Query psy16245
Match_columns 113
No_of_seqs 115 out of 1074
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 16:31:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16245.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16245hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 99.9 1.5E-28 3.2E-33 193.0 4.4 73 37-113 18-90 (432)
2 cd06959 NR_DBD_EcR_like The DN 99.9 5.3E-28 1.2E-32 153.0 5.1 70 40-113 1-70 (73)
3 cd06956 NR_DBD_RXR DNA-binding 99.9 7E-28 1.5E-32 153.9 4.8 70 40-113 2-71 (77)
4 cd07172 NR_DBD_GR_PR DNA-bindi 99.9 1.1E-27 2.3E-32 153.4 5.5 72 38-113 2-73 (78)
5 cd07173 NR_DBD_AR DNA-binding 99.9 1.4E-27 3E-32 154.2 5.9 71 39-113 4-74 (82)
6 cd07156 NR_DBD_VDR_like The DN 99.9 6.6E-28 1.4E-32 152.2 3.8 69 41-113 1-69 (72)
7 cd07171 NR_DBD_ER DNA-binding 99.9 1E-27 2.3E-32 154.8 4.8 71 39-113 4-74 (82)
8 cd07160 NR_DBD_LXR DNA-binding 99.9 1.6E-27 3.4E-32 159.3 5.6 72 38-113 18-89 (101)
9 cd07170 NR_DBD_ERR DNA-binding 99.9 1.1E-27 2.3E-32 159.1 4.5 72 38-113 4-75 (97)
10 cd06963 NR_DBD_GR_like The DNA 99.9 1.4E-27 3E-32 151.2 4.8 69 41-113 1-69 (73)
11 cd07179 2DBD_NR_DBD2 The secon 99.9 1.6E-27 3.5E-32 151.2 5.0 69 41-113 1-69 (74)
12 cd07161 NR_DBD_EcR DNA-binding 99.9 2.1E-27 4.6E-32 156.1 5.2 71 39-113 2-72 (91)
13 cd07155 NR_DBD_ER_like DNA-bin 99.9 1.5E-27 3.2E-32 151.7 4.2 69 41-113 1-69 (75)
14 cd06969 NR_DBD_NGFI-B DNA-bind 99.9 5.7E-28 1.2E-32 153.6 2.0 70 40-113 2-71 (75)
15 cd06961 NR_DBD_TR DNA-binding 99.9 1.7E-27 3.7E-32 154.7 4.1 70 40-113 1-70 (85)
16 cd07158 NR_DBD_Ppar_like The D 99.9 2.4E-27 5.3E-32 149.9 4.5 69 41-113 1-70 (73)
17 cd06958 NR_DBD_COUP_TF DNA-bin 99.9 1.9E-27 4.2E-32 150.4 4.1 69 41-113 1-69 (73)
18 cd06962 NR_DBD_FXR DNA-binding 99.9 9.2E-28 2E-32 155.7 2.3 71 39-113 2-72 (84)
19 cd07163 NR_DBD_TLX DNA-binding 99.9 8.5E-28 1.8E-32 158.2 1.8 76 36-113 4-79 (92)
20 smart00399 ZnF_C4 c4 zinc fing 99.9 2.7E-27 5.9E-32 148.5 3.7 70 40-113 1-70 (70)
21 cd07168 NR_DBD_DHR4_like DNA-b 99.9 3.8E-27 8.3E-32 154.5 4.5 72 38-113 6-77 (90)
22 cd06964 NR_DBD_RAR DNA-binding 99.9 1.1E-27 2.4E-32 155.6 1.7 72 38-113 4-75 (85)
23 cd06955 NR_DBD_VDR DNA-binding 99.9 2.6E-27 5.6E-32 159.7 3.4 73 37-113 5-77 (107)
24 PF00105 zf-C4: Zinc finger, C 99.9 5.4E-27 1.2E-31 146.8 4.2 69 40-112 2-70 (70)
25 cd07162 NR_DBD_PXR DNA-binding 99.9 6.3E-27 1.4E-31 152.6 4.6 70 40-113 1-70 (87)
26 cd07154 NR_DBD_PNR_like The DN 99.9 1.8E-27 3.9E-32 150.5 1.7 70 41-113 1-70 (73)
27 cd06967 NR_DBD_TR2_like DNA-bi 99.9 2.1E-27 4.6E-32 154.9 1.7 72 38-113 3-74 (87)
28 cd07169 NR_DBD_GCNF_like DNA-b 99.9 7.5E-27 1.6E-31 153.2 4.3 72 38-113 6-77 (90)
29 cd07164 NR_DBD_PNR_like_1 DNA- 99.9 8.5E-27 1.8E-31 149.2 4.1 69 41-113 1-69 (78)
30 cd06916 NR_DBD_like DNA-bindin 99.9 2E-27 4.3E-32 150.0 1.1 69 41-113 1-69 (72)
31 cd06970 NR_DBD_PNR DNA-binding 99.9 2.8E-27 6.1E-32 155.7 1.7 72 39-113 7-78 (92)
32 KOG4846|consensus 99.9 8E-27 1.7E-31 185.7 3.7 71 39-113 133-204 (538)
33 cd06968 NR_DBD_ROR DNA-binding 99.9 1.1E-26 2.4E-31 153.7 3.6 72 38-113 5-76 (95)
34 KOG4217|consensus 99.9 1.6E-26 3.5E-31 186.2 5.2 73 37-113 268-340 (605)
35 cd07167 NR_DBD_Lrh-1_like The 99.9 1.1E-26 2.4E-31 153.2 3.3 69 41-113 1-69 (93)
36 cd07157 2DBD_NR_DBD1 The first 99.9 6.1E-27 1.3E-31 152.4 2.0 70 40-113 2-73 (86)
37 cd06960 NR_DBD_HNF4A DNA-bindi 99.9 6.2E-27 1.3E-31 149.1 1.7 69 41-113 1-69 (76)
38 cd07165 NR_DBD_DmE78_like DNA- 99.9 2E-26 4.3E-31 148.4 3.7 69 41-113 1-69 (81)
39 cd06966 NR_DBD_CAR DNA-binding 99.9 8.4E-27 1.8E-31 154.0 1.9 70 40-113 2-71 (94)
40 cd06957 NR_DBD_PNR_like_2 DNA- 99.9 4.2E-27 9E-32 151.9 -0.3 70 41-113 1-70 (82)
41 cd07166 NR_DBD_REV_ERB DNA-bin 99.9 1.3E-26 2.8E-31 151.8 1.6 71 39-113 4-75 (89)
42 cd06965 NR_DBD_Ppar DNA-bindin 99.9 4.2E-26 9E-31 147.9 2.2 68 40-113 1-69 (84)
43 KOG4216|consensus 99.9 1.8E-24 4E-29 171.1 3.9 72 38-113 46-117 (479)
44 KOG4218|consensus 99.9 2.3E-22 5.1E-27 157.6 3.7 76 34-113 11-86 (475)
45 PF01412 ArfGap: Putative GTPa 69.8 1.8 3.8E-05 29.1 0.4 30 38-67 13-45 (116)
46 smart00105 ArfGap Putative GTP 59.2 7.3 0.00016 25.9 1.8 31 38-68 3-36 (112)
47 smart00401 ZnF_GATA zinc finge 44.9 16 0.00035 21.1 1.5 31 39-69 4-39 (52)
48 PRK00420 hypothetical protein; 39.4 9.2 0.0002 26.0 -0.1 29 37-65 22-50 (112)
49 PF10764 Gin: Inhibitor of sig 34.2 33 0.00072 19.5 1.7 23 40-62 1-25 (46)
50 PF00320 GATA: GATA zinc finge 32.8 25 0.00054 18.6 1.0 12 57-68 22-33 (36)
51 PF03107 C1_2: C1 domain; Int 30.9 25 0.00055 17.8 0.7 20 40-62 2-22 (30)
52 PF10013 DUF2256: Uncharacteri 30.3 34 0.00073 19.3 1.2 13 36-48 6-18 (42)
53 TIGR00269 conserved hypothetic 30.0 28 0.0006 22.8 1.0 20 39-63 81-100 (104)
54 PHA03124 dUTPase; Provisional 29.1 33 0.00072 28.2 1.5 16 56-71 191-206 (418)
55 PF15279 SOBP: Sine oculis-bin 28.1 57 0.0012 25.9 2.6 14 2-15 73-86 (306)
56 PTZ00218 40S ribosomal protein 26.8 35 0.00076 20.2 0.9 23 39-61 17-40 (54)
57 PF08394 Arc_trans_TRASH: Arch 26.5 71 0.0015 17.4 2.1 12 56-67 24-35 (37)
58 COG5347 GTPase-activating prot 25.8 30 0.00065 27.5 0.7 30 38-67 20-52 (319)
59 cd00202 ZnF_GATA Zinc finger D 25.5 49 0.0011 19.2 1.4 28 41-68 2-34 (54)
60 PF07649 C1_3: C1-like domain; 22.6 32 0.0007 17.2 0.2 15 40-54 2-17 (30)
61 cd00729 rubredoxin_SM Rubredox 22.4 40 0.00087 17.7 0.6 13 38-50 18-30 (34)
62 PF05970 PIF1: PIF1-like helic 22.2 30 0.00066 27.4 0.1 15 3-17 145-159 (364)
63 PF10080 DUF2318: Predicted me 22.0 36 0.00079 22.6 0.4 27 39-65 36-62 (102)
64 PRK12495 hypothetical protein; 20.9 33 0.00072 26.1 0.1 29 37-66 41-69 (226)
65 KOG0703|consensus 20.3 35 0.00076 26.9 0.1 30 38-67 25-57 (287)
66 PF00357 Integrin_alpha: Integ 20.2 46 0.001 14.6 0.4 9 63-71 3-11 (15)
No 1
>KOG4215|consensus
Probab=99.95 E-value=1.5e-28 Score=193.02 Aligned_cols=73 Identities=48% Similarity=1.153 Sum_probs=69.6
Q ss_pred CCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
....|.||||+++|.|||+.+|.+||+||||+|.++..|+|+.+. +|.|+++.|+.||||||+||+.+||++|
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k----~C~VDKdkRNaCRyCRfqKC~~aGMK~e 90 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNK----QCVVDKDKRNACRYCRFQKCVRAGMKRE 90 (432)
T ss_pred ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccc----cccccchhhhhhhHhhHHHHHHhcccHH
Confidence 357899999999999999999999999999999999999999974 7999999999999999999999999986
No 2
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=99.94 E-value=5.3e-28 Score=152.99 Aligned_cols=70 Identities=49% Similarity=1.126 Sum_probs=65.6
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 70 (73)
T cd06959 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGN----KCEMDMYMRRKCQECRLRKCKAAGMRPD 70 (73)
T ss_pred CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCC----cCCcCCcccccCccchhHHHHHhCCChh
Confidence 599999999999999999999999999999988889998764 7999999999999999999999999985
No 3
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR 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, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=99.94 E-value=7e-28 Score=153.87 Aligned_cols=70 Identities=51% Similarity=1.256 Sum_probs=65.6
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 71 (77)
T cd06956 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK----DCLIDKRQRNRCQYCRYQKCLAMGMKRE 71 (77)
T ss_pred CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCC----ccccCCCccccCccchhHHHhHhCCCHH
Confidence 599999999999999999999999999999998889998764 7999999999999999999999999864
No 4
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. 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. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=99.94 E-value=1.1e-27 Score=153.45 Aligned_cols=72 Identities=43% Similarity=0.959 Sum_probs=66.6
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+.+|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...|..|++|||+|||++||+.+
T Consensus 2 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 73 (78)
T cd07172 2 QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRN----DCIIDKIRRKNCPACRLRKCLQAGMNLG 73 (78)
T ss_pred CCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCC----ccccCCcccccCccchhHHHHHhCCCcc
Confidence 45799999999999999999999999999999999889998754 7999999999999999999999999863
No 5
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of 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 modul
Probab=99.94 E-value=1.4e-27 Score=154.22 Aligned_cols=71 Identities=42% Similarity=0.984 Sum_probs=66.3
Q ss_pred CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
.+|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||+++
T Consensus 4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 74 (82)
T cd07173 4 KTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRN----DCTIDKFRRKNCPSCRLRKCFEAGMTLG 74 (82)
T ss_pred CCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCC----ccccCCCccCcCcchhhhhhhhcCCCcC
Confidence 5799999999999999999999999999999988889998764 7999999999999999999999999874
No 6
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=99.94 E-value=6.6e-28 Score=152.19 Aligned_cols=69 Identities=48% Similarity=1.150 Sum_probs=64.8
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.++...|..|++|||+|||++||++|
T Consensus 1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 69 (72)
T cd07156 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNG----DCEITKDNRRHCQACRLKKCLDIGMKKE 69 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCC----ccccCCcccccCccchhHHHHHhCCCHH
Confidence 78999999999999999999999999999988889998754 7999999999999999999999999975
No 7
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. 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 domain, a non-conserv
Probab=99.94 E-value=1e-27 Score=154.80 Aligned_cols=71 Identities=51% Similarity=1.087 Sum_probs=66.3
Q ss_pred CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
.+|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||+++
T Consensus 4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 74 (82)
T cd07171 4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATN----QCTIDKNRRKSCQACRLRKCYEVGMMKG 74 (82)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCC----ccccCCcccccCccchhHHHhHhcCCHH
Confidence 5799999999999999999999999999999998889998754 7999999999999999999999999874
No 8
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells 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. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=99.94 E-value=1.6e-27 Score=159.34 Aligned_cols=72 Identities=44% Similarity=1.059 Sum_probs=67.1
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
..+|.|||++++|+||||.+|++|++||||++.....|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 89 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGG----KCQMDMYMRRKCQECRLRKCREAGMREQ 89 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCC----ccccCCcccccCccchhHHHHHhCCCHH
Confidence 46799999999999999999999999999999988889998764 7999999999999999999999999874
No 9
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=99.94 E-value=1.1e-27 Score=159.13 Aligned_cols=72 Identities=47% Similarity=0.996 Sum_probs=66.7
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
..+|.|||++++|+||||.+|+||++||||++.....|.|..++ .|.|+...|..|++|||+|||++||+++
T Consensus 4 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 75 (97)
T cd07170 4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATN----ECEITKRRRKSCQACRFMKCLKVGMLKE 75 (97)
T ss_pred CCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCC----ccccCcccCccCCccccchhhhcCCCHH
Confidence 45799999999999999999999999999999998889998754 7999999999999999999999999864
No 10
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate 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 have high sequence homology and sha
Probab=99.94 E-value=1.4e-27 Score=151.17 Aligned_cols=69 Identities=43% Similarity=1.028 Sum_probs=64.9
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 69 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRN----DCIIDKIRRKNCPACRLRKCYQAGMTLG 69 (73)
T ss_pred CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCC----ccccCCcccccCccchhhHHHHcCCChh
Confidence 78999999999999999999999999999999889998764 7999999999999999999999999875
No 11
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=99.94 E-value=1.6e-27 Score=151.18 Aligned_cols=69 Identities=41% Similarity=1.068 Sum_probs=65.0
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.++...|..|++|||+|||++||++|
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 69 (74)
T cd07179 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQ----NCAITPATRNACKSCRFRRCLAVGMSKT 69 (74)
T ss_pred CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCC----ccccCCcccccCccchhHHHHHhCCCHh
Confidence 78999999999999999999999999999998889998764 6999999999999999999999999975
No 12
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR 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 EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=99.94 E-value=2.1e-27 Score=156.05 Aligned_cols=71 Identities=45% Similarity=1.044 Sum_probs=66.3
Q ss_pred CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
++|.|||++++|+||||.+|++|++||||++.....|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 72 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGR----ACEMDMYMRRKCQECRLKKCLSVGMRPE 72 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCC----ccccCccccccCccchhhHHhHcCCCHH
Confidence 4699999999999999999999999999999998889998764 7999999999999999999999999874
No 13
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=99.94 E-value=1.5e-27 Score=151.68 Aligned_cols=69 Identities=49% Similarity=1.091 Sum_probs=64.7
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|..++ .|.|+...+..|++|||+|||++||+++
T Consensus 1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 69 (75)
T cd07155 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTS----ECEVDKKRRKSCQACRLQKCLKVGMLKE 69 (75)
T ss_pred CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCC----CcccCCcccccCccchhhhhhHhCCCHH
Confidence 78999999999999999999999999999988889998764 6999999999999999999999999874
No 14
>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B. DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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 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 transcrip
Probab=99.94 E-value=5.7e-28 Score=153.61 Aligned_cols=70 Identities=47% Similarity=1.165 Sum_probs=65.6
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++++||||.+|++|++||||++.....|.|..++ +|.|+...|..|++|||+|||++||++|
T Consensus 2 ~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 71 (75)
T cd06969 2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANK----NCPVDKRRRNRCQYCRFQKCLQVGMVKE 71 (75)
T ss_pred CCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCC----ccccCCcccccCcccHhHHHHHhCCCHH
Confidence 699999999999999999999999999999988889998754 7999999999999999999999999975
No 15
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates 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 he
Probab=99.94 E-value=1.7e-27 Score=154.70 Aligned_cols=70 Identities=50% Similarity=1.227 Sum_probs=65.7
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 70 (85)
T cd06961 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEG----KCEIDKVTRNQCQECRFKKCIAVGMAKD 70 (85)
T ss_pred CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCC----ccccCccccccCccchhhhhhhccCCHH
Confidence 599999999999999999999999999999998889998764 7999999999999999999999999874
No 16
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.94 E-value=2.4e-27 Score=149.88 Aligned_cols=69 Identities=49% Similarity=1.202 Sum_probs=64.7
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..| .|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 70 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGG----KCVIQRKNRNRCQYCRFKKCLSVGMSRN 70 (73)
T ss_pred CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCC----CcCCCccccccCccchhhhhhHccCChH
Confidence 78999999999999999999999999999998888 898764 6999999999999999999999999975
No 17
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. 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. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=99.94 E-value=1.9e-27 Score=150.41 Aligned_cols=69 Identities=58% Similarity=1.320 Sum_probs=64.6
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.++...|..|++|||+|||++||+++
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 69 (73)
T cd06958 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNR----NCPIDQHHRNQCQYCRLKKCLKVGMRRE 69 (73)
T ss_pred CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCC----cCccCCcccccCccchhhHhhHhCCCHH
Confidence 78999999999999999999999999999998888998754 7999999999999999999999999975
No 18
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=99.94 E-value=9.2e-28 Score=155.70 Aligned_cols=71 Identities=48% Similarity=1.064 Sum_probs=66.3
Q ss_pred CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
++|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 72 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGG----NCEMDMYMRRKCQECRLRKCKEMGMLAE 72 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCC----cCccCccccccCccchhhHHHHhCCChH
Confidence 4699999999999999999999999999999988889998764 7999999999999999999999999874
No 19
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.94 E-value=8.5e-28 Score=158.21 Aligned_cols=76 Identities=82% Similarity=1.585 Sum_probs=68.2
Q ss_pred CCCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 36 LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 36 ~~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
++..+|.|||++++|+||||.+|+||++||||++..+..|.|..+.+ +.|.|+...|..|++|||+|||++||+++
T Consensus 4 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~--~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 79 (92)
T cd07163 4 ILDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQ--GGCPVDKTHRNQCRACRLKKCFEVGMNKD 79 (92)
T ss_pred ccCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCC--CCCccCCCccccCccchhhhhhhhcCCHH
Confidence 34678999999999999999999999999999999888899987421 37999999999999999999999999874
No 20
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.93 E-value=2.7e-27 Score=148.45 Aligned_cols=70 Identities=43% Similarity=1.019 Sum_probs=65.7
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++++||||.+|++|++||||++..+..+.|..++ +|.|+...+..|++|||+|||++||++|
T Consensus 1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKN----NCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCc----ccccCCCccccCccCcChhHhhccCcCC
Confidence 499999999999999999999999999999988889998764 6999999999999999999999999986
No 21
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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
Probab=99.93 E-value=3.8e-27 Score=154.53 Aligned_cols=72 Identities=46% Similarity=1.102 Sum_probs=66.7
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
..+|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 6 ~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 77 (90)
T cd07168 6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDG----RCEITKAQRNRCQYCRFRKCIRKGMMLA 77 (90)
T ss_pred CCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCC----CccccccccccccccchhhhhhcCCCHH
Confidence 46799999999999999999999999999999998889998754 7999999999999999999999999864
No 22
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural 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. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=99.93 E-value=1.1e-27 Score=155.65 Aligned_cols=72 Identities=54% Similarity=1.168 Sum_probs=66.6
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
..+|.|||++++++||||.+|++|++||||++.....|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 75 (85)
T cd06964 4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDK----NCIINKVTRNRCQYCRLQKCFEVGMSKE 75 (85)
T ss_pred CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCC----ccccCCcccccCccchhhhhhhhCCCHH
Confidence 36799999999999999999999999999999988889998764 6999999999999999999999999874
No 23
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. 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 core
Probab=99.93 E-value=2.6e-27 Score=159.70 Aligned_cols=73 Identities=44% Similarity=1.055 Sum_probs=67.5
Q ss_pred CCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
.+.+|.|||+.++++||||.+|++|++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||+++
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 77 (107)
T cd06955 5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNG----DCRITKDNRRHCQACRLKRCVDIGMMKE 77 (107)
T ss_pred CCCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCC----ccccccCCccccccchhHHHHHcCCCch
Confidence 357899999999999999999999999999999998889998764 7999999999999999999999999874
No 24
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 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, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=99.93 E-value=5.4e-27 Score=146.80 Aligned_cols=69 Identities=51% Similarity=1.191 Sum_probs=61.3
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNK 112 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~ 112 (113)
+|.|||++++++||||.+|++|++||||++.....+.|..++ +|.++...+..|++|||+|||++||++
T Consensus 2 ~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~----~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 2 KCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNG----NCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSS----T---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred CCeECCCccCcccccccccccceeeeeecccccccccccccc----cccccccCCCEeCcchHHHHHHHCCcC
Confidence 699999999999999999999999999999999889999865 699999999999999999999999984
No 25
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The 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. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=99.93 E-value=6.3e-27 Score=152.62 Aligned_cols=70 Identities=47% Similarity=1.087 Sum_probs=65.4
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++++||||.+|++|++||||++.....|.|..++ +|.++...+..|++|||+|||++||++|
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 70 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQK----GCVITKSNRRQCQACRLRKCLSIGMKKE 70 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCC----ceecCCcccccCccchhhHHhHhCCCHH
Confidence 499999999999999999999999999999988888998764 6999999999999999999999999975
No 26
>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells 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
Probab=99.93 E-value=1.8e-27 Score=150.53 Aligned_cols=70 Identities=74% Similarity=1.453 Sum_probs=64.3
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|...+ ++|.|+...|..|++|||+|||++||+++
T Consensus 1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 70 (73)
T cd07154 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGN---GSCVVDKARRNQCQACRLKKCLEVSMNKD 70 (73)
T ss_pred CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCC---CCCccCCcccccCccchhhHhhHhCCChH
Confidence 78999999999999999999999999999998889998432 37999999999999999999999999975
No 27
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. 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. It has been 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
Probab=99.93 E-value=2.1e-27 Score=154.90 Aligned_cols=72 Identities=53% Similarity=1.146 Sum_probs=66.8
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
.++|.|||++++++||||.+|++|++||||++..+..+.|..++ .|.|+...|..|++|||+|||++||+++
T Consensus 3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 74 (87)
T cd06967 3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSK----DCVINKHHRNRCQYCRLQKCLAMGMKSD 74 (87)
T ss_pred CCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCC----ccccCccccccCccchhhhhhHcCCCHH
Confidence 46799999999999999999999999999999988889998754 7999999999999999999999999874
No 28
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.93 E-value=7.5e-27 Score=153.17 Aligned_cols=72 Identities=50% Similarity=1.142 Sum_probs=66.9
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
..+|.|||++++++||||.+|++|++||||++..+..|.|..++ .|.|+...|..|++|||+|||++||+++
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 77 (90)
T cd07169 6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDK----NCVMSRKQRNRCQYCRLLKCLQMGMNRK 77 (90)
T ss_pred CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCC----cccccccccccccccchhhhccccCCHH
Confidence 46799999999999999999999999999999998889998754 6999999999999999999999999874
No 29
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. 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. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=99.93 E-value=8.5e-27 Score=149.16 Aligned_cols=69 Identities=64% Similarity=1.344 Sum_probs=64.7
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||+++
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 69 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENG----SCVVDVARRNQCQACRFKKCLQVNMNRD 69 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCC----cccccCcccccCccchhhhhhHhcCCHH
Confidence 78999999999999999999999999999988889998864 7999999999999999999999999874
No 30
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. 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). Most nuclear receptors bind as homodimers or hetero
Probab=99.93 E-value=2e-27 Score=149.96 Aligned_cols=69 Identities=58% Similarity=1.297 Sum_probs=64.8
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|..++ .|.|+...|..|++|||+|||++||+++
T Consensus 1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 69 (72)
T cd06916 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGG----NCVIDKRNRNRCQACRLKKCLAVGMRKE 69 (72)
T ss_pred CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCC----ccccCCcccccCccchhhHhhHhCCChH
Confidence 78999999999999999999999999999988889998764 6999999999999999999999999975
No 31
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. 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. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=99.93 E-value=2.8e-27 Score=155.73 Aligned_cols=72 Identities=67% Similarity=1.418 Sum_probs=66.3
Q ss_pred CCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
.+|.|||++++|+||||.+|++|++||||++..+..|.|..+. ++|.|+...|..|++|||+|||++||+++
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 78 (92)
T cd06970 7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGT---GMCPVDKAHRNQCQACRLKKCLQAGMNKD 78 (92)
T ss_pred CCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCC---CcCccCCCccccCccchhhHhhHhCCCHH
Confidence 5799999999999999999999999999999999889998752 27999999999999999999999999874
No 32
>KOG4846|consensus
Probab=99.93 E-value=8e-27 Score=185.72 Aligned_cols=71 Identities=48% Similarity=1.102 Sum_probs=66.5
Q ss_pred CCceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
..|+||||+++|+||||.+|++||+||||+|+.+..| .|-+.. .|.|...+|++|++|||+|||.|||++|
T Consensus 133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e----~C~I~R~nRNRCQ~CRfKKCL~vGMSrD 204 (538)
T KOG4846|consen 133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQE----VCEIKRENRNRCQYCRFKKCLDVGMSRD 204 (538)
T ss_pred EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhh----ceehhhhccchhhhhhHHHHHhcccchh
Confidence 3699999999999999999999999999999999999 787764 7999999999999999999999999875
No 33
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which 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. RORbe
Probab=99.93 E-value=1.1e-26 Score=153.74 Aligned_cols=72 Identities=54% Similarity=1.225 Sum_probs=66.9
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
..+|.|||++++++||||.+|++|++||||++..+..|.|..++ +|.++...|..|++|||+|||++||+++
T Consensus 5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 76 (95)
T cd06968 5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQK----NCLIDRTNRNRCQHCRLQKCLALGMSRD 76 (95)
T ss_pred ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCc----ccccccCCceeccccchhhcccccCChh
Confidence 45899999999999999999999999999999988889998754 7999999999999999999999999874
No 34
>KOG4217|consensus
Probab=99.93 E-value=1.6e-26 Score=186.17 Aligned_cols=73 Identities=45% Similarity=1.105 Sum_probs=68.8
Q ss_pred CCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
....|+||||.+...||||.+|++||+||+|+|+++..|+|-.+. +|.|++..|++|++|||+|||+|||=+|
T Consensus 268 ~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanK----nCPVDKRrRnRCQyCRfQKCL~VGMVKE 340 (605)
T KOG4217|consen 268 AEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANK----NCPVDKRRRNRCQYCRFQKCLAVGMVKE 340 (605)
T ss_pred ccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCC----CCCcchhhhhhchhhhHhHHHHhhhhhh
Confidence 367899999999999999999999999999999999999998874 7999999999999999999999999765
No 35
>cd07167 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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 is required at several stages of development. Particularly, FTZ-F1 regulated 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 regu
Probab=99.93 E-value=1.1e-26 Score=153.17 Aligned_cols=69 Identities=46% Similarity=1.133 Sum_probs=64.9
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 69 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQ----NCQIDKTQRKRCPYCRFQKCLSVGMKLE 69 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCC----ccccCccccCcCCCcccchhhhccCCHH
Confidence 78999999999999999999999999999999999998864 7999999999999999999999999864
No 36
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=99.93 E-value=6.1e-27 Score=152.42 Aligned_cols=70 Identities=40% Similarity=0.926 Sum_probs=63.9
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCc--ccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR--VYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~--~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++++||||.+|++|++||||++.... .|.|..++ +|.++...|..|++|||+|||+|||+++
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 73 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGG----KCIIDKKNRTKCQACRYRKCLNVGMSLG 73 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCC----ccccCccccccCccchhhHHhHcCCCcc
Confidence 5999999999999999999999999999998664 78898764 7999999999999999999999999864
No 37
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. 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
Probab=99.93 E-value=6.2e-27 Score=149.06 Aligned_cols=69 Identities=55% Similarity=1.310 Sum_probs=64.6
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++..+..|.|..++ .|.|+...+..|++|||+|||++||+++
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 69 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGG----NCVVDKDKRNACRYCRFKKCLEVGMDPE 69 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCC----cccccCcccccCccchhhhhhhcCCCHH
Confidence 78999999999999999999999999999988889998764 7999999999999999999999999874
No 38
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. 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. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=99.93 E-value=2e-26 Score=148.45 Aligned_cols=69 Identities=52% Similarity=1.210 Sum_probs=64.7
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++++||||.+|++|++||||++.....|.|..++ +|.|+...+..|++|||+|||++||+++
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~ 69 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDG----KCEIIRLNRNRCQYCRFKKCLAAGMSKD 69 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCC----CccccccccccccchhhhhcccccCCHH
Confidence 78999999999999999999999999999988889998764 7999999999999999999999999874
No 39
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=99.92 E-value=8.4e-27 Score=154.03 Aligned_cols=70 Identities=36% Similarity=0.939 Sum_probs=65.6
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++++||||.+|++|++||||++.....|.|..++ +|.++...+..|++|||+|||++||+++
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 71 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNE----SCEINVVTRRFCQKCRLDKCFAIGMKKE 71 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCC----ccccCccccccCccchhhhCcccCCCHH
Confidence 699999999999999999999999999999988889998764 7999999999999999999999999874
No 40
>cd06957 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells 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
Probab=99.92 E-value=4.2e-27 Score=151.95 Aligned_cols=70 Identities=60% Similarity=1.276 Sum_probs=64.4
Q ss_pred ceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 41 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 41 C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
|.|||++++|+||||.+|++|++||||++..+..|.|...+ +.|.|+...|..|++|||+|||++||+++
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 70 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGN---GNCVVDKARRNWCPFCRLQKCFAVGMNRA 70 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCcc---CCCccCCCccCcccCcchhhcccccCCHH
Confidence 78999999999999999999999999999988889998532 37999999999999999999999999864
No 41
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors 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. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=99.92 E-value=1.3e-26 Score=151.75 Aligned_cols=71 Identities=46% Similarity=1.137 Sum_probs=65.5
Q ss_pred CCceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
.+|.|||++++++||||.+|++|++||||++..+..| .|..++ +|.|+...|..|++|||+|||++||+++
T Consensus 4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 75 (89)
T cd07166 4 VLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNE----TCSIMRINRNRCQYCRFKKCLAVGMSRD 75 (89)
T ss_pred CCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCC----cccccccccccccchhhhhcccccCCHH
Confidence 5799999999999999999999999999999988888 588764 7999999999999999999999999874
No 42
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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 elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=99.92 E-value=4.2e-26 Score=147.89 Aligned_cols=68 Identities=47% Similarity=1.158 Sum_probs=62.5
Q ss_pred CceecCCCCcceeeccccchhhHHHHHHHhhcCccc-ccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 40 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 40 ~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~-~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+|.|||++++|+||||.+|++|++||||++..+..| .|.. .|.|+...+..|++|||+|||++||+++
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~------~C~i~~~~r~~Cr~CRl~KCl~vGM~~~ 69 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDL------SCKIHKKSRNKCQYCRFQKCLNVGMSHN 69 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCcccccc------CCCcCccccccccchhhhhhhhccCCHH
Confidence 499999999999999999999999999999888878 4864 4999999999999999999999999864
No 43
>KOG4216|consensus
Probab=99.90 E-value=1.8e-24 Score=171.15 Aligned_cols=72 Identities=54% Similarity=1.220 Sum_probs=67.9
Q ss_pred CCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 38 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 38 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
-.+|.||||+++|.||||.+|++||+||||+-..+..|.|.+.. +|.|+..+|++|++|||+|||++||+.|
T Consensus 46 vIPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqk----nC~iDRtnRNRCQ~CRLqKClaLGMSRD 117 (479)
T KOG4216|consen 46 IIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQK----NCLIDRTNRNRCQHCRLQKCLALGMSRD 117 (479)
T ss_pred EEeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCccc----CCcccccccchhhHHHHHHHHHhccchh
Confidence 35799999999999999999999999999999999999998864 7999999999999999999999999875
No 44
>KOG4218|consensus
Probab=99.85 E-value=2.3e-22 Score=157.64 Aligned_cols=76 Identities=46% Similarity=1.073 Sum_probs=70.2
Q ss_pred CCCCCCCceecCCCCcceeeccccchhhHHHHHHHhhcCcccccccCCCCCCCCCCCCCCCCCCcchHHHHHHHhccCCC
Q psy16245 34 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 113 (113)
Q Consensus 34 ~~~~~~~C~VCg~~~~g~hyGv~sC~aC~~FFrR~v~~~~~~~C~~~~~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 113 (113)
+....+.|.||||+.+|+|||..+|+.||+||+|+|+.++.|+|.... +|.|++..|.+|.+|||+|||.+||+-|
T Consensus 11 dedl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~q----nC~iDkTqRKRCP~CRFQKCLtvGMklE 86 (475)
T KOG4218|consen 11 DEDLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQ----NCHIDKTQRKRCPSCRFQKCLTVGMKLE 86 (475)
T ss_pred ccccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceeccccc----ccccchHhhccCCchhHHHHhhhhhhHH
Confidence 344568999999999999999999999999999999999999998875 7999999999999999999999999754
No 45
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=69.80 E-value=1.8 Score=29.07 Aligned_cols=30 Identities=30% Similarity=0.815 Sum_probs=21.2
Q ss_pred CCCceecCCCCcc---eeeccccchhhHHHHHH
Q psy16245 38 DIPCKVCGDRSSG---KHYGIYSCDGCSGFFKR 67 (113)
Q Consensus 38 ~~~C~VCg~~~~g---~hyGv~sC~aC~~FFrR 67 (113)
+..|.-||.+... ..||+..|..|++..|.
T Consensus 13 N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~ 45 (116)
T PF01412_consen 13 NKVCADCGAPNPTWASLNYGIFLCLECAGIHRS 45 (116)
T ss_dssp CTB-TTT-SBS--EEETTTTEEE-HHHHHHHHH
T ss_pred cCcCCCCCCCCCCEEEeecChhhhHHHHHHHHH
Confidence 5679999987643 58999999999998665
No 46
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=59.17 E-value=7.3 Score=25.92 Aligned_cols=31 Identities=26% Similarity=0.689 Sum_probs=25.1
Q ss_pred CCCceecCCCCc---ceeeccccchhhHHHHHHH
Q psy16245 38 DIPCKVCGDRSS---GKHYGIYSCDGCSGFFKRS 68 (113)
Q Consensus 38 ~~~C~VCg~~~~---g~hyGv~sC~aC~~FFrR~ 68 (113)
+..|.-|+.+.. ...||+..|..|++..|..
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~l 36 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSL 36 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHHhc
Confidence 467999987653 4699999999999997754
No 47
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=44.95 E-value=16 Score=21.08 Aligned_cols=31 Identities=23% Similarity=0.583 Sum_probs=21.7
Q ss_pred CCceecCCCCcc----eeecc-ccchhhHHHHHHHh
Q psy16245 39 IPCKVCGDRSSG----KHYGI-YSCDGCSGFFKRSI 69 (113)
Q Consensus 39 ~~C~VCg~~~~g----~hyGv-~sC~aC~~FFrR~v 69 (113)
..|..|+...+- ...|. ..|++|..+|++.-
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 568888876543 13443 78999999998643
No 48
>PRK00420 hypothetical protein; Validated
Probab=39.43 E-value=9.2 Score=25.95 Aligned_cols=29 Identities=24% Similarity=0.361 Sum_probs=23.9
Q ss_pred CCCCceecCCCCcceeeccccchhhHHHH
Q psy16245 37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFF 65 (113)
Q Consensus 37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FF 65 (113)
....|.+||.+-...+-|...|-.|..+.
T Consensus 22 l~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred ccCCCCCCCCcceecCCCceECCCCCCee
Confidence 45789999999888788888999997654
No 49
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=34.17 E-value=33 Score=19.46 Aligned_cols=23 Identities=35% Similarity=1.094 Sum_probs=18.4
Q ss_pred CceecCCCCc-c-eeeccccchhhH
Q psy16245 40 PCKVCGDRSS-G-KHYGIYSCDGCS 62 (113)
Q Consensus 40 ~C~VCg~~~~-g-~hyGv~sC~aC~ 62 (113)
.|.||+.... | .-||...|..|-
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE 25 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCE 25 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHH
Confidence 4899998754 6 468999999996
No 50
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=32.75 E-value=25 Score=18.64 Aligned_cols=12 Identities=25% Similarity=0.938 Sum_probs=10.3
Q ss_pred cchhhHHHHHHH
Q psy16245 57 SCDGCSGFFKRS 68 (113)
Q Consensus 57 sC~aC~~FFrR~ 68 (113)
.|++|..+|++.
T Consensus 22 LCn~Cg~~~kk~ 33 (36)
T PF00320_consen 22 LCNACGLYYKKY 33 (36)
T ss_dssp EEHHHHHHHHHH
T ss_pred HHHHHHHHHHHh
Confidence 799999998864
No 51
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=30.93 E-value=25 Score=17.79 Aligned_cols=20 Identities=35% Similarity=0.926 Sum_probs=13.7
Q ss_pred CceecCCCCcce-eeccccchhhH
Q psy16245 40 PCKVCGDRSSGK-HYGIYSCDGCS 62 (113)
Q Consensus 40 ~C~VCg~~~~g~-hyGv~sC~aC~ 62 (113)
.|.||+....++ .| .|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y---~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFY---HCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeE---EeCCCC
Confidence 488888888887 55 455544
No 52
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.34 E-value=34 Score=19.29 Aligned_cols=13 Identities=38% Similarity=0.664 Sum_probs=9.5
Q ss_pred CCCCCceecCCCC
Q psy16245 36 LLDIPCKVCGDRS 48 (113)
Q Consensus 36 ~~~~~C~VCg~~~ 48 (113)
+...+|.|||.+-
T Consensus 6 lp~K~C~~C~rpf 18 (42)
T PF10013_consen 6 LPSKICPVCGRPF 18 (42)
T ss_pred CCCCcCcccCCcc
Confidence 4457899998763
No 53
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=29.96 E-value=28 Score=22.78 Aligned_cols=20 Identities=35% Similarity=0.956 Sum_probs=16.3
Q ss_pred CCceecCCCCcceeeccccchhhHH
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSG 63 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~ 63 (113)
..|.+||.++++- .|.+|..
T Consensus 81 ~~C~~CG~pss~~-----iC~~C~l 100 (104)
T TIGR00269 81 RRCERCGEPTSGR-----ICKACKF 100 (104)
T ss_pred CcCCcCcCcCCcc-----ccHhhhh
Confidence 4699999999864 7999873
No 54
>PHA03124 dUTPase; Provisional
Probab=29.14 E-value=33 Score=28.22 Aligned_cols=16 Identities=31% Similarity=1.026 Sum_probs=13.1
Q ss_pred ccchhhHHHHHHHhhc
Q psy16245 56 YSCDGCSGFFKRSIHR 71 (113)
Q Consensus 56 ~sC~aC~~FFrR~v~~ 71 (113)
.-|-+|++||||....
T Consensus 191 ~~~~~~~~~~~~~~~~ 206 (418)
T PHA03124 191 FGCMGCKAFYRRLFEC 206 (418)
T ss_pred ccccchHHHHHHHHHH
Confidence 3599999999998654
No 55
>PF15279 SOBP: Sine oculis-binding protein
Probab=28.09 E-value=57 Score=25.88 Aligned_cols=14 Identities=43% Similarity=0.816 Sum_probs=12.1
Q ss_pred ccccccccccCCCC
Q psy16245 2 ELFVGNCRQIPPRY 15 (113)
Q Consensus 2 ~~~~~~~~~~~~~~ 15 (113)
|||+.||+--++.-
T Consensus 73 elWl~~~~s~s~~~ 86 (306)
T PF15279_consen 73 ELWLRNCRSPSPSP 86 (306)
T ss_pred cccccccccCCCCC
Confidence 89999999887776
No 56
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=26.75 E-value=35 Score=20.24 Aligned_cols=23 Identities=35% Similarity=1.003 Sum_probs=18.2
Q ss_pred CCceecCCCCc-ceeeccccchhh
Q psy16245 39 IPCKVCGDRSS-GKHYGIYSCDGC 61 (113)
Q Consensus 39 ~~C~VCg~~~~-g~hyGv~sC~aC 61 (113)
..|.|||.+.. ...||...|.-|
T Consensus 17 r~C~vCg~~~gliRkygL~~CRqC 40 (54)
T PTZ00218 17 RQCRVCSNRHGLIRKYGLNVCRQC 40 (54)
T ss_pred CeeecCCCcchhhhhcCcchhhHH
Confidence 56999999753 458998888877
No 57
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=26.45 E-value=71 Score=17.40 Aligned_cols=12 Identities=33% Similarity=0.971 Sum_probs=9.2
Q ss_pred ccchhhHHHHHH
Q psy16245 56 YSCDGCSGFFKR 67 (113)
Q Consensus 56 ~sC~aC~~FFrR 67 (113)
..|+.|..=|++
T Consensus 24 fCC~tC~~~fk~ 35 (37)
T PF08394_consen 24 FCCPTCLSQFKK 35 (37)
T ss_pred EECHHHHHHHHh
Confidence 478999887765
No 58
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=25.82 E-value=30 Score=27.54 Aligned_cols=30 Identities=23% Similarity=0.755 Sum_probs=25.3
Q ss_pred CCCceecCCCCc---ceeeccccchhhHHHHHH
Q psy16245 38 DIPCKVCGDRSS---GKHYGIYSCDGCSGFFKR 67 (113)
Q Consensus 38 ~~~C~VCg~~~~---g~hyGv~sC~aC~~FFrR 67 (113)
+..|.-||.+.- ...|||..|--|++..|-
T Consensus 20 Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRs 52 (319)
T COG5347 20 NKKCADCGAPNPTWASVNLGVFLCIDCAGVHRS 52 (319)
T ss_pred cCccccCCCCCCceEecccCeEEEeecchhhhc
Confidence 568999998873 479999999999998654
No 59
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=25.47 E-value=49 Score=19.25 Aligned_cols=28 Identities=25% Similarity=0.724 Sum_probs=17.9
Q ss_pred ceecCCCCcc-----eeeccccchhhHHHHHHH
Q psy16245 41 CKVCGDRSSG-----KHYGIYSCDGCSGFFKRS 68 (113)
Q Consensus 41 C~VCg~~~~g-----~hyGv~sC~aC~~FFrR~ 68 (113)
|..|+...+- -.=+...|++|..+++..
T Consensus 2 C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~ 34 (54)
T cd00202 2 CSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKH 34 (54)
T ss_pred CCCCCCCCCcccccCCCCcchHHHHHHHHHHhc
Confidence 5566654432 123456899999998765
No 60
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=22.64 E-value=32 Score=17.24 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=5.8
Q ss_pred CceecCCCCcc-eeec
Q psy16245 40 PCKVCGDRSSG-KHYG 54 (113)
Q Consensus 40 ~C~VCg~~~~g-~hyG 54 (113)
.|.+|+.+..+ ..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~ 17 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYR 17 (30)
T ss_dssp --TTTS----S--EEE
T ss_pred cCCcCCCcCCCCceEE
Confidence 47788888776 6664
No 61
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=22.36 E-value=40 Score=17.69 Aligned_cols=13 Identities=23% Similarity=0.670 Sum_probs=8.6
Q ss_pred CCCceecCCCCcc
Q psy16245 38 DIPCKVCGDRSSG 50 (113)
Q Consensus 38 ~~~C~VCg~~~~g 50 (113)
+..|.|||.+...
T Consensus 18 p~~CP~Cg~~~~~ 30 (34)
T cd00729 18 PEKCPICGAPKEK 30 (34)
T ss_pred CCcCcCCCCchHH
Confidence 4578888876543
No 62
>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].
Probab=22.21 E-value=30 Score=27.40 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=12.1
Q ss_pred cccccccccCCCCCC
Q psy16245 3 LFVGNCRQIPPRYPQ 17 (113)
Q Consensus 3 ~~~~~~~~~~~~~~~ 17 (113)
+++||++|+||=-+.
T Consensus 145 il~GDf~QlpPV~~~ 159 (364)
T PF05970_consen 145 ILFGDFLQLPPVVPR 159 (364)
T ss_pred EeehhhhhcCCCccc
Confidence 578999999986544
No 63
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=21.97 E-value=36 Score=22.60 Aligned_cols=27 Identities=22% Similarity=0.578 Sum_probs=20.6
Q ss_pred CCceecCCCCcceeeccccchhhHHHH
Q psy16245 39 IPCKVCGDRSSGKHYGIYSCDGCSGFF 65 (113)
Q Consensus 39 ~~C~VCg~~~~g~hyGv~sC~aC~~FF 65 (113)
..|.||++......=+.+.|.+|..-|
T Consensus 36 daCeiC~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 36 DACEICGPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred EeccccCCCceEEECCEEEEecCCCEE
Confidence 469999877766666788999997543
No 64
>PRK12495 hypothetical protein; Provisional
Probab=20.89 E-value=33 Score=26.06 Aligned_cols=29 Identities=24% Similarity=0.452 Sum_probs=23.2
Q ss_pred CCCCceecCCCCcceeeccccchhhHHHHH
Q psy16245 37 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFK 66 (113)
Q Consensus 37 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFr 66 (113)
+...|.+||.+...+ =|+..|-.|...+-
T Consensus 41 sa~hC~~CG~PIpa~-pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIFRH-DGQEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCcccCC-CCeeECCCCCCccc
Confidence 456899999999843 69999999986554
No 65
>KOG0703|consensus
Probab=20.26 E-value=35 Score=26.86 Aligned_cols=30 Identities=23% Similarity=0.756 Sum_probs=24.8
Q ss_pred CCCceecCCCCc---ceeeccccchhhHHHHHH
Q psy16245 38 DIPCKVCGDRSS---GKHYGIYSCDGCSGFFKR 67 (113)
Q Consensus 38 ~~~C~VCg~~~~---g~hyGv~sC~aC~~FFrR 67 (113)
+..|.-||...- ..++||+.|-.|.+..|.
T Consensus 25 N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~ 57 (287)
T KOG0703|consen 25 NKVCADCGAKGPRWASWNLGVFICLRCAGIHRS 57 (287)
T ss_pred cCcccccCCCCCCeEEeecCeEEEeeccccccc
Confidence 567999998763 479999999999988654
No 66
>PF00357 Integrin_alpha: Integrin alpha cytoplasmic region; InterPro: IPR018184 Some alpha subunits are cleaved post- translationally to produce a heavy and a light chain linked by a disulphide bond [, ]. Integrin alpha chains share a conserved sequence which is found at the beginning of the cytoplasmic domain, just after the end of the transmembrane region. Within the N-terminal domain of alpha subunits, seven sequence repeats, each of approximately 60 amino acids, have been found []. It has been predicted that these repeats assume the beta-propeller fold. The domains contain seven four-stranded beta-sheets arranged in a torus around a pseudosymmetry axis []. Integrin ligands and a putative Mg2+ ion are predicted to bind to the upper face of the propeller, in a manner analogous to the way in which the trimeric G-protein beta subunit (G beta) (which also has a beta-propeller fold) binds the G protein alpha subunit []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences []. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first ten residues of the alpha-subunit cytoplasmic domain appear to form an alpha helix that is terminated by a proline residue. The remainder of the domain is highly acidic in nature and this loops back to contact the membrane-proximal lysine anchor residue. This entry represents the conserved site of the C-terminal integrin alpha chain. ; PDB: 2LKJ_A 2LKE_A 2K8O_A 1DPK_A 2K9J_A 1DPQ_A 1S4W_A 1M8O_A 2K1A_A 2KNC_A ....
Probab=20.18 E-value=46 Score=14.62 Aligned_cols=9 Identities=56% Similarity=0.899 Sum_probs=6.4
Q ss_pred HHHHHHhhc
Q psy16245 63 GFFKRSIHR 71 (113)
Q Consensus 63 ~FFrR~v~~ 71 (113)
+||.|....
T Consensus 3 GFFKR~~~~ 11 (15)
T PF00357_consen 3 GFFKRQRPP 11 (15)
T ss_dssp CHHHHHHHH
T ss_pred ccccccCcc
Confidence 589987543
Done!