 Score=37.60 Aligned_cols=114 Identities=21% Similarity=0.232 Sum_probs=67.6
Q ss_pred HHHHHHHhhhc-CCCceEeeCCceeecccCCCccccchhcchhHHH---HHHHHHhccCChhHHHHhHhhhhccCCcccc
Q 007965 399 LLQALLRSAMA-NSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLI---IKEQIKAENLTEAEEDYLSKLVLFCGNIGRL 474 (583)
Q Consensus 399 lL~~LL~SaKa-nS~GlllsD~~~EiT~~NrPkd~~fDWff~Pllv---iKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~ 474 (583)
+|...-||.-. +.+-+++.+| ++++..+-... .-.++-..... +=.+++.++++++|=.||+-++|++.|....
T Consensus 85 vL~~a~rs~~~~~~~~l~~~~g-~~~~~~~~~~~-~~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL 162 (237)
T cd07070 85 VFDHIYRQVQHGKEGSILLVTG-QEVELSTVAAQ-AGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFL 162 (237)
T ss_pred HHHHHHHhhhcCCCCceeecCC-CeechhHHHHH-HhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCccCC
Confidence 34444566644 3455777888 88876553211 11222222222 4457889999999999999999998775433
Q ss_pred cCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 475 KDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 475 ~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
.+.+ -.+..|..=.+| |+.-++ .++|.-..||-+++-.|-
T Consensus 163 -~~~~--~Ve~lQe~~~~a----L~~y~~--~~~p~~~~Rf~kLLl~Lp 202 (237)
T cd07070 163 -NNHS--LVKDAQEKANAA----LLDYTL--CHYPHCGDKFQQLLLRLV 202 (237)
T ss_pred -CCHH--HHHHHHHHHHHH----HHHHHH--hcCCCcchHHHHHHHHhH
Confidence 1111 122233222333 444444 478999999999865543
No 22
>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=77.53 E-value=23 Score=35.82 Aligned_cols=111 Identities=17% Similarity=0.134 Sum_probs=65.1
Q ss_pred Hhhhc-CCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccC-CcccccCCCCCCC
Q 007965 405 RSAMA-NSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCG-NIGRLKDLNVSPP 482 (583)
Q Consensus 405 ~SaKa-nS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~-d~~r~~d~~g~pp 482 (583)
||.-. +.+.+.+.+| ..++..+..+..+.+.. ..+.-+=++.++++++++|=.||+-++|++. |.... .+.. -
T Consensus 81 rs~~~~~~~~l~~~~~-~~l~~~~~~~~~~~~~~-~~l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~gL-~~~~--~ 155 (246)
T cd07073 81 RSFTNVNSRMLYFAPD-LVFNEYRMHKSRMYSQC-VRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGL-KNQK--F 155 (246)
T ss_pred hccccCCCCeEEecCC-eeechhhhccccHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcccc-cCHH--H
Confidence 56644 4555888888 77777665665666642 2333444578889999999999999999996 42212 1100 1
Q ss_pred chhhhHHHHHHHHHHhhhhhhcccCC-chhhhhHHHHHHHHHH
Q 007965 483 ESERKRAELGALARRLQGITKSVSRY-PTFRRQFDDLVKTLTE 524 (583)
Q Consensus 483 ~d~~rrAqLqai~RRLqGI~~s~SR~-PT~RRrf~~lvK~L~~ 524 (583)
-+++|..=+.| |+--+.+-... |.-..||-.+.-.|..
T Consensus 156 Ve~lQe~~~~a----L~~yi~~~~~~~~~~~~Rf~kLLl~Lp~ 194 (246)
T cd07073 156 FDELRMNYIKE----LDRIIACKRKNPTSCSRRFYQLTKLLDS 194 (246)
T ss_pred HHHHHHHHHHH----HHHHHHhcCCCCcccchHHHHHHHHHHH
Confidence 12222222223 33333322212 3557899988876643
No 23
>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=75.45 E-value=26 Score=35.25 Aligned_cols=103 Identities=7% Similarity=0.077 Sum_probs=64.7
Q ss_pred CCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHH
Q 007965 410 NSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRA 489 (583)
Q Consensus 410 nS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrA 489 (583)
..+.+++.+| .-.++.+. ...+-+ +.+++.-+=++++.++|+++|=.||+-++|++ |.... -..+.|.+-
T Consensus 98 ~~~~l~~~~g-~~~~~~~~-~~~~~~-~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf~-D~~gL------~~~~~Ve~l 167 (238)
T cd07071 98 VEGKLIFCNG-VVLHRLQC-VRGFGE-WIDSIVEFSSNLQNMNIDISAFSCIAALAMVT-ERHGL------KEPKRVEEL 167 (238)
T ss_pred CCCceEeeCC-ceechhhh-hhcHHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcC-CCCCC------CCHHHHHHH
Confidence 3455888888 66655442 333445 47788888899999999999999999999883 32212 222223222
Q ss_pred HHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 490 ELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 490 qLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
| +.+..-|+.-++.=...|.-..||-.+.-.|-
T Consensus 168 Q-e~~~~aL~~yi~~~~~~p~~~~rf~kLLl~Lp 200 (238)
T cd07071 168 Q-NKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLP 200 (238)
T ss_pred H-HHHHHHHHHHHHHhCCCCCcccHHHHHHHHhH
Confidence 2 12233455555443446788889988876554
No 24
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=73.30 E-value=30 Score=35.03 Aligned_cols=114 Identities=12% Similarity=0.048 Sum_probs=64.2
Q ss_pred HHHHHHHhhhcC-CCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCC
Q 007965 399 LLQALLRSAMAN-SPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDL 477 (583)
Q Consensus 399 lL~~LL~SaKan-S~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~ 477 (583)
+|..--||...+ ++-+++++| .-++...--+..+.| +.+++.-+=.++++++++++|=.||+-++|++.++.+
T Consensus 75 iL~~a~rs~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~-~~~~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~---- 148 (246)
T cd06947 75 VFALGWRSYKHVNSQMLYFAPD-LVFNEQRMHQSAMYS-LCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKD---- 148 (246)
T ss_pred HHHHHHhhccCCCCCeEEecCC-eeecHHHhhhccHHH-HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccc----
Confidence 334334666544 333667787 544433322334666 3466655566899999999999999999999963222
Q ss_pred CCCCCc---hhhhHHHHHHHHHHhhhhhhc-ccCCchhhhhHHHHHHHHH
Q 007965 478 NVSPPE---SERKRAELGALARRLQGITKS-VSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 478 ~g~pp~---d~~rrAqLqai~RRLqGI~~s-~SR~PT~RRrf~~lvK~L~ 523 (583)
|.-.. +++|..=+.|+- .-++. --..|...+||-++...|-
T Consensus 149 -gL~~~~~Ve~lqe~i~~AL~----~yi~~~~~~~~~~~~Rf~kLLllLp 193 (246)
T cd06947 149 -GLKSQAAFDEMRMNYIKELR----KAIVKREKNSSQSWQRFYQLTKLLD 193 (246)
T ss_pred -cccCHHHHHHHHHHHHHHHH----HHHHHhCCCCcccchHHHHHHHhhh
Confidence 12122 222222233333 22221 1124566788888876553
No 25
>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=73.17 E-value=41 Score=29.19 Aligned_cols=122 Identities=14% Similarity=0.118 Sum_probs=75.5
Q ss_pred cchHHHHHHHHHhhhcCCCceEeeCCceee-cccCCCccccc-hhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCc
Q 007965 394 LPAYCLLQALLRSAMANSPGILLSDSVTEI-TSSNRPKDVFF-DWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNI 471 (583)
Q Consensus 394 LPAyslL~~LL~SaKanS~GlllsD~~~Ei-T~~NrPkd~~f-DWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~ 471 (583)
-..+.+|...-+|.+.+....+..++ ... ...+.+..+.+ .=+-..+.-+-+.++.+++|++|=.+|+-+++++.+.
T Consensus 40 ~~~~~~L~~~~~s~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~ 118 (168)
T cd06157 40 WLELLVLDLAYRSYKNGLSLLLAPNG-GHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDR 118 (168)
T ss_pred hHHHHHHHHHHHHHhcCCCcEEeecc-cccccCchHHHHHhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCC
Confidence 45678899999999999988887777 432 12222222221 1222344456678899999999999999999998654
Q ss_pred ccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 472 GRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 472 ~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
.+ +....+.+ +..-+.+.+-|+-.+..-.. |..--||-+++..+.
T Consensus 119 ~~-----s~~~~~~~-~~~~~~~~~~L~~y~~~~~~-~~~~~R~~~ll~~l~ 163 (168)
T cd06157 119 KE-----SLEDRKIV-EELQERLLEALQDYLRKNYP-EEAPSRFAKLLLLLP 163 (168)
T ss_pred CC-----CccCHHHH-HHHHHHHHHHHHHHHHHhCC-ccchhHHHHHHHhch
Confidence 21 11112222 22334555666655544433 566667777776543
No 26
>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=73.08 E-value=16 Score=36.19 Aligned_cols=108 Identities=21% Similarity=0.284 Sum_probs=64.6
Q ss_pred HHHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHH---HHHHHHhccCChhHHHHhHhhhhccCCccccc
Q 007965 399 LLQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLI---IKEQIKAENLTEAEEDYLSKLVLFCGNIGRLK 475 (583)
Q Consensus 399 lL~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~Pllv---iKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~ 475 (583)
+|.+--+|...+.+-++..|| +.+...+ .+++-+ +.+.+-+ +=++++.+++|++|=.||+-++|++.|.....
T Consensus 77 lL~~a~~s~~~~~~~~~~~~g-~~~~~~~--~~~~~~-~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~~L~ 152 (236)
T cd06948 77 VLNAAQCCMPLHVAPLLAAAG-LHASPMS--ADRVVA-FMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLS 152 (236)
T ss_pred HHHHHHHcccccchhhhhccc-cccCccc--hhhHhH-HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCccccccc
Confidence 444445566666666777788 5443322 122222 2333322 23568999999999999999999997754431
Q ss_pred CCCCCCCchhhhHHH---HHHHHHHhhhhhhcccCCchhhhhHHHHHHHH
Q 007965 476 DLNVSPPESERKRAE---LGALARRLQGITKSVSRYPTFRRQFDDLVKTL 522 (583)
Q Consensus 476 d~~g~pp~d~~rrAq---Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L 522 (583)
..+.+++.| ++|+-+-.+ .++|.-..||-+++-.|
T Consensus 153 ------~~~~v~~~q~~~~~aL~~y~~------~~~~~~~~Rf~~LLl~L 190 (236)
T cd06948 153 ------DPAHIESLQEKSQCALEEYVR------TQYPNQPTRFGKLLLRL 190 (236)
T ss_pred ------CHHHHHHHHHHHHHHHHHHHH------HhCCCcccHHHHHHHHH
Confidence 122344443 555555443 45677778888877644
No 27
>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=72.70 E-value=30 Score=35.13 Aligned_cols=102 Identities=20% Similarity=0.282 Sum_probs=67.0
Q ss_pred cCCCceEeeCCceeecccC--CCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhh
Q 007965 409 ANSPGILLSDSVTEITSSN--RPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESER 486 (583)
Q Consensus 409 anS~GlllsD~~~EiT~~N--rPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~ 486 (583)
.|.+++++.+|-+-+|... ..+.. +.=+.+|+.-+=++++.++|+++|=.||+-++|++.|.... -..+.|
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~gL------~~~~~V 189 (259)
T cd06932 117 YNKDGLLFPEGNGYVTREFLESLRKP-FCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGL------INRKPV 189 (259)
T ss_pred cCCCCeEEeCCCEEeeHHHHHHhccc-HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccC------cCHHHH
Confidence 3567777776523233322 11111 22367788888999999999999999999999999875433 223345
Q ss_pred hHHH---HHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 487 KRAE---LGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 487 rrAq---Lqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
++.| ++|+-+.+. +++|..+.||-.++-.|-
T Consensus 190 e~lQe~~~~aL~~~i~------~~~p~~~~rf~kLLl~L~ 223 (259)
T cd06932 190 ERIQEHVLQALELQLK------KNHPDSPQLFAKLLQKMV 223 (259)
T ss_pred HHHHHHHHHHHHHHHh------hhCCCcccHHHHHHHHHH
Confidence 5444 445544432 457999999998876554
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=70.83 E-value=32 Score=34.68 Aligned_cols=113 Identities=16% Similarity=0.223 Sum_probs=68.5
Q ss_pred HHHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCC
Q 007965 399 LLQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLN 478 (583)
Q Consensus 399 lL~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~ 478 (583)
+|..--+|... ..-+++++| ..+++.+. ...+-+| .+++.-.=.+++.++++++|=.||+-++|+ .|....
T Consensus 88 vL~~a~r~~~~-~~~l~f~~~-~~~~r~~~-~~~~~~~-~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~gL---- 158 (238)
T cd07348 88 ILRLAYRSNPE-EGKLIFCNG-VVLHRTQC-VRGFGDW-IDSILEFSQSLHRMNLDVSAFSCLAALVII-TDRHGL---- 158 (238)
T ss_pred HHHHHHHcCCC-CCeEEeeCC-eeecHHHH-HhhHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCcCC----
Confidence 34444455444 345788888 77665553 3345565 466777788999999999999999999999 333222
Q ss_pred CCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 479 VSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 479 g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
--.+.|.+-| +.+..-|+.-++.-.+.|.-..||-+++-.|-
T Consensus 159 --~~~~~Ve~lQ-e~~~~aL~~yi~~~~~~p~~p~rf~kLLl~Lp 200 (238)
T cd07348 159 --KEPKRVEELQ-NRLISCLKEHVSGSASEPQRPNCLSRLLGKLP 200 (238)
T ss_pred --CCHHHHHHHH-HHHHHHHHHHHHhhCCCCccccHHHHHHHHHH
Confidence 2222333333 11223344444433346888889988875543
No 29
>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=66.33 E-value=39 Score=34.06 Aligned_cols=113 Identities=13% Similarity=0.198 Sum_probs=66.4
Q ss_pred HHHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCC
Q 007965 399 LLQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLN 478 (583)
Q Consensus 399 lL~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~ 478 (583)
+|..--+|... ..-+++++| ..++.....+ .+-+| .+++.-+=+++++++++++|=.||+-++|+. |..
T Consensus 89 ~L~~a~r~~~~-~~~l~~~~g-~~~~~~~~~~-~~~~~-~~~i~ef~~~l~~L~ld~~E~a~LkAivLf~-dr~------ 157 (239)
T cd07072 89 VLRLAYRTAPE-DTKLTFCNG-VVLHKQQCQR-SFGDW-LHAILEFSKSLHAMDIDISAFACLCALTLIT-ERH------ 157 (239)
T ss_pred HHHHHHHccCC-CCeEEeeCC-eeecHHHHHh-hHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhC-CCC------
Confidence 33434455444 344778888 6666554322 45564 5677777889999999999999999999993 221
Q ss_pred CCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 479 VSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 479 g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
|.-..+.|++-|=+ +..-|+.-++.-...|.-+.||-.++-.|-
T Consensus 158 gL~~~~~Ve~lQe~-~~~aL~~yi~~~~~~~~~~~rf~kLLl~Lp 201 (239)
T cd07072 158 GLKEPHKVEQLQMK-IISSLRDHVTYNAEAQKKPHYFSRLLGKLP 201 (239)
T ss_pred CCCCHHHHHHHHHH-HHHHHHHHHHHhCCCcccccHHHHHHHHhH
Confidence 22223334443311 122233333322245566678887765543
No 30
>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=64.61 E-value=45 Score=32.38 Aligned_cols=73 Identities=14% Similarity=0.182 Sum_probs=44.1
Q ss_pred hHHHHHHHHHhhhcCCCceEeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCc
Q 007965 396 AYCLLQALLRSAMANSPGILLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNI 471 (583)
Q Consensus 396 AyslL~~LL~SaKanS~GlllsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~ 471 (583)
.+.+|..--+|...+. -++..+| .-...........-++ .+++.-+=+.++.+++|++|=.||+-++|++.|.
T Consensus 71 el~lL~~a~~s~~~~~-~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~ 143 (221)
T cd06946 71 EILTLGVVFRSLPFNG-ELVFAED-FILDEELAREAGLLEL-YSACLQLVRRLQRLRLEKEEYVLLKALALANSDS 143 (221)
T ss_pred HHHHHHHHHHccCCCC-ceeecCC-eEEcHHHHhhcCHHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCC
Confidence 3455555667776653 3555565 3222111111112222 3445555578899999999999999999998774
No 31
>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=63.63 E-value=23 Score=35.12 Aligned_cols=71 Identities=17% Similarity=0.199 Sum_probs=48.0
Q ss_pred HHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHH
Q 007965 444 IKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLT 523 (583)
Q Consensus 444 iKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~ 523 (583)
+=.++++++++++|=.||+-+||++.|.... -..+.+++-|= .+..-|+..++ +++|.-..||-.++-.|-
T Consensus 120 ~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl------~~~~~V~~lqe-~~~~aL~~~~~--~~~p~~~~r~~kLLl~Lp 190 (222)
T cd07349 120 CLNKFWSLDLSPKEYAYLKGTILFNPDVPGL------TASSHVGHLQQ-EAQWALCEVLE--PLHPQDQGRFARILLTAS 190 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHcCCCcccC------CCHHHHHHHHH-HHHHHHHHHHH--HHCCCcccHHHHHHHHhH
Confidence 4468999999999999999999998765433 11233333332 22344555554 568999999988776554
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=62.65 E-value=85 Score=32.20 Aligned_cols=69 Identities=12% Similarity=0.124 Sum_probs=44.7
Q ss_pred HHHHHHHhhhcCCCce-EeeCCceeecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccC
Q 007965 399 LLQALLRSAMANSPGI-LLSDSVTEITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCG 469 (583)
Q Consensus 399 lL~~LL~SaKanS~Gl-llsD~~~EiT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~ 469 (583)
+|..--||.+.+++.. .+++| .-++..+..+..+.| +..++.-+-.+++.++++++|=.||+-++|++.
T Consensus 75 vL~~a~rS~~~~~~~~l~fa~d-~~~~~~~~~~~~~~~-~~~~m~e~~~~~~~L~ld~~Ey~cLKAIvLfnp 144 (248)
T cd07074 75 VFGLGWRSYKHVSGQMLYFAPD-LILNEQRMKESSFYS-LCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNT 144 (248)
T ss_pred HHHHHHhhhccCCCCeEEecCC-cccchhhhhhccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHCCC
Confidence 3344457888776654 45566 444333222234555 333443345689999999999999999999997
No 33
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=62.19 E-value=7.7 Score=35.90 Aligned_cols=48 Identities=25% Similarity=0.573 Sum_probs=38.6
Q ss_pred ccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHHH
Q 007965 451 ENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLTE 524 (583)
Q Consensus 451 ~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~ 524 (583)
.+|++++-.|++..+.-.||=+.. +|-| || -|||.|.|.++++++|-.
T Consensus 32 ~~L~~E~~~Fi~~Fi~~rGnlKe~--------------------e~~l-gi-----SYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 32 ARLSPEQLEFIKLFIKNRGNLKEM--------------------EKEL-GI-----SYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hcCCHHHHHHHHHHHHhcCCHHHH--------------------HHHH-CC-----CcHHHHHHHHHHHHHhCC
Confidence 589999999999999988886543 3333 44 399999999999999865
No 34
>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=60.99 E-value=45 Score=32.47 Aligned_cols=111 Identities=14% Similarity=0.156 Sum_probs=61.9
Q ss_pred hHHHHHHHHHHHhhhhhhHh-------cCCCChhchHHHHhcCCCcEEEeccchHHHHHHHHHhhhcCCCceEeeCCcee
Q 007965 350 LELLERLFKECQRHGEIWVS-------EGLITAKDIEDAKSNSGSQVVSIGLPAYCLLQALLRSAMANSPGILLSDSVTE 422 (583)
Q Consensus 350 vqiwd~lFk~ce~~G~~Ll~-------~G~It~~Diee~~~~k~~kvi~vgLPAyslL~~LL~SaKanS~GlllsD~~~E 422 (583)
+++|+++.+...+.=...++ =.-++.+|-..-+++. -..+.+|.+--+|+..+. ++.+.+| .-
T Consensus 26 ~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~--------~~~~~~l~~a~~s~~~~~-~~~~~~~-~~ 95 (221)
T cd07068 26 VSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSA--------WLEILMLGLVWRSLPHPG-KLVFAPD-LL 95 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHh--------hHHHHHHHHHHhhcCCCC-eEEeCCC-ce
Confidence 45666665444433222221 1224555544444443 344455555556665544 7888888 54
Q ss_pred ecccCCCccccchhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCc
Q 007965 423 ITSSNRPKDVFFDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNI 471 (583)
Q Consensus 423 iT~~NrPkd~~fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~ 471 (583)
.+.....+..+-+ +.+++.-+=..++.+++|++|=.+|+-+++++.|.
T Consensus 96 ~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~npd~ 143 (221)
T cd07068 96 LDREQARVEGLLE-IFDMLLQLVRRFRELGLQREEYVCLKAIILANSDV 143 (221)
T ss_pred ECHHHHhhccHHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCc
Confidence 4332211223222 23344445568999999999999999999996544
No 35
>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of
Probab=60.55 E-value=27 Score=34.49 Aligned_cols=74 Identities=16% Similarity=0.235 Sum_probs=48.7
Q ss_pred cchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHH---HHHHHHHhhhhhhcccCCc--hh
Q 007965 437 FFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAE---LGALARRLQGITKSVSRYP--TF 511 (583)
Q Consensus 437 ff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAq---Lqai~RRLqGI~~s~SR~P--T~ 511 (583)
+.+|+.-+=+++++++++++|=.||+-.+|++.|..... ..+.|.+-| ++|+-+.+ .+++| .-
T Consensus 117 ~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL~------~~~~Ve~lQe~~~~aL~~yi------~~~~p~~~~ 184 (226)
T cd06934 117 LLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVT------QHDVIDQLQEKMALTLKSYI------DSKRPGPEK 184 (226)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCc------ChHHHHHHHHHHHHHHHHHH------HHcCCCCCc
Confidence 567777788899999999999999999999998754431 122233322 34444332 13344 35
Q ss_pred hhhHHHHHHHH
Q 007965 512 RRQFDDLVKTL 522 (583)
Q Consensus 512 RRrf~~lvK~L 522 (583)
|.||-.++-.|
T Consensus 185 r~~f~kLLl~L 195 (226)
T cd06934 185 RFLYPKILACL 195 (226)
T ss_pred ccHHHHHHHHh
Confidence 55688887655
No 36
>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=59.74 E-value=43 Score=33.42 Aligned_cols=79 Identities=18% Similarity=0.303 Sum_probs=52.9
Q ss_pred cchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCc--hhhhh
Q 007965 437 FFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYP--TFRRQ 514 (583)
Q Consensus 437 ff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~P--T~RRr 514 (583)
+.+|+.-+-++++.++++++|=.||+-++|++.|.... -..+.|.+-| +.+..-|+.-++ +++| ..|.|
T Consensus 121 ~~~~l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~gL------~~~~~Ve~lQ-e~~~~aL~~yi~--~~~p~~~~~~~ 191 (238)
T cd06933 121 LLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGV------QDHALIEAIQ-DRLSDTLQTYIR--CRHPPPGSRLL 191 (238)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCCCC------cchHHHHHHH-HHHHHHHHHHHH--hcCCCCCchhH
Confidence 46788888889999999999999999999998764333 1122222222 122333444444 4555 67889
Q ss_pred HHHHHHHHHH
Q 007965 515 FDDLVKTLTE 524 (583)
Q Consensus 515 f~~lvK~L~~ 524 (583)
|-.++-.|.+
T Consensus 192 f~kLLl~L~~ 201 (238)
T cd06933 192 YAKMIQKLAD 201 (238)
T ss_pred HHHHHHHhHH
Confidence 9998877743
No 37
>PF06161 DUF975: Protein of unknown function (DUF975); InterPro: IPR010380 This is a family of uncharacterised bacterial proteins.
Probab=55.63 E-value=39 Score=32.94 Aligned_cols=41 Identities=27% Similarity=0.412 Sum_probs=27.1
Q ss_pred HHhhHHHHHHHHHHHhhHHHhhhhhhhhhhHhh------hhhhhccC
Q 007965 82 ICIPVFLILWPVVSIGASIIGGALYGFLSPIFA------TFDAVGEG 122 (583)
Q Consensus 82 i~lP~~l~LW~vvgI~GSvl~G~gYGff~P~~a------TFeAvgeg 122 (583)
......+++|.+++++..++.+..|.+-..+++ .+||+++.
T Consensus 142 ~~~~~~~~~~~l~~~i~~i~~~~~y~~~~yil~d~~~~~~~~al~~S 188 (243)
T PF06161_consen 142 ISLLLLLVLLLLLLIIPGIIVSYSYSMVPYILADNPELGAFEALKRS 188 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCHHHHHHHH
Confidence 334445566777788888888899988776653 45555543
No 38
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=55.16 E-value=55 Score=32.21 Aligned_cols=81 Identities=19% Similarity=0.215 Sum_probs=52.6
Q ss_pred chhcchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhh
Q 007965 434 FDWFFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRR 513 (583)
Q Consensus 434 fDWff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RR 513 (583)
.+=+.+|+.-+-+.++.+++|++|=.+|+-+++++.|.... .+ ..-.++.+..=++|+-+ .+. .++|....
T Consensus 112 ~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~gL-~~--~~~Ve~~Q~~~~~aL~~----y~~--~~~p~~p~ 182 (221)
T cd06936 112 SDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYL-KD--KEAVEKLQEPLLDLLQK----FCK--LYHPEDPQ 182 (221)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCcCC-CC--HHHHHHHHHHHHHHHHH----HHH--hhCCCchh
Confidence 34456777777888999999999999999999998875433 11 00112222222333333 332 47888889
Q ss_pred hHHHHHHHHH
Q 007965 514 QFDDLVKTLT 523 (583)
Q Consensus 514 rf~~lvK~L~ 523 (583)
||-.++-.|.
T Consensus 183 rf~~LL~~L~ 192 (221)
T cd06936 183 HFACLLGRLT 192 (221)
T ss_pred HHHHHHHHhH
Confidence 9988876553
No 39
>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=50.73 E-value=44 Score=32.63 Aligned_cols=77 Identities=14% Similarity=0.207 Sum_probs=49.1
Q ss_pred cchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHH
Q 007965 437 FFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFD 516 (583)
Q Consensus 437 ff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~ 516 (583)
+.+++.-+=.++++++++++|=.||+-+++++.|....++.. -.+..|..=.+|+-+..+ .++|....||-
T Consensus 113 ~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~---~Ve~lQ~~~~~aL~~y~~------~~~~~~p~Rf~ 183 (213)
T cd06953 113 VVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNAS---QLESLQKRYWYVLQDFTE------LNYPNQPNRFS 183 (213)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHH---HHHHHHHHHHHHHHHHHH------HhCCCcchHHH
Confidence 356666666789999999999999999999988764431111 022222222344444332 34588888998
Q ss_pred HHHHHH
Q 007965 517 DLVKTL 522 (583)
Q Consensus 517 ~lvK~L 522 (583)
++.-.|
T Consensus 184 ~LL~~L 189 (213)
T cd06953 184 DLLSCL 189 (213)
T ss_pred HHHHHh
Confidence 876555
No 40
>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=48.49 E-value=53 Score=32.97 Aligned_cols=76 Identities=16% Similarity=0.118 Sum_probs=50.1
Q ss_pred hhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHH
Q 007965 439 NPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDL 518 (583)
Q Consensus 439 ~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~l 518 (583)
+++.-+=+++++++++++|=.||+-+||++.|....+ ..+.|.+-|=+.. .-|+..++ +++|....||-.+
T Consensus 127 ~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~------~~~~Ve~lQe~~~-~aL~~yi~--~~~p~~~~rf~kL 197 (232)
T cd07350 127 RAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQ------CVQYIQGLQWEAQ-QALNEHVR--MIHRGDQARFAKL 197 (232)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCC------CHHHHHHHHHHHH-HHHHHHHH--hhCCChhhHHHHH
Confidence 4555566788999999999999999999998754331 1233443332222 23444444 4788888899887
Q ss_pred HHHHH
Q 007965 519 VKTLT 523 (583)
Q Consensus 519 vK~L~ 523 (583)
+-.|-
T Consensus 198 Ll~Lp 202 (232)
T cd07350 198 NIALS 202 (232)
T ss_pred HHHhH
Confidence 65543
No 41
>cd06952 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2. The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D
Probab=48.40 E-value=51 Score=31.98 Aligned_cols=73 Identities=16% Similarity=0.239 Sum_probs=47.6
Q ss_pred HHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHH
Q 007965 441 FLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVK 520 (583)
Q Consensus 441 llviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK 520 (583)
+.-+.++++++++++.|=.||+-++|++.|-...+ +..--+++|..=++|+.+ .++ +++|....||-+++-
T Consensus 115 l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~---~~~~v~~lq~~i~~aL~~----y~~--~~~p~~~~R~~klLl 185 (222)
T cd06952 115 LQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQE---LRQQIEKLQEKALMELRD----YVG--KTYPEDEYRLSKLLL 185 (222)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCc---CHHHHHHHHHHHHHHHHH----HHH--HhCCCcccHHHHHHH
Confidence 35678899999999999999999999998753321 111123333333334433 333 237888889988875
Q ss_pred HH
Q 007965 521 TL 522 (583)
Q Consensus 521 ~L 522 (583)
.|
T Consensus 186 ~L 187 (222)
T cd06952 186 RL 187 (222)
T ss_pred Hh
Confidence 44
No 42
>KOG2511 consensus Nicotinic acid phosphoribosyltransferase [Coenzyme transport and metabolism]
Probab=46.50 E-value=15 Score=40.27 Aligned_cols=23 Identities=43% Similarity=0.599 Sum_probs=19.7
Q ss_pred HHHHHH---hccCChhHHHHhHhhhh
Q 007965 444 IKEQIK---AENLTEAEEDYLSKLVL 466 (583)
Q Consensus 444 iKeQIk---~~~L~E~EE~yL~KlvL 466 (583)
++|||| +++||+||++||+|-.=
T Consensus 53 Lee~irfl~N~~lt~eei~~lkk~lP 78 (420)
T KOG2511|consen 53 LEEQIRFLANLKLTDEEIDYLKKELP 78 (420)
T ss_pred HHHHHHHHhhcCCCHHHHHHHHHhCC
Confidence 799987 67999999999998653
No 43
>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=43.36 E-value=61 Score=32.10 Aligned_cols=77 Identities=17% Similarity=0.020 Sum_probs=52.6
Q ss_pred cchhHHHHHHHHHhccCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHH
Q 007965 437 FFNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFD 516 (583)
Q Consensus 437 ff~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~ 516 (583)
+.+++.-+=.++++++++++|=.||+-++|++.|.. |. ..+.|++.|=+. ..=|+--++ +++|.-..||-
T Consensus 116 ~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~------gl-~~~~Ve~lQe~~-~~aL~~yi~--~~~p~~~~Rf~ 185 (222)
T cd06951 116 DVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPP------LL-CPHYIEALQKEA-QQALNEHTM--MTRPLEQLRSA 185 (222)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCC------cc-CHHHHHHHHHHH-HHHHHHHHH--hhCCCcccHHH
Confidence 467777788889999999999999999999997642 23 334444443221 122333333 57899999998
Q ss_pred HHHHHHH
Q 007965 517 DLVKTLT 523 (583)
Q Consensus 517 ~lvK~L~ 523 (583)
.+.=.|-
T Consensus 186 kLLl~Lp 192 (222)
T cd06951 186 RLLLMLS 192 (222)
T ss_pred HHHHHhH
Confidence 8765543
No 44
>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=40.00 E-value=35 Score=28.36 Aligned_cols=32 Identities=31% Similarity=0.506 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhceeEEEeecchhhhhHHHHHHHhhhhhhcccc
Q 007965 244 ILWPLAVVGAVLGSMVTSIFLGAYAGVVVYQESSLWFGLRYIIAALSIYDEYSND 298 (583)
Q Consensus 244 lLWPl~Vvgavl~sivsS~flG~yaaVVvYQE~Sf~~GL~Yvva~va~fDEYtND 298 (583)
-+||+.+-|+|..--|+|. -.+.+-=|||.||
T Consensus 9 P~wPFf~ag~iv~ygv~k~-----------------------~~a~~ns~E~~ND 40 (54)
T PF04911_consen 9 PMWPFFAAGAIVYYGVNKA-----------------------QNAMMNSDEFKND 40 (54)
T ss_pred hhhHHHHHHHHHHHHHHHH-----------------------HHHHhcCHHHhcC
Confidence 3799999998876544443 2233446999999
No 45
>PRK00523 hypothetical protein; Provisional
Probab=36.13 E-value=29 Score=30.25 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhhHHHhhhhhhhhh
Q 007965 87 FLILWPVVSIGASIIGGALYGFLS 110 (583)
Q Consensus 87 ~l~LW~vvgI~GSvl~G~gYGff~ 110 (583)
-+.||.+++|++ +++|+.-|||.
T Consensus 3 ~~~l~I~l~i~~-li~G~~~Gffi 25 (72)
T PRK00523 3 AIGLALGLGIPL-LIVGGIIGYFV 25 (72)
T ss_pred hHHHHHHHHHHH-HHHHHHHHHHH
Confidence 357888888888 88888888885
No 46
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=34.44 E-value=43 Score=34.80 Aligned_cols=48 Identities=25% Similarity=0.284 Sum_probs=25.8
Q ss_pred hhcccceeEEecccchhhhhhhhhhhhcccchhHHHHHHHHhhHHHHHHHHHHHhh
Q 007965 43 MTIGNSAIILGLLPAHVLWTYYCILRAKQLGPVLKLLTCICIPVFLILWPVVSIGA 98 (583)
Q Consensus 43 i~iGnsaVIlgLwP~Hv~WTyyci~rtkr~g~vlK~l~li~lP~~l~LW~vvgI~G 98 (583)
.+.|-|+|+-||.=. +|.+. .|.+..|..+ --.+-+..++|+++|..+
T Consensus 196 ~~gGaSGvVygL~g~--~~~~~--~~~p~~~~~l----p~~~~~f~llwl~~g~~~ 243 (276)
T PRK10907 196 WFGGLSGVVYALMGY--VWLRG--ERDPQSGIYL----PRGLIAFALLWLVAGYFD 243 (276)
T ss_pred hhhHHHHHHHHHHHH--HHHHh--ccccccchhh----hHHHHHHHHHHHHHHHHH
Confidence 467999999998762 34332 1222223222 112234567788766643
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=32.47 E-value=35 Score=20.48 Aligned_cols=27 Identities=22% Similarity=0.462 Sum_probs=20.4
Q ss_pred HHHHHHHHHhhhhhhHhcCCCChhchHHHHhc
Q 007965 353 LERLFKECQRHGEIWVSEGLITAKDIEDAKSN 384 (583)
Q Consensus 353 wd~lFk~ce~~G~~Ll~~G~It~~Diee~~~~ 384 (583)
|+.+|+.+..++ .|.|+..|+..++++
T Consensus 2 ~~~~f~~~d~~~-----~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDG-----DGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCC-----CCcEeHHHHHHHHHh
Confidence 567888887765 678888888877653
No 48
>PRK10110 bifunctional PTS system maltose and glucose-specific transporter subunits IICB; Provisional
Probab=31.22 E-value=1.4e+02 Score=33.77 Aligned_cols=51 Identities=24% Similarity=0.443 Sum_probs=31.1
Q ss_pred hhhhcccchhHHHH----------HHHHhhHHHH---HHHHHHHhhHH----------HhhhhhhhhhhHhhhh
Q 007965 66 ILRAKQLGPVLKLL----------TCICIPVFLI---LWPVVSIGASI----------IGGALYGFLSPIFATF 116 (583)
Q Consensus 66 i~rtkr~g~vlK~l----------~li~lP~~l~---LW~vvgI~GSv----------l~G~gYGff~P~~aTF 116 (583)
-.+.+++=..++.. +++++|+-++ +||+....++. +++.-||++.|++=-|
T Consensus 164 k~~k~~lP~~l~~f~G~rfvPiit~lv~~~l~~i~~~iwP~~~~~~~~~~~~~~~~g~ig~~i~G~l~r~LVp~ 237 (530)
T PRK10110 164 RFHNIRLPDALAFFGGTRFVPIISSLVMGLVGLVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPF 237 (530)
T ss_pred HHhcccCcHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHh
Confidence 34445666677764 4445555433 69998877643 4556677777766543
No 49
>PRK13735 conjugal transfer mating pair stabilization protein TraG; Provisional
Probab=28.53 E-value=1.8e+02 Score=35.53 Aligned_cols=70 Identities=14% Similarity=0.169 Sum_probs=47.7
Q ss_pred eEEecccc-----hhhhhhhhhhhhcccchhH--------------HHHHHHHhhHHHHHHHHHHHhhHHHhhhhhhhhh
Q 007965 50 IILGLLPA-----HVLWTYYCILRAKQLGPVL--------------KLLTCICIPVFLILWPVVSIGASIIGGALYGFLS 110 (583)
Q Consensus 50 VIlgLwP~-----Hv~WTyyci~rtkr~g~vl--------------K~l~li~lP~~l~LW~vvgI~GSvl~G~gYGff~ 110 (583)
+-|+|||+ |.+-++| .++.=.+.+| =++--+++-+|++=|-++=-.++++..++++|-.
T Consensus 365 iwLqlWppLfAIIN~~m~~~--~~~~G~~~tLs~~~~i~~~~sdia~~aGyL~msIP~LA~~ivkG~~~~~ssl~~~l~~ 442 (942)
T PRK13735 365 MWLQSWPLLYAILNSAMTFY--AKQNGAPVVLSELSQIQLKYSDLASTAGYLSMMIPPLSWGMVKGLGAGFSSVYSHFAS 442 (942)
T ss_pred HHHHHHHHHHHHHHHHHHHH--HhhcCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 34578985 6678888 3433322222 1233456678888888888899999999999988
Q ss_pred hHhhhhhhhcc
Q 007965 111 PIFATFDAVGE 121 (583)
Q Consensus 111 P~~aTFeAvge 121 (583)
+..++=++.+.
T Consensus 443 ~~~saa~~aAs 453 (942)
T PRK13735 443 SAISPTASAAS 453 (942)
T ss_pred hhhhHHHHHHH
Confidence 77776655553
No 50
>COG3790 Predicted membrane protein [Function unknown]
Probab=26.07 E-value=63 Score=29.61 Aligned_cols=33 Identities=24% Similarity=0.464 Sum_probs=28.7
Q ss_pred HhhHHHHHHHHHHHhhHHHhhhhh--------hhhhhHhhh
Q 007965 83 CIPVFLILWPVVSIGASIIGGALY--------GFLSPIFAT 115 (583)
Q Consensus 83 ~lP~~l~LW~vvgI~GSvl~G~gY--------Gff~P~~aT 115 (583)
.+|++..+..+-++..+++-|+|+ |+|+|+.|-
T Consensus 45 s~~a~~~llmiWavca~~IhGVGFrpr~~~wqg~FsPlla~ 85 (97)
T COG3790 45 SLEAWHGLLMIWAVCAGVIHGVGFRPRSVLWQGIFSPLLAD 85 (97)
T ss_pred CchHHHHHHHHHHHHHHHHhcccCchHHHHHHHHhhhHHHH
Confidence 468888888888999999999997 899999874
No 51
>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=26.05 E-value=1.1e+02 Score=30.74 Aligned_cols=35 Identities=23% Similarity=0.248 Sum_probs=30.8
Q ss_pred chhHHHHHHHHHhccCChhHHHHhHhhhhccCCcc
Q 007965 438 FNPFLIIKEQIKAENLTEAEEDYLSKLVLFCGNIG 472 (583)
Q Consensus 438 f~PllviKeQIk~~~L~E~EE~yL~KlvL~~~d~~ 472 (583)
.+++.-.=++++.++|+++|=.||+-+||++.|..
T Consensus 130 ~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~ 164 (241)
T cd06939 130 ISAVFDFAKSLCELKLTEDEIALFSALVLISADRP 164 (241)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCc
Confidence 46777788899999999999999999999997753
No 52
>PRK13511 6-phospho-beta-galactosidase; Provisional
Probab=24.50 E-value=1.1e+02 Score=33.61 Aligned_cols=54 Identities=13% Similarity=0.217 Sum_probs=37.4
Q ss_pred cCCCceEeeCCceeeccc-CCCcccc---------chhcchhHH------HHHHHHH----h----ccCChhHHHHhHh
Q 007965 409 ANSPGILLSDSVTEITSS-NRPKDVF---------FDWFFNPFL------IIKEQIK----A----ENLTEAEEDYLSK 463 (583)
Q Consensus 409 anS~GlllsD~~~EiT~~-NrPkd~~---------fDWff~Pll------viKeQIk----~----~~L~E~EE~yL~K 463 (583)
.+.-|+.+....++ -.. +.|+|.. ..||.+|+. .|+++++ . +++|++|.+.+++
T Consensus 209 ~g~IGi~~~~~~~~-P~~~~~~~d~~aa~~~~~~~~~~f~dp~~~G~Yp~~~~~~~~~~~~~~~~~l~~t~~d~~~ik~ 286 (469)
T PRK13511 209 KGEIGVVHALPTKY-PIDPDNPEDVRAAELEDIIHNKFILDATYLGYYSEETMEGVNHILEANGGSLDIRDEDFEILKA 286 (469)
T ss_pred CCeEEEEecCceEe-eCCCCCHHHHHHHHHHHHHhhhcccchhhCCCCCHHHHHHHHHhhhhcCCCCCCCHHHHHHHhc
Confidence 35678888887444 444 7788754 479999985 5677664 1 4688888887764
No 53
>PRK09695 glycolate transporter; Provisional
Probab=24.33 E-value=1.3e+02 Score=34.42 Aligned_cols=73 Identities=14% Similarity=0.300 Sum_probs=48.0
Q ss_pred HHHHhHHHHHHHHHHHhhhh-----hhhhhHHHHHHhhccc--c-----------eeEEecccch-----hhhhhhhhhh
Q 007965 12 WSFICFLPYFIGLLLLGIIK-----GIIFCPVICLMMTIGN--S-----------AIILGLLPAH-----VLWTYYCILR 68 (583)
Q Consensus 12 wsfi~FlP~F~~ll~LG~iK-----g~i~gP~a~lii~iGn--s-----------aVIlgLwP~H-----v~WTyyci~r 68 (583)
=.++.++|....+.+|+..| +.+++=+++.++++.. . ++..++||.= -+|.|++..+
T Consensus 17 ~~llA~lPIl~l~v~L~~~k~~a~~A~~i~~~~a~~iAi~~f~mp~~~~~~a~~~G~~~al~pI~~II~~AI~ly~~~~~ 96 (560)
T PRK09695 17 SALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMPIDMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVA 96 (560)
T ss_pred HHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677999888888887743 3334433343333322 1 4556778752 3589999999
Q ss_pred hcccchhHHHHHHHHh
Q 007965 69 AKQLGPVLKLLTCICI 84 (583)
Q Consensus 69 tkr~g~vlK~l~li~l 84 (583)
|..+...-+-+.-+.-
T Consensus 97 sGa~~~I~~~l~~is~ 112 (560)
T PRK09695 97 SGQFDIIRSSVISITD 112 (560)
T ss_pred hCcHHHHHHHHHhcCC
Confidence 9999988887776663
No 54
>PRK06814 acylglycerophosphoethanolamine acyltransferase; Provisional
Probab=23.99 E-value=2.7e+02 Score=32.76 Aligned_cols=19 Identities=21% Similarity=0.275 Sum_probs=12.1
Q ss_pred hhHHHhhhhhhhhhhHhhh
Q 007965 97 GASIIGGALYGFLSPIFAT 115 (583)
Q Consensus 97 ~GSvl~G~gYGff~P~~aT 115 (583)
++.++.|++.+++.|...+
T Consensus 113 ~~~~l~gi~~a~~~p~~~a 131 (1140)
T PRK06814 113 AALFLMGIHSALFGPIKYS 131 (1140)
T ss_pred HHHHHHHHHHHhhchHHHH
Confidence 4566777777777775443
No 55
>KOG2632 consensus Rhomboid family proteins [Function unknown]
Probab=23.73 E-value=98 Score=32.55 Aligned_cols=98 Identities=17% Similarity=0.298 Sum_probs=58.9
Q ss_pred HHhhhhhhhhhHHHHHHhhccccee--EEecccchhhhhhhhhhhhcccchhHHHHHHHHhhHHHHHHHHH---------
Q 007965 26 LLGIIKGIIFCPVICLMMTIGNSAI--ILGLLPAHVLWTYYCILRAKQLGPVLKLLTCICIPVFLILWPVV--------- 94 (583)
Q Consensus 26 ~LG~iKg~i~gP~a~lii~iGnsaV--IlgLwP~Hv~WTyyci~rtkr~g~vlK~l~li~lP~~l~LW~vv--------- 94 (583)
+++..-|++.+=+.....-...+-+ ++|+=|.||.|.--.=.+..+-... +-.++.+|..+.-|..+
T Consensus 99 llalf~gIl~ll~~~~~~~~d~~~~~~a~G~s~v~Fam~~~~~~~sp~r~~~--~fg~~siP~~l~Pw~lLi~~~~lvp~ 176 (258)
T KOG2632|consen 99 LLALFSGILYLLAYHVFLLSDLVYVEGAIGFSGVLFAMMAVLEVQSPVRSRS--VFGLFSIPIVLAPWALLIATQILVPQ 176 (258)
T ss_pred HHHHHHHHHHHHHHHHHhhcchhhhcccccccHHHHHHHHHHhhcCcccchh--hcccccccHHHHHHHHHHHHHHHccC
Confidence 3445555554444432222333333 4899999998876522333222211 12233356666666554
Q ss_pred ----HHhhHHHhhhhhhh----hhhHhhhhhhhccCccc
Q 007965 95 ----SIGASIIGGALYGF----LSPIFATFDAVGEGKTN 125 (583)
Q Consensus 95 ----gI~GSvl~G~gYGf----f~P~~aTFeAvgeg~~~ 125 (583)
|=++.+++|..|++ +.|.+..+.++.|....
T Consensus 177 aSFlghl~GllvG~ay~~~~f~lip~~~~~~~v~~~~~~ 215 (258)
T KOG2632|consen 177 ASFLGHLCGLLVGYAYAFSSFGLIPGIRNYRAVTEAAWS 215 (258)
T ss_pred chHHHHHHHHHHHHHHHHHhhccCCcchhHHHhhhhhhh
Confidence 44588999999999 89999999999986654
No 56
>PRK01844 hypothetical protein; Provisional
Probab=23.01 E-value=68 Score=28.04 Aligned_cols=22 Identities=23% Similarity=0.465 Sum_probs=15.7
Q ss_pred HHHHHHHHHhhHHHhhhhhhhhh
Q 007965 88 LILWPVVSIGASIIGGALYGFLS 110 (583)
Q Consensus 88 l~LW~vvgI~GSvl~G~gYGff~ 110 (583)
+.+|.+++|+ .+++|+.-|||.
T Consensus 3 ~~~~I~l~I~-~li~G~~~Gff~ 24 (72)
T PRK01844 3 IWLGILVGVV-ALVAGVALGFFI 24 (72)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHH
Confidence 4567777776 567777778875
No 57
>PRK00523 hypothetical protein; Provisional
Probab=21.86 E-value=1.1e+02 Score=26.73 Aligned_cols=26 Identities=23% Similarity=0.151 Sum_probs=18.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhh
Q 007965 240 GLAIILWPLAVVGAVLGSMVTSIFLG 265 (583)
Q Consensus 240 GLaIlLWPl~Vvgavl~sivsS~flG 265 (583)
|+++-+|=+.++.+.+++.+..||++
T Consensus 1 ~~~~~l~I~l~i~~li~G~~~Gffia 26 (72)
T PRK00523 1 GLAIGLALGLGIPLLIVGGIIGYFVS 26 (72)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777777777777777776666654
No 58
>PRK09598 lipid A phosphoethanolamine transferase; Reviewed
Probab=21.68 E-value=2.6e+02 Score=31.54 Aligned_cols=55 Identities=13% Similarity=0.165 Sum_probs=33.6
Q ss_pred hhhhhhHHHHHHhhcccceeEEecccchhhhhhhhhhhhcccch-----------------hHHHHHHHHhhHHHHHHH
Q 007965 31 KGIIFCPVICLMMTIGNSAIILGLLPAHVLWTYYCILRAKQLGP-----------------VLKLLTCICIPVFLILWP 92 (583)
Q Consensus 31 Kg~i~gP~a~lii~iGnsaVIlgLwP~Hv~WTyyci~rtkr~g~-----------------vlK~l~li~lP~~l~LW~ 92 (583)
..-+.-|+++++++++-.+ +++.++|=.++-+..++- ++-++++-.+|..++.|.
T Consensus 70 ~~~~~k~~~~~l~~~~a~~-------~yf~~~ygv~id~~mi~nv~~T~~~Ea~~~~~~~~~~~~~~l~~lp~~~~~~~ 141 (522)
T PRK09598 70 SRRLMRLSAIVFSLLNSIA-------FYFINTYKVFLNKSMMGNVLNTNTAESSGFLSVKLFIYIVVLGVLPGYIIYKI 141 (522)
T ss_pred hHHHHHHHHHHHHHHHHHH-------HHHHHhcCCeecHHHHHHHHhCCHHHHHHhcCHHHHHHHHHHHHHHHHHHHHh
Confidence 3345666666666654433 277788766666655543 445566667788886554
No 59
>cd01570 NAPRTase_A Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria and eukaryota (except funghi).
Probab=21.51 E-value=84 Score=33.15 Aligned_cols=44 Identities=23% Similarity=0.298 Sum_probs=27.1
Q ss_pred eeecccCCCccccchh--cchhHHHHHHHHHhccCChhHHHHhHhhhhc
Q 007965 421 TEITSSNRPKDVFFDW--FFNPFLIIKEQIKAENLTEAEEDYLSKLVLF 467 (583)
Q Consensus 421 ~EiT~~NrPkd~~fDW--ff~PllviKeQIk~~~L~E~EE~yL~KlvL~ 467 (583)
.|++..|.|..+ +| +.+==-+++ ++..+.+|++|.+||++...+
T Consensus 27 ~~~~~R~~p~~~--~~~v~~gl~~~l~-~L~~l~~t~~ei~~l~~~~~~ 72 (327)
T cd01570 27 FELFFRKLPFGG--GYAVFAGLEELLE-YLENFRFTEEDIDYLRSLGIF 72 (327)
T ss_pred EEEEECCCCCCC--cccHHHHHHHHHH-HHhcCCCCHHHHHHHHhCCCC
Confidence 577777777543 22 222112222 566677999999999996533
No 60
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.18 E-value=4.2e+02 Score=25.81 Aligned_cols=58 Identities=26% Similarity=0.296 Sum_probs=45.8
Q ss_pred cCChhHHHHhHhhhhccCCcccccCCCCCCCchhhhHHHHHHHHHHhhhhhhcccCCchhhhhHHHHHHHHHHHHHH
Q 007965 452 NLTEAEEDYLSKLVLFCGNIGRLKDLNVSPPESERKRAELGALARRLQGITKSVSRYPTFRRQFDDLVKTLTEDLAK 528 (583)
Q Consensus 452 ~L~E~EE~yL~KlvL~~~d~~r~~d~~g~pp~d~~rrAqLqai~RRLqGI~~s~SR~PT~RRrf~~lvK~L~~~~~~ 528 (583)
+|||-|.+.|+...=.+=- |.=||+.++.||..| ||++| |+-.|-++..+.|...+.+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYF-------------d~PR~~~l~dLA~~l-GISks-----t~~ehLRrAe~Kl~~~~~~ 212 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYF-------------DYPRRVSLKDLAKEL-GISKS-----TLSEHLRRAERKLIEAYFD 212 (215)
T ss_pred cCCHHHHHHHHHHHHcCCC-------------CCCccCCHHHHHHHh-CCCHH-----HHHHHHHHHHHHHHHHhhh
Confidence 8999999999876533322 334789999999987 88886 9999999988888887754
No 61
>PLN00151 potassium transporter; Provisional
Probab=20.03 E-value=1.2e+02 Score=36.54 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=20.8
Q ss_pred hhhhceeEEEeecchhhhhHHHHHHHh
Q 007965 263 FLGAYAGVVVYQESSLWFGLRYIIAAL 289 (583)
Q Consensus 263 flG~yaaVVvYQE~Sf~~GL~Yvva~v 289 (583)
.+++.+-++.||. |-..|=||=+|.+
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 5688999977754
Done!