Query psy16683
Match_columns 139
No_of_seqs 187 out of 1138
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 19:19:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16683.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16683hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07166 NR_DBD_REV_ERB DNA-bin 100.0 8.4E-32 1.8E-36 181.3 3.2 86 1-86 2-87 (89)
2 cd06964 NR_DBD_RAR DNA-binding 100.0 6E-31 1.3E-35 175.8 3.4 82 1-83 3-84 (85)
3 cd07163 NR_DBD_TLX DNA-binding 100.0 1.2E-30 2.6E-35 176.7 3.8 82 1-83 5-88 (92)
4 cd06967 NR_DBD_TR2_like DNA-bi 100.0 2.5E-30 5.4E-35 173.5 3.4 81 2-83 3-83 (87)
5 cd06957 NR_DBD_PNR_like_2 DNA- 100.0 3.2E-30 6.9E-35 171.2 3.8 78 5-83 1-79 (82)
6 cd06965 NR_DBD_Ppar DNA-bindin 100.0 2.7E-30 5.9E-35 172.3 3.3 81 4-86 1-81 (84)
7 cd06961 NR_DBD_TR DNA-binding 100.0 1.7E-30 3.6E-35 173.6 1.8 79 4-83 1-79 (85)
8 cd06970 NR_DBD_PNR DNA-binding 100.0 3.1E-30 6.8E-35 174.5 3.1 80 3-83 7-87 (92)
9 cd07168 NR_DBD_DHR4_like DNA-b 100.0 3.8E-30 8.2E-35 173.6 2.3 81 2-83 6-86 (90)
10 cd07170 NR_DBD_ERR DNA-binding 100.0 3.8E-30 8.3E-35 175.6 2.3 80 3-83 5-84 (97)
11 cd06956 NR_DBD_RXR DNA-binding 100.0 1.8E-30 3.9E-35 170.6 0.6 76 4-80 2-77 (77)
12 cd06960 NR_DBD_HNF4A DNA-bindi 100.0 5.2E-30 1.1E-34 168.0 2.8 76 5-81 1-76 (76)
13 cd07157 2DBD_NR_DBD1 The first 100.0 9.7E-30 2.1E-34 170.3 3.9 81 3-83 1-82 (86)
14 cd07164 NR_DBD_PNR_like_1 DNA- 100.0 4.5E-30 9.7E-35 169.0 2.2 77 5-82 1-77 (78)
15 cd07171 NR_DBD_ER DNA-binding 100.0 2.7E-30 5.9E-35 171.5 1.0 79 2-81 3-81 (82)
16 cd07155 NR_DBD_ER_like DNA-bin 100.0 3.2E-30 6.8E-35 168.6 1.0 75 5-80 1-75 (75)
17 cd07165 NR_DBD_DmE78_like DNA- 100.0 4.8E-30 1E-34 170.0 1.7 78 5-83 1-78 (81)
18 cd06968 NR_DBD_ROR DNA-binding 100.0 1.2E-29 2.6E-34 172.7 3.4 84 2-86 5-88 (95)
19 cd07160 NR_DBD_LXR DNA-binding 100.0 7.2E-30 1.6E-34 175.4 1.7 81 2-83 18-98 (101)
20 cd07169 NR_DBD_GCNF_like DNA-b 100.0 1.1E-29 2.4E-34 171.3 2.1 81 2-83 6-86 (90)
21 cd07161 NR_DBD_EcR DNA-binding 100.0 7.7E-30 1.7E-34 172.4 1.2 80 3-83 2-81 (91)
22 cd06966 NR_DBD_CAR DNA-binding 100.0 1.7E-29 3.6E-34 171.7 2.7 80 3-83 1-80 (94)
23 KOG4215|consensus 100.0 3.5E-30 7.6E-35 207.7 -1.2 82 2-84 19-100 (432)
24 cd06969 NR_DBD_NGFI-B DNA-bind 100.0 2.6E-29 5.6E-34 164.3 3.0 75 3-78 1-75 (75)
25 cd06962 NR_DBD_FXR DNA-binding 100.0 2E-29 4.4E-34 168.0 2.4 79 3-82 2-80 (84)
26 KOG4216|consensus 99.9 2.3E-29 5E-34 204.2 1.3 84 3-87 47-130 (479)
27 cd07179 2DBD_NR_DBD2 The secon 99.9 2E-29 4.3E-34 164.5 0.8 74 5-79 1-74 (74)
28 cd07167 NR_DBD_Lrh-1_like The 99.9 2.8E-29 6E-34 170.2 1.5 78 5-83 1-78 (93)
29 cd07154 NR_DBD_PNR_like The DN 99.9 9.3E-29 2E-33 160.9 2.9 72 5-77 1-73 (73)
30 cd06916 NR_DBD_like DNA-bindin 99.9 1.1E-28 2.4E-33 160.1 3.0 72 5-77 1-72 (72)
31 cd07158 NR_DBD_Ppar_like The D 99.9 7.3E-29 1.6E-33 161.4 1.8 73 5-77 1-73 (73)
32 cd06955 NR_DBD_VDR DNA-binding 99.9 1.3E-28 2.9E-33 170.6 3.1 79 2-81 6-84 (107)
33 cd06958 NR_DBD_COUP_TF DNA-bin 99.9 9.1E-29 2E-33 160.9 1.7 72 5-77 1-72 (73)
34 cd07156 NR_DBD_VDR_like The DN 99.9 1.2E-28 2.6E-33 160.0 1.8 71 5-76 1-71 (72)
35 KOG4846|consensus 99.9 2.2E-29 4.8E-34 205.7 -2.2 83 3-85 133-215 (538)
36 cd06959 NR_DBD_EcR_like The DN 99.9 1.9E-28 4.1E-33 159.4 1.4 73 4-77 1-73 (73)
37 cd07172 NR_DBD_GR_PR DNA-bindi 99.9 3.7E-28 8E-33 159.9 2.1 74 3-77 3-76 (78)
38 cd07162 NR_DBD_PXR DNA-binding 99.9 1.7E-28 3.7E-33 164.6 0.5 78 4-82 1-78 (87)
39 cd07173 NR_DBD_AR DNA-binding 99.9 3.2E-28 7E-33 161.5 1.2 74 2-76 3-76 (82)
40 cd06963 NR_DBD_GR_like The DNA 99.9 3.8E-28 8.2E-33 158.0 1.5 72 5-77 1-72 (73)
41 smart00399 ZnF_C4 c4 zinc fing 99.9 4.3E-27 9.4E-32 151.8 2.8 70 4-74 1-70 (70)
42 PF00105 zf-C4: Zinc finger, C 99.9 2.4E-26 5.3E-31 148.1 -1.4 69 3-72 1-69 (70)
43 KOG4217|consensus 99.9 4.1E-24 8.9E-29 177.1 -1.3 76 3-79 270-345 (605)
44 KOG4218|consensus 99.9 7.6E-24 1.7E-28 170.3 -1.2 80 2-82 15-94 (475)
45 PF01412 ArfGap: Putative GTPa 72.7 0.65 1.4E-05 32.2 -1.3 30 2-31 13-45 (116)
46 PF03107 C1_2: C1 domain; Int 64.3 3.7 8E-05 21.6 0.9 21 4-26 2-22 (30)
47 smart00105 ArfGap Putative GTP 63.7 2.4 5.1E-05 29.2 0.1 30 2-31 3-35 (112)
48 PRK00420 hypothetical protein; 48.1 12 0.00025 26.2 1.4 27 2-28 23-49 (112)
49 PF15446 zf-PHD-like: PHD/FYVE 47.8 17 0.00037 27.3 2.3 29 4-32 1-30 (175)
50 KOG3277|consensus 43.0 9.9 0.00021 28.1 0.5 26 4-29 81-114 (165)
51 COG1997 RPL43A Ribosomal prote 43.0 14 0.00029 24.8 1.1 27 3-29 36-63 (89)
52 PF00628 PHD: PHD-finger; Int 42.4 11 0.00024 21.6 0.6 24 4-29 1-24 (51)
53 PF03002 Somatostatin: Somatos 39.8 13 0.00029 17.5 0.5 10 24-33 6-15 (18)
54 PRK08359 transcription factor; 39.5 9.8 0.00021 28.6 0.0 30 2-31 6-42 (176)
55 PF10080 DUF2318: Predicted me 38.7 17 0.00038 24.8 1.1 25 5-29 38-62 (102)
56 PF07649 C1_3: C1-like domain; 37.7 16 0.00035 18.9 0.7 15 4-18 2-17 (30)
57 PF10764 Gin: Inhibitor of sig 36.3 18 0.0004 21.1 0.8 24 4-27 1-26 (46)
58 COG5347 GTPase-activating prot 36.0 16 0.00034 30.0 0.7 30 2-31 20-52 (319)
59 KOG0703|consensus 35.9 20 0.00043 29.1 1.2 31 2-32 25-58 (287)
60 PRK06424 transcription factor; 35.7 13 0.00029 26.9 0.2 25 5-30 3-34 (144)
61 PF09289 FOLN: Follistatin/Ost 35.6 13 0.00029 18.4 0.1 19 40-58 4-22 (22)
62 TIGR03655 anti_R_Lar restricti 35.2 31 0.00067 20.3 1.7 15 3-17 2-16 (53)
63 PF08273 Prim_Zn_Ribbon: Zinc- 34.9 24 0.00053 20.0 1.2 23 3-25 4-32 (40)
64 PHA03124 dUTPase; Provisional 31.6 10 0.00022 32.0 -1.0 17 18-34 189-205 (418)
65 smart00778 Prim_Zn_Ribbon Zinc 31.0 31 0.00066 19.2 1.1 9 3-11 4-12 (37)
66 cd00729 rubredoxin_SM Rubredox 27.0 28 0.0006 18.8 0.5 7 5-11 5-11 (34)
67 PF01286 XPA_N: XPA protein N- 26.9 15 0.00033 20.1 -0.6 24 3-26 4-31 (34)
68 PLN03114 ADP-ribosylation fact 26.4 31 0.00067 29.0 0.9 31 2-32 22-55 (395)
69 TIGR00270 conserved hypothetic 26.3 24 0.00051 25.8 0.2 25 4-28 2-33 (154)
70 PF01780 Ribosomal_L37ae: Ribo 26.1 24 0.00052 23.7 0.2 25 4-28 37-62 (90)
71 TIGR00009 L28 ribosomal protei 23.9 40 0.00086 20.4 0.8 12 1-12 1-12 (56)
72 PF01753 zf-MYND: MYND finger; 23.7 48 0.001 17.8 1.1 18 5-28 1-18 (37)
73 PTZ00255 60S ribosomal protein 23.2 54 0.0012 22.0 1.4 24 4-27 38-62 (90)
74 CHL00112 rpl28 ribosomal prote 23.1 43 0.00093 20.9 0.9 15 1-15 1-16 (63)
75 PF04216 FdhE: Protein involve 23.0 35 0.00076 27.2 0.6 13 15-27 207-219 (290)
76 smart00401 ZnF_GATA zinc finge 22.6 37 0.00081 20.1 0.5 31 2-32 3-38 (52)
77 PLN03119 putative ADP-ribosyla 22.5 44 0.00095 29.9 1.1 31 2-32 23-56 (648)
78 smart00249 PHD PHD zinc finger 22.2 46 0.00099 17.8 0.8 24 4-29 1-24 (47)
79 smart00154 ZnF_AN1 AN1-like Zi 21.8 52 0.0011 18.3 1.0 22 5-29 1-22 (39)
80 PLN03131 hypothetical protein; 21.8 44 0.00095 30.1 1.0 31 2-32 23-56 (705)
81 PLN02189 cellulose synthase 21.1 45 0.00097 31.7 0.9 22 3-26 35-60 (1040)
82 PF03884 DUF329: Domain of unk 20.8 15 0.00034 22.5 -1.4 26 1-26 1-29 (57)
83 PF04438 zf-HIT: HIT zinc fing 20.8 35 0.00077 17.9 0.1 19 2-26 2-20 (30)
84 cd02249 ZZ Zinc finger, ZZ typ 20.6 69 0.0015 18.1 1.4 13 5-17 3-15 (46)
85 COG4393 Predicted membrane pro 20.4 40 0.00087 28.2 0.4 23 5-27 337-359 (405)
86 PF06147 DUF968: Protein of un 20.2 50 0.0011 25.1 0.9 16 2-17 127-143 (200)
No 1
>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=99.97 E-value=8.4e-32 Score=181.32 Aligned_cols=86 Identities=47% Similarity=0.972 Sum_probs=78.5
Q ss_pred CCCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCC
Q psy16683 1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGR 80 (139)
Q Consensus 1 ~~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R 80 (139)
|..+|.|||++++|+||||++|+||++||||++..+..+..|..+++|.++...+..|++|||+||+++||++++||++|
T Consensus 2 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r 81 (89)
T cd07166 2 MVVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGR 81 (89)
T ss_pred CCCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCC
Confidence 57789999999999999999999999999999987655436998999999999999999999999999999999999999
Q ss_pred CCchhh
Q psy16683 81 RSNWFK 86 (139)
Q Consensus 81 ~~~~~k 86 (139)
++..+|
T Consensus 82 ~~~~~~ 87 (89)
T cd07166 82 IPKREK 87 (89)
T ss_pred CCCccc
Confidence 997543
No 2
>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=99.96 E-value=6e-31 Score=175.77 Aligned_cols=82 Identities=43% Similarity=0.948 Sum_probs=75.6
Q ss_pred CCCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCC
Q psy16683 1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGR 80 (139)
Q Consensus 1 ~~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R 80 (139)
+..+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||++|
T Consensus 3 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R 81 (85)
T cd06964 3 IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKN-MVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDR 81 (85)
T ss_pred cCCCCcccCCcCcccEECcceeeeeeeEEeeeecCC-CCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccc
Confidence 356899999999999999999999999999999864 4568998999999999999999999999999999999999999
Q ss_pred CCc
Q psy16683 81 RSN 83 (139)
Q Consensus 81 ~~~ 83 (139)
+++
T Consensus 82 ~~~ 84 (85)
T cd06964 82 NKK 84 (85)
T ss_pred cCC
Confidence 974
No 3
>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=99.96 E-value=1.2e-30 Score=176.67 Aligned_cols=82 Identities=38% Similarity=0.920 Sum_probs=75.0
Q ss_pred CCCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccC--CccccccccCcccccccccccceeecccccCccc
Q psy16683 1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKN--NNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRY 78 (139)
Q Consensus 1 ~~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~--~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~ 78 (139)
++.+|.|||++++|+||||++|+||++||||++..+. .+.|.. ++.|.++...+..|++|||+||+++||++++||+
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~-~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~ 83 (92)
T cd07163 5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNR-QYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQH 83 (92)
T ss_pred cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCC-CcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhc
Confidence 3678999999999999999999999999999998654 468986 4699999999999999999999999999999999
Q ss_pred CCCCc
Q psy16683 79 GRRSN 83 (139)
Q Consensus 79 ~R~~~ 83 (139)
+|++.
T Consensus 84 ~r~p~ 88 (92)
T cd07163 84 ERGPR 88 (92)
T ss_pred ccCcC
Confidence 99985
No 4
>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=99.96 E-value=2.5e-30 Score=173.48 Aligned_cols=81 Identities=42% Similarity=0.929 Sum_probs=75.2
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
..+|.|||++++|+||||++|+||++||||++..+ ..+.|..++.|.++...+..|++|||+||+++||++++||++||
T Consensus 3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~ 81 (87)
T cd06967 3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKN-LGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERK 81 (87)
T ss_pred CCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCC-CCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccC
Confidence 35799999999999999999999999999999864 45689999999999999999999999999999999999999999
Q ss_pred Cc
Q psy16683 82 SN 83 (139)
Q Consensus 82 ~~ 83 (139)
+.
T Consensus 82 ~~ 83 (87)
T cd06967 82 PI 83 (87)
T ss_pred CC
Confidence 84
No 5
>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=99.96 E-value=3.2e-30 Score=171.25 Aligned_cols=78 Identities=40% Similarity=0.929 Sum_probs=72.5
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCccccc-CCccccccccCcccccccccccceeecccccCcccCCCCc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECK-NNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSN 83 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~-~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~~ 83 (139)
|.|||++++|+||||++|+||++||||++..+ ..+.|. .++.|.++...+..|++|||+||+++||++++||++|++.
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~-~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~ 79 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKG-IIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPR 79 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCC-CceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcC
Confidence 89999999999999999999999999999864 457898 5689999999999999999999999999999999999985
No 6
>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=99.96 E-value=2.7e-30 Score=172.25 Aligned_cols=81 Identities=46% Similarity=0.972 Sum_probs=72.7
Q ss_pred cCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCCc
Q psy16683 4 TCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSN 83 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~~ 83 (139)
+|.|||++++|+||||++|+||++||||++..+..+..|.. .|.++...+..|++|||+||+++||++++||++|++.
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~--~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~ 78 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDL--SCKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPR 78 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCcccccc--CCCcCccccccccchhhhhhhhccCCHHHcccCCCCc
Confidence 59999999999999999999999999999987554335865 3999999999999999999999999999999999997
Q ss_pred hhh
Q psy16683 84 WFK 86 (139)
Q Consensus 84 ~~k 86 (139)
.+|
T Consensus 79 ~~~ 81 (84)
T cd06965 79 VEK 81 (84)
T ss_pred hhh
Confidence 554
No 7
>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=99.96 E-value=1.7e-30 Score=173.65 Aligned_cols=79 Identities=41% Similarity=0.920 Sum_probs=74.3
Q ss_pred cCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCCc
Q psy16683 4 TCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSN 83 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~~ 83 (139)
+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||++|++.
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~ 79 (85)
T cd06961 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKK-LSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRG 79 (85)
T ss_pred CCceeCCcCcceEEChhhhhhhhHhhHhhhccC-CccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCcc
Confidence 699999999999999999999999999999865 4568999999999999999999999999999999999999999985
No 8
>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=99.96 E-value=3.1e-30 Score=174.55 Aligned_cols=80 Identities=38% Similarity=0.930 Sum_probs=74.1
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCC-ccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNN-NECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~-~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
.+|.|||++++|+||||.+|+||++||||++..+ ..+.|..+ ++|.++...+..|++|||+||+++||++++||.+||
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~-~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~ 85 (92)
T cd06970 7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRK-LIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQ 85 (92)
T ss_pred CCCeecCCcCcccEECccEEeeeeeEeeeeeecC-CCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccC
Confidence 4699999999999999999999999999999864 45689875 899999989999999999999999999999999999
Q ss_pred Cc
Q psy16683 82 SN 83 (139)
Q Consensus 82 ~~ 83 (139)
+.
T Consensus 86 ~~ 87 (92)
T cd06970 86 PR 87 (92)
T ss_pred cc
Confidence 85
No 9
>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=99.96 E-value=3.8e-30 Score=173.58 Aligned_cols=81 Identities=38% Similarity=0.877 Sum_probs=75.4
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
..+|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||++++||++|+
T Consensus 6 ~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~-~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~ 84 (90)
T cd07168 6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKR-VYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRM 84 (90)
T ss_pred CCCCcccCCcCcceEECceehhhhhHhhhhhhcCCC-CccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccC
Confidence 467999999999999999999999999999998644 5689999999999999999999999999999999999999999
Q ss_pred Cc
Q psy16683 82 SN 83 (139)
Q Consensus 82 ~~ 83 (139)
+.
T Consensus 85 ~~ 86 (90)
T cd07168 85 PG 86 (90)
T ss_pred CC
Confidence 84
No 10
>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=99.96 E-value=3.8e-30 Score=175.60 Aligned_cols=80 Identities=45% Similarity=0.945 Sum_probs=74.3
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRS 82 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~ 82 (139)
.+|.|||++++|+||||++|+||++||||++..+ ..+.|..++.|.++...+..|++|||+||+++||++++||++|+.
T Consensus 5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~ 83 (97)
T cd07170 5 RLCLVCGDIASGYHYGVASCEACKAFFKRTIQGN-IEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVR 83 (97)
T ss_pred CCCeecCCcCcceEECceeehhhhHHHHHHhccC-CceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCC
Confidence 5699999999999999999999999999999865 456899999999999999999999999999999999999999987
Q ss_pred c
Q psy16683 83 N 83 (139)
Q Consensus 83 ~ 83 (139)
.
T Consensus 84 ~ 84 (97)
T cd07170 84 G 84 (97)
T ss_pred C
Confidence 4
No 11
>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=99.96 E-value=1.8e-30 Score=170.56 Aligned_cols=76 Identities=39% Similarity=1.017 Sum_probs=71.4
Q ss_pred cCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCC
Q psy16683 4 TCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGR 80 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R 80 (139)
+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||++|
T Consensus 2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKD-LTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred CCcccCCcCcceEECceeehhHHHHHHHHhhCC-CccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 699999999999999999999999999999864 4568998999999999999999999999999999999999987
No 12
>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=99.96 E-value=5.2e-30 Score=167.95 Aligned_cols=76 Identities=39% Similarity=0.966 Sum_probs=71.6
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
|.|||++++|+||||++|+||++||||++..+. .+.|..++.|.++...+..|++|||+||+++||++++||.+||
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~-~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNR-TYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCC-ceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 899999999999999999999999999998655 5689988999999999999999999999999999999999997
No 13
>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=99.96 E-value=9.7e-30 Score=170.29 Aligned_cols=81 Identities=68% Similarity=1.296 Sum_probs=74.3
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCC-CcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLP-SISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~-~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
.+|.|||++++|+||||++|+||++||||++..+. ..+.|..+++|.++...+..|++|||+||+++||++++++++|+
T Consensus 1 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~ 80 (86)
T cd07157 1 QTCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRR 80 (86)
T ss_pred CCCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCccccccccc
Confidence 37999999999999999999999999999987543 36789999999999989999999999999999999999999999
Q ss_pred Cc
Q psy16683 82 SN 83 (139)
Q Consensus 82 ~~ 83 (139)
..
T Consensus 81 ~~ 82 (86)
T cd07157 81 SD 82 (86)
T ss_pred cc
Confidence 74
No 14
>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=99.96 E-value=4.5e-30 Score=169.05 Aligned_cols=77 Identities=38% Similarity=0.935 Sum_probs=72.7
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCC
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRS 82 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~ 82 (139)
|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||++||+
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 77 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRN-LAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP 77 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCC-CCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence 88999999999999999999999999999865 456899999999999999999999999999999999999999997
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=99.96 E-value=2.7e-30 Score=171.50 Aligned_cols=79 Identities=48% Similarity=1.018 Sum_probs=73.5
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
+.+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||++|.
T Consensus 3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~ 81 (82)
T cd07171 3 THFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGH-NDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERR 81 (82)
T ss_pred CCCCeecCCcCcceEECceeehhhHHhHHHHeeCC-CceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhhc
Confidence 46899999999999999999999999999999874 45689999999999999999999999999999999999999875
No 16
>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=99.96 E-value=3.2e-30 Score=168.61 Aligned_cols=75 Identities=48% Similarity=1.026 Sum_probs=70.6
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCC
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGR 80 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R 80 (139)
|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||++++||++|
T Consensus 1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~-~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNL-GYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred CcccCccCcceEEChhhhhhhHHHHHHHhhCCC-ceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 899999999999999999999999999998654 568999999999999999999999999999999999999987
No 17
>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=99.95 E-value=4.8e-30 Score=170.03 Aligned_cols=78 Identities=49% Similarity=1.047 Sum_probs=73.4
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCCc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSN 83 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~~ 83 (139)
|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||++|++.
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~-~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~ 78 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQ-IEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPN 78 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccC-CceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCc
Confidence 89999999999999999999999999999864 4568999999999999999999999999999999999999999985
No 18
>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=99.95 E-value=1.2e-29 Score=172.65 Aligned_cols=84 Identities=43% Similarity=0.991 Sum_probs=77.4
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
+.+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||++|.
T Consensus 5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~ 83 (95)
T cd06968 5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNN-VSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRM 83 (95)
T ss_pred ccCCcccCCcCcceEECceeehhhHHhhHHheeCC-CceecCCCcccccccCCceeccccchhhcccccCChhhcccCcC
Confidence 46899999999999999999999999999999864 45689999999999999999999999999999999999999999
Q ss_pred Cchhh
Q psy16683 82 SNWFK 86 (139)
Q Consensus 82 ~~~~k 86 (139)
++..|
T Consensus 84 ~~~~~ 88 (95)
T cd06968 84 SKKQR 88 (95)
T ss_pred Chhhh
Confidence 97554
No 19
>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=7.2e-30 Score=175.37 Aligned_cols=81 Identities=40% Similarity=0.841 Sum_probs=74.9
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
+.+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||.+|+
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~ 96 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKG-AQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQ 96 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhhhhccccc-CccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhh
Confidence 35799999999999999999999999999999864 45789999999999999999999999999999999999999998
Q ss_pred Cc
Q psy16683 82 SN 83 (139)
Q Consensus 82 ~~ 83 (139)
..
T Consensus 97 ~~ 98 (101)
T cd07160 97 IR 98 (101)
T ss_pred hh
Confidence 74
No 20
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.95 E-value=1.1e-29 Score=171.26 Aligned_cols=81 Identities=40% Similarity=0.954 Sum_probs=74.8
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
..+|.|||++++|+||||++|+||++||||++..+. .+.|..++.|.++...+..|++|||+||+++||++++||.+|+
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~-~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~ 84 (90)
T cd07169 6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKR-VYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGM 84 (90)
T ss_pred CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCC-ceecCCCCcccccccccccccccchhhhccccCCHHHhccccC
Confidence 467999999999999999999999999999998644 4689988999999999999999999999999999999999998
Q ss_pred Cc
Q psy16683 82 SN 83 (139)
Q Consensus 82 ~~ 83 (139)
+.
T Consensus 85 ~~ 86 (90)
T cd07169 85 PG 86 (90)
T ss_pred CC
Confidence 74
No 21
>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=99.95 E-value=7.7e-30 Score=172.36 Aligned_cols=80 Identities=40% Similarity=0.874 Sum_probs=74.6
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRS 82 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~ 82 (139)
.+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||.+++.
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~ 80 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKS-AVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQC 80 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccC-CceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhh
Confidence 5799999999999999999999999999999864 456899889999999999999999999999999999999999987
Q ss_pred c
Q psy16683 83 N 83 (139)
Q Consensus 83 ~ 83 (139)
.
T Consensus 81 ~ 81 (91)
T cd07161 81 A 81 (91)
T ss_pred h
Confidence 5
No 22
>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=99.95 E-value=1.7e-29 Score=171.66 Aligned_cols=80 Identities=39% Similarity=0.772 Sum_probs=74.3
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRS 82 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~ 82 (139)
.+|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||++++||++||.
T Consensus 1 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~-~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~ 79 (94)
T cd06966 1 KICGVCGDKALGYNFNAITCESCKAFFRRNALKNK-EFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDK 79 (94)
T ss_pred CCCeeCCCcCcceEECcceeeeehheehhcccCCC-ccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhh
Confidence 36999999999999999999999999999998644 56899999999999999999999999999999999999999997
Q ss_pred c
Q psy16683 83 N 83 (139)
Q Consensus 83 ~ 83 (139)
.
T Consensus 80 ~ 80 (94)
T cd06966 80 S 80 (94)
T ss_pred h
Confidence 5
No 23
>KOG4215|consensus
Probab=99.95 E-value=3.5e-30 Score=207.67 Aligned_cols=82 Identities=35% Similarity=0.884 Sum_probs=77.5
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
+..|.||||+|.|.||||.+|.|||+||||+|++ +..|+|+.+.+|.++++.|+.|++|||+||+.+||++++||+.||
T Consensus 19 ~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk-~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERD 97 (432)
T KOG4215|consen 19 AEFCAICGDKATGKHYGAISCDGCKGFFRRSVRK-NHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERD 97 (432)
T ss_pred cchhheeCCcccccccceeecCcchHHHHHHHHh-cceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccc
Confidence 4579999999999999999999999999999996 566899999999999999999999999999999999999999999
Q ss_pred Cch
Q psy16683 82 SNW 84 (139)
Q Consensus 82 ~~~ 84 (139)
.+.
T Consensus 98 rIg 100 (432)
T KOG4215|consen 98 RIG 100 (432)
T ss_pred ccc
Confidence 863
No 24
>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=2.6e-29 Score=164.30 Aligned_cols=75 Identities=44% Similarity=0.895 Sum_probs=69.2
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCccc
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRY 78 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~ 78 (139)
.+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||.
T Consensus 1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~ 75 (75)
T cd06969 1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKN-AKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT 75 (75)
T ss_pred CCCeecCCcCcceEECcceeeeeeeeeeeeeecC-CcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence 4799999999999999999999999999999864 45689989999999999999999999999999999998873
No 25
>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=2e-29 Score=168.01 Aligned_cols=79 Identities=41% Similarity=0.873 Sum_probs=72.8
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRS 82 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~ 82 (139)
.+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++|+.++..
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~ 80 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKN-AVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQC 80 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccC-CceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHH
Confidence 5799999999999999999999999999999854 567899899999999999999999999999999999999887664
No 26
>KOG4216|consensus
Probab=99.95 E-value=2.3e-29 Score=204.20 Aligned_cols=84 Identities=42% Similarity=0.986 Sum_probs=78.1
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRS 82 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~ 82 (139)
.||+||||+++|.||||++|+|||+||||+-.+ ...|.|.+..+|.|++.+|+.|++|||+||+++||+.++|.|||++
T Consensus 47 IPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s-~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMS 125 (479)
T KOG4216|consen 47 IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQS-NANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMS 125 (479)
T ss_pred EeeeeccCCCCcceeeeEeeccchHhhhhhhhc-cccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhcccc
Confidence 479999999999999999999999999999886 4557999999999999999999999999999999999999999999
Q ss_pred chhhh
Q psy16683 83 NWFKI 87 (139)
Q Consensus 83 ~~~k~ 87 (139)
++.+.
T Consensus 126 KKQRd 130 (479)
T KOG4216|consen 126 KKQRD 130 (479)
T ss_pred HhhHH
Confidence 86543
No 27
>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=2e-29 Score=164.46 Aligned_cols=74 Identities=54% Similarity=1.131 Sum_probs=69.1
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccC
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYG 79 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~ 79 (139)
|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||++++|+++
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~-~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~ 74 (74)
T cd07179 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSN-SYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRIG 74 (74)
T ss_pred CcccCccCcceEECceeehhHHHHHHHHhhCCC-cccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeCc
Confidence 899999999999999999999999999998644 56899889999999999999999999999999999999875
No 28
>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=99.95 E-value=2.8e-29 Score=170.16 Aligned_cols=78 Identities=42% Similarity=0.932 Sum_probs=72.7
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCCc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSN 83 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~~ 83 (139)
|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||++++||++|+..
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~-~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~ 78 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK-RYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRG 78 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCC-ccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCC
Confidence 899999999999999999999999999998654 468999999999999999999999999999999999999999753
No 29
>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=9.3e-29 Score=160.87 Aligned_cols=72 Identities=43% Similarity=1.065 Sum_probs=66.6
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCccccc-CCccccccccCcccccccccccceeecccccCcc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECK-NNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSR 77 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~-~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq 77 (139)
|.|||++++|+||||++|+||++||||++..+. .+.|. .+++|.++...+..|++|||+||+++||++++||
T Consensus 1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~-~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNL-LYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred CcccCccCcceEECcceeeeeeeEeeeeecCCC-CcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 899999999999999999999999999998754 46898 6789999999999999999999999999999886
No 30
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or hetero
Probab=99.95 E-value=1.1e-28 Score=160.13 Aligned_cols=72 Identities=50% Similarity=1.123 Sum_probs=67.2
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSR 77 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq 77 (139)
|.|||++++|+||||++|+||++||||++..+. .+.|..++.|.++...+..|++|||+||+++||++++||
T Consensus 1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~-~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNL-EYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred CCccCccCcccEECcceeeeeeeeEeEeecCCC-CccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 899999999999999999999999999998654 468999999999999999999999999999999998876
No 31
>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=7.3e-29 Score=161.36 Aligned_cols=73 Identities=49% Similarity=1.141 Sum_probs=67.4
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSR 77 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq 77 (139)
|.|||++++|+||||++|+||++||||++..+..+..|..+++|.++...+..|++|||+||+++||++++||
T Consensus 1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 73 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence 8899999999999999999999999999987555448999999999999999999999999999999998875
No 32
>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=1.3e-28 Score=170.63 Aligned_cols=79 Identities=44% Similarity=0.935 Sum_probs=71.6
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
+.+|.|||+.++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||++++|+.+.+
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~-~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~ 84 (107)
T cd06955 6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKA-LFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEE 84 (107)
T ss_pred CCCCeecCCcCcccEECcceeeeecceecceeccCC-ccccCCCCccccccCCccccccchhHHHHHcCCCchhccCHHH
Confidence 467999999999999999999999999999998654 4689989999999999999999999999999999988877643
No 33
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=99.94 E-value=9.1e-29 Score=160.92 Aligned_cols=72 Identities=47% Similarity=1.057 Sum_probs=67.5
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSR 77 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq 77 (139)
|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||++++||
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~-~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (73)
T cd06958 1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNL-TYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred CCccCccCcceEEChhhhhhhhhhhhhhhcCCC-ceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 899999999999999999999999999998754 468999999999999999999999999999999999887
No 34
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=99.94 E-value=1.2e-28 Score=159.99 Aligned_cols=71 Identities=51% Similarity=1.052 Sum_probs=66.2
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGS 76 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~v 76 (139)
|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++|
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 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRK-ARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCc-CccccCCCCccccCCcccccCccchhHHHHHhCCCHHHc
Confidence 89999999999999999999999999999864 456899899999999999999999999999999999876
No 35
>KOG4846|consensus
Probab=99.94 E-value=2.2e-29 Score=205.66 Aligned_cols=83 Identities=43% Similarity=0.942 Sum_probs=78.4
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRS 82 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~ 82 (139)
..|+||||.|+|+||||.+|+|||+||||+|+.+-.|..|.+...|.|.+..|+.|+.|||+||+++||+.++|+||+++
T Consensus 133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~ 212 (538)
T KOG4846|consen 133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMK 212 (538)
T ss_pred EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhcccc
Confidence 46999999999999999999999999999999877777899999999999999999999999999999999999999998
Q ss_pred chh
Q psy16683 83 NWF 85 (139)
Q Consensus 83 ~~~ 85 (139)
.+.
T Consensus 213 ~rn 215 (538)
T KOG4846|consen 213 FRN 215 (538)
T ss_pred ccc
Confidence 755
No 36
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=99.94 E-value=1.9e-28 Score=159.42 Aligned_cols=73 Identities=44% Similarity=0.962 Sum_probs=67.2
Q ss_pred cCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcc
Q psy16683 4 TCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSR 77 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq 77 (139)
.|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||+++.|+
T Consensus 1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (73)
T cd06959 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKG-AVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73 (73)
T ss_pred CCceeCCcCcceEECceeehhhHHHHHHhhcCC-CCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence 599999999999999999999999999999864 4568998999999999999999999999999999988763
No 37
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=99.94 E-value=3.7e-28 Score=159.90 Aligned_cols=74 Identities=42% Similarity=0.935 Sum_probs=68.0
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcc
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSR 77 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq 77 (139)
.+|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||+..++.
T Consensus 3 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~-~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 3 KICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQH-NYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCC-ceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence 57999999999999999999999999999998754 468998999999999999999999999999999987654
No 38
>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=1.7e-28 Score=164.63 Aligned_cols=78 Identities=45% Similarity=0.943 Sum_probs=71.7
Q ss_pred cCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCCC
Q psy16683 4 TCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRS 82 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~~ 82 (139)
+|.|||++++|+||||++|+||++||||++..+ ..+.|..+++|.++...+..|++|||+||+++||++++||.+++.
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~-~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~ 78 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRN-ARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEAV 78 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccC-ceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHHH
Confidence 599999999999999999999999999999864 456899889999999999999999999999999999999988554
No 39
>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=3.2e-28 Score=161.54 Aligned_cols=74 Identities=43% Similarity=0.947 Sum_probs=67.0
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCc
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGS 76 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~v 76 (139)
..+|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||+++..
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~-~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~ 76 (82)
T cd07173 3 QKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQ-KYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGAR 76 (82)
T ss_pred CCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCC-ceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChH
Confidence 356999999999999999999999999999998654 46899999999999999999999999999999987643
No 40
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=99.94 E-value=3.8e-28 Score=158.01 Aligned_cols=72 Identities=42% Similarity=0.964 Sum_probs=66.4
Q ss_pred CcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSR 77 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq 77 (139)
|.|||++++|+||||++|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||+++++.
T Consensus 1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~-~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQH-NYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred CcccCccCcceEECceeehhhhHhHHHhhcCCC-ceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 899999999999999999999999999998754 468999999999999999999999999999999988753
No 41
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.93 E-value=4.3e-27 Score=151.81 Aligned_cols=70 Identities=49% Similarity=1.036 Sum_probs=64.6
Q ss_pred cCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeeccccc
Q psy16683 4 TCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKS 74 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~ 74 (139)
+|.|||++++|+||||.+|+||++||||++..+. .+.|..+++|.++...+..|++|||+||+++||+++
T Consensus 1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~-~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRY-KYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CCeEeCCcCcccEeCCcEechhhhhhhhheeCCC-CeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 5999999999999999999999999999998654 468998899999999999999999999999999863
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=99.91 E-value=2.4e-26 Score=148.12 Aligned_cols=69 Identities=51% Similarity=1.165 Sum_probs=59.8
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeeccc
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMS 72 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~ 72 (139)
..|.|||++++|+||||.+|++|++||||++... ..+.|..+++|.++...+..|++|||+||+++||+
T Consensus 1 ~~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~-~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~ 69 (70)
T PF00105_consen 1 KKCKVCGDPASGYHYGVLSCNACKMFFRRSVKKK-KPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMK 69 (70)
T ss_dssp -BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTT-CG-STSSSST---STTTTTTSHHHHHHHHHHTTBS
T ss_pred CCCeECCCccCcccccccccccceeeeeeccccc-ccccccccccccccccCCCEeCcchHHHHHHHCCc
Confidence 4799999999999999999999999999999864 44799999999999888899999999999999996
No 43
>KOG4217|consensus
Probab=99.87 E-value=4.1e-24 Score=177.06 Aligned_cols=76 Identities=43% Similarity=0.895 Sum_probs=71.3
Q ss_pred CcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccC
Q psy16683 3 QTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYG 79 (139)
Q Consensus 3 ~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~ 79 (139)
..|.||||.|..-||||-+|+|||+||+|+|++ +..|.|..+.+|.+++..|+.|++||||||++|||-.+-|+.|
T Consensus 270 ~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQK-naKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtd 345 (605)
T KOG4217|consen 270 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQK-NAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTD 345 (605)
T ss_pred ceeeecCChHHhhhcCccccccchHHHHHHHhc-CCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecc
Confidence 579999999999999999999999999999996 5678999999999999999999999999999999999988653
No 44
>KOG4218|consensus
Probab=99.87 E-value=7.6e-24 Score=170.30 Aligned_cols=80 Identities=41% Similarity=0.925 Sum_probs=74.4
Q ss_pred CCcCcccCCCCceeeeccccccccccceeeeeecCCCcccccCCccccccccCcccccccccccceeecccccCcccCCC
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRR 81 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~FFrR~~~~~~~~~~C~~~~~C~i~~~~~~~Ck~CRl~KCl~~GM~~~~vq~~R~ 81 (139)
.+.|.||||+-+|||||.++|++|++||+|+|+++. .|.|..+.+|.|++..|..|.+||||||+.+||..++|+-+|+
T Consensus 15 ~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK-~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRM 93 (475)
T KOG4218|consen 15 GELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNK-QYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRM 93 (475)
T ss_pred ccccccccCccccceeeeeehhhhhhHHHHHhhcCc-ceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhh
Confidence 357999999999999999999999999999999754 5799999999999999999999999999999999999988876
Q ss_pred C
Q psy16683 82 S 82 (139)
Q Consensus 82 ~ 82 (139)
.
T Consensus 94 R 94 (475)
T KOG4218|consen 94 R 94 (475)
T ss_pred c
Confidence 4
No 45
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=72.68 E-value=0.65 Score=32.24 Aligned_cols=30 Identities=30% Similarity=0.872 Sum_probs=21.1
Q ss_pred CCcCcccCCCCc---eeeeccccccccccceee
Q psy16683 2 NQTCKVCGEPAA---GFHFGAFTCEGCKSFFGR 31 (139)
Q Consensus 2 ~~~C~vC~~~a~---g~hyGv~sC~~C~~FFrR 31 (139)
|..|.-||.+.. ...||++.|..|++..|-
T Consensus 13 N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~ 45 (116)
T PF01412_consen 13 NKVCADCGAPNPTWASLNYGIFLCLECAGIHRS 45 (116)
T ss_dssp CTB-TTT-SBS--EEETTTTEEE-HHHHHHHHH
T ss_pred cCcCCCCCCCCCCEEEeecChhhhHHHHHHHHH
Confidence 667999997653 468999999999998644
No 46
>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=64.26 E-value=3.7 Score=21.57 Aligned_cols=21 Identities=33% Similarity=0.866 Sum_probs=16.6
Q ss_pred cCcccCCCCceeeeccccccccc
Q psy16683 4 TCKVCGEPAAGFHFGAFTCEGCK 26 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~sC~~C~ 26 (139)
.|.||+....|.. +..|..|-
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 4889998888885 56787776
No 47
>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=63.66 E-value=2.4 Score=29.21 Aligned_cols=30 Identities=30% Similarity=0.802 Sum_probs=24.5
Q ss_pred CCcCcccCCCCc---eeeeccccccccccceee
Q psy16683 2 NQTCKVCGEPAA---GFHFGAFTCEGCKSFFGR 31 (139)
Q Consensus 2 ~~~C~vC~~~a~---g~hyGv~sC~~C~~FFrR 31 (139)
|..|.-||.+.. ...||++.|..|++.-|.
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~ 35 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHRS 35 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHHh
Confidence 678999997643 579999999999998654
No 48
>PRK00420 hypothetical protein; Validated
Probab=48.13 E-value=12 Score=26.19 Aligned_cols=27 Identities=26% Similarity=0.560 Sum_probs=19.3
Q ss_pred CCcCcccCCCCceeeeccccccccccc
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCKSF 28 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~~F 28 (139)
...|.+||.+-...+=|-.-|-.|..+
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCe
Confidence 456888887776666677777777754
No 49
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=47.79 E-value=17 Score=27.30 Aligned_cols=29 Identities=31% Similarity=0.823 Sum_probs=20.9
Q ss_pred cCcccCCCCceeeecccc-ccccccceeee
Q psy16683 4 TCKVCGEPAAGFHFGAFT-CEGCKSFFGRS 32 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~s-C~~C~~FFrR~ 32 (139)
.|.+|+..+.+..=|.+. |-+|..-|-..
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~ 30 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKA 30 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhh
Confidence 488998776666667654 99998776444
No 50
>KOG3277|consensus
Probab=42.99 E-value=9.9 Score=28.14 Aligned_cols=26 Identities=38% Similarity=0.970 Sum_probs=18.8
Q ss_pred cCcccCCCCc------eeeeccc--cccccccce
Q psy16683 4 TCKVCGEPAA------GFHFGAF--TCEGCKSFF 29 (139)
Q Consensus 4 ~C~vC~~~a~------g~hyGv~--sC~~C~~FF 29 (139)
.|.||+.++. .||=|++ +|.+|+.+-
T Consensus 81 TCkvCntRs~ktisk~AY~~GvVivqC~gC~~~H 114 (165)
T KOG3277|consen 81 TCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH 114 (165)
T ss_pred EeeccCCccccccChhhhhCceEEEECCCCccce
Confidence 5999987654 3777774 688888753
No 51
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.98 E-value=14 Score=24.80 Aligned_cols=27 Identities=26% Similarity=0.790 Sum_probs=19.2
Q ss_pred CcCcccCCCCc-eeeeccccccccccce
Q psy16683 3 QTCKVCGEPAA-GFHFGAFTCEGCKSFF 29 (139)
Q Consensus 3 ~~C~vC~~~a~-g~hyGv~sC~~C~~FF 29 (139)
..|..|+..+. -.-.|.+.|+-|..-|
T Consensus 36 ~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 36 HVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 35888887764 3577888888887655
No 52
>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=42.40 E-value=11 Score=21.58 Aligned_cols=24 Identities=25% Similarity=0.832 Sum_probs=16.8
Q ss_pred cCcccCCCCceeeeccccccccccce
Q psy16683 4 TCKVCGEPAAGFHFGAFTCEGCKSFF 29 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv~sC~~C~~FF 29 (139)
.|.||+. .+..-..+.|..|..+|
T Consensus 1 ~C~vC~~--~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 1 YCPVCGQ--SDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp EBTTTTS--SCTTSSEEEBSTTSCEE
T ss_pred eCcCCCC--cCCCCCeEEcCCCChhh
Confidence 3788988 33344567899998765
No 53
>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=39.82 E-value=13 Score=17.45 Aligned_cols=10 Identities=50% Similarity=1.381 Sum_probs=7.5
Q ss_pred ccccceeeee
Q psy16683 24 GCKSFFGRSY 33 (139)
Q Consensus 24 ~C~~FFrR~~ 33 (139)
+|+.||..+.
T Consensus 6 ~CknffWK~~ 15 (18)
T PF03002_consen 6 GCKNFFWKTF 15 (18)
T ss_pred cccceeeccc
Confidence 6899997653
No 54
>PRK08359 transcription factor; Validated
Probab=39.48 E-value=9.8 Score=28.60 Aligned_cols=30 Identities=27% Similarity=0.757 Sum_probs=21.4
Q ss_pred CCcCcccCCCCceeeecc-------ccccccccceee
Q psy16683 2 NQTCKVCGEPAAGFHFGA-------FTCEGCKSFFGR 31 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv-------~sC~~C~~FFrR 31 (139)
+..|.+||.+..|.-|-| ..|..|+.=|-.
T Consensus 6 ~~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~G~ 42 (176)
T PRK08359 6 PRYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKYGR 42 (176)
T ss_pred cceeecCCCccCCCCeEEEEcCeEEehHHHHHHHhCC
Confidence 345999999988874444 579999944433
No 55
>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=38.71 E-value=17 Score=24.82 Aligned_cols=25 Identities=24% Similarity=0.639 Sum_probs=15.1
Q ss_pred CcccCCCCceeeeccccccccccce
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFF 29 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FF 29 (139)
|.||++.+-...=+.+.|.+|..=|
T Consensus 38 CeiC~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 38 CEICGPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred ccccCCCceEEECCEEEEecCCCEE
Confidence 6777655555555566677776533
No 56
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=37.70 E-value=16 Score=18.91 Aligned_cols=15 Identities=33% Similarity=1.152 Sum_probs=5.8
Q ss_pred cCcccCCCCce-eeec
Q psy16683 4 TCKVCGEPAAG-FHFG 18 (139)
Q Consensus 4 ~C~vC~~~a~g-~hyG 18 (139)
.|.+|+.+..+ ..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~ 17 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYR 17 (30)
T ss_dssp --TTTS----S--EEE
T ss_pred cCCcCCCcCCCCceEE
Confidence 58888888777 5554
No 57
>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=36.28 E-value=18 Score=21.08 Aligned_cols=24 Identities=33% Similarity=1.092 Sum_probs=18.6
Q ss_pred cCcccCCCC-cee-eecccccccccc
Q psy16683 4 TCKVCGEPA-AGF-HFGAFTCEGCKS 27 (139)
Q Consensus 4 ~C~vC~~~a-~g~-hyGv~sC~~C~~ 27 (139)
.|.||+++. .|. -||.+.|..|-.
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHHH
Confidence 489999764 475 488899999973
No 58
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=35.99 E-value=16 Score=30.05 Aligned_cols=30 Identities=33% Similarity=0.852 Sum_probs=25.0
Q ss_pred CCcCcccCCCC---ceeeeccccccccccceee
Q psy16683 2 NQTCKVCGEPA---AGFHFGAFTCEGCKSFFGR 31 (139)
Q Consensus 2 ~~~C~vC~~~a---~g~hyGv~sC~~C~~FFrR 31 (139)
|..|.-||.+. ....|||+.|--|++-.|-
T Consensus 20 Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRs 52 (319)
T COG5347 20 NKKCADCGAPNPTWASVNLGVFLCIDCAGVHRS 52 (319)
T ss_pred cCccccCCCCCCceEecccCeEEEeecchhhhc
Confidence 56799999876 3589999999999997654
No 59
>KOG0703|consensus
Probab=35.93 E-value=20 Score=29.08 Aligned_cols=31 Identities=29% Similarity=0.763 Sum_probs=25.1
Q ss_pred CCcCcccCCCC---ceeeeccccccccccceeee
Q psy16683 2 NQTCKVCGEPA---AGFHFGAFTCEGCKSFFGRS 32 (139)
Q Consensus 2 ~~~C~vC~~~a---~g~hyGv~sC~~C~~FFrR~ 32 (139)
|..|.-||... ....+||+.|--|++.-|..
T Consensus 25 N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~l 58 (287)
T KOG0703|consen 25 NKVCADCGAKGPRWASWNLGVFICLRCAGIHRSL 58 (287)
T ss_pred cCcccccCCCCCCeEEeecCeEEEeecccccccc
Confidence 56799998763 35899999999999987654
No 60
>PRK06424 transcription factor; Provisional
Probab=35.74 E-value=13 Score=26.91 Aligned_cols=25 Identities=24% Similarity=0.693 Sum_probs=18.8
Q ss_pred CcccCCCCceeeecc-------cccccccccee
Q psy16683 5 CKVCGEPAAGFHFGA-------FTCEGCKSFFG 30 (139)
Q Consensus 5 C~vC~~~a~g~hyGv-------~sC~~C~~FFr 30 (139)
|.+||....+.| -| ..|..|+-|=.
T Consensus 3 CE~CG~~~~~~~-~v~ieg~~l~vC~~Ca~~G~ 34 (144)
T PRK06424 3 CEMCGKKVPQTT-KVMIDGAILNVCDDCAKFGT 34 (144)
T ss_pred ccccCcccCCce-EEEEcCeeeehhHHHHHcCC
Confidence 999999888763 33 35999998743
No 61
>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=35.56 E-value=13 Score=18.41 Aligned_cols=19 Identities=21% Similarity=0.768 Sum_probs=12.5
Q ss_pred ccccCCccccccccCcccc
Q psy16683 40 SECKNNNECIINKKNRTSC 58 (139)
Q Consensus 40 ~~C~~~~~C~i~~~~~~~C 58 (139)
+.|..+..|.++..++..|
T Consensus 4 ~~Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 4 FHCKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp ---BTTEEEEEETTTCEEE
T ss_pred cccCCCCEeeeCCCCCcCC
Confidence 3688888999887776654
No 62
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=35.20 E-value=31 Score=20.35 Aligned_cols=15 Identities=20% Similarity=0.565 Sum_probs=11.0
Q ss_pred CcCcccCCCCceeee
Q psy16683 3 QTCKVCGEPAAGFHF 17 (139)
Q Consensus 3 ~~C~vC~~~a~g~hy 17 (139)
.+|.-||..+..+++
T Consensus 2 kPCPfCGg~~~~~~~ 16 (53)
T TIGR03655 2 KPCPFCGGADVYLRR 16 (53)
T ss_pred CCCCCCCCcceeeEe
Confidence 579999987765553
No 63
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=34.93 E-value=24 Score=19.97 Aligned_cols=23 Identities=30% Similarity=0.839 Sum_probs=10.1
Q ss_pred CcCcccCCCCceeee------cccccccc
Q psy16683 3 QTCKVCGEPAAGFHF------GAFTCEGC 25 (139)
Q Consensus 3 ~~C~vC~~~a~g~hy------Gv~sC~~C 25 (139)
.+|.+||....=..| |.+.|+.|
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCC
Confidence 478888754322212 55566666
No 64
>PHA03124 dUTPase; Provisional
Probab=31.60 E-value=10 Score=31.96 Aligned_cols=17 Identities=47% Similarity=1.249 Sum_probs=13.5
Q ss_pred ccccccccccceeeeee
Q psy16683 18 GAFTCEGCKSFFGRSYN 34 (139)
Q Consensus 18 Gv~sC~~C~~FFrR~~~ 34 (139)
|-+-|-+|++||||...
T Consensus 189 ~~~~~~~~~~~~~~~~~ 205 (418)
T PHA03124 189 GNFGCMGCKAFYRRLFE 205 (418)
T ss_pred ccccccchHHHHHHHHH
Confidence 33459999999999864
No 65
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=30.97 E-value=31 Score=19.23 Aligned_cols=9 Identities=33% Similarity=0.944 Sum_probs=6.3
Q ss_pred CcCcccCCC
Q psy16683 3 QTCKVCGEP 11 (139)
Q Consensus 3 ~~C~vC~~~ 11 (139)
.+|.+||..
T Consensus 4 ~pCP~CGG~ 12 (37)
T smart00778 4 GPCPNCGGS 12 (37)
T ss_pred cCCCCCCCc
Confidence 578888753
No 66
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=27.03 E-value=28 Score=18.82 Aligned_cols=7 Identities=57% Similarity=1.289 Sum_probs=3.3
Q ss_pred CcccCCC
Q psy16683 5 CKVCGEP 11 (139)
Q Consensus 5 C~vC~~~ 11 (139)
|.+||..
T Consensus 5 C~~CG~i 11 (34)
T cd00729 5 CPVCGYI 11 (34)
T ss_pred CCCCCCE
Confidence 5555543
No 67
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=26.93 E-value=15 Score=20.14 Aligned_cols=24 Identities=29% Similarity=0.785 Sum_probs=11.0
Q ss_pred CcCcccCCCC----ceeeeccccccccc
Q psy16683 3 QTCKVCGEPA----AGFHFGAFTCEGCK 26 (139)
Q Consensus 3 ~~C~vC~~~a----~g~hyGv~sC~~C~ 26 (139)
..|.-||++- --.||+...|..|+
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 3577787652 23688888888875
No 68
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=26.41 E-value=31 Score=29.04 Aligned_cols=31 Identities=26% Similarity=0.629 Sum_probs=25.1
Q ss_pred CCcCcccCCCC---ceeeeccccccccccceeee
Q psy16683 2 NQTCKVCGEPA---AGFHFGAFTCEGCKSFFGRS 32 (139)
Q Consensus 2 ~~~C~vC~~~a---~g~hyGv~sC~~C~~FFrR~ 32 (139)
|..|.-||.+. ....||++.|-.|++.-|..
T Consensus 22 Nk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsL 55 (395)
T PLN03114 22 NKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 55 (395)
T ss_pred CCcCccCCCCCCCceeeccceeehhhhhHhhccC
Confidence 56799998653 35899999999999987654
No 69
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=26.28 E-value=24 Score=25.83 Aligned_cols=25 Identities=32% Similarity=0.919 Sum_probs=18.7
Q ss_pred cCcccCCCCceeeecc-------ccccccccc
Q psy16683 4 TCKVCGEPAAGFHFGA-------FTCEGCKSF 28 (139)
Q Consensus 4 ~C~vC~~~a~g~hyGv-------~sC~~C~~F 28 (139)
.|.+||.+..|.-|-| ..|..|+-|
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~k~ 33 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECRKF 33 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHHhc
Confidence 3999999887764433 469999955
No 70
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=26.07 E-value=24 Score=23.68 Aligned_cols=25 Identities=28% Similarity=0.780 Sum_probs=18.1
Q ss_pred cCcccCCCCc-eeeeccccccccccc
Q psy16683 4 TCKVCGEPAA-GFHFGAFTCEGCKSF 28 (139)
Q Consensus 4 ~C~vC~~~a~-g~hyGv~sC~~C~~F 28 (139)
.|..||..+- -.-.|++.|..|.--
T Consensus 37 ~Cp~Cgk~~vkR~a~GIW~C~~C~~~ 62 (90)
T PF01780_consen 37 TCPFCGKTSVKRVATGIWKCKKCGKK 62 (90)
T ss_dssp EESSSSSSEEEEEETTEEEETTTTEE
T ss_pred cCCCCCCceeEEeeeEEeecCCCCCE
Confidence 5888887764 356788888888743
No 71
>TIGR00009 L28 ribosomal protein L28. This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included.
Probab=23.89 E-value=40 Score=20.40 Aligned_cols=12 Identities=25% Similarity=0.767 Sum_probs=9.6
Q ss_pred CCCcCcccCCCC
Q psy16683 1 MNQTCKVCGEPA 12 (139)
Q Consensus 1 ~~~~C~vC~~~a 12 (139)
|...|.|||...
T Consensus 1 Ms~~C~i~GK~~ 12 (56)
T TIGR00009 1 MSRKCQLTGKGP 12 (56)
T ss_pred CCCEeeeCCCcC
Confidence 677899999754
No 72
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=23.66 E-value=48 Score=17.78 Aligned_cols=18 Identities=56% Similarity=1.235 Sum_probs=9.8
Q ss_pred CcccCCCCceeeeccccccccccc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSF 28 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~F 28 (139)
|.+|+.++. ..|..|...
T Consensus 1 C~~C~~~~~------~~C~~C~~~ 18 (37)
T PF01753_consen 1 CAVCGKPAL------KRCSRCKSV 18 (37)
T ss_dssp -TTTSSCSS------EEETTTSSS
T ss_pred CcCCCCCcC------CcCCCCCCE
Confidence 566776332 267777644
No 73
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=23.17 E-value=54 Score=22.00 Aligned_cols=24 Identities=38% Similarity=0.951 Sum_probs=14.6
Q ss_pred cCcccCCCCc-eeeecccccccccc
Q psy16683 4 TCKVCGEPAA-GFHFGAFTCEGCKS 27 (139)
Q Consensus 4 ~C~vC~~~a~-g~hyGv~sC~~C~~ 27 (139)
.|..||..+- -..-|.+.|+.|..
T Consensus 38 ~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PTZ00255 38 FCPFCGKHAVKRQAVGIWRCKGCKK 62 (90)
T ss_pred cCCCCCCCceeeeeeEEEEcCCCCC
Confidence 4777765553 24457777777763
No 74
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=23.14 E-value=43 Score=20.88 Aligned_cols=15 Identities=33% Similarity=0.935 Sum_probs=10.9
Q ss_pred CCCcCcccCCCC-cee
Q psy16683 1 MNQTCKVCGEPA-AGF 15 (139)
Q Consensus 1 ~~~~C~vC~~~a-~g~ 15 (139)
|...|.|||... .|.
T Consensus 1 Msr~C~i~GK~~~~Gn 16 (63)
T CHL00112 1 MSKKCQLTGKKANNGY 16 (63)
T ss_pred CCCeeccCCCcCccCc
Confidence 677899999654 453
No 75
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=22.96 E-value=35 Score=27.18 Aligned_cols=13 Identities=23% Similarity=0.685 Sum_probs=5.0
Q ss_pred eeecccccccccc
Q psy16683 15 FHFGAFTCEGCKS 27 (139)
Q Consensus 15 ~hyGv~sC~~C~~ 27 (139)
.||.-..|-.|..
T Consensus 207 W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 207 WRFVRIKCPYCGN 219 (290)
T ss_dssp EE--TTS-TTT--
T ss_pred eeecCCCCcCCCC
Confidence 4555566666663
No 76
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=22.61 E-value=37 Score=20.06 Aligned_cols=31 Identities=19% Similarity=0.607 Sum_probs=20.5
Q ss_pred CCcCcccCCCCce----eeecc-ccccccccceeee
Q psy16683 2 NQTCKVCGEPAAG----FHFGA-FTCEGCKSFFGRS 32 (139)
Q Consensus 2 ~~~C~vC~~~a~g----~hyGv-~sC~~C~~FFrR~ 32 (139)
...|..|+...+- .-.|. .-|.+|..+|+..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~ 38 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKH 38 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHc
Confidence 4568888865432 23444 6799999888764
No 77
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=22.47 E-value=44 Score=29.86 Aligned_cols=31 Identities=23% Similarity=0.522 Sum_probs=25.1
Q ss_pred CCcCcccCCCCc---eeeeccccccccccceeee
Q psy16683 2 NQTCKVCGEPAA---GFHFGAFTCEGCKSFFGRS 32 (139)
Q Consensus 2 ~~~C~vC~~~a~---g~hyGv~sC~~C~~FFrR~ 32 (139)
|..|.-||...- ...||++.|-.|++.-|..
T Consensus 23 Nk~CADCgs~~P~WASiNlGIFICi~CSGIHRsL 56 (648)
T PLN03119 23 NRRCINCNSLGPQYVCTTFWTFVCMACSGIHREF 56 (648)
T ss_pred CCccccCCCCCCCceeeccceEEeccchhhhccC
Confidence 567999987543 5799999999999987654
No 78
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=21.82 E-value=52 Score=18.29 Aligned_cols=22 Identities=27% Similarity=0.843 Sum_probs=11.6
Q ss_pred CcccCCCCceeeeccccccccccce
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKSFF 29 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~FF 29 (139)
|.+|+....-. ...|+.|..-|
T Consensus 1 C~~C~~~~~l~---~f~C~~C~~~F 22 (39)
T smart00154 1 CHFCRKKVGLT---GFKCRHCGNLF 22 (39)
T ss_pred CcccCCccccc---CeECCccCCcc
Confidence 45555544332 34677776544
No 80
>PLN03131 hypothetical protein; Provisional
Probab=21.82 E-value=44 Score=30.15 Aligned_cols=31 Identities=23% Similarity=0.515 Sum_probs=25.1
Q ss_pred CCcCcccCCCCc---eeeeccccccccccceeee
Q psy16683 2 NQTCKVCGEPAA---GFHFGAFTCEGCKSFFGRS 32 (139)
Q Consensus 2 ~~~C~vC~~~a~---g~hyGv~sC~~C~~FFrR~ 32 (139)
|..|.-|+...- ...||++.|-.|++.-|..
T Consensus 23 Nk~CADCga~~P~WASiNlGIFICi~CSGIHRsL 56 (705)
T PLN03131 23 NRRCINCNSLGPQFVCTNFWTFICMTCSGIHREF 56 (705)
T ss_pred CCccccCCCCCCCeeEeccceEEchhchhhhccc
Confidence 567999987543 5899999999999987664
No 81
>PLN02189 cellulose synthase
Probab=21.06 E-value=45 Score=31.72 Aligned_cols=22 Identities=36% Similarity=1.037 Sum_probs=17.4
Q ss_pred CcCcccCCC----Cceeeeccccccccc
Q psy16683 3 QTCKVCGEP----AAGFHFGAFTCEGCK 26 (139)
Q Consensus 3 ~~C~vC~~~----a~g~hyGv~sC~~C~ 26 (139)
..|.||||. +.|--| ++|..|+
T Consensus 35 ~~C~iCgd~vg~~~~g~~f--vaC~~C~ 60 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLF--VACNECG 60 (1040)
T ss_pred ccccccccccCcCCCCCEE--EeeccCC
Confidence 369999987 678777 6788876
No 82
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=20.81 E-value=15 Score=22.48 Aligned_cols=26 Identities=38% Similarity=0.892 Sum_probs=11.0
Q ss_pred CCCcCcccCCCCc---eeeeccccccccc
Q psy16683 1 MNQTCKVCGEPAA---GFHFGAFTCEGCK 26 (139)
Q Consensus 1 ~~~~C~vC~~~a~---g~hyGv~sC~~C~ 26 (139)
|...|.+||++.. ..-|.-+....|+
T Consensus 1 m~v~CP~C~k~~~~~~~n~~rPFCS~RCk 29 (57)
T PF03884_consen 1 MTVKCPICGKPVEWSPENPFRPFCSERCK 29 (57)
T ss_dssp -EEE-TTT--EEE-SSSSS--SSSSHHHH
T ss_pred CcccCCCCCCeecccCCCCcCCcccHhhc
Confidence 5567888886542 2344444444444
No 83
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=20.78 E-value=35 Score=17.95 Aligned_cols=19 Identities=32% Similarity=0.983 Sum_probs=9.3
Q ss_pred CCcCcccCCCCceeeeccccccccc
Q psy16683 2 NQTCKVCGEPAAGFHFGAFTCEGCK 26 (139)
Q Consensus 2 ~~~C~vC~~~a~g~hyGv~sC~~C~ 26 (139)
...|.||+. .+-.+|..|.
T Consensus 2 ~~~C~vC~~------~~kY~Cp~C~ 20 (30)
T PF04438_consen 2 RKLCSVCGN------PAKYRCPRCG 20 (30)
T ss_dssp -EEETSSSS------EESEE-TTT-
T ss_pred cCCCccCcC------CCEEECCCcC
Confidence 456788875 2333566555
No 84
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=20.62 E-value=69 Score=18.13 Aligned_cols=13 Identities=31% Similarity=0.930 Sum_probs=6.0
Q ss_pred CcccCCCCceeee
Q psy16683 5 CKVCGEPAAGFHF 17 (139)
Q Consensus 5 C~vC~~~a~g~hy 17 (139)
|.+|+.+..|.+|
T Consensus 3 C~~C~~~i~g~r~ 15 (46)
T cd02249 3 CDGCLKPIVGVRY 15 (46)
T ss_pred CcCCCCCCcCCEE
Confidence 4455544444433
No 85
>COG4393 Predicted membrane protein [Function unknown]
Probab=20.43 E-value=40 Score=28.18 Aligned_cols=23 Identities=22% Similarity=0.674 Sum_probs=21.0
Q ss_pred CcccCCCCceeeecccccccccc
Q psy16683 5 CKVCGEPAAGFHFGAFTCEGCKS 27 (139)
Q Consensus 5 C~vC~~~a~g~hyGv~sC~~C~~ 27 (139)
|.+|||.+--+.=|-+.|-+|..
T Consensus 337 C~iCGd~GYv~e~dqvICv~C~V 359 (405)
T COG4393 337 CDICGDQGYVMEGDQVICVRCDV 359 (405)
T ss_pred HHhccccceEeECCEEEEEEccE
Confidence 99999999888888999999985
No 86
>PF06147 DUF968: Protein of unknown function (DUF968); InterPro: IPR010373 This is a family of uncharacterised prophage proteins that are also found in bacteria and humans.
Probab=20.23 E-value=50 Score=25.11 Aligned_cols=16 Identities=38% Similarity=0.974 Sum_probs=11.8
Q ss_pred CCcCcccCCC-Cceeee
Q psy16683 2 NQTCKVCGEP-AAGFHF 17 (139)
Q Consensus 2 ~~~C~vC~~~-a~g~hy 17 (139)
..+|.|||.+ +.-.|+
T Consensus 127 ~~~C~iCGk~~~d~hH~ 143 (200)
T PF06147_consen 127 SRPCVICGKPPADIHHI 143 (200)
T ss_pred cCccccCCCCcccccee
Confidence 5789999975 555665
Done!