Query psy9231
Match_columns 134
No_of_seqs 190 out of 1200
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 22:15:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 100.0 1.5E-30 3.2E-35 214.3 0.5 75 60-134 18-92 (432)
2 cd06969 NR_DBD_NGFI-B DNA-bind 100.0 1.9E-29 4.1E-34 167.9 4.4 72 63-134 2-73 (75)
3 cd07156 NR_DBD_VDR_like The DN 100.0 1.2E-29 2.7E-34 167.5 2.5 71 64-134 1-71 (72)
4 cd06962 NR_DBD_FXR DNA-binding 100.0 2.7E-29 5.9E-34 170.5 4.3 73 62-134 2-74 (84)
5 cd06964 NR_DBD_RAR DNA-binding 100.0 2.4E-29 5.3E-34 171.1 3.6 75 60-134 3-77 (85)
6 cd06959 NR_DBD_EcR_like The DN 100.0 1.8E-29 3.8E-34 167.2 1.8 72 63-134 1-72 (73)
7 cd07154 NR_DBD_PNR_like The DN 100.0 4.7E-29 1E-33 165.1 3.8 71 64-134 1-72 (73)
8 cd06916 NR_DBD_like DNA-bindin 100.0 4.7E-29 1E-33 164.6 3.8 71 64-134 1-71 (72)
9 cd07172 NR_DBD_GR_PR DNA-bindi 100.0 4.6E-29 1E-33 167.2 3.4 74 61-134 2-75 (78)
10 cd06963 NR_DBD_GR_like The DNA 99.9 2.7E-29 5.8E-34 166.4 2.1 71 64-134 1-71 (73)
11 cd06958 NR_DBD_COUP_TF DNA-bin 99.9 4.3E-29 9.3E-34 165.3 2.0 71 64-134 1-71 (73)
12 cd07179 2DBD_NR_DBD2 The secon 99.9 2.9E-29 6.3E-34 166.6 0.9 71 64-134 1-71 (74)
13 cd06967 NR_DBD_TR2_like DNA-bi 99.9 1.1E-28 2.5E-33 168.4 3.8 74 61-134 3-76 (87)
14 cd06956 NR_DBD_RXR DNA-binding 99.9 2.1E-29 4.6E-34 168.4 0.1 72 63-134 2-73 (77)
15 cd07171 NR_DBD_ER DNA-binding 99.9 4.5E-29 9.7E-34 168.8 1.6 73 62-134 4-76 (82)
16 cd07160 NR_DBD_LXR DNA-binding 99.9 9.2E-29 2E-33 173.1 3.2 74 61-134 18-91 (101)
17 cd06970 NR_DBD_PNR DNA-binding 99.9 1.7E-28 3.6E-33 169.2 4.2 74 61-134 6-80 (92)
18 cd07158 NR_DBD_Ppar_like The D 99.9 5.9E-29 1.3E-33 164.5 1.4 71 64-134 1-72 (73)
19 cd06955 NR_DBD_VDR DNA-binding 99.9 2.7E-28 5.8E-33 172.3 4.5 74 61-134 6-79 (107)
20 cd07163 NR_DBD_TLX DNA-binding 99.9 2.1E-28 4.5E-33 168.7 3.8 75 60-134 5-81 (92)
21 cd07170 NR_DBD_ERR DNA-binding 99.9 8.3E-29 1.8E-33 172.2 1.6 73 62-134 5-77 (97)
22 cd07155 NR_DBD_ER_like DNA-bin 99.9 4.2E-29 9.2E-34 166.1 0.1 71 64-134 1-71 (75)
23 cd07161 NR_DBD_EcR DNA-binding 99.9 1.1E-28 2.4E-33 169.8 1.7 73 62-134 2-74 (91)
24 cd06961 NR_DBD_TR DNA-binding 99.9 8.8E-29 1.9E-33 168.3 1.2 72 63-134 1-72 (85)
25 cd06957 NR_DBD_PNR_like_2 DNA- 99.9 1.8E-28 3.8E-33 165.7 2.5 71 64-134 1-72 (82)
26 cd06960 NR_DBD_HNF4A DNA-bindi 99.9 1.7E-28 3.8E-33 163.4 2.3 71 64-134 1-71 (76)
27 KOG4846|consensus 99.9 9.3E-29 2E-33 206.4 0.8 79 56-134 127-206 (538)
28 cd07157 2DBD_NR_DBD1 The first 99.9 5.8E-28 1.3E-32 164.6 4.2 72 63-134 2-75 (86)
29 cd07166 NR_DBD_REV_ERB DNA-bin 99.9 2.6E-28 5.6E-33 167.3 2.3 74 61-134 3-77 (89)
30 cd07173 NR_DBD_AR DNA-binding 99.9 1.9E-28 4.1E-33 165.7 1.6 73 61-133 3-75 (82)
31 cd07168 NR_DBD_DHR4_like DNA-b 99.9 1.7E-28 3.7E-33 168.5 1.3 75 60-134 5-79 (90)
32 cd07164 NR_DBD_PNR_like_1 DNA- 99.9 2.5E-28 5.4E-33 163.5 1.8 71 64-134 1-71 (78)
33 cd07162 NR_DBD_PXR DNA-binding 99.9 2.6E-28 5.6E-33 166.6 1.7 72 63-134 1-72 (87)
34 cd07169 NR_DBD_GCNF_like DNA-b 99.9 2.3E-28 4.9E-33 167.9 0.7 75 60-134 5-79 (90)
35 smart00399 ZnF_C4 c4 zinc fing 99.9 9.2E-28 2E-32 157.5 3.5 70 63-132 1-70 (70)
36 cd06966 NR_DBD_CAR DNA-binding 99.9 4.3E-28 9.2E-33 167.7 2.0 72 63-134 2-73 (94)
37 cd06968 NR_DBD_ROR DNA-binding 99.9 6.6E-28 1.4E-32 167.1 1.5 74 61-134 5-78 (95)
38 cd07167 NR_DBD_Lrh-1_like The 99.9 3.8E-28 8.3E-33 167.7 -0.2 71 64-134 1-71 (93)
39 KOG4217|consensus 99.9 1.5E-27 3.3E-32 201.5 3.2 79 56-134 264-342 (605)
40 cd07165 NR_DBD_DmE78_like DNA- 99.9 4.7E-28 1E-32 163.3 0.0 71 64-134 1-71 (81)
41 cd06965 NR_DBD_Ppar DNA-bindin 99.9 4.8E-27 1E-31 159.4 2.7 70 63-134 1-71 (84)
42 PF00105 zf-C4: Zinc finger, C 99.9 1.3E-27 2.8E-32 156.4 -2.2 69 63-131 2-70 (70)
43 KOG4216|consensus 99.9 6.8E-27 1.5E-31 193.9 1.3 72 63-134 48-119 (479)
44 KOG4218|consensus 99.9 3.2E-25 6.9E-30 182.1 -0.2 75 60-134 14-88 (475)
45 PF10764 Gin: Inhibitor of sig 52.0 7.4 0.00016 23.3 0.8 23 63-85 1-25 (46)
46 PF09289 FOLN: Follistatin/Ost 45.5 8.5 0.00019 19.7 0.3 20 97-116 3-22 (22)
47 PRK00420 hypothetical protein; 40.3 16 0.00035 26.0 1.2 30 60-89 22-51 (112)
48 PF03107 C1_2: C1 domain; Int 38.3 16 0.00034 19.5 0.7 21 63-85 2-22 (30)
49 PF01412 ArfGap: Putative GTPa 37.7 3.5 7.7E-05 28.9 -2.5 31 60-90 12-45 (116)
50 PF13901 DUF4206: Domain of un 36.6 19 0.00041 27.8 1.2 30 62-91 153-185 (202)
51 PF10080 DUF2318: Predicted me 31.8 24 0.00052 24.6 1.0 28 62-89 36-63 (102)
52 PF03002 Somatostatin: Somatos 31.8 21 0.00046 17.3 0.5 10 83-92 6-15 (18)
53 PF00628 PHD: PHD-finger; Int 31.0 16 0.00034 21.3 -0.1 25 64-90 2-26 (51)
54 smart00401 ZnF_GATA zinc finge 29.5 18 0.00039 21.9 0.0 31 61-91 3-38 (52)
55 KOG3277|consensus 28.4 27 0.00058 26.5 0.8 26 63-88 81-114 (165)
56 smart00105 ArfGap Putative GTP 27.6 14 0.0003 25.7 -0.8 30 61-90 3-35 (112)
57 PF14260 zf-C4pol: C4-type zin 26.2 24 0.00051 22.4 0.1 27 61-91 45-73 (73)
58 TIGR00269 conserved hypothetic 26.1 26 0.00057 24.0 0.4 20 62-86 81-100 (104)
59 PRK12495 hypothetical protein; 21.7 51 0.0011 26.3 1.2 30 60-90 41-70 (226)
60 PTZ00218 40S ribosomal protein 21.6 35 0.00076 21.3 0.2 24 61-84 16-40 (54)
61 COG1997 RPL43A Ribosomal prote 20.4 50 0.0011 22.6 0.8 27 62-88 36-63 (89)
No 1
>KOG4215|consensus
Probab=99.96 E-value=1.5e-30 Score=214.28 Aligned_cols=75 Identities=52% Similarity=1.224 Sum_probs=72.9
Q ss_pred CCccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 60 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
....|.||||++.|.|||+.+|++||+||||+|.++..|.|+++.+|.|+++.|+.|||||||||+++||++|||
T Consensus 18 ~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAi 92 (432)
T KOG4215|consen 18 VAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAI 92 (432)
T ss_pred ccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhh
Confidence 466899999999999999999999999999999999999999999999999999999999999999999999997
No 2
>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=99.95 E-value=1.9e-29 Score=167.86 Aligned_cols=72 Identities=56% Similarity=1.224 Sum_probs=69.3
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+|.|||+.++++|||+.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|
T Consensus 2 ~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 73 (75)
T cd06969 2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVV 73 (75)
T ss_pred CCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHc
Confidence 599999999999999999999999999999988889999999999999999999999999999999999887
No 3
>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=99.95 E-value=1.2e-29 Score=167.52 Aligned_cols=71 Identities=42% Similarity=1.118 Sum_probs=68.5
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||++++++||||.+|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|
T Consensus 1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (72)
T cd07156 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence 78999999999999999999999999999988889999999999999999999999999999999999987
No 4
>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=99.95 E-value=2.7e-29 Score=170.48 Aligned_cols=73 Identities=49% Similarity=1.086 Sum_probs=69.8
Q ss_pred ccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 62 VLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 62 ~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+.|.|||++++++||||.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 74 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECL 74 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHc
Confidence 4699999999999999999999999999999988899999999999999999999999999999999999886
No 5
>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=99.95 E-value=2.4e-29 Score=171.05 Aligned_cols=75 Identities=47% Similarity=1.111 Sum_probs=70.5
Q ss_pred CCccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 60 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+..+|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 3 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 77 (85)
T cd06964 3 IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESV 77 (85)
T ss_pred cCCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHh
Confidence 345799999999999999999999999999999988889999999999999999999999999999999998876
No 6
>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=99.95 E-value=1.8e-29 Score=167.17 Aligned_cols=72 Identities=50% Similarity=1.061 Sum_probs=69.1
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||+++.|
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 599999999999999999999999999999988889999999999999999999999999999999999886
No 7
>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=99.95 E-value=4.7e-29 Score=165.07 Aligned_cols=71 Identities=73% Similarity=1.434 Sum_probs=67.8
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCccccee-cCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCK-ERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~-~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||+.++++|||+.+|+||++||||++..+..|.|. .+++|.|+...|..|++|||+|||++||++++|
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 78999999999999999999999999999988899998 678999999999999999999999999999987
No 8
>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=99.95 E-value=4.7e-29 Score=164.65 Aligned_cols=71 Identities=62% Similarity=1.349 Sum_probs=68.4
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||++++++||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|
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 78999999999999999999999999999988889999999999999999999999999999999999886
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=99.95 E-value=4.6e-29 Score=167.22 Aligned_cols=74 Identities=49% Similarity=1.027 Sum_probs=70.1
Q ss_pred CccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
...|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||+..||
T Consensus 2 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~ 75 (78)
T cd07172 2 QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGAR 75 (78)
T ss_pred CCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCcccc
Confidence 34699999999999999999999999999999999899999999999999999999999999999999999875
No 10
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=99.95 E-value=2.7e-29 Score=166.39 Aligned_cols=71 Identities=48% Similarity=1.036 Sum_probs=68.5
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||+.++++||||.+|++|++||||++..+..|.|..+++|.|+...|..|++|||+|||++||+++||
T Consensus 1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~ 71 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGAR 71 (73)
T ss_pred CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChhhc
Confidence 88999999999999999999999999999988889999999999999999999999999999999999986
No 11
>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=99.95 E-value=4.3e-29 Score=165.30 Aligned_cols=71 Identities=59% Similarity=1.246 Sum_probs=68.4
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|
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 88999999999999999999999999999988889999999999999999999999999999999999887
No 12
>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=99.95 E-value=2.9e-29 Score=166.56 Aligned_cols=71 Identities=42% Similarity=1.058 Sum_probs=68.6
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||++++++|||+.+|++|++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|
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 88999999999999999999999999999988899999999999999999999999999999999999987
No 13
>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=99.95 E-value=1.1e-28 Score=168.40 Aligned_cols=74 Identities=55% Similarity=1.200 Sum_probs=70.0
Q ss_pred CccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
.+.|.|||+.++++|||+.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 76 (87)
T cd06967 3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSV 76 (87)
T ss_pred CCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHh
Confidence 45699999999999999999999999999999988889999999999999999999999999999999998876
No 14
>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=99.95 E-value=2.1e-29 Score=168.36 Aligned_cols=72 Identities=54% Similarity=1.324 Sum_probs=69.1
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+|.|||++++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|
T Consensus 2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 73 (77)
T cd06956 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV 73 (77)
T ss_pred CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHh
Confidence 599999999999999999999999999999988999999999999999999999999999999999999876
No 15
>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=99.95 E-value=4.5e-29 Score=168.75 Aligned_cols=73 Identities=49% Similarity=1.078 Sum_probs=69.7
Q ss_pred ccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 62 VLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 62 ~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
..|.|||+.++++|||+.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 76 (82)
T cd07171 4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGI 76 (82)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHH
Confidence 4699999999999999999999999999999988899999999999999999999999999999999999876
No 16
>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=99.95 E-value=9.2e-29 Score=173.08 Aligned_cols=74 Identities=49% Similarity=1.101 Sum_probs=70.5
Q ss_pred CccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
...|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 91 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCV 91 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHh
Confidence 45799999999999999999999999999999988899999999999999999999999999999999999876
No 17
>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=99.95 E-value=1.7e-28 Score=169.21 Aligned_cols=74 Identities=62% Similarity=1.275 Sum_probs=69.3
Q ss_pred CccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecC-CceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKER-GHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~-~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
...|.|||+.++++|||+.+|+||++||||++..+..|.|..+ ++|.++...|..|++|||+|||++||++++|
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 80 (92)
T cd06970 6 GLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAV 80 (92)
T ss_pred CCCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHc
Confidence 3469999999999999999999999999999999899999986 8999999999999999999999999998875
No 18
>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=99.95 E-value=5.9e-29 Score=164.51 Aligned_cols=71 Identities=61% Similarity=1.299 Sum_probs=68.3
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCccc-ceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEY-VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~-~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||+.++++||||.+|++|++||||++..+..| .|..+++|.++...+..|++|||+|||++||++++|
T Consensus 1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 72 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAV 72 (73)
T ss_pred CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHc
Confidence 78999999999999999999999999999988888 899999999999999999999999999999999987
No 19
>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=99.95 E-value=2.7e-28 Score=172.32 Aligned_cols=74 Identities=38% Similarity=1.022 Sum_probs=70.1
Q ss_pred CccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
...|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 79 (107)
T cd06955 6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFI 79 (107)
T ss_pred CCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhc
Confidence 35699999999999999999999999999999988899999999999999999999999999999999999876
No 20
>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=99.95 E-value=2.1e-28 Score=168.67 Aligned_cols=75 Identities=67% Similarity=1.356 Sum_probs=69.6
Q ss_pred CCccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecC--CceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKER--GHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 60 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~--~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+...|.|||+.++++||||.+|+||++||||++..+..|.|... ++|.++...|..|++|||+|||++||++++|
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 81 (92)
T cd07163 5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAV 81 (92)
T ss_pred cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHh
Confidence 45679999999999999999999999999999998889999874 6899999999999999999999999999876
No 21
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=99.94 E-value=8.3e-29 Score=172.21 Aligned_cols=73 Identities=53% Similarity=1.126 Sum_probs=69.5
Q ss_pred ccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 62 VLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 62 ~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
..|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|
T Consensus 5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 77 (97)
T cd07170 5 RLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGV 77 (97)
T ss_pred CCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHc
Confidence 4699999999999999999999999999999988889999999999999999999999999999999998876
No 22
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=99.94 E-value=4.2e-29 Score=166.11 Aligned_cols=71 Identities=55% Similarity=1.143 Sum_probs=68.1
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||++++++|||+.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 71 (75)
T cd07155 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGV 71 (75)
T ss_pred CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHc
Confidence 88999999999999999999999999999988889999999999999999999999999999999999876
No 23
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=99.94 E-value=1.1e-28 Score=169.79 Aligned_cols=73 Identities=47% Similarity=1.042 Sum_probs=69.5
Q ss_pred ccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 62 VLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 62 ~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+.|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 74 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECV 74 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHc
Confidence 3699999999999999999999999999999988899999999999999999999999999999999999876
No 24
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=99.94 E-value=8.8e-29 Score=168.28 Aligned_cols=72 Identities=51% Similarity=1.188 Sum_probs=68.9
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+|.|||+.++++|||+.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (85)
T cd06961 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLV 72 (85)
T ss_pred CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHc
Confidence 499999999999999999999999999999988899999999999999999999999999999999998876
No 25
>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=99.94 E-value=1.8e-28 Score=165.73 Aligned_cols=71 Identities=59% Similarity=1.221 Sum_probs=67.2
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCccccee-cCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCK-ERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~-~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||+.++++||||.+|+||++||||++..+..|.|. .+++|.|+...+..|++|||+|||++||++++|
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 72 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAV 72 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHh
Confidence 88999999999999999999999999999988999998 468899999999999999999999999998876
No 26
>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=99.94 E-value=1.7e-28 Score=163.42 Aligned_cols=71 Identities=58% Similarity=1.313 Sum_probs=68.0
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||+.++++|||+.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v 71 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAV 71 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHc
Confidence 78999999999999999999999999999988889999999999999999999999999999999998876
No 27
>KOG4846|consensus
Probab=99.94 E-value=9.3e-29 Score=206.36 Aligned_cols=79 Identities=54% Similarity=1.127 Sum_probs=73.6
Q ss_pred ccccCCccceEcCcCCCceeecCccCcCCCceeeeeEecCccc-ceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 56 GITSMDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEY-VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 56 ~~~~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~-~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+....-.+|+||||+++||||||.+|++||+||||+|+.+..| .|-+..+|.|..+.|++|++|||+|||++||.++||
T Consensus 127 ~~~~~~~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaV 206 (538)
T KOG4846|consen 127 QIGKAISLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAV 206 (538)
T ss_pred cccceeEeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhh
Confidence 3444556899999999999999999999999999999999999 699999999999999999999999999999999987
No 28
>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=99.94 E-value=5.8e-28 Score=164.58 Aligned_cols=72 Identities=42% Similarity=0.877 Sum_probs=66.9
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCc--ccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNL--EYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~--~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
.|.|||+.++++||||.+|+||++||||++..+. .|.|..+++|.++...+..|++|||+|||++||+++++
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~ 75 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGP 75 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccc
Confidence 5999999999999999999999999999998654 78899999999999999999999999999999998764
No 29
>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=99.94 E-value=2.6e-28 Score=167.30 Aligned_cols=74 Identities=58% Similarity=1.206 Sum_probs=69.6
Q ss_pred CccceEcCcCCCceeecCccCcCCCceeeeeEecCccc-ceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEY-VCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~-~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
..+|.|||+.++++|||+.+|+||++||||++..+..| .|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 77 (89)
T cd07166 3 VVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAV 77 (89)
T ss_pred CCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHh
Confidence 45799999999999999999999999999999988888 599999999999999999999999999999998876
No 30
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=99.94 E-value=1.9e-28 Score=165.72 Aligned_cols=73 Identities=41% Similarity=0.969 Sum_probs=68.8
Q ss_pred CccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCC
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDA 133 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~a 133 (134)
...|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||+++.
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~ 75 (82)
T cd07173 3 QKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGA 75 (82)
T ss_pred CCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcCh
Confidence 4469999999999999999999999999999998888999999999999999999999999999999999764
No 31
>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=99.94 E-value=1.7e-28 Score=168.48 Aligned_cols=75 Identities=44% Similarity=1.029 Sum_probs=70.3
Q ss_pred CCccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 60 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
....|.|||+.++++|||+.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|
T Consensus 5 ~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 79 (90)
T cd07168 5 SPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAV 79 (90)
T ss_pred cCCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHh
Confidence 345799999999999999999999999999999988889999999999999999999999999999999998765
No 32
>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=99.94 E-value=2.5e-28 Score=163.53 Aligned_cols=71 Identities=86% Similarity=1.630 Sum_probs=68.1
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||+.++++|||+.+|++|++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 71 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAV 71 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHh
Confidence 88999999999999999999999999999988889999999999999999999999999999999998875
No 33
>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=99.94 E-value=2.6e-28 Score=166.57 Aligned_cols=72 Identities=42% Similarity=1.113 Sum_probs=68.8
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+|.|||+.++++|||+.+|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 72 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELI 72 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHc
Confidence 499999999999999999999999999999988889999999999999999999999999999999999876
No 34
>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=99.94 E-value=2.3e-28 Score=167.90 Aligned_cols=75 Identities=49% Similarity=1.073 Sum_probs=70.6
Q ss_pred CCccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 60 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
....|.|||+.++++||||.+|++|++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 79 (90)
T cd07169 5 EQRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAI 79 (90)
T ss_pred cCCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHh
Confidence 355799999999999999999999999999999988889999999999999999999999999999999998876
No 35
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.94 E-value=9.2e-28 Score=157.51 Aligned_cols=70 Identities=44% Similarity=1.046 Sum_probs=66.9
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRD 132 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~ 132 (134)
+|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||+++
T Consensus 1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 4999999999999999999999999999999888899999999999999999999999999999999975
No 36
>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=99.94 E-value=4.3e-28 Score=167.74 Aligned_cols=72 Identities=36% Similarity=0.923 Sum_probs=68.9
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
.|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 73 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWI 73 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHc
Confidence 599999999999999999999999999999988889999999999999999999999999999999998775
No 37
>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=99.94 E-value=6.6e-28 Score=167.09 Aligned_cols=74 Identities=53% Similarity=1.193 Sum_probs=70.1
Q ss_pred CccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
...|.|||+.+.++|||+.+|++|++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|
T Consensus 5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V 78 (95)
T cd06968 5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAV 78 (95)
T ss_pred ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhc
Confidence 34699999999999999999999999999999988889999999999999999999999999999999998876
No 38
>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=99.94 E-value=3.8e-28 Score=167.71 Aligned_cols=71 Identities=49% Similarity=1.138 Sum_probs=68.2
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||++++++||||.+|++|++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V 71 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAV 71 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHh
Confidence 89999999999999999999999999999999999999999999999999999999999999999998765
No 39
>KOG4217|consensus
Probab=99.93 E-value=1.5e-27 Score=201.49 Aligned_cols=79 Identities=51% Similarity=1.096 Sum_probs=73.9
Q ss_pred ccccCCccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 56 GITSMDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 56 ~~~~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+....+..|+||||.+..-||||.+|++||+||+|+|+++.+|+|..+++|.||+..|++|+||||||||+|||-+|.|
T Consensus 264 s~~~~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVV 342 (605)
T KOG4217|consen 264 SSLSAEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVV 342 (605)
T ss_pred cCCCccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhhe
Confidence 3334567899999999999999999999999999999999999999999999999999999999999999999998865
No 40
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=99.93 E-value=4.7e-28 Score=163.26 Aligned_cols=71 Identities=58% Similarity=1.245 Sum_probs=68.2
Q ss_pred ceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
|.|||+.++++|||+.+|++|++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++|
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V 71 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSV 71 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHc
Confidence 88999999999999999999999999999988889999999999999999999999999999999998876
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=99.93 E-value=4.8e-27 Score=159.43 Aligned_cols=70 Identities=56% Similarity=1.201 Sum_probs=64.8
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccc-eecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYV-CKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~-C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
.|.|||+.++++||||.+|+||++||||++..+..|. |... |.|+...+..|++|||+|||++||++++|
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v 71 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAI 71 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHc
Confidence 4999999999999999999999999999999888885 9753 99999999999999999999999998875
No 42
>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=99.92 E-value=1.3e-27 Score=156.42 Aligned_cols=69 Identities=52% Similarity=1.190 Sum_probs=62.3
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNR 131 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~ 131 (134)
.|.|||++++++||||.+|++|++||||++..+..+.|+.+++|.++...+..|++|||+|||++||++
T Consensus 2 ~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 2 KCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred CCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence 699999999999999999999999999999988889999999999999889999999999999999984
No 43
>KOG4216|consensus
Probab=99.92 E-value=6.8e-27 Score=193.94 Aligned_cols=72 Identities=54% Similarity=1.213 Sum_probs=70.6
Q ss_pred cceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
+|.||||+++|.||||.+|++||+||||+-..+..|.|.+..||.||...|++|++|||||||++||+++||
T Consensus 48 PCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAV 119 (479)
T KOG4216|consen 48 PCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAV 119 (479)
T ss_pred eeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhH
Confidence 599999999999999999999999999999999999999999999999999999999999999999999997
No 44
>KOG4218|consensus
Probab=99.90 E-value=3.2e-25 Score=182.14 Aligned_cols=75 Identities=49% Similarity=1.141 Sum_probs=72.7
Q ss_pred CCccceEcCcCCCceeecCccCcCCCceeeeeEecCcccceecCCceeecCCCCCCCcchhhHHHHHccCCCCCC
Q psy9231 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKRSIRRNLEYVCKERGHCIVDVTRRNQCQACRFSKCLQVKMNRDAM 134 (134)
Q Consensus 60 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrRtv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRf~KCl~vGM~~~aV 134 (134)
..++|.||||+.+|||||.++|++||+||+|+|+.++.|.|..+.+|.|++..|.+|.+|||||||.+||+.|||
T Consensus 14 l~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAV 88 (475)
T KOG4218|consen 14 LGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAV 88 (475)
T ss_pred cccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHH
Confidence 567899999999999999999999999999999999999999999999999999999999999999999999987
No 45
>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=52.03 E-value=7.4 Score=23.33 Aligned_cols=23 Identities=39% Similarity=1.037 Sum_probs=18.4
Q ss_pred cceEcCcCC-Ccee-ecCccCcCCC
Q psy9231 63 LCKVCGDKA-SGKH-YGVPSCDGCR 85 (134)
Q Consensus 63 ~C~VCg~~a-~g~h-yGv~sC~aCk 85 (134)
.|.||++.. .|.| ||...|..|-
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE 25 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCE 25 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHH
Confidence 389999875 4765 8889999985
No 46
>PF09289 FOLN: Follistatin/Osteonectin-like EGF domain; InterPro: IPR015369 This domain is predominantly found in osteonectin and follistatin. They adopt an EGF-like structure [, ]. Follistatin is involved in diverse activities from embryonic development to cell secretion. ; GO: 0005515 protein binding; PDB: 1LR7_A 1LR8_A 1LR9_A 2ARP_F 3B4V_H 2KCX_A 3SEK_C 2P6A_D 3HH2_C 2B0U_D ....
Probab=45.46 E-value=8.5 Score=19.70 Aligned_cols=20 Identities=30% Similarity=0.735 Sum_probs=12.9
Q ss_pred ccceecCCceeecCCCCCCC
Q psy9231 97 EYVCKERGHCIVDVTRRNQC 116 (134)
Q Consensus 97 ~~~C~~~~~C~i~~~~r~~C 116 (134)
.+.|+.+..|.++...+..|
T Consensus 3 n~~Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 3 NFHCKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp T---BTTEEEEEETTTCEEE
T ss_pred CcccCCCCEeeeCCCCCcCC
Confidence 35699999999987766544
No 47
>PRK00420 hypothetical protein; Validated
Probab=40.26 E-value=16 Score=25.99 Aligned_cols=30 Identities=20% Similarity=0.307 Sum_probs=24.7
Q ss_pred CCccceEcCcCCCceeecCccCcCCCceee
Q psy9231 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFK 89 (134)
Q Consensus 60 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFr 89 (134)
....|.+||.+-...+-|...|..|..+..
T Consensus 22 l~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCCcceecCCCceECCCCCCeee
Confidence 346799999988887888999999997653
No 48
>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=38.30 E-value=16 Score=19.52 Aligned_cols=21 Identities=33% Similarity=0.733 Sum_probs=15.5
Q ss_pred cceEcCcCCCceeecCccCcCCC
Q psy9231 63 LCKVCGDKASGKHYGVPSCDGCR 85 (134)
Q Consensus 63 ~C~VCg~~a~g~hyGv~sC~aCk 85 (134)
.|.||++...++. ...|+.|.
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 4889999888884 44677766
No 49
>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=37.73 E-value=3.5 Score=28.92 Aligned_cols=31 Identities=26% Similarity=0.678 Sum_probs=21.2
Q ss_pred CCccceEcCcCCC---ceeecCccCcCCCceeee
Q psy9231 60 MDVLCKVCGDKAS---GKHYGVPSCDGCRGFFKR 90 (134)
Q Consensus 60 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFrR 90 (134)
.+..|.-||.... ...||+..|..|++..|.
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 4667999998764 358999999999987543
No 50
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=36.64 E-value=19 Score=27.77 Aligned_cols=30 Identities=20% Similarity=0.661 Sum_probs=22.9
Q ss_pred ccceEcCcCCCceee---cCccCcCCCceeeee
Q psy9231 62 VLCKVCGDKASGKHY---GVPSCDGCRGFFKRS 91 (134)
Q Consensus 62 ~~C~VCg~~a~g~hy---Gv~sC~aCk~FFrRt 91 (134)
..|.+|.+...-|-| .+..|..|++.|.+.
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~ 185 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKS 185 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchh
Confidence 469999987665554 556799999998776
No 51
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=31.82 E-value=24 Score=24.60 Aligned_cols=28 Identities=25% Similarity=0.528 Sum_probs=21.3
Q ss_pred ccceEcCcCCCceeecCccCcCCCceee
Q psy9231 62 VLCKVCGDKASGKHYGVPSCDGCRGFFK 89 (134)
Q Consensus 62 ~~C~VCg~~a~g~hyGv~sC~aCk~FFr 89 (134)
..|.||++......=+.+.|.+|..-|.
T Consensus 36 daCeiC~~~GY~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 36 DACEICGPKGYYQEGDQLVCKNCGVRFN 63 (102)
T ss_pred EeccccCCCceEEECCEEEEecCCCEEe
Confidence 3599998777666667789999986553
No 52
>PF03002 Somatostatin: Somatostatin/Cortistatin family; InterPro: IPR018142 Somatostatin inhibits the release of the pituitary growth hormone, somatotropin and inhibits the release of glucagon and insulin from the pancreas of fasted animals. Cortistatin is a cortical neuropeptide with neuronal depressant and sleep-modulating properties [].; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=31.75 E-value=21 Score=17.32 Aligned_cols=10 Identities=40% Similarity=1.228 Sum_probs=7.5
Q ss_pred CCCceeeeeE
Q psy9231 83 GCRGFFKRSI 92 (134)
Q Consensus 83 aCk~FFrRtv 92 (134)
+|+.||..+.
T Consensus 6 ~CknffWK~~ 15 (18)
T PF03002_consen 6 GCKNFFWKTF 15 (18)
T ss_pred cccceeeccc
Confidence 6889987653
No 53
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=31.03 E-value=16 Score=21.30 Aligned_cols=25 Identities=28% Similarity=0.905 Sum_probs=16.8
Q ss_pred ceEcCcCCCceeecCccCcCCCceeee
Q psy9231 64 CKVCGDKASGKHYGVPSCDGCRGFFKR 90 (134)
Q Consensus 64 C~VCg~~a~g~hyGv~sC~aCk~FFrR 90 (134)
|.||+.. ...-..+.|..|...|..
T Consensus 2 C~vC~~~--~~~~~~i~C~~C~~~~H~ 26 (51)
T PF00628_consen 2 CPVCGQS--DDDGDMIQCDSCNRWYHQ 26 (51)
T ss_dssp BTTTTSS--CTTSSEEEBSTTSCEEET
T ss_pred CcCCCCc--CCCCCeEEcCCCChhhCc
Confidence 7788882 223345789999987743
No 54
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=29.47 E-value=18 Score=21.91 Aligned_cols=31 Identities=23% Similarity=0.598 Sum_probs=21.3
Q ss_pred CccceEcCcCCCc-e---eecC-ccCcCCCceeeee
Q psy9231 61 DVLCKVCGDKASG-K---HYGV-PSCDGCRGFFKRS 91 (134)
Q Consensus 61 ~~~C~VCg~~a~g-~---hyGv-~sC~aCk~FFrRt 91 (134)
...|..|+...+- . -.|. ..|++|..+|++.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~ 38 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKH 38 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHc
Confidence 3468888876542 2 3454 7799999998764
No 55
>KOG3277|consensus
Probab=28.42 E-value=27 Score=26.48 Aligned_cols=26 Identities=35% Similarity=0.908 Sum_probs=19.9
Q ss_pred cceEcCcCCC------ceeecCc--cCcCCCcee
Q psy9231 63 LCKVCGDKAS------GKHYGVP--SCDGCRGFF 88 (134)
Q Consensus 63 ~C~VCg~~a~------g~hyGv~--sC~aCk~FF 88 (134)
.|.||+.+.+ .|+-|+. .|.+|+.+.
T Consensus 81 TCkvCntRs~ktisk~AY~~GvVivqC~gC~~~H 114 (165)
T KOG3277|consen 81 TCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH 114 (165)
T ss_pred EeeccCCccccccChhhhhCceEEEECCCCccce
Confidence 3999998764 3677765 799999864
No 56
>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=27.58 E-value=14 Score=25.74 Aligned_cols=30 Identities=27% Similarity=0.592 Sum_probs=24.0
Q ss_pred CccceEcCcCCC---ceeecCccCcCCCceeee
Q psy9231 61 DVLCKVCGDKAS---GKHYGVPSCDGCRGFFKR 90 (134)
Q Consensus 61 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFrR 90 (134)
+..|.-|+.... ...||+..|..|.+..|.
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~ 35 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHRS 35 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHHh
Confidence 557999998653 468999999999987654
No 57
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=26.19 E-value=24 Score=22.40 Aligned_cols=27 Identities=30% Similarity=0.740 Sum_probs=17.4
Q ss_pred CccceEcCcCCCceeecCccCcC--CCceeeee
Q psy9231 61 DVLCKVCGDKASGKHYGVPSCDG--CRGFFKRS 91 (134)
Q Consensus 61 ~~~C~VCg~~a~g~hyGv~sC~a--Ck~FFrRt 91 (134)
...|..|. +...+...|.+ |..||+|.
T Consensus 45 ~~iC~~C~----~~~~~~~~C~s~DCpV~Y~R~ 73 (73)
T PF14260_consen 45 WTICQSCS----GSLHEEIECDSLDCPVFYERV 73 (73)
T ss_pred HHHHHHhc----CcCCCCCcccCCCCCcceeeC
Confidence 34577777 44344555655 88998874
No 58
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=26.09 E-value=26 Score=23.99 Aligned_cols=20 Identities=35% Similarity=0.974 Sum_probs=15.8
Q ss_pred ccceEcCcCCCceeecCccCcCCCc
Q psy9231 62 VLCKVCGDKASGKHYGVPSCDGCRG 86 (134)
Q Consensus 62 ~~C~VCg~~a~g~hyGv~sC~aCk~ 86 (134)
..|.+||.++++- .|.+|+.
T Consensus 81 ~~C~~CG~pss~~-----iC~~C~l 100 (104)
T TIGR00269 81 RRCERCGEPTSGR-----ICKACKF 100 (104)
T ss_pred CcCCcCcCcCCcc-----ccHhhhh
Confidence 4599999999763 7888863
No 59
>PRK12495 hypothetical protein; Provisional
Probab=21.74 E-value=51 Score=26.31 Aligned_cols=30 Identities=23% Similarity=0.507 Sum_probs=23.8
Q ss_pred CCccceEcCcCCCceeecCccCcCCCceeee
Q psy9231 60 MDVLCKVCGDKASGKHYGVPSCDGCRGFFKR 90 (134)
Q Consensus 60 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFrR 90 (134)
....|.+||.+...+ =|+..|-.|...+.+
T Consensus 41 sa~hC~~CG~PIpa~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIFRH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCcccCC-CCeeECCCCCCcccc
Confidence 455799999998743 699999999977654
No 60
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=21.61 E-value=35 Score=21.26 Aligned_cols=24 Identities=29% Similarity=0.912 Sum_probs=18.2
Q ss_pred CccceEcCcCCC-ceeecCccCcCC
Q psy9231 61 DVLCKVCGDKAS-GKHYGVPSCDGC 84 (134)
Q Consensus 61 ~~~C~VCg~~a~-g~hyGv~sC~aC 84 (134)
...|.|||.+.. -..||...|+-|
T Consensus 16 sr~C~vCg~~~gliRkygL~~CRqC 40 (54)
T PTZ00218 16 SRQCRVCSNRHGLIRKYGLNVCRQC 40 (54)
T ss_pred CCeeecCCCcchhhhhcCcchhhHH
Confidence 456999999753 357888888777
No 61
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=20.43 E-value=50 Score=22.62 Aligned_cols=27 Identities=26% Similarity=0.643 Sum_probs=21.4
Q ss_pred ccceEcCcCCC-ceeecCccCcCCCcee
Q psy9231 62 VLCKVCGDKAS-GKHYGVPSCDGCRGFF 88 (134)
Q Consensus 62 ~~C~VCg~~a~-g~hyGv~sC~aCk~FF 88 (134)
-.|..|+.... -...|++.|+.|..-|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 35999999864 3578999999998665
Done!