Query psy12688
Match_columns 222
No_of_seqs 186 out of 1115
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 17:05:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12688.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12688hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4215|consensus 100.0 7.3E-30 1.6E-34 235.1 4.7 87 125-211 17-103 (432)
2 cd06956 NR_DBD_RXR DNA-binding 99.9 1.1E-27 2.4E-32 178.0 5.0 76 129-204 2-77 (77)
3 cd07171 NR_DBD_ER DNA-binding 99.9 2.2E-27 4.7E-32 178.7 4.5 79 128-206 4-82 (82)
4 cd07160 NR_DBD_LXR DNA-binding 99.9 2.7E-27 5.9E-32 184.7 5.1 80 127-206 18-97 (101)
5 cd07155 NR_DBD_ER_like DNA-bin 99.9 2.5E-27 5.4E-32 175.2 4.6 75 130-204 1-75 (75)
6 cd06961 NR_DBD_TR DNA-binding 99.9 2.7E-27 5.9E-32 179.1 4.4 79 129-207 1-79 (85)
7 cd07170 NR_DBD_ERR DNA-binding 99.9 4.9E-27 1.1E-31 182.0 5.3 81 128-208 5-85 (97)
8 cd06964 NR_DBD_RAR DNA-binding 99.9 1.4E-27 3.1E-32 180.7 2.2 80 127-206 4-83 (85)
9 KOG4846|consensus 99.9 6.8E-27 1.5E-31 218.3 7.0 77 125-201 130-207 (538)
10 cd06967 NR_DBD_TR2_like DNA-bi 99.9 1.8E-27 3.8E-32 180.9 2.3 82 127-208 3-84 (87)
11 cd07164 NR_DBD_PNR_like_1 DNA- 99.9 5.7E-27 1.2E-31 174.5 4.6 77 130-206 1-77 (78)
12 cd07161 NR_DBD_EcR DNA-binding 99.9 7.7E-27 1.7E-31 178.9 4.6 79 128-206 2-80 (91)
13 cd07168 NR_DBD_DHR4_like DNA-b 99.9 9.1E-27 2E-31 178.0 4.8 81 127-207 6-86 (90)
14 cd06970 NR_DBD_PNR DNA-binding 99.9 3.4E-27 7.5E-32 181.2 2.3 81 128-208 7-88 (92)
15 cd06960 NR_DBD_HNF4A DNA-bindi 99.9 4.3E-27 9.4E-32 174.1 2.6 76 130-205 1-76 (76)
16 cd07179 2DBD_NR_DBD2 The secon 99.9 1.4E-26 3.1E-31 170.8 4.9 73 130-202 1-73 (74)
17 cd07173 NR_DBD_AR DNA-binding 99.9 1.8E-26 4E-31 173.8 5.3 79 128-206 4-82 (82)
18 cd06959 NR_DBD_EcR_like The DN 99.9 1.6E-26 3.6E-31 170.0 5.0 73 129-201 1-73 (73)
19 cd07163 NR_DBD_TLX DNA-binding 99.9 5E-27 1.1E-31 180.1 2.2 83 126-208 5-89 (92)
20 cd06962 NR_DBD_FXR DNA-binding 99.9 4.6E-27 9.9E-32 177.7 1.6 78 128-205 2-79 (84)
21 KOG4217|consensus 99.9 4.8E-26 1E-30 215.1 8.8 79 125-203 267-345 (605)
22 cd07156 NR_DBD_VDR_like The DN 99.9 1.6E-26 3.5E-31 169.6 4.0 72 130-201 1-72 (72)
23 cd07172 NR_DBD_GR_PR DNA-bindi 99.9 2.8E-26 6.1E-31 171.1 5.4 75 128-202 3-77 (78)
24 cd06963 NR_DBD_GR_like The DNA 99.9 3E-26 6.6E-31 168.8 4.9 72 130-201 1-72 (73)
25 cd06969 NR_DBD_NGFI-B DNA-bind 99.9 8.4E-27 1.8E-31 172.5 1.9 73 129-201 2-74 (75)
26 cd07169 NR_DBD_GCNF_like DNA-b 99.9 2E-26 4.3E-31 176.2 3.9 80 127-206 6-85 (90)
27 cd06958 NR_DBD_COUP_TF DNA-bin 99.9 2.4E-26 5.3E-31 169.1 4.2 72 130-201 1-72 (73)
28 cd07158 NR_DBD_Ppar_like The D 99.9 2.6E-26 5.7E-31 168.7 4.4 72 130-201 1-73 (73)
29 cd07165 NR_DBD_DmE78_like DNA- 99.9 2.6E-26 5.7E-31 172.1 4.2 77 130-206 1-77 (81)
30 cd07162 NR_DBD_PXR DNA-binding 99.9 2.7E-26 5.8E-31 174.2 4.2 76 129-204 1-76 (87)
31 cd06957 NR_DBD_PNR_like_2 DNA- 99.9 6.7E-27 1.5E-31 175.8 0.6 78 130-207 1-79 (82)
32 cd07167 NR_DBD_Lrh-1_like The 99.9 2.3E-26 5E-31 177.0 3.5 77 130-206 1-77 (93)
33 cd07166 NR_DBD_REV_ERB DNA-bin 99.9 1.6E-26 3.5E-31 176.3 2.2 80 127-206 3-83 (89)
34 cd06966 NR_DBD_CAR DNA-binding 99.9 1.6E-26 3.4E-31 178.0 1.6 79 129-207 2-80 (94)
35 cd07154 NR_DBD_PNR_like The DN 99.9 2.1E-26 4.7E-31 169.3 2.0 72 130-201 1-73 (73)
36 cd07157 2DBD_NR_DBD1 The first 99.9 3E-26 6.6E-31 173.8 2.6 79 129-207 2-82 (86)
37 cd06916 NR_DBD_like DNA-bindin 99.9 2.1E-26 4.7E-31 168.9 1.5 72 130-201 1-72 (72)
38 cd06968 NR_DBD_ROR DNA-binding 99.9 6E-26 1.3E-30 175.2 3.7 81 127-207 5-85 (95)
39 cd06955 NR_DBD_VDR DNA-binding 99.9 5.4E-26 1.2E-30 179.1 3.1 78 126-203 5-82 (107)
40 cd06965 NR_DBD_Ppar DNA-bindin 99.9 1.1E-25 2.3E-30 170.1 2.7 78 129-208 1-79 (84)
41 smart00399 ZnF_C4 c4 zinc fing 99.9 5.1E-25 1.1E-29 160.4 3.6 70 129-198 1-70 (70)
42 PF00105 zf-C4: Zinc finger, C 99.9 8.3E-25 1.8E-29 158.7 4.5 70 128-197 1-70 (70)
43 KOG4216|consensus 99.9 7.3E-25 1.6E-29 203.4 3.2 77 128-204 47-123 (479)
44 KOG4218|consensus 99.9 7.1E-25 1.5E-29 201.4 3.0 81 124-204 12-92 (475)
45 PF01412 ArfGap: Putative GTPa 64.6 4.6 9.9E-05 31.8 1.9 32 125-156 11-45 (116)
46 PF10764 Gin: Inhibitor of sig 55.9 6.2 0.00013 26.8 1.0 22 130-151 2-25 (46)
47 smart00105 ArfGap Putative GTP 40.8 20 0.00043 28.0 1.9 31 127-157 3-36 (112)
48 PF09788 Tmemb_55A: Transmembr 37.9 81 0.0018 28.9 5.6 43 127-169 65-112 (256)
49 KOG4399|consensus 35.9 15 0.00034 33.9 0.7 59 128-192 262-321 (325)
50 KOG3277|consensus 34.9 14 0.0003 31.6 0.2 26 129-154 81-114 (165)
51 smart00401 ZnF_GATA zinc finge 32.1 39 0.00085 23.1 2.1 30 128-157 4-38 (52)
52 PF03107 C1_2: C1 domain; Int 31.8 23 0.00051 21.4 0.8 21 129-151 2-22 (30)
53 PF12760 Zn_Tnp_IS1595: Transp 29.9 30 0.00065 22.8 1.1 40 148-188 4-46 (46)
54 PHA03124 dUTPase; Provisional 29.3 29 0.00063 33.6 1.4 15 145-159 191-205 (418)
55 PF04783 DUF630: Protein of un 28.2 32 0.0007 24.7 1.1 13 12-24 11-23 (60)
56 PTZ00218 40S ribosomal protein 26.5 47 0.001 23.5 1.7 26 125-150 14-40 (54)
57 PF09289 FOLN: Follistatin/Ost 26.0 16 0.00034 21.4 -0.7 19 164-182 4-22 (22)
58 PRK00420 hypothetical protein; 24.1 28 0.00061 27.9 0.2 28 127-154 23-50 (112)
59 PF00320 GATA: GATA zinc finge 21.2 70 0.0015 20.2 1.6 28 130-157 1-33 (36)
No 1
>KOG4215|consensus
Probab=99.96 E-value=7.3e-30 Score=235.12 Aligned_cols=87 Identities=43% Similarity=1.018 Sum_probs=83.0
Q ss_pred CCCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST 204 (222)
Q Consensus 125 ~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r 204 (222)
...+.|.||||+++|.|||+.+|.|||+||||+|.++..|.|+++.+|.|+|++|+.||||||+||+.+||++||||++|
T Consensus 17 ~~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnER 96 (432)
T KOG4215|consen 17 GVAEFCAICGDKATGKHYGAISCDGCKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNER 96 (432)
T ss_pred cccchhheeCCcccccccceeecCcchHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhccc
Confidence 44678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcceec
Q psy12688 205 HGVVVIW 211 (222)
Q Consensus 205 ~g~~~~~ 211 (222)
|.+..-.
T Consensus 97 DrIg~Rr 103 (432)
T KOG4215|consen 97 DRIGSRR 103 (432)
T ss_pred ccccccC
Confidence 9998733
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=99.94 E-value=1.1e-27 Score=178.02 Aligned_cols=76 Identities=54% Similarity=1.200 Sum_probs=73.4
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST 204 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r 204 (222)
+|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++||.+|
T Consensus 2 ~C~VC~~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 77 (77)
T cd06956 2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77 (77)
T ss_pred CCcccCCcCcceEECceeehhHHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence 5999999999999999999999999999999999999999999999999999999999999999999999999876
No 3
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=99.94 E-value=2.2e-27 Score=178.73 Aligned_cols=79 Identities=48% Similarity=1.026 Sum_probs=75.3
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
..|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.++-|
T Consensus 4 ~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~~~ 82 (82)
T cd07171 4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERRG 82 (82)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhhcC
Confidence 4699999999999999999999999999999988899999999999999999999999999999999999999998764
No 4
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=99.94 E-value=2.7e-27 Score=184.67 Aligned_cols=80 Identities=43% Similarity=0.970 Sum_probs=76.1
Q ss_pred CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
..+|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+++-
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~ 97 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQI 97 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhh
Confidence 45799999999999999999999999999999988999999999999999999999999999999999999999998864
No 5
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=99.94 E-value=2.5e-27 Score=175.18 Aligned_cols=75 Identities=52% Similarity=1.065 Sum_probs=72.5
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST 204 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r 204 (222)
|.|||+.++|+||||.+|+||++||||++..+..|.|..++.|.|+...|..|++|||+|||++||++++||.+|
T Consensus 1 C~VC~~~~~g~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r 75 (75)
T cd07155 1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75 (75)
T ss_pred CcccCccCcceEEChhhhhhhHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence 899999999999999999999999999999888999999999999999999999999999999999999999876
No 6
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=99.93 E-value=2.7e-27 Score=179.11 Aligned_cols=79 Identities=51% Similarity=1.056 Sum_probs=75.9
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV 207 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~ 207 (222)
+|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+++..
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~ 79 (85)
T cd06961 1 PCVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRG 79 (85)
T ss_pred CCceeCCcCcceEEChhhhhhhhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCcc
Confidence 4999999999999999999999999999999889999999999999999999999999999999999999999998875
No 7
>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=99.93 E-value=4.9e-27 Score=181.99 Aligned_cols=81 Identities=51% Similarity=0.966 Sum_probs=75.9
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV 207 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~ 207 (222)
..|.|||+.++|+||||.+|+||++||||++..+..|.|..++.|.|+...|..|++|||+|||++||++++|+.+++-.
T Consensus 5 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~ 84 (97)
T cd07170 5 RLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRG 84 (97)
T ss_pred CCCeecCCcCcceEECceeehhhhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCC
Confidence 45999999999999999999999999999999888999999999999999999999999999999999999999987554
Q ss_pred c
Q psy12688 208 V 208 (222)
Q Consensus 208 ~ 208 (222)
.
T Consensus 85 ~ 85 (97)
T cd07170 85 G 85 (97)
T ss_pred C
Confidence 3
No 8
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=99.93 E-value=1.4e-27 Score=180.69 Aligned_cols=80 Identities=50% Similarity=1.073 Sum_probs=76.2
Q ss_pred CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
.++|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|+.
T Consensus 4 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~ 83 (85)
T cd06964 4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK 83 (85)
T ss_pred CCCCcccCCcCcccEECcceeeeeeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccC
Confidence 45799999999999999999999999999999988889999999999999999999999999999999999999999986
No 9
>KOG4846|consensus
Probab=99.93 E-value=6.8e-27 Score=218.28 Aligned_cols=77 Identities=49% Similarity=1.157 Sum_probs=73.3
Q ss_pred CCCccccccCCCCcceeeccccchhhhHHHHhHhhcCcee-ccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 125 ~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~-~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
....+|.||||+|+||||||.+|||||+||||+|+.+..| .|-+...|.|....|++|++|||+|||.|||.++|||
T Consensus 130 ~~~~lCkVCgDkASGfHYGV~aCEGCKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVR 207 (538)
T KOG4846|consen 130 KAISLCKVCGDKASGFHYGVTACEGCKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVR 207 (538)
T ss_pred ceeEeehhhccccccceeceeecccchHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhh
Confidence 3456899999999999999999999999999999999888 7999999999999999999999999999999999999
No 10
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=99.93 E-value=1.8e-27 Score=180.91 Aligned_cols=82 Identities=48% Similarity=1.037 Sum_probs=77.7
Q ss_pred CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
.++|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|+.
T Consensus 3 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~ 82 (87)
T cd06967 3 VELCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKP 82 (87)
T ss_pred CCCCeecCCcCCcCEeCcceEeeeeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCC
Confidence 45699999999999999999999999999999988899999999999999999999999999999999999999999997
Q ss_pred cc
Q psy12688 207 VV 208 (222)
Q Consensus 207 ~~ 208 (222)
+.
T Consensus 83 ~~ 84 (87)
T cd06967 83 ID 84 (87)
T ss_pred CC
Confidence 54
No 11
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=99.93 E-value=5.7e-27 Score=174.46 Aligned_cols=77 Identities=42% Similarity=1.022 Sum_probs=74.4
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
|.|||+.++|+||||.+|++|++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|+.
T Consensus 1 C~VCg~~~~g~hyG~~~C~~C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 77 (78)
T cd07164 1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAP 77 (78)
T ss_pred CcccCccCcceEECcchhhhhhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCC
Confidence 89999999999999999999999999999988899999999999999999999999999999999999999999984
No 12
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=99.93 E-value=7.7e-27 Score=178.91 Aligned_cols=79 Identities=51% Similarity=1.083 Sum_probs=74.9
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
++|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+++-
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~ 80 (91)
T cd07161 2 ELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQC 80 (91)
T ss_pred CCCeeCCCcCcceEECceeehhhHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhh
Confidence 4599999999999999999999999999999988899999999999999999999999999999999999999988653
No 13
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=99.93 E-value=9.1e-27 Score=178.02 Aligned_cols=81 Identities=54% Similarity=1.154 Sum_probs=76.7
Q ss_pred CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
...|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|..
T Consensus 6 ~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~ 85 (90)
T cd07168 6 PKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMP 85 (90)
T ss_pred CCCCcccCCcCcceEECceehhhhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCC
Confidence 34699999999999999999999999999999988899999999999999999999999999999999999999999876
Q ss_pred c
Q psy12688 207 V 207 (222)
Q Consensus 207 ~ 207 (222)
.
T Consensus 86 ~ 86 (90)
T cd07168 86 G 86 (90)
T ss_pred C
Confidence 4
No 14
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=99.93 E-value=3.4e-27 Score=181.22 Aligned_cols=81 Identities=43% Similarity=0.968 Sum_probs=76.4
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccC-cccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAE-RSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~-~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
.+|.|||+.++|+||||.+|+||++||||++..+..|.|..+ ++|.++...|..|++|||+|||++||++++|+.+|+.
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~ 86 (92)
T cd06970 7 LLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQP 86 (92)
T ss_pred CCCeecCCcCcccEECccEEeeeeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCc
Confidence 359999999999999999999999999999998889999886 8999999999999999999999999999999999986
Q ss_pred cc
Q psy12688 207 VV 208 (222)
Q Consensus 207 ~~ 208 (222)
..
T Consensus 87 ~~ 88 (92)
T cd06970 87 RN 88 (92)
T ss_pred cc
Confidence 54
No 15
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=99.93 E-value=4.3e-27 Score=174.06 Aligned_cols=76 Identities=49% Similarity=1.154 Sum_probs=73.5
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH 205 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~ 205 (222)
|.|||+.++++||||.+|+||++||||++..+..|.|...+.|.|+...|..|++|||+|||++||++++|+.+||
T Consensus 1 C~vCg~~~~~~hygv~~C~aC~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~ 76 (76)
T cd06960 1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD 76 (76)
T ss_pred CCccCccCcccEECcceeeeehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence 8999999999999999999999999999998889999999999999999999999999999999999999999886
No 16
>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=99.93 E-value=1.4e-26 Score=170.83 Aligned_cols=73 Identities=48% Similarity=1.042 Sum_probs=70.5
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCcccccc
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQ 202 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~ 202 (222)
|.|||++++++||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++||.
T Consensus 1 C~VCg~~~~g~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~ 73 (74)
T cd07179 1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI 73 (74)
T ss_pred CcccCccCcceEECceeehhHHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence 8999999999999999999999999999999889999999999999999999999999999999999999985
No 17
>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=99.93 E-value=1.8e-26 Score=173.76 Aligned_cols=79 Identities=49% Similarity=1.042 Sum_probs=74.4
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
..|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||+++.++.++.|
T Consensus 4 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~~~~ 82 (82)
T cd07173 4 KTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKKLG 82 (82)
T ss_pred CCCeecCCcCcceEECcchhhhHHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhhccC
Confidence 4599999999999999999999999999999988999999999999999999999999999999999999988877654
No 18
>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=99.93 E-value=1.6e-26 Score=170.01 Aligned_cols=73 Identities=47% Similarity=1.065 Sum_probs=70.0
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
+|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.+++..|..|++|||+|||++||+++.|+
T Consensus 1 ~C~vCg~~~~~~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~ 73 (73)
T cd06959 1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL 73 (73)
T ss_pred CCceeCCcCcceEECceeehhhHHHHHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence 5999999999999999999999999999999888999999999999999999999999999999999999874
No 19
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=99.93 E-value=5e-27 Score=180.12 Aligned_cols=83 Identities=40% Similarity=0.969 Sum_probs=76.8
Q ss_pred CCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccC--cccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAE--RSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS 203 (222)
Q Consensus 126 ~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~--~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~ 203 (222)
+...|.|||+.++|+||||.+|+||++||||++..+..|.|... +.|.++...|..|++|||+|||++||++++|+.+
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~ 84 (92)
T cd07163 5 LDIPCKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHE 84 (92)
T ss_pred cCCCCcccCCcCcccEECceeeeeeeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcc
Confidence 45679999999999999999999999999999998889999873 6899999999999999999999999999999999
Q ss_pred CCCcc
Q psy12688 204 THGVV 208 (222)
Q Consensus 204 r~g~~ 208 (222)
|+...
T Consensus 85 r~p~~ 89 (92)
T cd07163 85 RGPRN 89 (92)
T ss_pred cCcCC
Confidence 88653
No 20
>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=99.93 E-value=4.6e-27 Score=177.70 Aligned_cols=78 Identities=49% Similarity=1.043 Sum_probs=74.0
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH 205 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~ 205 (222)
++|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+.+
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~ 79 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQ 79 (84)
T ss_pred CCCeecCCcCcceEECcceeecceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHH
Confidence 469999999999999999999999999999998889999999999999999999999999999999999999998764
No 21
>KOG4217|consensus
Probab=99.93 E-value=4.8e-26 Score=215.09 Aligned_cols=79 Identities=56% Similarity=1.141 Sum_probs=75.7
Q ss_pred CCCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS 203 (222)
Q Consensus 125 ~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~ 203 (222)
.....|.||||.|..-||||.+|||||+||+|||+++.+|+|-.+++|.|+|..|++|+||||||||+|||-+|.||.+
T Consensus 267 ~~e~~CAVCgDnAaCqHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtd 345 (605)
T KOG4217|consen 267 SAEGLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTD 345 (605)
T ss_pred CccceeeecCChHHhhhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecc
Confidence 4478899999999999999999999999999999999999999999999999999999999999999999999999954
No 22
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=99.93 E-value=1.6e-26 Score=169.64 Aligned_cols=72 Identities=47% Similarity=1.128 Sum_probs=69.4
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+
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 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL 72 (72)
T ss_pred CCccCccCcccEECcceehhhhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence 899999999999999999999999999999888999999999999999999999999999999999999884
No 23
>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=99.93 E-value=2.8e-26 Score=171.11 Aligned_cols=75 Identities=51% Similarity=1.091 Sum_probs=71.4
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCcccccc
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQ 202 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~ 202 (222)
.+|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||+..+++.
T Consensus 3 ~~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~ 77 (78)
T cd07172 3 KICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKT 77 (78)
T ss_pred CCCeecCCcCcceEECceeehhhHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCcccccC
Confidence 469999999999999999999999999999999989999999999999999999999999999999999998864
No 24
>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=99.92 E-value=3e-26 Score=168.81 Aligned_cols=72 Identities=50% Similarity=1.108 Sum_probs=69.5
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||+++||.
T Consensus 1 C~VCg~~a~~~hygv~sC~aCk~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~ 72 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK 72 (73)
T ss_pred CcccCccCcceEECceeehhhhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence 899999999999999999999999999999888999999999999999999999999999999999999885
No 25
>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=99.92 E-value=8.4e-27 Score=172.49 Aligned_cols=73 Identities=59% Similarity=1.229 Sum_probs=70.5
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
+|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|++..|..|++|||+|||++||++++||
T Consensus 2 ~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~ 74 (75)
T cd06969 2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74 (75)
T ss_pred CCeecCCcCcceEECcceeeeeeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHcc
Confidence 5999999999999999999999999999999888999999999999999999999999999999999999997
No 26
>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=99.92 E-value=2e-26 Score=176.21 Aligned_cols=80 Identities=43% Similarity=1.092 Sum_probs=75.6
Q ss_pred CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
..+|.|||+.++++||||.+|+||++||||++..+..|.|..++.|.|+...|..|++|||+|||++||++++||.++..
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~ 85 (90)
T cd07169 6 QRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP 85 (90)
T ss_pred CCCCeecCCcCcceEECcceehhhHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccCC
Confidence 45699999999999999999999999999999988899999999999999999999999999999999999999998753
No 27
>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=99.92 E-value=2.4e-26 Score=169.11 Aligned_cols=72 Identities=54% Similarity=1.179 Sum_probs=69.7
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+
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 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72 (73)
T ss_pred CCccCccCcceEEChhhhhhhhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence 899999999999999999999999999999888899999999999999999999999999999999999987
No 28
>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=99.92 E-value=2.6e-26 Score=168.66 Aligned_cols=72 Identities=51% Similarity=1.209 Sum_probs=69.5
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCcee-ccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~-~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
|.|||+.++|+||||.+|++|++||||++..+..| .|..+++|.|+...|..|++|||+|||++||++++||
T Consensus 1 C~VCg~~~~g~hyGv~~C~aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 73 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73 (73)
T ss_pred CcccCccCcceEECcchhhHHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence 89999999999999999999999999999988888 8999999999999999999999999999999999986
No 29
>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=99.92 E-value=2.6e-26 Score=172.11 Aligned_cols=77 Identities=47% Similarity=1.097 Sum_probs=74.2
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...+..|++|||+|||++||++++||.+|..
T Consensus 1 C~VCg~~~~g~hyG~~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~ 77 (81)
T cd07165 1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIP 77 (81)
T ss_pred CCccCccCcceEECchhhhhHHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCC
Confidence 89999999999999999999999999999988899999999999999999999999999999999999999998875
No 30
>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=99.92 E-value=2.7e-26 Score=174.24 Aligned_cols=76 Identities=42% Similarity=1.049 Sum_probs=72.7
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST 204 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r 204 (222)
+|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+.++
T Consensus 1 ~C~VCg~~~~g~hygv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~ 76 (87)
T cd07162 1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDE 76 (87)
T ss_pred CCcccCCcCcceEECcceehhhHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHH
Confidence 4999999999999999999999999999999888999999999999999999999999999999999999998874
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=99.92 E-value=6.7e-27 Score=175.79 Aligned_cols=78 Identities=45% Similarity=1.034 Sum_probs=73.8
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccc-cCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCV-AERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV 207 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~-~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~ 207 (222)
|.|||+.++|+||||.+|+||++||||++..+..|.|. .++.|.|+...|..|++|||+|||++||++++|+.+|+..
T Consensus 1 C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~ 79 (82)
T cd06957 1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPR 79 (82)
T ss_pred CCccCccCcceEECcceEeeeeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcC
Confidence 89999999999999999999999999999988899998 4689999999999999999999999999999999988764
No 32
>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=99.92 E-value=2.3e-26 Score=177.01 Aligned_cols=77 Identities=78% Similarity=1.461 Sum_probs=74.2
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.++..
T Consensus 1 C~VCg~~a~g~hyGv~sC~aCk~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~ 77 (93)
T cd07167 1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMR 77 (93)
T ss_pred CcccCccCcceEECchhhhhHHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999854
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=99.92 E-value=1.6e-26 Score=176.29 Aligned_cols=80 Identities=48% Similarity=1.064 Sum_probs=75.3
Q ss_pred CccccccCCCCcceeeccccchhhhHHHHhHhhcCcee-ccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCC
Q psy12688 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVY-TCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTH 205 (222)
Q Consensus 127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~-~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~ 205 (222)
..+|.|||+.++|+||||.+|+||++||||++..+..| .|..+++|.|+...|..|++|||+|||++||++++|+.+|.
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~ 82 (89)
T cd07166 3 VVLCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRI 82 (89)
T ss_pred CCCCcccCccCcceEEChhhhhhHhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCC
Confidence 34699999999999999999999999999999988888 59999999999999999999999999999999999999986
Q ss_pred C
Q psy12688 206 G 206 (222)
Q Consensus 206 g 206 (222)
.
T Consensus 83 ~ 83 (89)
T cd07166 83 P 83 (89)
T ss_pred C
Confidence 5
No 34
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=99.92 E-value=1.6e-26 Score=178.04 Aligned_cols=79 Identities=41% Similarity=0.899 Sum_probs=75.1
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV 207 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~ 207 (222)
.|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.++...+..|++|||+|||++||++++|+.+++-.
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~ 80 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS 80 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhh
Confidence 5999999999999999999999999999999888999999999999999999999999999999999999999987643
No 35
>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear
Probab=99.92 E-value=2.1e-26 Score=169.27 Aligned_cols=72 Identities=47% Similarity=1.119 Sum_probs=68.9
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccc-cCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCV-AERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~-~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
|.|||+.++++||||.+|+||++||||++..+..|.|. .+++|.|+...|..|++|||+|||++||++++||
T Consensus 1 C~vCg~~~~~~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq 73 (73)
T cd07154 1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73 (73)
T ss_pred CcccCccCcceEECcceeeeeeeEeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence 89999999999999999999999999999988899998 6789999999999999999999999999999986
No 36
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=99.92 E-value=3e-26 Score=173.82 Aligned_cols=79 Identities=38% Similarity=0.854 Sum_probs=73.4
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCc--eeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKK--VYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~--~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
.|.|||+.++|+||||.+|+||++||||++..+. .|.|..+++|.++...|..|++|||+|||++||++++++.+|+.
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aCk~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~ 81 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS 81 (86)
T ss_pred CCcccCCcCcccEECcceeeEeeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence 4999999999999999999999999999988654 88999999999999999999999999999999999999988765
Q ss_pred c
Q psy12688 207 V 207 (222)
Q Consensus 207 ~ 207 (222)
+
T Consensus 82 ~ 82 (86)
T cd07157 82 D 82 (86)
T ss_pred c
Confidence 4
No 37
>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=99.92 E-value=2.1e-26 Score=168.86 Aligned_cols=72 Identities=60% Similarity=1.233 Sum_probs=69.6
Q ss_pred ccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccc
Q psy12688 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSS 201 (222)
Q Consensus 130 C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr 201 (222)
|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++||
T Consensus 1 C~vC~~~~~~~hygv~sC~aC~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~ 72 (72)
T cd06916 1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72 (72)
T ss_pred CCccCccCcccEECcceeeeeeeeEeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence 899999999999999999999999999999888899999999999999999999999999999999999886
No 38
>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=99.92 E-value=6e-26 Score=175.21 Aligned_cols=81 Identities=47% Similarity=1.015 Sum_probs=75.8
Q ss_pred CccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCC
Q psy12688 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHG 206 (222)
Q Consensus 127 ~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g 206 (222)
..+|.|||+.+.|+||||.+|+||++||||++..+..|.|..+++|.++...|..|++|||+|||++||++++|+.++..
T Consensus 5 ~~~C~VCg~~~~g~hyGv~sC~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~ 84 (95)
T cd06968 5 VIPCKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMS 84 (95)
T ss_pred ccCCcccCCcCcceEECceeehhhHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCC
Confidence 34699999999999999999999999999999988899999999999999999999999999999999999999988754
Q ss_pred c
Q psy12688 207 V 207 (222)
Q Consensus 207 ~ 207 (222)
.
T Consensus 85 ~ 85 (95)
T cd06968 85 K 85 (95)
T ss_pred h
Confidence 3
No 39
>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=99.92 E-value=5.4e-26 Score=179.08 Aligned_cols=78 Identities=38% Similarity=1.037 Sum_probs=73.5
Q ss_pred CCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688 126 IEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS 203 (222)
Q Consensus 126 ~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~ 203 (222)
....|.|||+.++|+||||.+|+||++||||++..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+
T Consensus 5 ~~~~C~VCg~~a~g~hyGv~sC~aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~ 82 (107)
T cd06955 5 VPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD 82 (107)
T ss_pred CCCCCeecCCcCcccEECcceeeeecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence 346699999999999999999999999999999988899999999999999999999999999999999999988876
No 40
>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=99.91 E-value=1.1e-25 Score=170.07 Aligned_cols=78 Identities=51% Similarity=1.076 Sum_probs=71.9
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCceec-cccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCCCCc
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGV 207 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~-C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r~g~ 207 (222)
+|.|||+.++|+||||.+|+||++||||++..+..|. |... |.|+...|..|++|||+|||++||++++|+.+|...
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~ 78 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPR 78 (84)
T ss_pred CCcccCccCcceEEChhhhhhhhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCc
Confidence 4999999999999999999999999999998888884 9753 999999999999999999999999999999998764
Q ss_pred c
Q psy12688 208 V 208 (222)
Q Consensus 208 ~ 208 (222)
.
T Consensus 79 ~ 79 (84)
T cd06965 79 V 79 (84)
T ss_pred h
Confidence 3
No 41
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=99.90 E-value=5.1e-25 Score=160.39 Aligned_cols=70 Identities=50% Similarity=1.095 Sum_probs=66.9
Q ss_pred cccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCcc
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~e 198 (222)
+|.|||+.++++||||.+|+||++||||++..+..|.|..+++|.+++..|..|++|||+|||++||+++
T Consensus 1 ~C~vC~~~~~~~hygv~~C~aC~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~ 70 (70)
T smart00399 1 LCCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70 (70)
T ss_pred CCeEeCCcCcccEeCCcEechhhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence 4999999999999999999999999999999888899999999999999999999999999999999874
No 42
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=99.90 E-value=8.3e-25 Score=158.66 Aligned_cols=70 Identities=59% Similarity=1.247 Sum_probs=62.4
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCc
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKL 197 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~ 197 (222)
+.|+|||++++++||||.+|++|++||+|++..+..+.|..+++|.+++..+..|++|||+|||++||++
T Consensus 1 ~~C~VCg~~~~~~~ygv~sC~~C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k 70 (70)
T PF00105_consen 1 KKCKVCGDPASGYHYGVLSCNACKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK 70 (70)
T ss_dssp -BSTTTSSBESEEETTEEEEHHHHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred CCCeECCCccCcccccccccccceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence 3699999999999999999999999999999988889999999999999999999999999999999974
No 43
>KOG4216|consensus
Probab=99.90 E-value=7.3e-25 Score=203.42 Aligned_cols=77 Identities=48% Similarity=1.075 Sum_probs=73.5
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccCC
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQST 204 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~r 204 (222)
.+|.||||+++|.||||.+|||||+||||+-+.+..|.|.+.++|.|+...|++|++|||+|||++||+.+||..-|
T Consensus 47 IPCKiCGDKSSGiHYGVITCEGCKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGR 123 (479)
T KOG4216|consen 47 IPCKICGDKSSGIHYGVITCEGCKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGR 123 (479)
T ss_pred EeeeeccCCCCcceeeeEeeccchHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhcc
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999997544
No 44
>KOG4218|consensus
Probab=99.90 E-value=7.1e-25 Score=201.41 Aligned_cols=81 Identities=79% Similarity=1.426 Sum_probs=77.2
Q ss_pred cCCCccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcchHhHHHHHhcCCccccccC
Q psy12688 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQS 203 (222)
Q Consensus 124 ~~~~~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~CRl~KCLevGM~~eaVr~~ 203 (222)
+...++|.||||+.+|||||..+||.||+||+|+|++++.|.|....+|.|++..|++|.+|||+|||.+||+.||||.|
T Consensus 12 edl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRAD 91 (475)
T KOG4218|consen 12 EDLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRAD 91 (475)
T ss_pred cccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHh
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999977
Q ss_pred C
Q psy12688 204 T 204 (222)
Q Consensus 204 r 204 (222)
|
T Consensus 92 R 92 (475)
T KOG4218|consen 92 R 92 (475)
T ss_pred h
Confidence 6
No 45
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=64.63 E-value=4.6 Score=31.78 Aligned_cols=32 Identities=25% Similarity=0.730 Sum_probs=21.9
Q ss_pred CCCccccccCCCCcc---eeeccccchhhhHHHHh
Q psy12688 125 GIEELCPVCGDKVSG---YHYGLLTCESCKGFFKR 156 (222)
Q Consensus 125 ~~~~~C~VCGd~asg---~HYGV~sCeaCk~FFRR 156 (222)
..+..|.-||..... ..||++.|..|.++.|.
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 345679999977644 47999999999999764
No 46
>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=55.86 E-value=6.2 Score=26.80 Aligned_cols=22 Identities=41% Similarity=1.223 Sum_probs=18.8
Q ss_pred ccccCCCC-ccee-eccccchhhh
Q psy12688 130 CPVCGDKV-SGYH-YGLLTCESCK 151 (222)
Q Consensus 130 C~VCGd~a-sg~H-YGV~sCeaCk 151 (222)
|.||+... .|.| ||.+.|..|-
T Consensus 2 CiiC~~~~~~GI~I~~~fIC~~CE 25 (46)
T PF10764_consen 2 CIICGKEKEEGIHIYGKFICSDCE 25 (46)
T ss_pred eEeCCCcCCCCEEEECeEehHHHH
Confidence 89999764 5876 9999999996
No 47
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=40.85 E-value=20 Score=28.00 Aligned_cols=31 Identities=23% Similarity=0.636 Sum_probs=24.8
Q ss_pred CccccccCCCCc---ceeeccccchhhhHHHHhH
Q psy12688 127 EELCPVCGDKVS---GYHYGLLTCESCKGFFKRT 157 (222)
Q Consensus 127 ~~~C~VCGd~as---g~HYGV~sCeaCk~FFRRt 157 (222)
+..|.-|+.+.- ...||++.|..|.+..|..
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~l 36 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSL 36 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHHHHHhc
Confidence 457999997653 3589999999999998753
No 48
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=37.91 E-value=81 Score=28.86 Aligned_cols=43 Identities=21% Similarity=0.449 Sum_probs=27.1
Q ss_pred CccccccCCC---Ccceeeccccchhhh--HHHHhHhhcCceeccccC
Q psy12688 127 EELCPVCGDK---VSGYHYGLLTCESCK--GFFKRTVQNKKVYTCVAE 169 (222)
Q Consensus 127 ~~~C~VCGd~---asg~HYGV~sCeaCk--~FFRRtv~~~~~~~C~~~ 169 (222)
...|.||+.. ....|--|+-|..|. .--|++=..++...|.-+
T Consensus 65 ~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCPCN 112 (256)
T PF09788_consen 65 VVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCPCN 112 (256)
T ss_pred eEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecCCc
Confidence 4569999964 445788899999995 333444334444456433
No 49
>KOG4399|consensus
Probab=35.92 E-value=15 Score=33.90 Aligned_cols=59 Identities=17% Similarity=0.216 Sum_probs=33.3
Q ss_pred ccccccCCCCcceeeccccchhhhHHHHhHhhcCceeccccCcccccCCCCCCCCcch-HhHHHHH
Q psy12688 128 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFC-RFQKCLE 192 (222)
Q Consensus 128 ~~C~VCGd~asg~HYGV~sCeaCk~FFRRtv~~~~~~~C~~~~~C~i~~~~R~~Cr~C-Rl~KCLe 192 (222)
.-|.|||.-.+.- .+|..|++- |.+...+..+|+....|....++-..|+-| |+.+|.+
T Consensus 262 ~~C~iC~~~~~~R----~~C~~~kA~--~~~~Q~K~N~~~~~~~~~q~~~H~s~~~R~~~~~R~~Q 321 (325)
T KOG4399|consen 262 HGCFICGELDHKR----STCPNIKAV--RKQKQRKSNKMKMETTKGQSMNHTSATRRKKRRERAHQ 321 (325)
T ss_pred cceeecccccccc----ccCccHHHH--HHHHhcccchhhhhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 3477777554332 578888765 444444555676666666654444455544 4555654
No 50
>KOG3277|consensus
Probab=34.92 E-value=14 Score=31.57 Aligned_cols=26 Identities=31% Similarity=0.912 Sum_probs=20.7
Q ss_pred cccccCCCCc------ceeeccc--cchhhhHHH
Q psy12688 129 LCPVCGDKVS------GYHYGLL--TCESCKGFF 154 (222)
Q Consensus 129 ~C~VCGd~as------g~HYGV~--sCeaCk~FF 154 (222)
-|.||+.+.+ .||-|++ .|.+|+.+.
T Consensus 81 TCkvCntRs~ktisk~AY~~GvVivqC~gC~~~H 114 (165)
T KOG3277|consen 81 TCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH 114 (165)
T ss_pred EeeccCCccccccChhhhhCceEEEECCCCccce
Confidence 4999998764 3777875 899999875
No 51
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=32.12 E-value=39 Score=23.09 Aligned_cols=30 Identities=23% Similarity=0.685 Sum_probs=21.4
Q ss_pred ccccccCCCCcc-e---eecc-ccchhhhHHHHhH
Q psy12688 128 ELCPVCGDKVSG-Y---HYGL-LTCESCKGFFKRT 157 (222)
Q Consensus 128 ~~C~VCGd~asg-~---HYGV-~sCeaCk~FFRRt 157 (222)
..|..|+...+- . -.|. ..|++|..||++.
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~ 38 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKH 38 (52)
T ss_pred CCcCCCCCCCCCccccCCCCCCcEeecccHHHHHc
Confidence 458899876543 2 3454 7899999999764
No 52
>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=31.83 E-value=23 Score=21.41 Aligned_cols=21 Identities=33% Similarity=0.988 Sum_probs=16.1
Q ss_pred cccccCCCCcceeeccccchhhh
Q psy12688 129 LCPVCGDKVSGYHYGLLTCESCK 151 (222)
Q Consensus 129 ~C~VCGd~asg~HYGV~sCeaCk 151 (222)
.|.||++...++. ...|+.|.
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCC
Confidence 3899999998884 45677766
No 53
>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=29.91 E-value=30 Score=22.83 Aligned_cols=40 Identities=23% Similarity=0.591 Sum_probs=21.5
Q ss_pred hhhhHHHHhHhhcCceecccc---CcccccCCCCCCCCcchHhH
Q psy12688 148 ESCKGFFKRTVQNKKVYTCVA---ERSCHIDKTQRKRCPFCRFQ 188 (222)
Q Consensus 148 eaCk~FFRRtv~~~~~~~C~~---~~~C~i~~~~R~~Cr~CRl~ 188 (222)
+.|..||... .=...+.|.. .....+....+..|+.||.+
T Consensus 4 ~~c~~~l~~~-RW~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 4 EACREYLEEI-RWPDGFVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred HHHHHHHHHh-cCCCCCCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 3567777654 2223354532 22334444566788888754
No 54
>PHA03124 dUTPase; Provisional
Probab=29.26 E-value=29 Score=33.58 Aligned_cols=15 Identities=33% Similarity=1.021 Sum_probs=12.7
Q ss_pred ccchhhhHHHHhHhh
Q psy12688 145 LTCESCKGFFKRTVQ 159 (222)
Q Consensus 145 ~sCeaCk~FFRRtv~ 159 (222)
+-|-+|++||||...
T Consensus 191 ~~~~~~~~~~~~~~~ 205 (418)
T PHA03124 191 FGCMGCKAFYRRLFE 205 (418)
T ss_pred ccccchHHHHHHHHH
Confidence 349999999999864
No 55
>PF04783 DUF630: Protein of unknown function (DUF630); InterPro: IPR006868 This region is sometimes found at the N terminus of putative plant bZIP proteins IPR006867 from INTERPRO. The function of this conserved region is not known.
Probab=28.21 E-value=32 Score=24.72 Aligned_cols=13 Identities=46% Similarity=0.784 Sum_probs=11.2
Q ss_pred HHHHHHHhhhhhc
Q psy12688 12 LDLVQRCKKRKKL 24 (222)
Q Consensus 12 ~~~~~~~~~~~~~ 24 (222)
.+.|++||.||++
T Consensus 11 eeaV~~CkeRkr~ 23 (60)
T PF04783_consen 11 EEAVSLCKERKRL 23 (60)
T ss_pred cHHHHHHHHHHHH
Confidence 3789999999986
No 56
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=26.51 E-value=47 Score=23.53 Aligned_cols=26 Identities=31% Similarity=0.718 Sum_probs=19.7
Q ss_pred CCCccccccCCCCcc-eeeccccchhh
Q psy12688 125 GIEELCPVCGDKVSG-YHYGLLTCESC 150 (222)
Q Consensus 125 ~~~~~C~VCGd~asg-~HYGV~sCeaC 150 (222)
...+.|.|||....- -.||...|+-|
T Consensus 14 kGsr~C~vCg~~~gliRkygL~~CRqC 40 (54)
T PTZ00218 14 KGSRQCRVCSNRHGLIRKYGLNVCRQC 40 (54)
T ss_pred CCCCeeecCCCcchhhhhcCcchhhHH
Confidence 345679999987543 36999888888
No 57
>PF09289 FOLN: Follistatin/Osteonectin-like EGF domain; InterPro: IPR015369 This domain is predominantly found in osteonectin and follistatin. They adopt an EGF-like structure [, ]. Follistatin is involved in diverse activities from embryonic development to cell secretion. ; GO: 0005515 protein binding; PDB: 1LR7_A 1LR8_A 1LR9_A 2ARP_F 3B4V_H 2KCX_A 3SEK_C 2P6A_D 3HH2_C 2B0U_D ....
Probab=26.04 E-value=16 Score=21.43 Aligned_cols=19 Identities=21% Similarity=0.863 Sum_probs=12.5
Q ss_pred eccccCcccccCCCCCCCC
Q psy12688 164 YTCVAERSCHIDKTQRKRC 182 (222)
Q Consensus 164 ~~C~~~~~C~i~~~~R~~C 182 (222)
+.|+.++.|.+++..+..|
T Consensus 4 ~~Ck~GKvC~~d~~~~P~C 22 (22)
T PF09289_consen 4 FHCKRGKVCKVDEQGKPHC 22 (22)
T ss_dssp ---BTTEEEEEETTTCEEE
T ss_pred cccCCCCEeeeCCCCCcCC
Confidence 6799999999987766544
No 58
>PRK00420 hypothetical protein; Validated
Probab=24.06 E-value=28 Score=27.92 Aligned_cols=28 Identities=25% Similarity=0.581 Sum_probs=23.4
Q ss_pred CccccccCCCCcceeeccccchhhhHHH
Q psy12688 127 EELCPVCGDKVSGYHYGLLTCESCKGFF 154 (222)
Q Consensus 127 ~~~C~VCGd~asg~HYGV~sCeaCk~FF 154 (222)
...|.+||.+-...+-|...|-.|..+.
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCee
Confidence 3579999988888888889999998654
No 59
>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=21.21 E-value=70 Score=20.16 Aligned_cols=28 Identities=25% Similarity=0.750 Sum_probs=15.5
Q ss_pred ccccCCCCcc-ee---eccc-cchhhhHHHHhH
Q psy12688 130 CPVCGDKVSG-YH---YGLL-TCESCKGFFKRT 157 (222)
Q Consensus 130 C~VCGd~asg-~H---YGV~-sCeaCk~FFRRt 157 (222)
|..|+...+- .+ .|.. .|++|..+|++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~ 33 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKY 33 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHh
Confidence 4556654332 22 3444 799999999864
Done!