Query psy11507
Match_columns 113
No_of_seqs 108 out of 1034
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 20:10:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11507.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11507hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07170 NR_DBD_ERR DNA-binding 99.9 2.8E-25 6.2E-30 150.4 4.7 75 38-112 3-82 (97)
2 cd06956 NR_DBD_RXR DNA-binding 99.9 3.5E-25 7.7E-30 144.0 4.8 71 41-111 2-77 (77)
3 cd07160 NR_DBD_LXR DNA-binding 99.9 8E-25 1.7E-29 149.1 5.2 74 38-111 17-95 (101)
4 cd07168 NR_DBD_DHR4_like DNA-b 99.9 6.4E-25 1.4E-29 146.7 4.5 76 37-112 4-84 (90)
5 cd07155 NR_DBD_ER_like DNA-bin 99.9 9E-25 1.9E-29 141.4 4.6 70 42-111 1-75 (75)
6 cd06961 NR_DBD_TR DNA-binding 99.9 1E-24 2.2E-29 144.3 4.3 72 41-112 1-77 (85)
7 cd06959 NR_DBD_EcR_like The DN 99.9 1.5E-24 3.3E-29 139.7 4.7 67 41-107 1-72 (73)
8 cd07173 NR_DBD_AR DNA-binding 99.9 2.6E-24 5.6E-29 141.7 5.8 70 39-108 3-77 (82)
9 cd07172 NR_DBD_GR_PR DNA-bindi 99.9 2.1E-24 4.6E-29 140.8 5.2 67 39-105 2-73 (78)
10 cd07171 NR_DBD_ER DNA-binding 99.9 1.8E-24 4E-29 142.3 4.8 71 39-109 3-78 (82)
11 cd06964 NR_DBD_RAR DNA-binding 99.9 4E-25 8.6E-30 146.3 1.5 74 39-112 4-82 (85)
12 cd07161 NR_DBD_EcR DNA-binding 99.9 2.5E-24 5.5E-29 144.2 4.9 71 40-110 2-77 (91)
13 cd06970 NR_DBD_PNR DNA-binding 99.9 5.2E-25 1.1E-29 147.8 1.3 76 37-112 4-85 (92)
14 cd06967 NR_DBD_TR2_like DNA-bi 99.9 5.7E-25 1.2E-29 146.1 1.3 75 38-112 2-81 (87)
15 cd07164 NR_DBD_PNR_like_1 DNA- 99.9 3.5E-24 7.5E-29 139.6 3.9 71 42-112 1-76 (78)
16 cd06969 NR_DBD_NGFI-B DNA-bind 99.9 1.3E-24 2.7E-29 140.8 1.3 69 40-108 1-74 (75)
17 cd07179 2DBD_NR_DBD2 The secon 99.9 6.2E-24 1.3E-28 137.2 4.5 66 42-107 1-71 (74)
18 cd07165 NR_DBD_DmE78_like DNA- 99.9 4.9E-24 1.1E-28 139.8 4.1 71 42-112 1-76 (81)
19 cd06963 NR_DBD_GR_like The DNA 99.9 6.8E-24 1.5E-28 136.8 4.6 64 42-105 1-69 (73)
20 cd07169 NR_DBD_GCNF_like DNA-b 99.9 6.7E-24 1.5E-28 141.8 4.4 73 39-111 6-83 (90)
21 cd06958 NR_DBD_COUP_TF DNA-bin 99.9 6E-24 1.3E-28 136.9 4.0 66 42-107 1-71 (73)
22 cd07156 NR_DBD_VDR_like The DN 99.9 4.1E-24 9E-29 137.3 3.3 65 42-106 1-70 (72)
23 KOG4846|consensus 99.9 2.6E-24 5.7E-29 175.2 2.3 69 40-108 133-207 (538)
24 cd06960 NR_DBD_HNF4A DNA-bindi 99.9 2.5E-24 5.5E-29 139.5 1.7 71 42-112 1-76 (76)
25 cd07158 NR_DBD_Ppar_like The D 99.9 9.5E-24 2.1E-28 135.8 4.2 65 42-106 1-71 (73)
26 cd07167 NR_DBD_Lrh-1_like The 99.9 6.9E-24 1.5E-28 142.6 3.6 70 42-111 1-75 (93)
27 cd06966 NR_DBD_CAR DNA-binding 99.9 2.7E-24 5.8E-29 144.8 1.6 71 41-111 2-77 (94)
28 cd07163 NR_DBD_TLX DNA-binding 99.9 2.6E-24 5.7E-29 144.3 1.0 75 38-112 5-86 (92)
29 cd06962 NR_DBD_FXR DNA-binding 99.9 3.8E-24 8.2E-29 141.4 1.6 69 40-108 2-75 (84)
30 cd06968 NR_DBD_ROR DNA-binding 99.9 1.1E-23 2.3E-28 142.2 3.8 74 39-112 5-83 (95)
31 cd07157 2DBD_NR_DBD1 The first 99.9 3.3E-24 7.2E-29 142.2 1.2 71 41-111 2-79 (86)
32 cd07162 NR_DBD_PXR DNA-binding 99.9 1.7E-23 3.7E-28 139.0 4.4 68 41-108 1-73 (87)
33 smart00399 ZnF_C4 c4 zinc fing 99.9 1.5E-23 3.1E-28 133.8 3.3 64 41-104 1-69 (70)
34 cd06955 NR_DBD_VDR DNA-binding 99.9 1E-23 2.2E-28 145.0 2.6 69 38-106 5-78 (107)
35 cd07154 NR_DBD_PNR_like The DN 99.9 4.7E-24 1E-28 137.3 0.9 66 42-107 1-72 (73)
36 cd06916 NR_DBD_like DNA-bindin 99.9 4.3E-24 9.3E-29 137.2 0.3 66 42-107 1-71 (72)
37 PF00105 zf-C4: Zinc finger, C 99.9 2.4E-23 5.1E-28 132.5 3.7 65 40-104 1-70 (70)
38 cd07166 NR_DBD_REV_ERB DNA-bin 99.9 7.8E-24 1.7E-28 141.2 1.5 73 40-112 4-82 (89)
39 cd06957 NR_DBD_PNR_like_2 DNA- 99.9 3.1E-24 6.7E-29 141.1 -0.7 71 42-112 1-77 (82)
40 KOG4215|consensus 99.9 4.6E-23 1E-27 165.8 4.5 75 38-112 18-97 (432)
41 cd06965 NR_DBD_Ppar DNA-bindin 99.9 3.8E-23 8.2E-28 136.5 2.2 70 41-112 1-76 (84)
42 KOG4217|consensus 99.9 3.4E-22 7.3E-27 164.9 4.1 73 38-110 268-345 (605)
43 KOG4216|consensus 99.8 8E-22 1.7E-26 159.7 3.5 70 39-108 46-120 (479)
44 KOG4218|consensus 99.8 5.1E-20 1.1E-24 147.8 3.3 74 38-111 14-92 (475)
45 PF01412 ArfGap: Putative GTPa 73.3 1.9 4E-05 29.5 1.1 31 38-68 12-45 (116)
46 smart00105 ArfGap Putative GTP 57.7 7.9 0.00017 26.2 1.8 31 39-69 3-36 (112)
47 PTZ00218 40S ribosomal protein 48.0 16 0.00035 22.2 1.9 27 36-62 13-40 (54)
48 PRK00420 hypothetical protein; 39.4 10 0.00023 26.2 0.1 27 39-65 23-49 (112)
49 smart00401 ZnF_GATA zinc finge 38.3 20 0.00044 21.1 1.3 31 39-69 3-38 (52)
50 PRK04179 rpl37e 50S ribosomal 37.5 28 0.0006 21.8 1.8 25 37-63 15-39 (62)
51 PF10013 DUF2256: Uncharacteri 31.3 31 0.00068 19.9 1.2 14 35-48 4-17 (42)
52 PF00320 GATA: GATA zinc finge 29.6 33 0.00072 18.6 1.1 16 54-69 17-33 (36)
53 KOG3506|consensus 29.5 33 0.00071 21.0 1.2 30 34-63 13-43 (56)
54 PF03107 C1_2: C1 domain; Int 29.1 20 0.00044 18.6 0.2 21 41-63 2-22 (30)
55 COG2126 RPL37A Ribosomal prote 28.6 31 0.00068 21.4 1.0 35 26-63 4-38 (61)
56 PF10764 Gin: Inhibitor of sig 28.2 44 0.00096 19.4 1.5 24 41-64 1-26 (46)
57 KOG0706|consensus 28.0 28 0.0006 29.6 0.9 31 38-68 22-55 (454)
58 PF09889 DUF2116: Uncharacteri 27.0 31 0.00068 21.2 0.8 32 38-72 2-34 (59)
59 COG5347 GTPase-activating prot 26.5 29 0.00063 28.1 0.7 31 38-68 19-52 (319)
60 cd00729 rubredoxin_SM Rubredox 25.3 29 0.00063 18.7 0.4 14 38-51 17-30 (34)
61 PHA03124 dUTPase; Provisional 23.9 44 0.00096 28.1 1.3 15 57-71 191-205 (418)
62 COG4068 Uncharacterized protei 23.6 53 0.0012 20.5 1.4 14 35-48 4-17 (64)
63 PF10705 Ycf15: Chloroplast pr 23.4 25 0.00055 23.4 -0.1 7 1-7 33-39 (93)
64 PF00357 Integrin_alpha: Integ 20.3 50 0.0011 15.0 0.6 9 64-72 3-11 (15)
65 PF11781 RRN7: RNA polymerase 20.2 43 0.00094 18.4 0.4 24 39-62 8-31 (36)
66 PF13901 DUF4206: Domain of un 20.1 35 0.00077 25.4 0.1 34 40-73 153-189 (202)
No 1
>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=99.91 E-value=2.8e-25 Score=150.36 Aligned_cols=75 Identities=51% Similarity=0.746 Sum_probs=67.0
Q ss_pred CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
+..+|.||++++.|+||||.+|++|++||||++.....|.|..++.|.+ ..|++|||+|||+|||..+..+..|.
T Consensus 3 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~ 82 (97)
T cd07170 3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRV 82 (97)
T ss_pred CCCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccC
Confidence 3456999999999999999999999999999999998999998888853 47999999999999999987777663
No 2
>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=99.91 E-value=3.5e-25 Score=144.01 Aligned_cols=71 Identities=37% Similarity=0.598 Sum_probs=64.9
Q ss_pred cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||..+..+..|
T Consensus 2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 5999999999999999999999999999999999999998888853 4799999999999999998777655
No 3
>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=99.91 E-value=8e-25 Score=149.13 Aligned_cols=74 Identities=35% Similarity=0.576 Sum_probs=66.1
Q ss_pred CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
...+|.||+++++++||||.+|++|++||||++.....|.|..++.|.+ ..|++|||+|||++||+.+..+..|
T Consensus 17 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~ 95 (101)
T cd07160 17 GNEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEE 95 (101)
T ss_pred CCCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChh
Confidence 3567999999999999999999999999999999999999998888853 4799999999999999998765543
No 4
>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=99.91 E-value=6.4e-25 Score=146.73 Aligned_cols=76 Identities=29% Similarity=0.534 Sum_probs=68.0
Q ss_pred CCCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 37 ~~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
....+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||.....+..|
T Consensus 4 ~~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R 83 (90)
T cd07168 4 ESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDR 83 (90)
T ss_pred ccCCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhccc
Confidence 34567999999999999999999999999999999988999998888853 4799999999999999998877776
Q ss_pred C
Q psy11507 112 F 112 (113)
Q Consensus 112 ~ 112 (113)
.
T Consensus 84 ~ 84 (90)
T cd07168 84 M 84 (90)
T ss_pred C
Confidence 4
No 5
>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=99.91 E-value=9e-25 Score=141.41 Aligned_cols=70 Identities=50% Similarity=0.723 Sum_probs=63.8
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||+.+..+.+|
T Consensus 1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 789999999999999999999999999999999999998888853 4799999999999999998776655
No 6
>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=99.90 E-value=1e-24 Score=144.34 Aligned_cols=72 Identities=35% Similarity=0.581 Sum_probs=65.3
Q ss_pred cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
+|.||++.++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||+++..+..|.
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~ 77 (85)
T cd06961 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRK 77 (85)
T ss_pred CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccC
Confidence 4999999999999999999999999999999999999998888853 47999999999999999987776653
No 7
>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=99.90 E-value=1.5e-24 Score=139.70 Aligned_cols=67 Identities=39% Similarity=0.629 Sum_probs=61.3
Q ss_pred cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD 107 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~ 107 (113)
+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||.++..
T Consensus 1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (73)
T cd06959 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL 72 (73)
T ss_pred CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhc
Confidence 5999999999999999999999999999999889999998888853 479999999999999998753
No 8
>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=99.90 E-value=2.6e-24 Score=141.69 Aligned_cols=70 Identities=29% Similarity=0.567 Sum_probs=63.1
Q ss_pred CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchh
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDT 108 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~ 108 (113)
..+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||......
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~ 77 (82)
T cd07173 3 QKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARK 77 (82)
T ss_pred CCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHH
Confidence 456999999999999999999999999999999999999998888853 4799999999999999987544
No 9
>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=99.90 E-value=2.1e-24 Score=140.82 Aligned_cols=67 Identities=33% Similarity=0.618 Sum_probs=61.4
Q ss_pred CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCcc
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDS 105 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~ 105 (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 QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLG 73 (78)
T ss_pred CCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCcc
Confidence 457999999999999999999999999999999999999998888853 4799999999999999875
No 10
>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=99.90 E-value=1.8e-24 Score=142.35 Aligned_cols=71 Identities=38% Similarity=0.583 Sum_probs=63.8
Q ss_pred CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhh
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTT 109 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~ 109 (113)
..+|.||+++++++||||.+|++|++||||++.....|.|..++.|.+ ..|++|||+|||++||.++....
T Consensus 3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~ 78 (82)
T cd07171 3 THFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRR 78 (82)
T ss_pred CCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHH
Confidence 356999999999999999999999999999999999999998888853 47999999999999999975544
No 11
>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=99.90 E-value=4e-25 Score=146.34 Aligned_cols=74 Identities=32% Similarity=0.568 Sum_probs=66.7
Q ss_pred CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
..+|.||+++++++||||.+|++|++||||++.....|.|..++.|.+ ..|++|||+|||++||.++..+..|.
T Consensus 4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~ 82 (85)
T cd06964 4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN 82 (85)
T ss_pred CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhcccc
Confidence 357999999999999999999999999999999888899998888853 47999999999999999988877764
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=99.90 E-value=2.5e-24 Score=144.17 Aligned_cols=71 Identities=35% Similarity=0.611 Sum_probs=64.1
Q ss_pred CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhc
Q psy11507 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTN 110 (113)
Q Consensus 40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~ 110 (113)
.+|.||+++++++||||.+|++|++||||++.....|.|..++.|.+ ..|++|||+|||++||++...+..
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 77 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPE 77 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCch
Confidence 35999999999999999999999999999999999999998888853 479999999999999999866554
No 13
>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=99.90 E-value=5.2e-25 Score=147.81 Aligned_cols=76 Identities=32% Similarity=0.518 Sum_probs=66.9
Q ss_pred CCCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCC-CCCCC-----CCCcchHHhHhHHhcCCccchhhc
Q psy11507 37 LPRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRG-HEPQK-----KSSQIPKEKYNLAYLMSDSLDTTN 110 (113)
Q Consensus 37 ~~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~-~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~ 110 (113)
.+..+|.||+++++++|||+.+|++|++||||++..+..|.|..+ +.|.+ ..|++|||+|||++||..+..+..
T Consensus 4 ~p~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~ 83 (92)
T cd06970 4 NPGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNE 83 (92)
T ss_pred CCCCCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccc
Confidence 345579999999999999999999999999999999999999885 67753 479999999999999999877766
Q ss_pred cC
Q psy11507 111 RF 112 (113)
Q Consensus 111 ~~ 112 (113)
|+
T Consensus 84 R~ 85 (92)
T cd06970 84 RQ 85 (92)
T ss_pred cC
Confidence 64
No 14
>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=99.90 E-value=5.7e-25 Score=146.14 Aligned_cols=75 Identities=37% Similarity=0.584 Sum_probs=67.7
Q ss_pred CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
|..+|.||++.+.++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||+....+..|+
T Consensus 2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~ 81 (87)
T cd06967 2 PVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERK 81 (87)
T ss_pred CCCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccC
Confidence 4567999999999999999999999999999999888999998888853 47999999999999999988877764
No 15
>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=99.89 E-value=3.5e-24 Score=139.58 Aligned_cols=71 Identities=37% Similarity=0.575 Sum_probs=64.9
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||+|||.....+..|.
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~ 76 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERA 76 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCC
Confidence 789999999999999999999999999999889999998888853 47999999999999999988777664
No 16
>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=99.89 E-value=1.3e-24 Score=140.79 Aligned_cols=69 Identities=39% Similarity=0.605 Sum_probs=62.2
Q ss_pred CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchh
Q psy11507 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDT 108 (113)
Q Consensus 40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~ 108 (113)
++|.||++++.++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||+++..+
T Consensus 1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 74 (75)
T cd06969 1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74 (75)
T ss_pred CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHcc
Confidence 36999999999999999999999999999999888999998877753 4799999999999999987543
No 17
>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=99.89 E-value=6.2e-24 Score=137.23 Aligned_cols=66 Identities=36% Similarity=0.621 Sum_probs=60.6
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD 107 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~ 107 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||+++..
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (74)
T cd07179 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGS 71 (74)
T ss_pred CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHe
Confidence 789999999999999999999999999999999999998888853 479999999999999998754
No 18
>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=99.89 E-value=4.9e-24 Score=139.82 Aligned_cols=71 Identities=44% Similarity=0.680 Sum_probs=64.9
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
|.||+++++++||||.+|++|++||||++.....|.|..++.|.+ ..|++|||+|||++||.+...+..|.
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~ 76 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRI 76 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCC
Confidence 789999999999999999999999999999899999998888853 47999999999999999988777764
No 19
>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=99.89 E-value=6.8e-24 Score=136.76 Aligned_cols=64 Identities=33% Similarity=0.604 Sum_probs=59.5
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCcc
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDS 105 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~ 105 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||..+
T Consensus 1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 69 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLG 69 (73)
T ss_pred CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChh
Confidence 789999999999999999999999999999999999998888853 4799999999999999876
No 20
>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=99.89 E-value=6.7e-24 Score=141.83 Aligned_cols=73 Identities=34% Similarity=0.586 Sum_probs=65.2
Q ss_pred CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
..+|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||.++..+..|
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 83 (90)
T cd07169 6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDG 83 (90)
T ss_pred CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhcccc
Confidence 456999999999999999999999999999999999999998888853 4799999999999999998665544
No 21
>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=99.89 E-value=6e-24 Score=136.90 Aligned_cols=66 Identities=33% Similarity=0.569 Sum_probs=60.5
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD 107 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~ 107 (113)
|.||++++.++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||+++..
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (73)
T cd06958 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAV 71 (73)
T ss_pred CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHc
Confidence 789999999999999999999999999999998999998888853 479999999999999998754
No 22
>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=99.89 E-value=4.1e-24 Score=137.33 Aligned_cols=65 Identities=31% Similarity=0.632 Sum_probs=59.9
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccc
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSL 106 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~ 106 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||+++.
T Consensus 1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~ 70 (72)
T cd07156 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEM 70 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHH
Confidence 789999999999999999999999999999888899998888853 47999999999999999864
No 23
>KOG4846|consensus
Probab=99.89 E-value=2.6e-24 Score=175.20 Aligned_cols=69 Identities=43% Similarity=0.693 Sum_probs=63.3
Q ss_pred CcceEcCCCCcceeechhcchhhHHHHHHhHhhccce-ecCCCCCCCCC-----CCcchHHhHhHHhcCCccchh
Q psy11507 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL-VSLRGHEPQKK-----SSQIPKEKYNLAYLMSDSLDT 108 (113)
Q Consensus 40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~-~C~~~~~c~~~-----~C~~CR~~kcl~~GM~~~~~~ 108 (113)
.+|.||||.++||||||.+|+|||+||||+|+.+..| .|-+..+|.+. .|+.|||+|||+|||+...++
T Consensus 133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVR 207 (538)
T KOG4846|consen 133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVR 207 (538)
T ss_pred EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhh
Confidence 5799999999999999999999999999999999999 59999888544 699999999999999998665
No 24
>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=99.89 E-value=2.5e-24 Score=139.46 Aligned_cols=71 Identities=32% Similarity=0.543 Sum_probs=64.6
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||.+...+..|+
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 789999999999999999999999999999888999998888853 47999999999999999987776664
No 25
>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=99.89 E-value=9.5e-24 Score=135.83 Aligned_cols=65 Identities=48% Similarity=0.737 Sum_probs=59.8
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccce-ecCCCCCCCC-----CCCcchHHhHhHHhcCCccc
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASL-VSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSL 106 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~-~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~ 106 (113)
|.||+++++++||||.+|++|++||||++..+..| .|..++.|.+ ..|++|||+|||++||++..
T Consensus 1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~ 71 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNA 71 (73)
T ss_pred CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHH
Confidence 78999999999999999999999999999999888 7998888853 47999999999999999864
No 26
>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=99.89 E-value=6.9e-24 Score=142.62 Aligned_cols=70 Identities=36% Similarity=0.647 Sum_probs=63.9
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||..+..+..|
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r 75 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADR 75 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcc
Confidence 789999999999999999999999999999999999999888853 4799999999999999998766655
No 27
>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=99.89 E-value=2.7e-24 Score=144.76 Aligned_cols=71 Identities=25% Similarity=0.446 Sum_probs=64.7
Q ss_pred cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
+|.||+++++++||||.+|.+|++||||++.....|.|..++.|.+ ..|++|||+|||++||.++.....|
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r 77 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEE 77 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchh
Confidence 6999999999999999999999999999999888999998888853 4799999999999999998776654
No 28
>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=99.88 E-value=2.6e-24 Score=144.27 Aligned_cols=75 Identities=28% Similarity=0.464 Sum_probs=66.0
Q ss_pred CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCC--CCCC-----CCCCcchHHhHhHHhcCCccchhhc
Q psy11507 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRG--HEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTN 110 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~--~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~ 110 (113)
...+|.||+++++++||||.+|++|++||||++..+..|.|..+ +.|. ...|++|||+|||++||++...+..
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~ 84 (92)
T cd07163 5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHE 84 (92)
T ss_pred cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcc
Confidence 35679999999999999999999999999999998999999873 5664 3479999999999999999887776
Q ss_pred cC
Q psy11507 111 RF 112 (113)
Q Consensus 111 ~~ 112 (113)
|.
T Consensus 85 r~ 86 (92)
T cd07163 85 RG 86 (92)
T ss_pred cC
Confidence 63
No 29
>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=99.88 E-value=3.8e-24 Score=141.42 Aligned_cols=69 Identities=33% Similarity=0.596 Sum_probs=62.6
Q ss_pred CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchh
Q psy11507 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDT 108 (113)
Q Consensus 40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~ 108 (113)
.+|.||+++++++||||.+|++|++||||++..+..|.|..++.|. ...|++|||+|||++||......
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~ 75 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLL 75 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHcc
Confidence 4599999999999999999999999999999988999999888885 34799999999999999987544
No 30
>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=99.88 E-value=1.1e-23 Score=142.16 Aligned_cols=74 Identities=35% Similarity=0.537 Sum_probs=65.9
Q ss_pred CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
..+|.|||+++.++|||+.+|++|++||||++..+..|.|..++.|.. ..|++|||+|||++||.....+..|.
T Consensus 5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~ 83 (95)
T cd06968 5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRM 83 (95)
T ss_pred ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcC
Confidence 457999999999999999999999999999999888999998888853 47999999999999999987665553
No 31
>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=99.88 E-value=3.3e-24 Score=142.19 Aligned_cols=71 Identities=34% Similarity=0.445 Sum_probs=63.1
Q ss_pred cceEcCCCCcceeechhcchhhHHHHHHhHhhcc--ceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhcc
Q psy11507 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARA--SLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~--~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
+|.||+++++++||||.+|++|++||||++.... .|.|..++.|.+ ..|++|||+|||+|||.......+|
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~ 79 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGR 79 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccc
Confidence 5999999999999999999999999999998664 788998888853 4799999999999999988766665
No 32
>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=99.88 E-value=1.7e-23 Score=138.96 Aligned_cols=68 Identities=31% Similarity=0.607 Sum_probs=61.7
Q ss_pred cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchh
Q psy11507 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDT 108 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~ 108 (113)
+|.||+++++++||||.+|++|++||||++.....|.|..++.|. ...|++|||+|||++||.++...
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 73 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIM 73 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHcc
Confidence 499999999999999999999999999999998999999888885 34799999999999999997543
No 33
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.88 E-value=1.5e-23 Score=133.83 Aligned_cols=64 Identities=44% Similarity=0.715 Sum_probs=59.2
Q ss_pred cceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCc
Q psy11507 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSD 104 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~ 104 (113)
+|.||+++++++||||.+|++|++||||++..+..|.|..++.|. ...|++|||+|||++||..
T Consensus 1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~ 69 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDP 69 (70)
T ss_pred CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcC
Confidence 499999999999999999999999999999989889999888785 3479999999999999986
No 34
>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=99.88 E-value=1e-23 Score=145.03 Aligned_cols=69 Identities=30% Similarity=0.598 Sum_probs=62.6
Q ss_pred CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccc
Q psy11507 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSL 106 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~ 106 (113)
.+.+|.||++.++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||..+.
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~ 78 (107)
T cd06955 5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEF 78 (107)
T ss_pred CCCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchh
Confidence 4567999999999999999999999999999999999999998888853 47999999999999998854
No 35
>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=99.88 E-value=4.7e-24 Score=137.32 Aligned_cols=66 Identities=33% Similarity=0.563 Sum_probs=59.4
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecC-CCCCCC-----CCCCcchHHhHhHHhcCCccch
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSL-RGHEPQ-----KKSSQIPKEKYNLAYLMSDSLD 107 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~-~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~ 107 (113)
|.||+++++++||||.+|++|++||||++..+..|.|. .++.|. ...|++|||+|||++||+++..
T Consensus 1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (73)
T cd07154 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAV 72 (73)
T ss_pred CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHC
Confidence 78999999999999999999999999999999999998 566674 3479999999999999998753
No 36
>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=99.88 E-value=4.3e-24 Score=137.18 Aligned_cols=66 Identities=38% Similarity=0.652 Sum_probs=60.4
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccch
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLD 107 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~ 107 (113)
|.||+++++++||||.+|++|++||||++..+..|.|..++.|.+ ..|++|||+|||++||.++..
T Consensus 1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (72)
T cd06916 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAV 71 (72)
T ss_pred CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHc
Confidence 789999999999999999999999999999998999998888853 479999999999999998643
No 37
>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=99.88 E-value=2.4e-23 Score=132.46 Aligned_cols=65 Identities=34% Similarity=0.660 Sum_probs=56.3
Q ss_pred CcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCc
Q psy11507 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSD 104 (113)
Q Consensus 40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~ 104 (113)
+.|.||++++.+.||||.+|++|++||||++.....+.|..++.|.+ ..|++|||+|||++||..
T Consensus 1 ~~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 1 KKCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp -BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred CCCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence 36999999999999999999999999999999998899998877743 479999999999999973
No 38
>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=99.88 E-value=7.8e-24 Score=141.20 Aligned_cols=73 Identities=41% Similarity=0.644 Sum_probs=65.3
Q ss_pred CcceEcCCCCcceeechhcchhhHHHHHHhHhhccce-ecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 40 RLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASL-VSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 40 ~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~-~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
.+|.||++++.++|||+.+|++|++||||++..+..| .|..++.|.+ ..|++|||+|||++||.++..+..|.
T Consensus 4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~ 82 (89)
T cd07166 4 VLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRI 82 (89)
T ss_pred CCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCC
Confidence 4699999999999999999999999999999988888 5988888853 47999999999999999988777663
No 39
>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=99.88 E-value=3.1e-24 Score=141.12 Aligned_cols=71 Identities=27% Similarity=0.464 Sum_probs=63.3
Q ss_pred ceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCC-CCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 42 CLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLR-GHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 42 C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~-~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
|.||+++++++||||.+|++|++||||++.....|.|.. ++.|.+ ..|++|||+|||++||..+..+..|.
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~ 77 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERG 77 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccC
Confidence 789999999999999999999999999999999999984 566743 47999999999999999987776663
No 40
>KOG4215|consensus
Probab=99.87 E-value=4.6e-23 Score=165.75 Aligned_cols=75 Identities=24% Similarity=0.459 Sum_probs=68.0
Q ss_pred CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCCC-----CCCcchHHhHhHHhcCCccchhhccC
Q psy11507 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQK-----KSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~~-----~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
....|.||||++.|.|||+.+|+|||+||||+|.++..|+|+-+++|.. +.||+|||+||+++||..+..+.-|+
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERD 97 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERD 97 (432)
T ss_pred ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccc
Confidence 3567999999999999999999999999999999999999999988853 26999999999999999987777664
No 41
>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=99.87 E-value=3.8e-23 Score=136.54 Aligned_cols=70 Identities=39% Similarity=0.610 Sum_probs=61.3
Q ss_pred cceEcCCCCcceeechhcchhhHHHHHHhHhhcccee-cCCCCCCC-----CCCCcchHHhHhHHhcCCccchhhccC
Q psy11507 41 LCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLV-SLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTNRF 112 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~-C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~~~ 112 (113)
+|.||++.++++||||.+|++|++||||++..+..|. |... |. ...|++|||+|||++||..+..+..|.
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~ 76 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRM 76 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCC
Confidence 4999999999999999999999999999999888885 8754 53 347999999999999999987776663
No 42
>KOG4217|consensus
Probab=99.85 E-value=3.4e-22 Score=164.86 Aligned_cols=73 Identities=40% Similarity=0.628 Sum_probs=66.5
Q ss_pred CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchhhc
Q psy11507 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTN 110 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~ 110 (113)
..+.|.||||.+..-||||.+|+|||+||+|+|+++.+|+|..+++|- .+.|++|||+|||+|||..+++++.
T Consensus 268 ~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtd 345 (605)
T KOG4217|consen 268 AEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTD 345 (605)
T ss_pred ccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecc
Confidence 367899999999999999999999999999999999999999999883 2369999999999999999877653
No 43
>KOG4216|consensus
Probab=99.84 E-value=8e-22 Score=159.67 Aligned_cols=70 Identities=36% Similarity=0.579 Sum_probs=63.9
Q ss_pred CCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchh
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDT 108 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~ 108 (113)
-.+|.||||.++|.||||.+|+|||+||||+...+..|.|.+.++|. .+.|++||++|||++||++..+-
T Consensus 46 vIPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVK 120 (479)
T KOG4216|consen 46 IIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVK 120 (479)
T ss_pred EEeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHH
Confidence 35799999999999999999999999999999999999999999994 34799999999999999997543
No 44
>KOG4218|consensus
Probab=99.78 E-value=5.1e-20 Score=147.82 Aligned_cols=74 Identities=34% Similarity=0.588 Sum_probs=67.3
Q ss_pred CCCcceEcCCCCcceeechhcchhhHHHHHHhHhhccceecCCCCCCC-----CCCCcchHHhHhHHhcCCccchhhcc
Q psy11507 38 PRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQARASLVSLRGHEPQ-----KKSSQIPKEKYNLAYLMSDSLDTTNR 111 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C~~C~~FFRRsv~~~~~~~C~~~~~c~-----~~~C~~CR~~kcl~~GM~~~~~~~~~ 111 (113)
..+.|.||||+.+|+|||..+|+.|++||+|+|+.+..|+|....+|. .+.|-+|||+|||.|||.-+.+++.|
T Consensus 14 l~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADR 92 (475)
T KOG4218|consen 14 LGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADR 92 (475)
T ss_pred cccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhh
Confidence 356899999999999999999999999999999999999999998884 44799999999999999988777655
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=73.35 E-value=1.9 Score=29.47 Aligned_cols=31 Identities=23% Similarity=0.705 Sum_probs=21.1
Q ss_pred CCCcceEcCCCCcc---eeechhcchhhHHHHHH
Q psy11507 38 PRRLCLVCGDVASG---FHYGVASCEACKAFFKR 68 (113)
Q Consensus 38 ~~~~C~VC~~~~~g---~hyGv~~C~~C~~FFRR 68 (113)
....|.-|+.+... ..||+..|..|++..|.
T Consensus 12 ~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~ 45 (116)
T PF01412_consen 12 GNKVCADCGAPNPTWASLNYGIFLCLECAGIHRS 45 (116)
T ss_dssp TCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHH
T ss_pred CcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHH
Confidence 35679999976533 58999999999999654
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=57.68 E-value=7.9 Score=26.19 Aligned_cols=31 Identities=23% Similarity=0.630 Sum_probs=24.4
Q ss_pred CCcceEcCCCC---cceeechhcchhhHHHHHHh
Q psy11507 39 RRLCLVCGDVA---SGFHYGVASCEACKAFFKRT 69 (113)
Q Consensus 39 ~~~C~VC~~~~---~g~hyGv~~C~~C~~FFRRs 69 (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 45688898654 33699999999999998653
No 47
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=48.02 E-value=16 Score=22.24 Aligned_cols=27 Identities=30% Similarity=0.650 Sum_probs=20.7
Q ss_pred CCCCCcceEcCCC-Ccceeechhcchhh
Q psy11507 36 ELPRRLCLVCGDV-ASGFHYGVASCEAC 62 (113)
Q Consensus 36 ~~~~~~C~VC~~~-~~g~hyGv~~C~~C 62 (113)
..-...|.||+.+ +.-..||...|.-|
T Consensus 13 GkGsr~C~vCg~~~gliRkygL~~CRqC 40 (54)
T PTZ00218 13 GKGSRQCRVCSNRHGLIRKYGLNVCRQC 40 (54)
T ss_pred CCCCCeeecCCCcchhhhhcCcchhhHH
Confidence 4445789999986 44468999888887
No 48
>PRK00420 hypothetical protein; Validated
Probab=39.36 E-value=10 Score=26.23 Aligned_cols=27 Identities=22% Similarity=0.405 Sum_probs=23.2
Q ss_pred CCcceEcCCCCcceeechhcchhhHHH
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEACKAF 65 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C~~F 65 (113)
...|.+||.+-...+-|...|..|..+
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCe
Confidence 367999999998888999999999754
No 49
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=38.30 E-value=20 Score=21.12 Aligned_cols=31 Identities=29% Similarity=0.754 Sum_probs=21.2
Q ss_pred CCcceEcCCCCcc-e---eech-hcchhhHHHHHHh
Q psy11507 39 RRLCLVCGDVASG-F---HYGV-ASCEACKAFFKRT 69 (113)
Q Consensus 39 ~~~C~VC~~~~~g-~---hyGv-~~C~~C~~FFRRs 69 (113)
...|..|+...+. . -.|. ..|++|..+|+..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~ 38 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKH 38 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHc
Confidence 4568888854332 2 3443 7899999999764
No 50
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=37.46 E-value=28 Score=21.78 Aligned_cols=25 Identities=24% Similarity=0.570 Sum_probs=20.7
Q ss_pred CCCCcceEcCCCCcceeechhcchhhH
Q psy11507 37 LPRRLCLVCGDVASGFHYGVASCEACK 63 (113)
Q Consensus 37 ~~~~~C~VC~~~~~g~hyGv~~C~~C~ 63 (113)
.++.+|..||..+ +|.--..|.+|.
T Consensus 15 ~tHt~CrRCG~~s--yh~qK~~CasCG 39 (62)
T PRK04179 15 KTHIRCRRCGRHS--YNVRKKYCAACG 39 (62)
T ss_pred cccchhcccCccc--ccccccchhhcC
Confidence 3688999999885 888888898885
No 51
>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=31.33 E-value=31 Score=19.92 Aligned_cols=14 Identities=43% Similarity=1.108 Sum_probs=10.4
Q ss_pred CCCCCCcceEcCCC
Q psy11507 35 EELPRRLCLVCGDV 48 (113)
Q Consensus 35 ~~~~~~~C~VC~~~ 48 (113)
...+..+|.||+.+
T Consensus 4 ~~lp~K~C~~C~rp 17 (42)
T PF10013_consen 4 SNLPSKICPVCGRP 17 (42)
T ss_pred ccCCCCcCcccCCc
Confidence 35567889999875
No 52
>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=29.63 E-value=33 Score=18.57 Aligned_cols=16 Identities=31% Similarity=0.802 Sum_probs=12.1
Q ss_pred echh-cchhhHHHHHHh
Q psy11507 54 YGVA-SCEACKAFFKRT 69 (113)
Q Consensus 54 yGv~-~C~~C~~FFRRs 69 (113)
.|.. .|++|-.+|++.
T Consensus 17 ~g~~~LCn~Cg~~~kk~ 33 (36)
T PF00320_consen 17 NGNRTLCNACGLYYKKY 33 (36)
T ss_dssp TSEE-EEHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 3444 899999999764
No 53
>KOG3506|consensus
Probab=29.49 E-value=33 Score=21.00 Aligned_cols=30 Identities=27% Similarity=0.504 Sum_probs=22.0
Q ss_pred CCCCCCCcceEcCCCC-cceeechhcchhhH
Q psy11507 34 EEELPRRLCLVCGDVA-SGFHYGVASCEACK 63 (113)
Q Consensus 34 ~~~~~~~~C~VC~~~~-~g~hyGv~~C~~C~ 63 (113)
+-.+-...|.||.+.. ---.||...|.-|-
T Consensus 13 kfg~GsrsC~vCsn~~gLIrKYGL~vcr~cf 43 (56)
T KOG3506|consen 13 KFGQGSRSCRVCSNRHGLIRKYGLNVCRQCF 43 (56)
T ss_pred ccCCCCcceeeeccchhHHHHhhhHHhHHHH
Confidence 3344567899999764 44689999888774
No 54
>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=29.14 E-value=20 Score=18.59 Aligned_cols=21 Identities=33% Similarity=0.760 Sum_probs=14.6
Q ss_pred cceEcCCCCcceeechhcchhhH
Q psy11507 41 LCLVCGDVASGFHYGVASCEACK 63 (113)
Q Consensus 41 ~C~VC~~~~~g~hyGv~~C~~C~ 63 (113)
.|.||++...++. ...|..|.
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 4889988888873 34666654
No 55
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=28.64 E-value=31 Score=21.42 Aligned_cols=35 Identities=23% Similarity=0.497 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCCCCCcceEcCCCCcceeechhcchhhH
Q psy11507 26 RGSTDGIKEEELPRRLCLVCGDVASGFHYGVASCEACK 63 (113)
Q Consensus 26 ~~s~~~~~~~~~~~~~C~VC~~~~~g~hyGv~~C~~C~ 63 (113)
++++-..... .++..|.-||..+ +|---..|.+|.
T Consensus 4 GT~S~GKrnk-~tH~~CRRCGr~s--yhv~k~~CaaCG 38 (61)
T COG2126 4 GTPSFGKRNK-KTHIRCRRCGRRS--YHVRKKYCAACG 38 (61)
T ss_pred CCccccccCC-cceehhhhccchh--eeeccceecccC
Confidence 3344343333 6678899999887 676677888885
No 56
>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=28.22 E-value=44 Score=19.40 Aligned_cols=24 Identities=33% Similarity=0.955 Sum_probs=18.5
Q ss_pred cceEcCCC-Ccc-eeechhcchhhHH
Q psy11507 41 LCLVCGDV-ASG-FHYGVASCEACKA 64 (113)
Q Consensus 41 ~C~VC~~~-~~g-~hyGv~~C~~C~~ 64 (113)
.|.||++. ..| .-+|...|..|-.
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHHH
Confidence 38999975 446 4689999999963
No 57
>KOG0706|consensus
Probab=28.02 E-value=28 Score=29.63 Aligned_cols=31 Identities=26% Similarity=0.759 Sum_probs=25.4
Q ss_pred CCCcceEcCCCC---cceeechhcchhhHHHHHH
Q psy11507 38 PRRLCLVCGDVA---SGFHYGVASCEACKAFFKR 68 (113)
Q Consensus 38 ~~~~C~VC~~~~---~g~hyGv~~C~~C~~FFRR 68 (113)
..+.|.-|+.+. ....||+..|--|.+-+|.
T Consensus 22 ~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRn 55 (454)
T KOG0706|consen 22 ENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRN 55 (454)
T ss_pred CCceecccCCCCCCceeecceEEEEEecchhhhc
Confidence 467899999764 4579999999999998754
No 58
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=26.96 E-value=31 Score=21.20 Aligned_cols=32 Identities=22% Similarity=0.658 Sum_probs=20.8
Q ss_pred CCCcceEcCCCCcceeechhcc-hhhHHHHHHhHhh
Q psy11507 38 PRRLCLVCGDVASGFHYGVASC-EACKAFFKRTIQA 72 (113)
Q Consensus 38 ~~~~C~VC~~~~~g~hyGv~~C-~~C~~FFRRsv~~ 72 (113)
+++.|.+||.+--. .-..| ..|+.-+++...+
T Consensus 2 ~HkHC~~CG~~Ip~---~~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 2 PHKHCPVCGKPIPP---DESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CCCcCCcCCCcCCc---chhhhCHHHHHHHHHHHHH
Confidence 57899999976432 23345 5788777655443
No 59
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=26.49 E-value=29 Score=28.13 Aligned_cols=31 Identities=23% Similarity=0.596 Sum_probs=25.1
Q ss_pred CCCcceEcCCCC---cceeechhcchhhHHHHHH
Q psy11507 38 PRRLCLVCGDVA---SGFHYGVASCEACKAFFKR 68 (113)
Q Consensus 38 ~~~~C~VC~~~~---~g~hyGv~~C~~C~~FFRR 68 (113)
....|.-|+.+. ....|||+.|--|++-.|-
T Consensus 19 ~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRs 52 (319)
T COG5347 19 SNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRS 52 (319)
T ss_pred ccCccccCCCCCCceEecccCeEEEeecchhhhc
Confidence 356799999876 3479999999999998654
No 60
>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=25.29 E-value=29 Score=18.69 Aligned_cols=14 Identities=21% Similarity=0.589 Sum_probs=9.4
Q ss_pred CCCcceEcCCCCcc
Q psy11507 38 PRRLCLVCGDVASG 51 (113)
Q Consensus 38 ~~~~C~VC~~~~~g 51 (113)
++..|.||+.+...
T Consensus 17 ~p~~CP~Cg~~~~~ 30 (34)
T cd00729 17 APEKCPICGAPKEK 30 (34)
T ss_pred CCCcCcCCCCchHH
Confidence 35578888876543
No 61
>PHA03124 dUTPase; Provisional
Probab=23.92 E-value=44 Score=28.08 Aligned_cols=15 Identities=40% Similarity=1.023 Sum_probs=12.6
Q ss_pred hcchhhHHHHHHhHh
Q psy11507 57 ASCEACKAFFKRTIQ 71 (113)
Q Consensus 57 ~~C~~C~~FFRRsv~ 71 (113)
.-|.+|++||||...
T Consensus 191 ~~~~~~~~~~~~~~~ 205 (418)
T PHA03124 191 FGCMGCKAFYRRLFE 205 (418)
T ss_pred ccccchHHHHHHHHH
Confidence 359999999999865
No 62
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=23.62 E-value=53 Score=20.47 Aligned_cols=14 Identities=43% Similarity=1.082 Sum_probs=11.0
Q ss_pred CCCCCCcceEcCCC
Q psy11507 35 EELPRRLCLVCGDV 48 (113)
Q Consensus 35 ~~~~~~~C~VC~~~ 48 (113)
...+++.|.|||+.
T Consensus 4 ~v~PH~HC~VCg~a 17 (64)
T COG4068 4 GVVPHRHCVVCGKA 17 (64)
T ss_pred CCCCCccccccCCc
Confidence 34578899999975
No 63
>PF10705 Ycf15: Chloroplast protein precursor Ycf15 putative; InterPro: IPR019645 In some species of plants the ycf15 gene is probably not a protein-coding gene because the protein in these species has premature stop codons. Most of the members of the family are hypothetical or uncharacterised [].
Probab=23.40 E-value=25 Score=23.44 Aligned_cols=7 Identities=29% Similarity=0.653 Sum_probs=5.8
Q ss_pred CCCCCCc
Q psy11507 1 MLRWSSK 7 (113)
Q Consensus 1 ~~~~~~~ 7 (113)
||.|||-
T Consensus 33 mygwyel 39 (93)
T PF10705_consen 33 MYGWYEL 39 (93)
T ss_pred chhhhhc
Confidence 8999974
No 64
>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=20.34 E-value=50 Score=14.96 Aligned_cols=9 Identities=44% Similarity=0.744 Sum_probs=6.5
Q ss_pred HHHHHhHhh
Q psy11507 64 AFFKRTIQA 72 (113)
Q Consensus 64 ~FFRRsv~~ 72 (113)
+||+|....
T Consensus 3 GFFKR~~~~ 11 (15)
T PF00357_consen 3 GFFKRQRPP 11 (15)
T ss_dssp CHHHHHHHH
T ss_pred ccccccCcc
Confidence 589987654
No 65
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=20.21 E-value=43 Score=18.36 Aligned_cols=24 Identities=29% Similarity=0.552 Sum_probs=13.4
Q ss_pred CCcceEcCCCCcceeechhcchhh
Q psy11507 39 RRLCLVCGDVASGFHYGVASCEAC 62 (113)
Q Consensus 39 ~~~C~VC~~~~~g~hyGv~~C~~C 62 (113)
..+|.+|+..-....=|-..|..|
T Consensus 8 ~~~C~~C~~~~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 8 NEPCPVCGSRWFYSDDGFYYCDRC 31 (36)
T ss_pred CCcCCCCCCeEeEccCCEEEhhhC
Confidence 456999987633334444445444
No 66
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=20.14 E-value=35 Score=25.45 Aligned_cols=34 Identities=21% Similarity=0.562 Sum_probs=24.9
Q ss_pred CcceEcCCCCcc--eee-chhcchhhHHHHHHhHhhc
Q psy11507 40 RLCLVCGDVASG--FHY-GVASCEACKAFFKRTIQAR 73 (113)
Q Consensus 40 ~~C~VC~~~~~g--~hy-Gv~~C~~C~~FFRRsv~~~ 73 (113)
..|.+|.+...- +.. ++.-|..|.+.|.+....+
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~ 189 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK 189 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC
Confidence 469999866544 444 6788999999998765543
Done!