Query psy6599
Match_columns 93
No_of_seqs 156 out of 1060
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 22:12:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6599.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6599hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 100.0 2.9E-32 6.3E-37 197.8 3.8 81 9-93 13-93 (432)
2 cd06956 NR_DBD_RXR DNA-binding 100.0 6.9E-32 1.5E-36 160.3 3.9 73 17-93 2-74 (77)
3 cd06969 NR_DBD_NGFI-B DNA-bind 100.0 5.3E-32 1.2E-36 160.1 3.0 74 16-93 1-74 (75)
4 cd07163 NR_DBD_TLX DNA-binding 100.0 4.6E-32 9.9E-37 165.8 2.6 81 11-93 2-82 (92)
5 cd07160 NR_DBD_LXR DNA-binding 100.0 2.1E-31 4.6E-36 165.2 5.1 77 13-93 16-92 (101)
6 cd07170 NR_DBD_ERR DNA-binding 100.0 1.4E-31 3E-36 165.0 4.2 76 14-93 3-78 (97)
7 cd06958 NR_DBD_COUP_TF DNA-bin 100.0 1.7E-31 3.6E-36 157.2 3.9 72 18-93 1-72 (73)
8 cd06959 NR_DBD_EcR_like The DN 100.0 2.8E-31 6.1E-36 156.2 4.9 73 17-93 1-73 (73)
9 cd07161 NR_DBD_EcR DNA-binding 100.0 2.9E-31 6.2E-36 162.0 4.9 74 16-93 2-75 (91)
10 cd07155 NR_DBD_ER_like DNA-bin 100.0 1.6E-31 3.5E-36 158.0 3.6 72 18-93 1-72 (75)
11 cd07179 2DBD_NR_DBD2 The secon 100.0 2.5E-31 5.4E-36 156.8 4.3 72 18-93 1-72 (74)
12 cd07171 NR_DBD_ER DNA-binding 100.0 2E-31 4.4E-36 159.9 3.9 74 16-93 4-77 (82)
13 cd06964 NR_DBD_RAR DNA-binding 100.0 7.5E-32 1.6E-36 162.8 1.9 76 14-93 3-78 (85)
14 cd07172 NR_DBD_GR_PR DNA-bindi 100.0 5.8E-31 1.3E-35 156.6 5.7 75 15-93 2-76 (78)
15 cd06961 NR_DBD_TR DNA-binding 100.0 2.1E-31 4.6E-36 160.8 3.6 73 17-93 1-73 (85)
16 cd06962 NR_DBD_FXR DNA-binding 100.0 1.7E-31 3.8E-36 160.8 3.2 74 16-93 2-75 (84)
17 cd07154 NR_DBD_PNR_like The DN 100.0 1.4E-31 3.1E-36 157.5 2.7 73 18-93 1-73 (73)
18 cd07158 NR_DBD_Ppar_like The D 100.0 4E-31 8.6E-36 155.6 4.2 72 18-93 1-73 (73)
19 cd07156 NR_DBD_VDR_like The DN 100.0 3.5E-31 7.5E-36 155.5 3.9 72 18-93 1-72 (72)
20 cd06963 NR_DBD_GR_like The DNA 100.0 6.1E-31 1.3E-35 154.8 4.6 72 18-93 1-72 (73)
21 cd06916 NR_DBD_like DNA-bindin 100.0 1.8E-31 4E-36 156.6 2.2 72 18-93 1-72 (72)
22 cd06955 NR_DBD_VDR DNA-binding 100.0 6.5E-31 1.4E-35 164.4 4.2 78 12-93 3-80 (107)
23 cd07168 NR_DBD_DHR4_like DNA-b 100.0 6.1E-31 1.3E-35 160.3 3.8 76 14-93 5-80 (90)
24 cd06967 NR_DBD_TR2_like DNA-bi 100.0 3.3E-31 7.2E-36 160.6 2.3 76 14-93 2-77 (87)
25 cd07169 NR_DBD_GCNF_like DNA-b 100.0 7.6E-31 1.7E-35 159.8 3.8 77 13-93 4-80 (90)
26 cd06970 NR_DBD_PNR DNA-binding 100.0 4.6E-31 9.9E-36 161.3 2.5 75 16-93 7-81 (92)
27 cd07164 NR_DBD_PNR_like_1 DNA- 100.0 1.4E-30 3E-35 155.0 3.5 72 18-93 1-72 (78)
28 cd07162 NR_DBD_PXR DNA-binding 100.0 2.1E-30 4.6E-35 157.0 4.4 73 17-93 1-73 (87)
29 cd07173 NR_DBD_AR DNA-binding 100.0 3.5E-30 7.5E-35 154.5 5.1 73 15-91 3-75 (82)
30 cd06960 NR_DBD_HNF4A DNA-bindi 100.0 8.3E-31 1.8E-35 155.3 2.1 72 18-93 1-72 (76)
31 cd06957 NR_DBD_PNR_like_2 DNA- 100.0 4.7E-31 1E-35 158.3 0.8 73 18-93 1-73 (82)
32 cd06968 NR_DBD_ROR DNA-binding 100.0 2E-30 4.4E-35 159.3 3.6 77 13-93 3-79 (95)
33 cd07166 NR_DBD_REV_ERB DNA-bin 100.0 1E-30 2.2E-35 159.0 2.1 75 15-93 3-78 (89)
34 cd07167 NR_DBD_Lrh-1_like The 100.0 1.8E-30 3.9E-35 159.0 2.6 72 18-93 1-72 (93)
35 cd07165 NR_DBD_DmE78_like DNA- 100.0 2.9E-30 6.2E-35 154.6 3.4 72 18-93 1-72 (81)
36 cd06966 NR_DBD_CAR DNA-binding 100.0 1.6E-30 3.5E-35 159.5 2.2 73 17-93 2-74 (94)
37 cd07157 2DBD_NR_DBD1 The first 100.0 4.4E-30 9.5E-35 155.4 3.2 73 17-93 2-76 (86)
38 smart00399 ZnF_C4 c4 zinc fing 100.0 1.7E-29 3.7E-34 147.5 3.8 70 17-90 1-70 (70)
39 cd06965 NR_DBD_Ppar DNA-bindin 100.0 8.7E-30 1.9E-34 153.5 2.6 71 17-93 1-72 (84)
40 PF00105 zf-C4: Zinc finger, C 100.0 2.6E-29 5.7E-34 146.5 3.5 70 16-89 1-70 (70)
41 KOG4846|consensus 100.0 1.7E-29 3.6E-34 185.9 2.3 74 16-93 133-207 (538)
42 KOG4216|consensus 99.9 2.2E-28 4.8E-33 178.8 3.2 75 15-93 46-120 (479)
43 KOG4217|consensus 99.9 8E-28 1.7E-32 179.1 3.8 76 14-93 268-343 (605)
44 KOG4218|consensus 99.9 3.2E-26 7E-31 165.8 2.9 79 11-93 11-89 (475)
45 PF10764 Gin: Inhibitor of sig 74.5 2.5 5.3E-05 22.5 1.5 24 17-40 1-26 (46)
46 PRK00420 hypothetical protein; 71.4 1.5 3.2E-05 27.7 0.3 31 12-42 20-50 (112)
47 PF01412 ArfGap: Putative GTPa 70.5 2 4.4E-05 26.8 0.8 32 13-44 11-45 (116)
48 KOG2879|consensus 57.2 12 0.00027 27.3 2.8 52 2-56 226-281 (298)
49 smart00401 ZnF_GATA zinc finge 56.1 7.9 0.00017 20.8 1.3 31 15-45 3-38 (52)
50 PF03107 C1_2: C1 domain; Int 56.0 5.1 0.00011 19.0 0.5 21 17-39 2-22 (30)
51 cd00729 rubredoxin_SM Rubredox 53.8 5.7 0.00012 19.5 0.5 14 14-27 17-30 (34)
52 smart00105 ArfGap Putative GTP 52.3 9.5 0.0002 23.6 1.4 30 15-44 3-35 (112)
53 TIGR00269 conserved hypothetic 50.1 8.5 0.00018 23.5 0.9 21 15-40 80-100 (104)
54 PTZ00218 40S ribosomal protein 48.6 9.4 0.0002 21.0 0.8 23 16-38 17-40 (54)
55 PHA03124 dUTPase; Provisional 45.7 11 0.00023 28.8 1.0 16 32-47 190-205 (418)
56 PLN02915 cellulose synthase A 44.5 16 0.00035 31.2 1.9 36 1-38 1-40 (1044)
57 PF03002 Somatostatin: Somatos 42.8 5.9 0.00013 16.9 -0.4 10 37-46 6-15 (18)
58 PF06677 Auto_anti-p27: Sjogre 40.3 10 0.00022 19.6 0.2 27 12-38 14-40 (41)
59 PRK12495 hypothetical protein; 35.7 15 0.00032 25.9 0.4 33 11-44 38-70 (226)
60 PF00320 GATA: GATA zinc finge 35.4 17 0.00037 17.9 0.5 16 30-45 17-33 (36)
61 PF13901 DUF4206: Domain of un 34.2 25 0.00053 24.1 1.3 34 15-48 152-188 (202)
62 cd00350 rubredoxin_like Rubred 33.6 16 0.00034 17.6 0.2 14 14-27 16-29 (33)
63 KOG3277|consensus 33.6 16 0.00035 24.5 0.3 26 17-42 81-114 (165)
64 PF10013 DUF2256: Uncharacteri 33.1 28 0.0006 18.2 1.1 13 12-24 5-17 (42)
65 PF00357 Integrin_alpha: Integ 32.7 19 0.00041 14.7 0.3 8 40-47 3-10 (15)
66 PF08273 Prim_Zn_Ribbon: Zinc- 32.3 22 0.00048 18.2 0.6 24 15-38 3-32 (40)
67 PRK04179 rpl37e 50S ribosomal 31.3 53 0.0011 18.6 2.1 24 14-39 16-39 (62)
68 smart00778 Prim_Zn_Ribbon Zinc 30.4 27 0.00058 17.6 0.7 10 15-24 3-12 (37)
69 PF00628 PHD: PHD-finger; Int 30.3 8.3 0.00018 20.0 -1.2 25 18-44 2-26 (51)
70 TIGR03124 ctirate_citX holo-AC 29.4 23 0.00049 23.7 0.5 13 14-26 129-141 (165)
71 PRK08359 transcription factor; 27.7 37 0.0008 23.0 1.3 31 14-44 5-42 (176)
72 PF07649 C1_3: C1-like domain; 27.5 21 0.00046 16.6 0.1 14 17-30 2-16 (30)
73 COG1592 Rubrerythrin [Energy p 26.8 20 0.00043 24.2 -0.2 14 13-26 147-160 (166)
74 PRK01392 citX 2'-(5''-triphosp 26.7 26 0.00056 23.8 0.4 14 13-26 137-150 (180)
75 PF03802 CitX: Apo-citrate lya 26.2 26 0.00056 23.4 0.3 13 14-26 131-143 (170)
76 PTZ00073 60S ribosomal protein 25.8 74 0.0016 19.3 2.2 26 12-39 13-38 (91)
77 PRK06424 transcription factor; 25.6 29 0.00063 22.7 0.5 27 17-43 2-34 (144)
78 PRK05766 rps14P 30S ribosomal 25.5 89 0.0019 16.9 2.3 27 12-38 11-38 (52)
79 PF11781 RRN7: RNA polymerase 25.1 35 0.00076 16.9 0.6 9 16-24 9-17 (36)
80 COG2260 Predicted Zn-ribbon RN 25.0 31 0.00067 19.3 0.4 16 14-29 16-31 (59)
81 PF09180 ProRS-C_1: Prolyl-tRN 24.8 36 0.00079 19.1 0.7 18 11-28 44-61 (68)
82 TIGR00270 conserved hypothetic 24.0 33 0.00072 22.6 0.5 25 17-41 2-33 (154)
83 PRK01343 zinc-binding protein; 23.8 73 0.0016 17.7 1.8 27 14-41 8-34 (57)
84 PF00130 C1_1: Phorbol esters/ 23.6 20 0.00044 18.6 -0.5 28 14-41 10-37 (53)
85 COG1997 RPL43A Ribosomal prote 23.5 28 0.00061 21.1 0.1 28 15-42 35-63 (89)
86 PF10080 DUF2318: Predicted me 22.7 29 0.00063 21.4 0.1 29 14-42 34-62 (102)
87 PF06147 DUF968: Protein of un 22.3 48 0.001 22.7 1.1 18 13-30 125-143 (200)
88 KOG3116|consensus 22.3 48 0.001 22.2 1.0 9 78-86 29-37 (177)
89 PF12760 Zn_Tnp_IS1595: Transp 21.4 47 0.001 17.0 0.7 11 70-80 36-46 (46)
90 smart00109 C1 Protein kinase C 20.8 89 0.0019 15.3 1.7 25 15-40 11-35 (49)
91 PF08394 Arc_trans_TRASH: Arch 20.5 95 0.0021 15.6 1.7 27 18-44 1-35 (37)
92 TIGR03655 anti_R_Lar restricti 20.4 67 0.0014 17.0 1.2 15 16-30 2-16 (53)
No 1
>KOG4215|consensus
Probab=99.97 E-value=2.9e-32 Score=197.78 Aligned_cols=81 Identities=43% Similarity=1.027 Sum_probs=76.0
Q ss_pred CCCCCCCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCC
Q psy6599 9 LGDRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMN 88 (93)
Q Consensus 9 ~~~~~~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~ 88 (93)
.+++.....|.||||+++|.|||+.+|++||+||||+|.++..|+|+.+. +|.|+++.|+.||||||+||+.+||+
T Consensus 13 ~~~s~~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k----~C~VDKdkRNaCRyCRfqKC~~aGMK 88 (432)
T KOG4215|consen 13 QSSSGVAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNK----QCVVDKDKRNACRYCRFQKCVRAGMK 88 (432)
T ss_pred CCcccccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccc----cccccchhhhhhhHhhHHHHHHhccc
Confidence 34445889999999999999999999999999999999999999999886 69999999999999999999999999
Q ss_pred CCCCC
Q psy6599 89 KDDFK 93 (93)
Q Consensus 89 ~~~vq 93 (93)
++|||
T Consensus 89 ~eAiQ 93 (432)
T KOG4215|consen 89 REAIQ 93 (432)
T ss_pred HHhhh
Confidence 99997
No 2
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=99.97 E-value=6.9e-32 Score=160.29 Aligned_cols=73 Identities=49% Similarity=1.210 Sum_probs=69.0
Q ss_pred CceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 74 (77)
T cd06956 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK----DCLIDKRQRNRCQYCRYQKCLAMGMKREAVQ 74 (77)
T ss_pred CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCC----ccccCCCccccCccchhHHHhHhCCCHHHhc
Confidence 699999999999999999999999999999999999998764 6999999999999999999999999999887
No 3
>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=99.97 E-value=5.3e-32 Score=160.06 Aligned_cols=74 Identities=45% Similarity=1.081 Sum_probs=69.3
Q ss_pred CCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 16 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 16 ~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
.+|.|||++++++|||+.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 1 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 74 (75)
T cd06969 1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANK----NCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74 (75)
T ss_pred CCCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCC----ccccCCcccccCcccHhHHHHHhCCCHHHcc
Confidence 3699999999999999999999999999999988889998764 6999999999999999999999999999987
No 4
>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=99.97 E-value=4.6e-32 Score=165.83 Aligned_cols=81 Identities=78% Similarity=1.514 Sum_probs=73.3
Q ss_pred CCCCCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCC
Q psy6599 11 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 90 (93)
Q Consensus 11 ~~~~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 90 (93)
+++...+|.|||++++++||||.+|+||++||||++..+..|.|..+++ ++|.++...|..|++|||+|||++||+++
T Consensus 2 ~~~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~--~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~ 79 (92)
T cd07163 2 SRILDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQ--GGCPVDKTHRNQCRACRLKKCFEVGMNKD 79 (92)
T ss_pred CcccCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCC--CCCccCCCccccCccchhhhhhhhcCCHH
Confidence 5567889999999999999999999999999999999888999987421 36999998899999999999999999999
Q ss_pred CCC
Q psy6599 91 DFK 93 (93)
Q Consensus 91 ~vq 93 (93)
+||
T Consensus 80 ~Vq 82 (92)
T cd07163 80 AVQ 82 (92)
T ss_pred Hhh
Confidence 886
No 5
>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=99.97 E-value=2.1e-31 Score=165.18 Aligned_cols=77 Identities=43% Similarity=0.966 Sum_probs=71.7
Q ss_pred CCCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCC
Q psy6599 13 LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDF 92 (93)
Q Consensus 13 ~~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~v 92 (93)
+...+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++|
T Consensus 16 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V 91 (101)
T cd07160 16 LGNEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGG----KCQMDMYMRRKCQECRLRKCREAGMREQCV 91 (101)
T ss_pred cCCCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCC----ccccCCcccccCccchhHHHHHhCCCHHHh
Confidence 4567899999999999999999999999999999988999999865 699999999999999999999999999988
Q ss_pred C
Q psy6599 93 K 93 (93)
Q Consensus 93 q 93 (93)
|
T Consensus 92 ~ 92 (101)
T cd07160 92 L 92 (101)
T ss_pred c
Confidence 6
No 6
>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=99.97 E-value=1.4e-31 Score=164.97 Aligned_cols=76 Identities=45% Similarity=0.946 Sum_probs=70.4
Q ss_pred CCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
...+|.|||++++|+||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 3 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq 78 (97)
T cd07170 3 PKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATN----ECEITKRRRKSCQACRFMKCLKVGMLKEGVR 78 (97)
T ss_pred CCCCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCC----ccccCcccCccCCccccchhhhcCCCHHHcc
Confidence 346799999999999999999999999999999998889998764 6999999999999999999999999999886
No 7
>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=99.97 E-value=1.7e-31 Score=157.20 Aligned_cols=72 Identities=56% Similarity=1.271 Sum_probs=68.0
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.++...+..|++|||+|||++||++++||
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 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNR----NCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCC----cCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 78999999999999999999999999999998889998764 6999999999999999999999999999987
No 8
>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=99.97 E-value=2.8e-31 Score=156.22 Aligned_cols=73 Identities=47% Similarity=1.065 Sum_probs=68.4
Q ss_pred CceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.++...+..|++|||+|||++||+++.|+
T Consensus 1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (73)
T cd06959 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGN----KCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73 (73)
T ss_pred CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCC----cCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence 599999999999999999999999999999988889998764 6999999999999999999999999999875
No 9
>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=99.97 E-value=2.9e-31 Score=161.98 Aligned_cols=74 Identities=43% Similarity=0.980 Sum_probs=69.6
Q ss_pred CCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 16 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 16 ~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
++|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~ 75 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGR----ACEMDMYMRRKCQECRLKKCLSVGMRPECVV 75 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCC----ccccCccccccCccchhhHHhHcCCCHHHcC
Confidence 5699999999999999999999999999999999999998764 6999999999999999999999999999886
No 10
>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=99.97 E-value=1.6e-31 Score=157.98 Aligned_cols=72 Identities=47% Similarity=1.059 Sum_probs=68.0
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++|||+.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 72 (75)
T cd07155 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTS----ECEVDKKRRKSCQACRLQKCLKVGMLKEGVR 72 (75)
T ss_pred CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCC----CcccCCcccccCccchhhhhhHhCCCHHHcc
Confidence 78999999999999999999999999999988899998765 6999999999999999999999999999886
No 11
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=99.97 E-value=2.5e-31 Score=156.82 Aligned_cols=72 Identities=39% Similarity=1.024 Sum_probs=67.9
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.++...+..|++|||+|||++||++++|+
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (74)
T cd07179 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQ----NCAITPATRNACKSCRFRRCLAVGMSKTGSR 72 (74)
T ss_pred CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCC----ccccCCcccccCccchhHHHHHhCCCHhHee
Confidence 78999999999999999999999999999999999999865 5999999999999999999999999999985
No 12
>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=99.97 E-value=2e-31 Score=159.91 Aligned_cols=74 Identities=49% Similarity=1.060 Sum_probs=69.2
Q ss_pred CCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 16 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 16 ~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
.+|.|||++++++|||+.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 77 (82)
T cd07171 4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATN----QCTIDKNRRKSCQACRLRKCYEVGMMKGGIR 77 (82)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCC----ccccCCcccccCccchhHHHhHhcCCHHHHH
Confidence 5799999999999999999999999999999998899998764 6999999999999999999999999999875
No 13
>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=99.97 E-value=7.5e-32 Score=162.76 Aligned_cols=76 Identities=51% Similarity=1.133 Sum_probs=70.4
Q ss_pred CCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
.+.+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 3 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 78 (85)
T cd06964 3 IYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDK----NCIINKVTRNRCQYCRLQKCFEVGMSKESVR 78 (85)
T ss_pred cCCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCC----ccccCCcccccCccchhhhhhhhCCCHHHhh
Confidence 346899999999999999999999999999999988889998765 6999999999999999999999999999886
No 14
>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=99.97 E-value=5.8e-31 Score=156.62 Aligned_cols=75 Identities=43% Similarity=0.919 Sum_probs=69.4
Q ss_pred CCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 15 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 15 ~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
..+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++.+++
T Consensus 2 ~~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (78)
T cd07172 2 QKICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRN----DCIIDKIRRKNCPACRLRKCLQAGMNLGARK 76 (78)
T ss_pred CCCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCC----ccccCCcccccCccchhHHHHHhCCCccccc
Confidence 45799999999999999999999999999999999999998764 6999999999999999999999999998864
No 15
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=99.97 E-value=2.1e-31 Score=160.81 Aligned_cols=73 Identities=48% Similarity=1.149 Sum_probs=68.9
Q ss_pred CceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
+|.|||++++++|||+.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (85)
T cd06961 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEG----KCEIDKVTRNQCQECRFKKCIAVGMAKDLVL 73 (85)
T ss_pred CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCC----ccccCccccccCccchhhhhhhccCCHHHcc
Confidence 599999999999999999999999999999999999999865 6999999999999999999999999999886
No 16
>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=99.97 E-value=1.7e-31 Score=160.85 Aligned_cols=74 Identities=46% Similarity=1.006 Sum_probs=69.4
Q ss_pred CCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 16 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 16 ~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
++|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~ 75 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGG----NCEMDMYMRRKCQECRLRKCKEMGMLAECLL 75 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCC----cCccCccccccCccchhhHHHHhCCChHHcc
Confidence 5799999999999999999999999999999988899998765 6999998899999999999999999999886
No 17
>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=99.97 E-value=1.4e-31 Score=157.47 Aligned_cols=73 Identities=71% Similarity=1.399 Sum_probs=67.5
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++|||+.+|+||++||||++..+..|.|...+ ++|.|+...+..|++|||+|||++||++++||
T Consensus 1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGN---GSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCC---CCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 78999999999999999999999999999999999998432 26999999999999999999999999999997
No 18
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=99.97 E-value=4e-31 Score=155.57 Aligned_cols=72 Identities=47% Similarity=1.164 Sum_probs=67.9
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCcee-ccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~-~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|++|++||||++..+..| .|..++ +|.|+...+..|++|||+|||++||++++||
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 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGG----KCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCC----CcCCCccccccCccchhhhhhHccCChHHcC
Confidence 78999999999999999999999999999998888 898765 5999999999999999999999999999986
No 19
>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=99.97 E-value=3.5e-31 Score=155.48 Aligned_cols=72 Identities=46% Similarity=1.083 Sum_probs=67.5
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.++...+..|++|||+|||++||++++|.
T Consensus 1 C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd07156 1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNG----DCEITKDNRRHCQACRLKKCLDIGMKKEMIL 72 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCC----ccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence 78999999999999999999999999999988889998764 6999999999999999999999999999874
No 20
>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=99.97 E-value=6.1e-31 Score=154.81 Aligned_cols=72 Identities=43% Similarity=0.983 Sum_probs=67.5
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||+++++.
T Consensus 1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRN----DCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCC----ccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 78999999999999999999999999999999889998765 6999999999999999999999999999873
No 21
>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=99.96 E-value=1.8e-31 Score=156.64 Aligned_cols=72 Identities=56% Similarity=1.255 Sum_probs=68.2
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGG----NCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCC----ccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 78999999999999999999999999999988889998765 6999999999999999999999999999997
No 22
>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=99.96 E-value=6.5e-31 Score=164.42 Aligned_cols=78 Identities=42% Similarity=0.971 Sum_probs=71.5
Q ss_pred CCCCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCC
Q psy6599 12 RLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDD 91 (93)
Q Consensus 12 ~~~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~ 91 (93)
...+.+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++
T Consensus 3 ~~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~ 78 (107)
T cd06955 3 RNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNG----DCRITKDNRRHCQACRLKRCVDIGMMKEF 78 (107)
T ss_pred CCCCCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCC----ccccccCCccccccchhHHHHHcCCCchh
Confidence 34668899999999999999999999999999999999999998764 69999988999999999999999999987
Q ss_pred CC
Q psy6599 92 FK 93 (93)
Q Consensus 92 vq 93 (93)
|+
T Consensus 79 v~ 80 (107)
T cd06955 79 IL 80 (107)
T ss_pred cc
Confidence 75
No 23
>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=6.1e-31 Score=160.28 Aligned_cols=76 Identities=43% Similarity=1.045 Sum_probs=70.5
Q ss_pred CCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
.+.+|.|||++++++|||+.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 5 ~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 80 (90)
T cd07168 5 SPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDG----RCEITKAQRNRCQYCRFRKCIRKGMMLAAVR 80 (90)
T ss_pred cCCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCC----CccccccccccccccchhhhhhcCCCHHHhh
Confidence 456799999999999999999999999999999998899999764 6999999999999999999999999998876
No 24
>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=3.3e-31 Score=160.56 Aligned_cols=76 Identities=50% Similarity=1.085 Sum_probs=70.3
Q ss_pred CCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
..++|.|||++++++|||+.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 2 ~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq 77 (87)
T cd06967 2 PVELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSK----DCVINKHHRNRCQYCRLQKCLAMGMKSDSVQ 77 (87)
T ss_pred CCCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCC----ccccCccccccCccchhhhhhHcCCCHHHhc
Confidence 346799999999999999999999999999999988889998764 6999999999999999999999999999886
No 25
>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=99.96 E-value=7.6e-31 Score=159.83 Aligned_cols=77 Identities=47% Similarity=1.066 Sum_probs=71.2
Q ss_pred CCCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCC
Q psy6599 13 LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDF 92 (93)
Q Consensus 13 ~~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~v 92 (93)
....+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++|
T Consensus 4 ~~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v 79 (90)
T cd07169 4 AEQRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDK----NCVMSRKQRNRCQYCRLLKCLQMGMNRKAI 79 (90)
T ss_pred ccCCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCC----cccccccccccccccchhhhccccCCHHHh
Confidence 4567799999999999999999999999999999999999998764 699999999999999999999999999988
Q ss_pred C
Q psy6599 93 K 93 (93)
Q Consensus 93 q 93 (93)
|
T Consensus 80 ~ 80 (90)
T cd07169 80 R 80 (90)
T ss_pred c
Confidence 6
No 26
>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=4.6e-31 Score=161.34 Aligned_cols=75 Identities=64% Similarity=1.367 Sum_probs=69.1
Q ss_pred CCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 16 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 16 ~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
++|.|||++++++|||+.+|+||++||||++..+..|.|..+. ++|.++...|..|++|||+|||++||++++||
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 81 (92)
T cd06970 7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGT---GMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQ 81 (92)
T ss_pred CCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCC---CcCccCCCccccCccchhhHhhHhCCCHHHcc
Confidence 4699999999999999999999999999999999999998752 26999998899999999999999999999886
No 27
>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=1.4e-30 Score=155.00 Aligned_cols=72 Identities=61% Similarity=1.294 Sum_probs=67.8
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++|||+.+|++|++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 72 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENG----SCVVDVARRNQCQACRFKKCLQVNMNRDAVQ 72 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCC----cccccCcccccCccchhhhhhHhcCCHHHhc
Confidence 78999999999999999999999999999988899998865 6999999999999999999999999999886
No 28
>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=99.96 E-value=2.1e-30 Score=157.02 Aligned_cols=73 Identities=45% Similarity=1.023 Sum_probs=68.2
Q ss_pred CceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
+|.|||++++++|||+.+|+||++||||++..+..|.|..++ +|.++...+..|++|||+|||++||++++||
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 73 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQK----GCVITKSNRRQCQACRLRKCLSIGMKKELIM 73 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCC----ceecCCcccccCccchhhHHhHhCCCHHHcc
Confidence 499999999999999999999999999999988889998764 5999999999999999999999999999875
No 29
>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=99.96 E-value=3.5e-30 Score=154.54 Aligned_cols=73 Identities=41% Similarity=0.960 Sum_probs=67.5
Q ss_pred CCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCC
Q psy6599 15 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDD 91 (93)
Q Consensus 15 ~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~ 91 (93)
..+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||+++.
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~ 75 (82)
T cd07173 3 QKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRN----DCTIDKFRRKNCPSCRLRKCFEAGMTLGA 75 (82)
T ss_pred CCCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCC----ccccCCCccCcCcchhhhhhhhcCCCcCh
Confidence 35699999999999999999999999999999999999998765 69999999999999999999999999874
No 30
>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=8.3e-31 Score=155.26 Aligned_cols=72 Identities=53% Similarity=1.261 Sum_probs=67.8
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGG----NCVVDKDKRNACRYCRFKKCLEVGMDPEAVQ 72 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCC----cccccCcccccCccchhhhhhhcCCCHHHcc
Confidence 78999999999999999999999999999988899998765 6999999999999999999999999999886
No 31
>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=4.7e-31 Score=158.34 Aligned_cols=73 Identities=58% Similarity=1.230 Sum_probs=67.5
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|+||++||||++..+..|.|...+ ++|.|+...+..|++|||+|||++||++++||
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~---~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGN---GNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQ 73 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCcc---CCCccCCCccCcccCcchhhcccccCCHHHhc
Confidence 78999999999999999999999999999998999998532 26999999999999999999999999999886
No 32
>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=99.96 E-value=2e-30 Score=159.32 Aligned_cols=77 Identities=52% Similarity=1.159 Sum_probs=71.1
Q ss_pred CCCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCC
Q psy6599 13 LLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDF 92 (93)
Q Consensus 13 ~~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~v 92 (93)
+...+|.|||++++++|||+.+|++|++||||++..+..|.|..++ +|.++...+..|++|||+|||++||++++|
T Consensus 3 ~~~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V 78 (95)
T cd06968 3 IEVIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQK----NCLIDRTNRNRCQHCRLQKCLALGMSRDAV 78 (95)
T ss_pred ccccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCc----ccccccCCceeccccchhhcccccCChhhc
Confidence 3456899999999999999999999999999999988889998764 699999999999999999999999999988
Q ss_pred C
Q psy6599 93 K 93 (93)
Q Consensus 93 q 93 (93)
|
T Consensus 79 ~ 79 (95)
T cd06968 79 K 79 (95)
T ss_pred c
Confidence 6
No 33
>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=99.96 E-value=1e-30 Score=158.98 Aligned_cols=75 Identities=44% Similarity=1.074 Sum_probs=69.3
Q ss_pred CCCceecCCCCceeeeCcccchhhhhhhhhhhccCcee-ccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 15 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 15 ~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~-~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
..+|.|||++++++|||+.+|+||++||||++..+..| .|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~ 78 (89)
T cd07166 3 VVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNE----TCSIMRINRNRCQYCRFKKCLAVGMSRDAVR 78 (89)
T ss_pred CCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCC----cccccccccccccchhhhhcccccCCHHHhc
Confidence 46799999999999999999999999999999988888 598765 6999999999999999999999999999886
No 34
>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=99.96 E-value=1.8e-30 Score=158.97 Aligned_cols=72 Identities=44% Similarity=1.097 Sum_probs=67.9
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~----~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq 72 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQ----NCQIDKTQRKRCPYCRFQKCLSVGMKLEAVR 72 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCC----ccccCccccCcCCCcccchhhhccCCHHHhh
Confidence 78999999999999999999999999999999999999865 6999999999999999999999999998876
No 35
>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=99.96 E-value=2.9e-30 Score=154.63 Aligned_cols=72 Identities=50% Similarity=1.175 Sum_probs=67.9
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
|.|||++++++|||+.+|+||++||||++..+..|.|..++ +|.|+...+..|++|||+|||++||++++||
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~ 72 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDG----KCEIIRLNRNRCQYCRFKKCLAAGMSKDSVR 72 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCC----CccccccccccccchhhhhcccccCCHHHcc
Confidence 78999999999999999999999999999988889998865 6999999999999999999999999999886
No 36
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=99.96 E-value=1.6e-30 Score=159.53 Aligned_cols=73 Identities=34% Similarity=0.875 Sum_probs=68.7
Q ss_pred CceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.++...+..|++|||+|||++||++++||
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 74 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNE----SCEINVVTRRFCQKCRLDKCFAIGMKKEWIM 74 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCC----ccccCccccccCccchhhhCcccCCCHHHcc
Confidence 699999999999999999999999999999988889999765 6999999999999999999999999999886
No 37
>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=4.4e-30 Score=155.35 Aligned_cols=73 Identities=38% Similarity=0.883 Sum_probs=66.4
Q ss_pred CceecCCCCceeeeCcccchhhhhhhhhhhccCc--eeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNR--VYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~--~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
+|.|||++++++||||.+|+||++||||++..+. .|.|..++ +|.++...+..|++|||+|||++||++++++
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~----~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~ 76 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGG----KCIIDKKNRTKCQACRYRKCLNVGMSLGGPR 76 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCC----ccccCccccccCccchhhHHhHcCCCccccc
Confidence 6999999999999999999999999999998664 78898764 6999988899999999999999999988764
No 38
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.95 E-value=1.7e-29 Score=147.50 Aligned_cols=70 Identities=43% Similarity=1.019 Sum_probs=65.5
Q ss_pred CceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCC
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 90 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 90 (93)
+|.|||++++++||||.+|+||++||||++..+..|.|..++ +|.++...+..|++|||+|||++||+++
T Consensus 1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~----~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKN----NCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCc----ccccCCCccccCccCcChhHhhccCcCC
Confidence 599999999999999999999999999999988889999875 5999999999999999999999999975
No 39
>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=99.95 E-value=8.7e-30 Score=153.46 Aligned_cols=71 Identities=45% Similarity=1.125 Sum_probs=65.6
Q ss_pred CceecCCCCceeeeCcccchhhhhhhhhhhccCceec-cccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYT-CKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~-C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
+|.|||++++++||||.+|+||++||||++..+..|. |.. .|.|+...+..|++|||+|||++||++++||
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~------~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~ 72 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDL------SCKIHKKSRNKCQYCRFQKCLNVGMSHNAIR 72 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCcccccc------CCCcCccccccccchhhhhhhhccCCHHHcc
Confidence 5999999999999999999999999999999888884 864 3999999999999999999999999999886
No 40
>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=99.95 E-value=2.6e-29 Score=146.51 Aligned_cols=70 Identities=50% Similarity=1.164 Sum_probs=61.1
Q ss_pred CCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCC
Q psy6599 16 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNK 89 (93)
Q Consensus 16 ~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~ 89 (93)
.+|+|||++++++||||.+|++|++||+|++..+..+.|..++ +|.++...+..|++|||+|||++||++
T Consensus 1 ~~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~----~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 1 KKCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNG----NCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp -BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSS----T---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred CCCeECCCccCcccccccccccceeeeeecccccccccccccc----cccccccCCCEeCcchHHHHHHHCCcC
Confidence 3699999999999999999999999999999998889999875 599998888999999999999999974
No 41
>KOG4846|consensus
Probab=99.95 E-value=1.7e-29 Score=185.85 Aligned_cols=74 Identities=46% Similarity=1.069 Sum_probs=69.9
Q ss_pred CCceecCCCCceeeeCcccchhhhhhhhhhhccCcee-ccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 16 IPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVY-TCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 16 ~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~-~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
..|+||||.++||||||.+|++||+||||+|+.+..| .|-+.. +|.|...+|++|++|||+|||+|||++++|+
T Consensus 133 ~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e----~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVR 207 (538)
T KOG4846|consen 133 SLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQE----VCEIKRENRNRCQYCRFKKCLDVGMSRDAVR 207 (538)
T ss_pred EeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhh----ceehhhhccchhhhhhHHHHHhcccchhhhh
Confidence 5699999999999999999999999999999999999 688764 6999999999999999999999999999986
No 42
>KOG4216|consensus
Probab=99.94 E-value=2.2e-28 Score=178.75 Aligned_cols=75 Identities=53% Similarity=1.184 Sum_probs=71.2
Q ss_pred CCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 15 DIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 15 ~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
-.||.||||.++|.||||.+|++||+||||+-..+..|.|.++. +|.|+..+|++|++|||+|||++||+.+||.
T Consensus 46 vIPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqk----nC~iDRtnRNRCQ~CRLqKClaLGMSRDAVK 120 (479)
T KOG4216|consen 46 IIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQK----NCLIDRTNRNRCQHCRLQKCLALGMSRDAVK 120 (479)
T ss_pred EEeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCccc----CCcccccccchhhHHHHHHHHHhccchhhHH
Confidence 36799999999999999999999999999999999999999986 6999999999999999999999999999874
No 43
>KOG4217|consensus
Probab=99.94 E-value=8e-28 Score=179.11 Aligned_cols=76 Identities=43% Similarity=1.061 Sum_probs=71.5
Q ss_pred CCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCCCCC
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKDDFK 93 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~~vq 93 (93)
....|.||||.+.--||||.+|++||+||+|||+++..|+|..++ +|+|++..|++|++|||||||+|||-+|-||
T Consensus 268 ~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanK----nCPVDKRrRnRCQyCRfQKCL~VGMVKEVVR 343 (605)
T KOG4217|consen 268 AEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANK----NCPVDKRRRNRCQYCRFQKCLAVGMVKEVVR 343 (605)
T ss_pred ccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCC----CCCcchhhhhhchhhhHhHHHHhhhhhhhee
Confidence 457899999999999999999999999999999999999999986 6999999999999999999999999887664
No 44
>KOG4218|consensus
Probab=99.92 E-value=3.2e-26 Score=165.85 Aligned_cols=79 Identities=44% Similarity=1.043 Sum_probs=73.9
Q ss_pred CCCCCCCceecCCCCceeeeCcccchhhhhhhhhhhccCceeccccCCCCCCCCCCCCCCCCCCcchHHHHhHHhcCCCC
Q psy6599 11 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKRSIHRNRVYTCKAQGDLKGHCPIDKTHRNQCRACRLNKCFMSAMNKD 90 (93)
Q Consensus 11 ~~~~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR~~~~~~~~~C~~~~~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 90 (93)
+.-..+.|.||||..+|||||..+|++||+||+|+++.++.|.|..+. +|.|++..|.+|.+|||+|||.+||+.|
T Consensus 11 dedl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~q----nC~iDkTqRKRCP~CRFQKCLtvGMklE 86 (475)
T KOG4218|consen 11 DEDLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQ----NCHIDKTQRKRCPSCRFQKCLTVGMKLE 86 (475)
T ss_pred ccccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceeccccc----ccccchHhhccCCchhHHHHhhhhhhHH
Confidence 445678999999999999999999999999999999999999998875 6999999999999999999999999999
Q ss_pred CCC
Q psy6599 91 DFK 93 (93)
Q Consensus 91 ~vq 93 (93)
||+
T Consensus 87 AVR 89 (475)
T KOG4218|consen 87 AVR 89 (475)
T ss_pred HHH
Confidence 885
No 45
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=74.45 E-value=2.5 Score=22.45 Aligned_cols=24 Identities=38% Similarity=1.110 Sum_probs=19.1
Q ss_pred CceecCCCC-ceee-eCcccchhhhh
Q psy6599 17 PCKVCGDRS-SGKH-YGIYSCDGCSG 40 (93)
Q Consensus 17 ~C~VCg~~~-~~~h-yGv~~C~~C~~ 40 (93)
.|.||+.+. .|.| ||...|..|-.
T Consensus 1 ~CiiC~~~~~~GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEEGIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCCCEEEECeEehHHHHH
Confidence 489999874 4765 99999999963
No 46
>PRK00420 hypothetical protein; Validated
Probab=71.45 E-value=1.5 Score=27.71 Aligned_cols=31 Identities=23% Similarity=0.397 Sum_probs=25.7
Q ss_pred CCCCCCceecCCCCceeeeCcccchhhhhhh
Q psy6599 12 RLLDIPCKVCGDRSSGKHYGIYSCDGCSGFF 42 (93)
Q Consensus 12 ~~~~~~C~VCg~~~~~~hyGv~~C~~C~~FF 42 (93)
.+....|++||.+-...+-|...|..|..+.
T Consensus 20 ~ml~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 20 KMLSKHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred HHccCCCCCCCCcceecCCCceECCCCCCee
Confidence 3456889999999888888999999998754
No 47
>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=70.50 E-value=2 Score=26.76 Aligned_cols=32 Identities=28% Similarity=0.695 Sum_probs=21.3
Q ss_pred CCCCCceecCCCCce---eeeCcccchhhhhhhhh
Q psy6599 13 LLDIPCKVCGDRSSG---KHYGIYSCDGCSGFFKR 44 (93)
Q Consensus 13 ~~~~~C~VCg~~~~~---~hyGv~~C~~C~~FFrR 44 (93)
.....|.-||.+... ..||+..|..|++..|.
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~ 45 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRS 45 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHH
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHH
Confidence 345679999987643 58999999999998654
No 48
>KOG2879|consensus
Probab=57.22 E-value=12 Score=27.29 Aligned_cols=52 Identities=23% Similarity=0.331 Sum_probs=32.4
Q ss_pred CCCCCCCCCCCCCCCCceecCCCCceeeeC----cccchhhhhhhhhhhccCceecccc
Q psy6599 2 NVGTDNSLGDRLLDIPCKVCGDRSSGKHYG----IYSCDGCSGFFKRSIHRNRVYTCKA 56 (93)
Q Consensus 2 ~~~~~~~~~~~~~~~~C~VCg~~~~~~hyG----v~~C~~C~~FFrR~~~~~~~~~C~~ 56 (93)
+.+++.+.+.......|.+||.+....|-+ ...|..|..- +..-...+.|..
T Consensus 226 ~~ap~~sss~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~t---s~~~~asf~Cp~ 281 (298)
T KOG2879|consen 226 DRAPKFSSSTGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIAT---SRLWDASFTCPL 281 (298)
T ss_pred cCCCCcccccccCCceeeccCCCCCCCeeeccccceeehhhhhh---hhcchhhcccCc
Confidence 445666677777788899999887665543 3567777631 222233456654
No 49
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=56.09 E-value=7.9 Score=20.81 Aligned_cols=31 Identities=23% Similarity=0.607 Sum_probs=22.1
Q ss_pred CCCceecCCCCce-e---eeCc-ccchhhhhhhhhh
Q psy6599 15 DIPCKVCGDRSSG-K---HYGI-YSCDGCSGFFKRS 45 (93)
Q Consensus 15 ~~~C~VCg~~~~~-~---hyGv-~~C~~C~~FFrR~ 45 (93)
+..|..|+...+- . -.|. ..|++|..+|+..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~ 38 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKH 38 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHc
Confidence 4678889876543 2 3454 7899999999864
No 50
>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=56.01 E-value=5.1 Score=18.99 Aligned_cols=21 Identities=33% Similarity=0.865 Sum_probs=14.5
Q ss_pred CceecCCCCceeeeCcccchhhh
Q psy6599 17 PCKVCGDRSSGKHYGIYSCDGCS 39 (93)
Q Consensus 17 ~C~VCg~~~~~~hyGv~~C~~C~ 39 (93)
.|.||+...+++. ...|..|.
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 4788888888874 44666655
No 51
>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=53.78 E-value=5.7 Score=19.51 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=9.5
Q ss_pred CCCCceecCCCCce
Q psy6599 14 LDIPCKVCGDRSSG 27 (93)
Q Consensus 14 ~~~~C~VCg~~~~~ 27 (93)
.+..|.|||.+...
T Consensus 17 ~p~~CP~Cg~~~~~ 30 (34)
T cd00729 17 APEKCPICGAPKEK 30 (34)
T ss_pred CCCcCcCCCCchHH
Confidence 45678888876543
No 52
>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=52.27 E-value=9.5 Score=23.58 Aligned_cols=30 Identities=27% Similarity=0.736 Sum_probs=23.8
Q ss_pred CCCceecCCCCc---eeeeCcccchhhhhhhhh
Q psy6599 15 DIPCKVCGDRSS---GKHYGIYSCDGCSGFFKR 44 (93)
Q Consensus 15 ~~~C~VCg~~~~---~~hyGv~~C~~C~~FFrR 44 (93)
...|.-|+.+.. ...||+..|..|.+.-|.
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~ 35 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHRS 35 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHHh
Confidence 456888887643 468999999999998765
No 53
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=50.09 E-value=8.5 Score=23.50 Aligned_cols=21 Identities=33% Similarity=0.847 Sum_probs=16.6
Q ss_pred CCCceecCCCCceeeeCcccchhhhh
Q psy6599 15 DIPCKVCGDRSSGKHYGIYSCDGCSG 40 (93)
Q Consensus 15 ~~~C~VCg~~~~~~hyGv~~C~~C~~ 40 (93)
...|.+||.++++- .|.+|+.
T Consensus 80 ~~~C~~CG~pss~~-----iC~~C~l 100 (104)
T TIGR00269 80 LRRCERCGEPTSGR-----ICKACKF 100 (104)
T ss_pred CCcCCcCcCcCCcc-----ccHhhhh
Confidence 35699999999863 7888873
No 54
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=48.63 E-value=9.4 Score=21.03 Aligned_cols=23 Identities=35% Similarity=1.003 Sum_probs=18.3
Q ss_pred CCceecCCCCc-eeeeCcccchhh
Q psy6599 16 IPCKVCGDRSS-GKHYGIYSCDGC 38 (93)
Q Consensus 16 ~~C~VCg~~~~-~~hyGv~~C~~C 38 (93)
..|.|||.+.. ...||...|.-|
T Consensus 17 r~C~vCg~~~gliRkygL~~CRqC 40 (54)
T PTZ00218 17 RQCRVCSNRHGLIRKYGLNVCRQC 40 (54)
T ss_pred CeeecCCCcchhhhhcCcchhhHH
Confidence 66999998753 457999888877
No 55
>PHA03124 dUTPase; Provisional
Probab=45.65 E-value=11 Score=28.84 Aligned_cols=16 Identities=31% Similarity=1.014 Sum_probs=13.0
Q ss_pred cccchhhhhhhhhhhc
Q psy6599 32 IYSCDGCSGFFKRSIH 47 (93)
Q Consensus 32 v~~C~~C~~FFrR~~~ 47 (93)
-.-|-+|++||||...
T Consensus 190 ~~~~~~~~~~~~~~~~ 205 (418)
T PHA03124 190 NFGCMGCKAFYRRLFE 205 (418)
T ss_pred cccccchHHHHHHHHH
Confidence 3459999999999864
No 56
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=44.53 E-value=16 Score=31.19 Aligned_cols=36 Identities=25% Similarity=0.617 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCCCCCCCceecCCC----CceeeeCcccchhh
Q psy6599 1 MNVGTDNSLGDRLLDIPCKVCGDR----SSGKHYGIYSCDGC 38 (93)
Q Consensus 1 ~~~~~~~~~~~~~~~~~C~VCg~~----~~~~hyGv~~C~~C 38 (93)
|++-.+....+......|+|||+. .+|--| .+|+.|
T Consensus 1 ~~~~~~~~~~~~~~~~~c~iCGd~vg~~~~Ge~F--VAC~eC 40 (1044)
T PLN02915 1 MDDEDRPPTRQSADAKTCRVCGDEVGVKEDGQPF--VACHVC 40 (1044)
T ss_pred CCcccCCccccCCCcchhhccccccCcCCCCCEE--EEeccC
Confidence 455555556667777889999986 345444 344444
No 57
>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=42.83 E-value=5.9 Score=16.89 Aligned_cols=10 Identities=40% Similarity=1.142 Sum_probs=7.0
Q ss_pred hhhhhhhhhh
Q psy6599 37 GCSGFFKRSI 46 (93)
Q Consensus 37 ~C~~FFrR~~ 46 (93)
+|+.||..+.
T Consensus 6 ~CknffWK~~ 15 (18)
T PF03002_consen 6 GCKNFFWKTF 15 (18)
T ss_pred cccceeeccc
Confidence 5888887553
No 58
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=40.31 E-value=10 Score=19.55 Aligned_cols=27 Identities=30% Similarity=0.604 Sum_probs=16.4
Q ss_pred CCCCCCceecCCCCceeeeCcccchhh
Q psy6599 12 RLLDIPCKVCGDRSSGKHYGIYSCDGC 38 (93)
Q Consensus 12 ~~~~~~C~VCg~~~~~~hyGv~~C~~C 38 (93)
.+..+.|..|+.+-...+=|...|-.|
T Consensus 14 ~ML~~~Cp~C~~PL~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 14 TMLDEHCPDCGTPLMRDKDGKIYCVSC 40 (41)
T ss_pred hHhcCccCCCCCeeEEecCCCEECCCC
Confidence 355677888877655544455555544
No 59
>PRK12495 hypothetical protein; Provisional
Probab=35.66 E-value=15 Score=25.94 Aligned_cols=33 Identities=21% Similarity=0.424 Sum_probs=25.8
Q ss_pred CCCCCCCceecCCCCceeeeCcccchhhhhhhhh
Q psy6599 11 DRLLDIPCKVCGDRSSGKHYGIYSCDGCSGFFKR 44 (93)
Q Consensus 11 ~~~~~~~C~VCg~~~~~~hyGv~~C~~C~~FFrR 44 (93)
..+....|.+||.+...+ =|+..|-.|...+-+
T Consensus 38 atmsa~hC~~CG~PIpa~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 38 ATMTNAHCDECGDPIFRH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred cccchhhcccccCcccCC-CCeeECCCCCCcccc
Confidence 345667899999998843 699999999976643
No 60
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=35.45 E-value=17 Score=17.90 Aligned_cols=16 Identities=25% Similarity=0.717 Sum_probs=12.0
Q ss_pred eCcc-cchhhhhhhhhh
Q psy6599 30 YGIY-SCDGCSGFFKRS 45 (93)
Q Consensus 30 yGv~-~C~~C~~FFrR~ 45 (93)
.|.. .|++|-.+|++.
T Consensus 17 ~g~~~LCn~Cg~~~kk~ 33 (36)
T PF00320_consen 17 NGNRTLCNACGLYYKKY 33 (36)
T ss_dssp TSEE-EEHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 3444 799999998864
No 61
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=34.16 E-value=25 Score=24.08 Aligned_cols=34 Identities=21% Similarity=0.551 Sum_probs=25.6
Q ss_pred CCCceecCCCCceeee---Ccccchhhhhhhhhhhcc
Q psy6599 15 DIPCKVCGDRSSGKHY---GIYSCDGCSGFFKRSIHR 48 (93)
Q Consensus 15 ~~~C~VCg~~~~~~hy---Gv~~C~~C~~FFrR~~~~ 48 (93)
...|.+|.+....|-| .+..|..|++.|.+....
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~ 188 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR 188 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC
Confidence 4579999987766655 457799999999876543
No 62
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain 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), but iron can also be replaced by cobalt, nickel or zinc 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=33.63 E-value=16 Score=17.62 Aligned_cols=14 Identities=29% Similarity=0.601 Sum_probs=9.4
Q ss_pred CCCCceecCCCCce
Q psy6599 14 LDIPCKVCGDRSSG 27 (93)
Q Consensus 14 ~~~~C~VCg~~~~~ 27 (93)
.+..|.+||.+...
T Consensus 16 ~~~~CP~Cg~~~~~ 29 (33)
T cd00350 16 APWVCPVCGAPKDK 29 (33)
T ss_pred CCCcCcCCCCcHHH
Confidence 55678888876543
No 63
>KOG3277|consensus
Probab=33.56 E-value=16 Score=24.46 Aligned_cols=26 Identities=38% Similarity=0.917 Sum_probs=19.1
Q ss_pred CceecCCCCce------eeeCcc--cchhhhhhh
Q psy6599 17 PCKVCGDRSSG------KHYGIY--SCDGCSGFF 42 (93)
Q Consensus 17 ~C~VCg~~~~~------~hyGv~--~C~~C~~FF 42 (93)
.|.||+.+++- ||-|+. .|.+|+.+.
T Consensus 81 TCkvCntRs~ktisk~AY~~GvVivqC~gC~~~H 114 (165)
T KOG3277|consen 81 TCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH 114 (165)
T ss_pred EeeccCCccccccChhhhhCceEEEECCCCccce
Confidence 39999987642 566754 699998764
No 64
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.09 E-value=28 Score=18.18 Aligned_cols=13 Identities=38% Similarity=0.743 Sum_probs=9.3
Q ss_pred CCCCCCceecCCC
Q psy6599 12 RLLDIPCKVCGDR 24 (93)
Q Consensus 12 ~~~~~~C~VCg~~ 24 (93)
.+....|.|||.+
T Consensus 5 ~lp~K~C~~C~rp 17 (42)
T PF10013_consen 5 NLPSKICPVCGRP 17 (42)
T ss_pred cCCCCcCcccCCc
Confidence 3455779999865
No 65
>PF00357 Integrin_alpha: Integrin alpha cytoplasmic region; InterPro: IPR018184 Some alpha subunits are cleaved post- translationally to produce a heavy and a light chain linked by a disulphide bond [, ]. Integrin alpha chains share a conserved sequence which is found at the beginning of the cytoplasmic domain, just after the end of the transmembrane region. Within the N-terminal domain of alpha subunits, seven sequence repeats, each of approximately 60 amino acids, have been found []. It has been predicted that these repeats assume the beta-propeller fold. The domains contain seven four-stranded beta-sheets arranged in a torus around a pseudosymmetry axis []. Integrin ligands and a putative Mg2+ ion are predicted to bind to the upper face of the propeller, in a manner analogous to the way in which the trimeric G-protein beta subunit (G beta) (which also has a beta-propeller fold) binds the G protein alpha subunit []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences []. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first ten residues of the alpha-subunit cytoplasmic domain appear to form an alpha helix that is terminated by a proline residue. The remainder of the domain is highly acidic in nature and this loops back to contact the membrane-proximal lysine anchor residue. This entry represents the conserved site of the C-terminal integrin alpha chain. ; PDB: 2LKJ_A 2LKE_A 2K8O_A 1DPK_A 2K9J_A 1DPQ_A 1S4W_A 1M8O_A 2K1A_A 2KNC_A ....
Probab=32.69 E-value=19 Score=14.66 Aligned_cols=8 Identities=63% Similarity=1.049 Sum_probs=5.7
Q ss_pred hhhhhhhc
Q psy6599 40 GFFKRSIH 47 (93)
Q Consensus 40 ~FFrR~~~ 47 (93)
+||+|.-.
T Consensus 3 GFFKR~~~ 10 (15)
T PF00357_consen 3 GFFKRQRP 10 (15)
T ss_dssp CHHHHHHH
T ss_pred ccccccCc
Confidence 58988653
No 66
>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=32.27 E-value=22 Score=18.22 Aligned_cols=24 Identities=29% Similarity=0.959 Sum_probs=10.5
Q ss_pred CCCceecCCCCceeee------Ccccchhh
Q psy6599 15 DIPCKVCGDRSSGKHY------GIYSCDGC 38 (93)
Q Consensus 15 ~~~C~VCg~~~~~~hy------Gv~~C~~C 38 (93)
..+|++||....-..| |...|+.|
T Consensus 3 h~pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 3 HGPCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp EE--TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCCCcCccccccCcCcccCCCEECCCC
Confidence 3578899864322213 44556555
No 67
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=31.26 E-value=53 Score=18.57 Aligned_cols=24 Identities=25% Similarity=0.663 Sum_probs=19.6
Q ss_pred CCCCceecCCCCceeeeCcccchhhh
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCS 39 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~ 39 (93)
.+.+|..||.. .||.--..|.+|-
T Consensus 16 tHt~CrRCG~~--syh~qK~~CasCG 39 (62)
T PRK04179 16 THIRCRRCGRH--SYNVRKKYCAACG 39 (62)
T ss_pred ccchhcccCcc--cccccccchhhcC
Confidence 67889999977 4787778888886
No 68
>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=30.41 E-value=27 Score=17.60 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=7.4
Q ss_pred CCCceecCCC
Q psy6599 15 DIPCKVCGDR 24 (93)
Q Consensus 15 ~~~C~VCg~~ 24 (93)
..+|++||..
T Consensus 3 ~~pCP~CGG~ 12 (37)
T smart00778 3 HGPCPNCGGS 12 (37)
T ss_pred ccCCCCCCCc
Confidence 4678999864
No 69
>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=30.28 E-value=8.3 Score=19.96 Aligned_cols=25 Identities=32% Similarity=0.978 Sum_probs=15.6
Q ss_pred ceecCCCCceeeeCcccchhhhhhhhh
Q psy6599 18 CKVCGDRSSGKHYGIYSCDGCSGFFKR 44 (93)
Q Consensus 18 C~VCg~~~~~~hyGv~~C~~C~~FFrR 44 (93)
|.||+. ....-..+.|..|..+|..
T Consensus 2 C~vC~~--~~~~~~~i~C~~C~~~~H~ 26 (51)
T PF00628_consen 2 CPVCGQ--SDDDGDMIQCDSCNRWYHQ 26 (51)
T ss_dssp BTTTTS--SCTTSSEEEBSTTSCEEET
T ss_pred CcCCCC--cCCCCCeEEcCCCChhhCc
Confidence 677877 2223346678888876643
No 70
>TIGR03124 ctirate_citX holo-ACP synthase CitX. Members of this protein family are the CitX protein, or CitX domain of the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems.
Probab=29.45 E-value=23 Score=23.71 Aligned_cols=13 Identities=15% Similarity=0.501 Sum_probs=10.9
Q ss_pred CCCCceecCCCCc
Q psy6599 14 LDIPCKVCGDRSS 26 (93)
Q Consensus 14 ~~~~C~VCg~~~~ 26 (93)
.++.|.||++++.
T Consensus 129 ~~R~CliC~~~Ak 141 (165)
T TIGR03124 129 PPRKCLLCEEDAK 141 (165)
T ss_pred CCCeeecCCchHH
Confidence 5688999999874
No 71
>PRK08359 transcription factor; Validated
Probab=27.65 E-value=37 Score=23.04 Aligned_cols=31 Identities=26% Similarity=0.606 Sum_probs=22.0
Q ss_pred CCCCceecCCCCceeeeC-------cccchhhhhhhhh
Q psy6599 14 LDIPCKVCGDRSSGKHYG-------IYSCDGCSGFFKR 44 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyG-------v~~C~~C~~FFrR 44 (93)
.+..|-+||.+..|.-|- ...|..|+.=|..
T Consensus 5 ~~~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~G~ 42 (176)
T PRK08359 5 KPRYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKYGR 42 (176)
T ss_pred CcceeecCCCccCCCCeEEEEcCeEEehHHHHHHHhCC
Confidence 345699999998776333 3589999944444
No 72
>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=27.45 E-value=21 Score=16.62 Aligned_cols=14 Identities=36% Similarity=0.914 Sum_probs=4.7
Q ss_pred CceecCCCCce-eee
Q psy6599 17 PCKVCGDRSSG-KHY 30 (93)
Q Consensus 17 ~C~VCg~~~~~-~hy 30 (93)
+|.+|+.+..+ ..|
T Consensus 2 ~C~~C~~~~~~~~~Y 16 (30)
T PF07649_consen 2 RCDACGKPIDGGWFY 16 (30)
T ss_dssp --TTTS----S--EE
T ss_pred cCCcCCCcCCCCceE
Confidence 47777777666 445
No 73
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=26.84 E-value=20 Score=24.16 Aligned_cols=14 Identities=21% Similarity=0.525 Sum_probs=8.9
Q ss_pred CCCCCceecCCCCc
Q psy6599 13 LLDIPCKVCGDRSS 26 (93)
Q Consensus 13 ~~~~~C~VCg~~~~ 26 (93)
..|..|+|||.+..
T Consensus 147 e~P~~CPiCga~k~ 160 (166)
T COG1592 147 EAPEVCPICGAPKE 160 (166)
T ss_pred CCCCcCCCCCChHH
Confidence 35667777776643
No 74
>PRK01392 citX 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase; Reviewed
Probab=26.73 E-value=26 Score=23.80 Aligned_cols=14 Identities=29% Similarity=0.686 Sum_probs=11.3
Q ss_pred CCCCCceecCCCCc
Q psy6599 13 LLDIPCKVCGDRSS 26 (93)
Q Consensus 13 ~~~~~C~VCg~~~~ 26 (93)
..++.|.||++++.
T Consensus 137 ~p~R~CliC~~~Ak 150 (180)
T PRK01392 137 LPPRRCLLCGQDAK 150 (180)
T ss_pred CCCCeeecCCchHH
Confidence 35688999999874
No 75
>PF03802 CitX: Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; InterPro: IPR005551 Members of this protein family are annotated as CitX, containing the CitX domain, the domain is also found in the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25 from EC), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems.; GO: 0051191 prosthetic group biosynthetic process
Probab=26.18 E-value=26 Score=23.44 Aligned_cols=13 Identities=23% Similarity=0.623 Sum_probs=10.9
Q ss_pred CCCCceecCCCCc
Q psy6599 14 LDIPCKVCGDRSS 26 (93)
Q Consensus 14 ~~~~C~VCg~~~~ 26 (93)
.++.|.||++++.
T Consensus 131 ~~R~CliC~~~Ak 143 (170)
T PF03802_consen 131 PPRRCLICGRPAK 143 (170)
T ss_pred CCCcccCCChhHH
Confidence 6688999999874
No 76
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=25.85 E-value=74 Score=19.34 Aligned_cols=26 Identities=31% Similarity=0.648 Sum_probs=20.5
Q ss_pred CCCCCCceecCCCCceeeeCcccchhhh
Q psy6599 12 RLLDIPCKVCGDRSSGKHYGIYSCDGCS 39 (93)
Q Consensus 12 ~~~~~~C~VCg~~~~~~hyGv~~C~~C~ 39 (93)
...+.+|..||..+ ||.--..|.+|-
T Consensus 13 ~ktHtlCrRCG~~s--yH~qK~~CasCG 38 (91)
T PTZ00073 13 GKTHTLCRRCGKRS--FHVQKKRCASCG 38 (91)
T ss_pred CcCcchhcccCccc--cccccccchhcC
Confidence 34678899999765 777777899886
No 77
>PRK06424 transcription factor; Provisional
Probab=25.59 E-value=29 Score=22.67 Aligned_cols=27 Identities=26% Similarity=0.701 Sum_probs=19.6
Q ss_pred CceecCCCCceeee------Ccccchhhhhhhh
Q psy6599 17 PCKVCGDRSSGKHY------GIYSCDGCSGFFK 43 (93)
Q Consensus 17 ~C~VCg~~~~~~hy------Gv~~C~~C~~FFr 43 (93)
.|.+||....+.+. -...|..|+-|=.
T Consensus 2 ~CE~CG~~~~~~~~v~ieg~~l~vC~~Ca~~G~ 34 (144)
T PRK06424 2 ECEMCGKKVPQTTKVMIDGAILNVCDDCAKFGT 34 (144)
T ss_pred cccccCcccCCceEEEEcCeeeehhHHHHHcCC
Confidence 39999998776632 1348999998854
No 78
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=25.49 E-value=89 Score=16.87 Aligned_cols=27 Identities=30% Similarity=0.801 Sum_probs=18.9
Q ss_pred CCCCCCceecCCCCce-eeeCcccchhh
Q psy6599 12 RLLDIPCKVCGDRSSG-KHYGIYSCDGC 38 (93)
Q Consensus 12 ~~~~~~C~VCg~~~~~-~hyGv~~C~~C 38 (93)
......|.|||.+..- ..||...|.-|
T Consensus 11 ~r~~nrC~~~Gr~rgvirkf~l~lcR~~ 38 (52)
T PRK05766 11 GKGARECQRCGRKQGLIRKYGLYLCRQC 38 (52)
T ss_pred CCCCceeecCCCCceeHHhhCCcccHHH
Confidence 3344679999987544 47887777765
No 79
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=25.14 E-value=35 Score=16.94 Aligned_cols=9 Identities=67% Similarity=1.571 Sum_probs=6.5
Q ss_pred CCceecCCC
Q psy6599 16 IPCKVCGDR 24 (93)
Q Consensus 16 ~~C~VCg~~ 24 (93)
.+|.+|+..
T Consensus 9 ~~C~~C~~~ 17 (36)
T PF11781_consen 9 EPCPVCGSR 17 (36)
T ss_pred CcCCCCCCe
Confidence 458888865
No 80
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=25.01 E-value=31 Score=19.30 Aligned_cols=16 Identities=38% Similarity=0.773 Sum_probs=11.5
Q ss_pred CCCCceecCCCCceee
Q psy6599 14 LDIPCKVCGDRSSGKH 29 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~h 29 (93)
+.+.|.+||..+...|
T Consensus 16 Lke~Cp~CG~~t~~~~ 31 (59)
T COG2260 16 LKEKCPVCGGDTKVPH 31 (59)
T ss_pred ecccCCCCCCccccCC
Confidence 4478999998765544
No 81
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=24.76 E-value=36 Score=19.14 Aligned_cols=18 Identities=22% Similarity=0.340 Sum_probs=10.5
Q ss_pred CCCCCCCceecCCCCcee
Q psy6599 11 DRLLDIPCKVCGDRSSGK 28 (93)
Q Consensus 11 ~~~~~~~C~VCg~~~~~~ 28 (93)
+......|.+||+++...
T Consensus 44 ~~~~~~~Ci~cgk~a~~~ 61 (68)
T PF09180_consen 44 QEPEGGKCIVCGKPAKKW 61 (68)
T ss_dssp CEBTT-B-TTT-SB-SCE
T ss_pred CCCCCCeeecCCChhhEE
Confidence 456678899999998754
No 82
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=23.97 E-value=33 Score=22.60 Aligned_cols=25 Identities=32% Similarity=0.982 Sum_probs=18.5
Q ss_pred CceecCCCCceeeeC-------cccchhhhhh
Q psy6599 17 PCKVCGDRSSGKHYG-------IYSCDGCSGF 41 (93)
Q Consensus 17 ~C~VCg~~~~~~hyG-------v~~C~~C~~F 41 (93)
.|-+||.+..+.-|- ...|..|+-|
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~k~ 33 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECRKF 33 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHHhc
Confidence 499999887765332 4589999955
No 83
>PRK01343 zinc-binding protein; Provisional
Probab=23.77 E-value=73 Score=17.67 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=17.7
Q ss_pred CCCCceecCCCCceeeeCcccchhhhhh
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCSGF 41 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~~F 41 (93)
....|.||+.+... .|--+....|+..
T Consensus 8 p~~~CP~C~k~~~~-~~rPFCS~RC~~i 34 (57)
T PRK01343 8 PTRPCPECGKPSTR-EAYPFCSERCRDI 34 (57)
T ss_pred CCCcCCCCCCcCcC-CCCcccCHHHhhh
Confidence 45779999998653 3445566667643
No 84
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.56 E-value=20 Score=18.62 Aligned_cols=28 Identities=29% Similarity=0.452 Sum_probs=16.3
Q ss_pred CCCCceecCCCCceeeeCcccchhhhhh
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCSGF 41 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~~F 41 (93)
.+..|.+|++.-.|.-.-..-|..|...
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCCh
Confidence 4556888887765544445567777643
No 85
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=23.49 E-value=28 Score=21.06 Aligned_cols=28 Identities=29% Similarity=0.724 Sum_probs=20.8
Q ss_pred CCCceecCCCCc-eeeeCcccchhhhhhh
Q psy6599 15 DIPCKVCGDRSS-GKHYGIYSCDGCSGFF 42 (93)
Q Consensus 15 ~~~C~VCg~~~~-~~hyGv~~C~~C~~FF 42 (93)
.-.|+.|+.... -...|++.|..|..-|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 345999998854 3578999999997544
No 86
>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=22.67 E-value=29 Score=21.41 Aligned_cols=29 Identities=21% Similarity=0.473 Sum_probs=19.9
Q ss_pred CCCCceecCCCCceeeeCcccchhhhhhh
Q psy6599 14 LDIPCKVCGDRSSGKHYGIYSCDGCSGFF 42 (93)
Q Consensus 14 ~~~~C~VCg~~~~~~hyGv~~C~~C~~FF 42 (93)
....|.||++..-...=+...|.+|..=|
T Consensus 34 a~daCeiC~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 34 AFDACEICGPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred EEEeccccCCCceEEECCEEEEecCCCEE
Confidence 34569999666555555677899997544
No 87
>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=22.28 E-value=48 Score=22.72 Aligned_cols=18 Identities=28% Similarity=0.722 Sum_probs=12.6
Q ss_pred CCCCCceecCCC-Cceeee
Q psy6599 13 LLDIPCKVCGDR-SSGKHY 30 (93)
Q Consensus 13 ~~~~~C~VCg~~-~~~~hy 30 (93)
+...+|.|||.+ +...|+
T Consensus 125 v~~~~C~iCGk~~~d~hH~ 143 (200)
T PF06147_consen 125 VKSRPCVICGKPPADIHHI 143 (200)
T ss_pred hccCccccCCCCcccccee
Confidence 355789999975 445565
No 88
>KOG3116|consensus
Probab=22.26 E-value=48 Score=22.21 Aligned_cols=9 Identities=33% Similarity=0.785 Sum_probs=7.9
Q ss_pred HHHHhHHhc
Q psy6599 78 RLNKCFMSA 86 (93)
Q Consensus 78 R~~KCl~~G 86 (93)
|-||||++|
T Consensus 29 rCQKClq~G 37 (177)
T KOG3116|consen 29 RCQKCLQAG 37 (177)
T ss_pred hHHHHHhhc
Confidence 778999998
No 89
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=21.42 E-value=47 Score=17.04 Aligned_cols=11 Identities=45% Similarity=1.053 Sum_probs=7.0
Q ss_pred CCCCCcchHHH
Q psy6599 70 HRNQCRACRLN 80 (93)
Q Consensus 70 ~r~~C~~CR~~ 80 (93)
.+..|+.||.+
T Consensus 36 ~~~~C~~C~~q 46 (46)
T PF12760_consen 36 GRYRCKACRKQ 46 (46)
T ss_pred CeEECCCCCCc
Confidence 45578777753
No 90
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=20.75 E-value=89 Score=15.32 Aligned_cols=25 Identities=24% Similarity=0.442 Sum_probs=13.7
Q ss_pred CCCceecCCCCceeeeCcccchhhhh
Q psy6599 15 DIPCKVCGDRSSGKHYGIYSCDGCSG 40 (93)
Q Consensus 15 ~~~C~VCg~~~~~~hyGv~~C~~C~~ 40 (93)
+..|.+|++...+.. -..-|..|+.
T Consensus 11 ~~~C~~C~~~i~~~~-~~~~C~~C~~ 35 (49)
T smart00109 11 PTKCCVCRKSIWGSF-QGLRCSWCKV 35 (49)
T ss_pred CCCccccccccCcCC-CCcCCCCCCc
Confidence 455777777654322 2345666654
No 91
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=20.45 E-value=95 Score=15.62 Aligned_cols=27 Identities=33% Similarity=0.924 Sum_probs=15.2
Q ss_pred ceecCCCCce----eeeC----cccchhhhhhhhh
Q psy6599 18 CKVCGDRSSG----KHYG----IYSCDGCSGFFKR 44 (93)
Q Consensus 18 C~VCg~~~~~----~hyG----v~~C~~C~~FFrR 44 (93)
|..||++..+ +.++ ...|+.|..=|++
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~fk~ 35 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQFKK 35 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHHHh
Confidence 4566665443 2222 3467888777654
No 92
>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=20.44 E-value=67 Score=16.99 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=10.9
Q ss_pred CCceecCCCCceeee
Q psy6599 16 IPCKVCGDRSSGKHY 30 (93)
Q Consensus 16 ~~C~VCg~~~~~~hy 30 (93)
.+|+.||.....+++
T Consensus 2 kPCPfCGg~~~~~~~ 16 (53)
T TIGR03655 2 KPCPFCGGADVYLRR 16 (53)
T ss_pred CCCCCCCCcceeeEe
Confidence 479999987765553
Done!