Query 033819
Match_columns 111
No_of_seqs 14 out of 16
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 06:39:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033819.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033819hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03207 stomagen; Provisional 100.0 2.8E-55 6.1E-60 319.3 4.4 105 3-111 9-113 (113)
2 PF07172 GRP: Glycine rich pro 70.6 3.5 7.6E-05 28.7 2.0 17 1-18 1-17 (95)
3 PF06679 DUF1180: Protein of u 45.1 24 0.00051 27.0 2.8 25 12-36 17-41 (163)
4 PF07561 DUF1540: Domain of Un 41.4 18 0.00039 21.2 1.3 19 73-95 7-26 (43)
5 PF09401 NSP10: RNA synthesis 34.1 14 0.0003 28.0 0.1 20 81-100 82-101 (124)
6 PF04885 Stig1: Stigma-specifi 32.5 38 0.00082 25.2 2.2 20 76-95 84-103 (136)
7 cd07155 NR_DBD_ER_like DNA-bin 28.6 20 0.00044 23.2 0.1 14 63-76 26-39 (75)
8 TIGR02052 MerP mercuric transp 26.9 48 0.001 18.9 1.5 15 8-22 6-20 (92)
9 PF06589 CRA: Circumsporozoite 26.3 51 0.0011 25.9 2.0 15 5-19 2-16 (157)
10 cd07157 2DBD_NR_DBD1 The first 25.8 34 0.00075 22.9 0.9 25 63-87 28-66 (86)
11 smart00132 LIM Zinc-binding do 25.2 40 0.00087 17.4 0.9 10 98-107 18-27 (39)
12 PTZ00264 circumsporozoite-rela 24.5 60 0.0013 25.3 2.0 15 5-19 2-16 (148)
13 cd07158 NR_DBD_Ppar_like The D 24.1 35 0.00076 21.8 0.7 14 63-76 26-40 (73)
14 cd07171 NR_DBD_ER DNA-binding 23.8 29 0.00064 23.1 0.2 14 63-76 31-44 (82)
15 PF10511 Cementoin: Trappin pr 23.1 42 0.00091 17.8 0.7 10 90-99 8-17 (17)
16 cd06959 NR_DBD_EcR_like The DN 23.1 31 0.00067 22.2 0.2 14 63-76 27-40 (73)
17 cd06963 NR_DBD_GR_like The DNA 22.8 30 0.00066 22.4 0.2 25 63-87 26-62 (73)
18 PF07246 Phlebovirus_NSM: Phle 22.3 59 0.0013 27.0 1.8 24 10-33 4-27 (264)
19 cd07164 NR_DBD_PNR_like_1 DNA- 22.3 43 0.00093 21.8 0.8 14 63-76 26-39 (78)
20 TIGR02803 ExbD_1 TonB system t 22.3 1.1E+02 0.0025 20.6 2.9 15 5-19 8-22 (122)
21 cd07163 NR_DBD_TLX DNA-binding 22.0 49 0.0011 22.4 1.1 14 63-76 34-47 (92)
22 PF02472 ExbD: Biopolymer tran 21.5 31 0.00067 22.6 0.0 15 5-19 12-26 (130)
23 PF09716 ETRAMP: Malarial earl 21.3 93 0.002 20.9 2.3 23 1-23 1-23 (84)
24 PF15240 Pro-rich: Proline-ric 20.8 47 0.001 26.1 0.9 11 10-20 2-12 (179)
25 smart00399 ZnF_C4 c4 zinc fing 20.0 55 0.0012 20.6 0.9 14 63-76 27-40 (70)
No 1
>PLN03207 stomagen; Provisional
Probab=100.00 E-value=2.8e-55 Score=319.29 Aligned_cols=105 Identities=59% Similarity=1.008 Sum_probs=94.9
Q ss_pred chhhHHHHHHHHHHHhhcccceeeecCccccccccccccCCCCCcccccchhhhhccccccceecccCCCccccccccCc
Q 033819 3 SIKLCNFVLLLLLVQLLAPAYVVVQGSRTQVGIPHHQSFSPSSPVHFKESSKAKVMNRNSRRLMIGSTAPTCTYNECRGC 82 (111)
Q Consensus 3 n~kl~~~~~Ll~~~il~~~Aa~viqgs~t~e~~p~~~s~s~~~q~~~~~~~~gg~~~~~~rr~miGStAPtCTYNECRgC 82 (111)
.++.+.+|||||+||| |++|+||+|+++++|++++.+.++|... +.+.|+..++++||+||||+||||||||||||
T Consensus 9 tt~~~~lffLl~~lll---a~~v~qgsr~~~~~~~~~~~s~~~q~~~-~~l~g~~~~k~srr~~igs~aptctynecrgc 84 (113)
T PLN03207 9 TTRCLTLFFLLFFLLL---GAYVIQGSRNQSILPYDQSISYPHQETV-KLLNGGHLSKSSRRLMIGSTAPTCTYNECRGC 84 (113)
T ss_pred cchhHHHHHHHHHHHH---HHHHHhccccccccCcccccccCchhcc-ccccccccchhhhhhhhcCcCCccccccccCc
Confidence 3556777888888889 9999999999999999999998886544 44556677889999999999999999999999
Q ss_pred cccccceeecccCCCCCCCcceeeeccCC
Q 033819 83 KYKCRAEQVPVEGNDPINSAYHYKCVCHR 111 (111)
Q Consensus 83 k~kC~aeqVPv~~ndP~nSayhy~cvchr 111 (111)
||||+||||||||||||||||||+|||||
T Consensus 85 r~kc~~eqvpv~~~dp~nsayhy~cvchR 113 (113)
T PLN03207 85 RYKCRAEQVPVEGNDPINSAYHYKCVCHR 113 (113)
T ss_pred cccccceeccccCCCCCccccccccCCCC
Confidence 99999999999999999999999999998
No 2
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=70.56 E-value=3.5 Score=28.70 Aligned_cols=17 Identities=47% Similarity=0.389 Sum_probs=7.0
Q ss_pred CcchhhHHHHHHHHHHHh
Q 033819 1 MASIKLCNFVLLLLLVQL 18 (111)
Q Consensus 1 man~kl~~~~~Ll~~~il 18 (111)
|++ |..-||.|||+++|
T Consensus 1 MaS-K~~llL~l~LA~lL 17 (95)
T PF07172_consen 1 MAS-KAFLLLGLLLAALL 17 (95)
T ss_pred Cch-hHHHHHHHHHHHHH
Confidence 774 43333333333333
No 3
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=45.10 E-value=24 Score=27.01 Aligned_cols=25 Identities=40% Similarity=0.509 Sum_probs=13.6
Q ss_pred HHHHHHhhcccceeeecCccccccc
Q 033819 12 LLLLVQLLAPAYVVVQGSRTQVGIP 36 (111)
Q Consensus 12 Ll~~~il~~~Aa~viqgs~t~e~~p 36 (111)
||++..|+++++..-....++..-|
T Consensus 17 LlLL~~L~~~~a~~~~A~sa~~~~P 41 (163)
T PF06679_consen 17 LLLLALLLAPAALASTAESAAPPTP 41 (163)
T ss_pred HHHHHHhhhhhhhhccccccCCCCC
Confidence 3344456667776655555554333
No 4
>PF07561 DUF1540: Domain of Unknown Function (DUF1540); InterPro: IPR011437 These proteins have four conserved cysteines, which is suggestive of a metal binding function. This domain may be found on its own or duplicated in the proteins.
Probab=41.35 E-value=18 Score=21.15 Aligned_cols=19 Identities=42% Similarity=0.906 Sum_probs=14.0
Q ss_pred cccc-ccccCccccccceeecccC
Q 033819 73 TCTY-NECRGCKYKCRAEQVPVEG 95 (111)
Q Consensus 73 tCTY-NECRgCk~kC~aeqVPv~~ 95 (111)
.|.| |+ ...|.|++|-|..
T Consensus 7 ~C~y~n~----~~~C~a~~I~V~~ 26 (43)
T PF07561_consen 7 NCKYWNE----DNECTAESIEVSS 26 (43)
T ss_pred cCCccCC----CCcEeCCeeEEec
Confidence 5667 54 4569999999973
No 5
>PF09401 NSP10: RNA synthesis protein NSP10; InterPro: IPR018995 Non-structural protein 10 (NSP10) is involved in RNA synthesis. It is synthesised as part of a replicase polyprotein, whose cleavage generates many non-structural proteins []. NSP10 contains two zinc binding motifs and forms two anti-parallel helices which are stacked against an irregular beta sheet []. A cluster of basic residues on the protein surface suggests a nucleic acid-binding function. ; GO: 0003723 RNA binding, 0008270 zinc ion binding, 0019079 viral genome replication, 0048471 perinuclear region of cytoplasm; PDB: 2XYQ_B 2XYR_B 2XYV_B 3R24_B 2GA6_I 2G9T_V 2FYG_A.
Probab=34.11 E-value=14 Score=27.98 Aligned_cols=20 Identities=40% Similarity=0.820 Sum_probs=16.3
Q ss_pred CccccccceeecccCCCCCC
Q 033819 81 GCKYKCRAEQVPVEGNDPIN 100 (111)
Q Consensus 81 gCk~kC~aeqVPv~~ndP~n 100 (111)
-|++|=+..|||.+-+||+.
T Consensus 82 ~c~~kgkfvqiP~~~~dPv~ 101 (124)
T PF09401_consen 82 RCKYKGKFVQIPTGTKDPVR 101 (124)
T ss_dssp S-SSTTSEEEEEGGTT-HHH
T ss_pred eeeccceEEECCCCCcCcch
Confidence 59999999999998899985
No 6
>PF04885 Stig1: Stigma-specific protein, Stig1; InterPro: IPR006969 This family represents the Stig1 cysteine rich plant protein.The tobacco stigma-specific gene, STIG1 is developmentally regulated and expressed specifically in the stigmatic secretory zone. Pistils of transgenic STIG1-barnase tobacco plants undergo normal development, but lack the stigmatic secretory zone and are female sterile. Pollen grains are unable to penetrate the surface of the ablated pistils. Application of stigmatic exudate from wild-type pistils to the ablated surface increases the efficiency of pollen tube germination and growth and restores the capacity of pollen tubes to penetrate the style []. The function of STIG1 is unknown.
Probab=32.50 E-value=38 Score=25.22 Aligned_cols=20 Identities=35% Similarity=0.652 Sum_probs=15.5
Q ss_pred cccccCccccccceeecccC
Q 033819 76 YNECRGCKYKCRAEQVPVEG 95 (111)
Q Consensus 76 YNECRgCk~kC~aeqVPv~~ 95 (111)
.+.|..|..+|..-|+.-+|
T Consensus 84 ~~nCG~Cg~~C~~g~~cC~G 103 (136)
T PF04885_consen 84 RNNCGACGNKCPYGQTCCGG 103 (136)
T ss_pred ccccHhhcCCCCCCceecCC
Confidence 45566899999988887766
No 7
>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=28.59 E-value=20 Score=23.21 Aligned_cols=14 Identities=21% Similarity=0.513 Sum_probs=10.2
Q ss_pred cceecccCCCcccc
Q 033819 63 RRLMIGSTAPTCTY 76 (111)
Q Consensus 63 rr~miGStAPtCTY 76 (111)
||.+.+....+|..
T Consensus 26 RR~~~~~~~~~C~~ 39 (75)
T cd07155 26 KRTIQGNLGYSCPS 39 (75)
T ss_pred HHHhhCCCceeCCc
Confidence 77777777777764
No 8
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=26.94 E-value=48 Score=18.94 Aligned_cols=15 Identities=33% Similarity=0.370 Sum_probs=6.0
Q ss_pred HHHHHHHHHHhhccc
Q 033819 8 NFVLLLLLVQLLAPA 22 (111)
Q Consensus 8 ~~~~Ll~~~il~~~A 22 (111)
-+|+|||.+.+++-|
T Consensus 6 ~~~~~~~~~~~~~~~ 20 (92)
T TIGR02052 6 TLLALFVLTSLPAWA 20 (92)
T ss_pred HHHHHHHHhcchhhh
Confidence 334444444443333
No 9
>PF06589 CRA: Circumsporozoite-related antigen (CRA); InterPro: IPR009512 The mode of choroquine action or resistance of the malarial parasite Plasmodium falciparum is not fully elucidated and presents a huge challenge world wide. Plasmodial EXP-1 protein, also called circumsporozoite-related antigen, changes under chloroquine treatment, making it a potential chloroquine resistance marker []. Although there are no authentic repeats in this antigen, there are a number of internal homologies (N-A-N-P) and (N-A-D-P). The first of these tetramers is the dominant repeat found in the circumsporozoite protein (CSP) of P. falciparum and reacts with antibodies against circumsporozoite-related antigen (CRA). It is possible that immune responses to CRA may act against the CSP also. The CRA is found in many parasitic strains.
Probab=26.33 E-value=51 Score=25.87 Aligned_cols=15 Identities=33% Similarity=0.385 Sum_probs=11.8
Q ss_pred hhHHHHHHHHHHHhh
Q 033819 5 KLCNFVLLLLLVQLL 19 (111)
Q Consensus 5 kl~~~~~Ll~~~il~ 19 (111)
|+--++||||++||.
T Consensus 2 kl~s~~FllF~~il~ 16 (157)
T PF06589_consen 2 KLLSAFFLLFCLILC 16 (157)
T ss_pred cHHHHHHHHHHHHHh
Confidence 667788889888873
No 10
>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=25.82 E-value=34 Score=22.93 Aligned_cols=25 Identities=24% Similarity=0.744 Sum_probs=15.3
Q ss_pred cceecccC--CCcccc-----------ccccCcccc-cc
Q 033819 63 RRLMIGST--APTCTY-----------NECRGCKYK-CR 87 (111)
Q Consensus 63 rr~miGSt--APtCTY-----------NECRgCk~k-C~ 87 (111)
||.+.... ..+|.. +.||.||++ |-
T Consensus 28 RR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl 66 (86)
T cd07157 28 MRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCL 66 (86)
T ss_pred ecceecCCCccccCCCCCccccCccccccCccchhhHHh
Confidence 67666654 556653 557777763 54
No 11
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=25.20 E-value=40 Score=17.38 Aligned_cols=10 Identities=20% Similarity=0.780 Sum_probs=7.2
Q ss_pred CCCCcceeee
Q 033819 98 PINSAYHYKC 107 (111)
Q Consensus 98 P~nSayhy~c 107 (111)
..+..||-.|
T Consensus 18 ~~~~~~H~~C 27 (39)
T smart00132 18 ALGKVWHPEC 27 (39)
T ss_pred eCCccccccC
Confidence 3567888877
No 12
>PTZ00264 circumsporozoite-related antigen; Provisional
Probab=24.46 E-value=60 Score=25.26 Aligned_cols=15 Identities=40% Similarity=0.421 Sum_probs=12.3
Q ss_pred hhHHHHHHHHHHHhh
Q 033819 5 KLCNFVLLLLLVQLL 19 (111)
Q Consensus 5 kl~~~~~Ll~~~il~ 19 (111)
|+-.++||||++||.
T Consensus 2 kils~vFllF~~il~ 16 (148)
T PTZ00264 2 KLLSAVFLLFCAILC 16 (148)
T ss_pred hHHHHHHHHHHHHHh
Confidence 677789999999973
No 13
>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=24.15 E-value=35 Score=21.83 Aligned_cols=14 Identities=21% Similarity=0.311 Sum_probs=9.0
Q ss_pred cceecccCCC-cccc
Q 033819 63 RRLMIGSTAP-TCTY 76 (111)
Q Consensus 63 rr~miGStAP-tCTY 76 (111)
||.+.+...+ +|..
T Consensus 26 RR~v~~~~~~~~C~~ 40 (73)
T cd07158 26 RRTIQHNLTYRRCLN 40 (73)
T ss_pred hhhhcCCCCcccCCC
Confidence 6777666666 6653
No 14
>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=23.81 E-value=29 Score=23.15 Aligned_cols=14 Identities=21% Similarity=0.434 Sum_probs=9.9
Q ss_pred cceecccCCCcccc
Q 033819 63 RRLMIGSTAPTCTY 76 (111)
Q Consensus 63 rr~miGStAPtCTY 76 (111)
||.+.+....+|..
T Consensus 31 RR~v~~~~~~~C~~ 44 (82)
T cd07171 31 KRSIQGHNDYICPA 44 (82)
T ss_pred HHHeeCCCceeCCC
Confidence 77777777777763
No 15
>PF10511 Cementoin: Trappin protein transglutaminase binding domain; InterPro: IPR019541 Trappin-2,a protease inhibitor, has a unique N-terminal domain that enables it to become cross-linked to extracellular matrix proteins by transglutaminase []. This domain contains several repeated motifs (rpresented by this entry) with the consensus sequence Gly-Gln-Asp-Pro-Val-Lys, and these together can anchor the whole molecule to extracellular matrix proteins, such as laminin, fibronectin, beta-crystallin, collagen IV, fibrinogen, and elastin, by transglutaminase-catalysed cross-links. The whole domain is rich in glutamine and lysine, thus allowing and transglutaminase(s) to catalyse the formation of an intermolecular epsilon-(gamma-glutamyl)lysine isopeptide bond []. Cementoin is associated with the WAP family, IPR008197 from INTERPRO, at the C terminus. ; PDB: 2REL_A.
Probab=23.10 E-value=42 Score=17.84 Aligned_cols=10 Identities=70% Similarity=1.365 Sum_probs=4.8
Q ss_pred eecccCCCCC
Q 033819 90 QVPVEGNDPI 99 (111)
Q Consensus 90 qVPv~~ndP~ 99 (111)
++||.|.||+
T Consensus 8 ~~~vKGQd~v 17 (17)
T PF10511_consen 8 QVPVKGQDPV 17 (17)
T ss_dssp ---SSSSS-S
T ss_pred cccccCcCCC
Confidence 6788888875
No 16
>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=23.08 E-value=31 Score=22.23 Aligned_cols=14 Identities=21% Similarity=0.536 Sum_probs=8.8
Q ss_pred cceecccCCCcccc
Q 033819 63 RRLMIGSTAPTCTY 76 (111)
Q Consensus 63 rr~miGStAPtCTY 76 (111)
||.+++.....|..
T Consensus 27 RR~v~~~~~~~C~~ 40 (73)
T cd06959 27 RRSVTKGAVYACKF 40 (73)
T ss_pred HHhhcCCCCccCCC
Confidence 66666666666653
No 17
>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=22.78 E-value=30 Score=22.41 Aligned_cols=25 Identities=24% Similarity=0.695 Sum_probs=15.1
Q ss_pred cceecccCCCcccc-----------ccccCcccc-cc
Q 033819 63 RRLMIGSTAPTCTY-----------NECRGCKYK-CR 87 (111)
Q Consensus 63 rr~miGStAPtCTY-----------NECRgCk~k-C~ 87 (111)
||.+.+...++|.. +.||.||++ |-
T Consensus 26 RR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl 62 (73)
T cd06963 26 KRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCY 62 (73)
T ss_pred HHhhcCCCceeCCCCCccccCCcccccCccchhhHHH
Confidence 66666666666653 457777764 43
No 18
>PF07246 Phlebovirus_NSM: Phlebovirus nonstructural protein NS-M; InterPro: IPR009879 This entry consists of several Phlebovirus nonstructural NS-M proteins, which represent the N-terminal region of the M polyprotein precursor. The function of this family is unknown.
Probab=22.33 E-value=59 Score=27.02 Aligned_cols=24 Identities=25% Similarity=0.199 Sum_probs=17.3
Q ss_pred HHHHHHHHhhcccceeeecCcccc
Q 033819 10 VLLLLLVQLLAPAYVVVQGSRTQV 33 (111)
Q Consensus 10 ~~Ll~~~il~~~Aa~viqgs~t~e 33 (111)
++.+|+.+.+|-|||+|.++..+.
T Consensus 4 iL~iL~~~~~a~aay~l~~w~~~g 27 (264)
T PF07246_consen 4 ILAILTNIVLAMAAYSLHGWGPDG 27 (264)
T ss_pred HHHHHHHHHHHHhheeEEecCCCC
Confidence 333445666777999999988765
No 19
>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=22.30 E-value=43 Score=21.82 Aligned_cols=14 Identities=21% Similarity=0.292 Sum_probs=9.4
Q ss_pred cceecccCCCcccc
Q 033819 63 RRLMIGSTAPTCTY 76 (111)
Q Consensus 63 rr~miGStAPtCTY 76 (111)
||.+.+....+|..
T Consensus 26 RR~~~~~~~~~C~~ 39 (78)
T cd07164 26 KRSIRRNLAYVCKE 39 (78)
T ss_pred hhhccCCCCccCCC
Confidence 67776666667764
No 20
>TIGR02803 ExbD_1 TonB system transport protein ExbD, group 1. Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR family modeled by TIGRFAMs TIGR02801. Members always are encoded next to a protein designated ExbB (TIGR02797), related to the TolQ family modeled by TIGRFAMs TIGR02796. ExbD and ExbB together form a proton channel through which they can harness the proton-motive force to energize TonB, which in turn energizes TonB-dependent receptors in the outer membrane. TonB-dependent receptors with known specificity tend to import siderophores or vitamin B12. A TonB system and Tol-Pal system often will co-exist in a single bacterial genome.
Probab=22.26 E-value=1.1e+02 Score=20.64 Aligned_cols=15 Identities=20% Similarity=0.576 Sum_probs=9.1
Q ss_pred hhHHHHHHHHHHHhh
Q 033819 5 KLCNFVLLLLLVQLL 19 (111)
Q Consensus 5 kl~~~~~Ll~~~il~ 19 (111)
-+-+++|+|+.|.++
T Consensus 8 PlIDVvflLLiFFmv 22 (122)
T TIGR02803 8 PFIDVMLVLLIIFMV 22 (122)
T ss_pred cHHHHHHHHHHHHHH
Confidence 455677777655543
No 21
>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=22.00 E-value=49 Score=22.44 Aligned_cols=14 Identities=14% Similarity=0.275 Sum_probs=10.0
Q ss_pred cceecccCCCcccc
Q 033819 63 RRLMIGSTAPTCTY 76 (111)
Q Consensus 63 rr~miGStAPtCTY 76 (111)
||.+.+....+|..
T Consensus 34 RR~v~~~~~~~C~~ 47 (92)
T cd07163 34 KRSIRRNRQYVCKS 47 (92)
T ss_pred eeeecCCCCcCCCC
Confidence 77777777667764
No 22
>PF02472 ExbD: Biopolymer transport protein ExbD/TolR; InterPro: IPR003400 This group of proteins are membrane bound transport proteins essential for ferric ion uptake in bacteria []. The family consists of ExbD, and TolR which are involved in TonB-dependent transport of various receptor bound substrates including colicins [].; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2JWL_A 2JWK_A 2PFU_A.
Probab=21.52 E-value=31 Score=22.62 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHhh
Q 033819 5 KLCNFVLLLLLVQLL 19 (111)
Q Consensus 5 kl~~~~~Ll~~~il~ 19 (111)
-+-.++|+|+.|+++
T Consensus 12 pmiDv~flLLiFfm~ 26 (130)
T PF02472_consen 12 PMIDVVFLLLIFFMV 26 (130)
T ss_dssp ---------------
T ss_pred cHHHHHHHHHHHHHH
Confidence 345677777766664
No 23
>PF09716 ETRAMP: Malarial early transcribed membrane protein (ETRAMP); InterPro: IPR006389 These sequences represent a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rodent parasite Plasmodium yoelii []. A homologue from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane []. Members have an initial hydrophobic, Phe/Tyr-rich stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region, and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both Plasmodium falciparum and P. yoelii chromosomes.
Probab=21.33 E-value=93 Score=20.94 Aligned_cols=23 Identities=35% Similarity=0.556 Sum_probs=11.3
Q ss_pred CcchhhHHHHHHHHHHHhhcccc
Q 033819 1 MASIKLCNFVLLLLLVQLLAPAY 23 (111)
Q Consensus 1 man~kl~~~~~Ll~~~il~~~Aa 23 (111)
|-=+|...|+.+||.+-++.|..
T Consensus 1 MKi~kv~~ff~~Ll~i~~l~p~~ 23 (84)
T PF09716_consen 1 MKISKVFYFFAFLLAINLLTPCL 23 (84)
T ss_pred CcHHHHHHHHHHHHHHHhCcCcc
Confidence 33345544555555555655543
No 24
>PF15240 Pro-rich: Proline-rich
Probab=20.80 E-value=47 Score=26.14 Aligned_cols=11 Identities=64% Similarity=0.821 Sum_probs=6.2
Q ss_pred HHHHHHHHhhc
Q 033819 10 VLLLLLVQLLA 20 (111)
Q Consensus 10 ~~Ll~~~il~~ 20 (111)
|++||++.|||
T Consensus 2 LlVLLSvALLA 12 (179)
T PF15240_consen 2 LLVLLSVALLA 12 (179)
T ss_pred hhHHHHHHHHH
Confidence 45556666654
No 25
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=20.01 E-value=55 Score=20.62 Aligned_cols=14 Identities=21% Similarity=0.154 Sum_probs=9.2
Q ss_pred cceecccCCCcccc
Q 033819 63 RRLMIGSTAPTCTY 76 (111)
Q Consensus 63 rr~miGStAPtCTY 76 (111)
||.+.......|..
T Consensus 27 RR~v~~~~~~~C~~ 40 (70)
T smart00399 27 RRTVNLRYKYRCDR 40 (70)
T ss_pred hhheeCCCCeecCC
Confidence 67777766666653
Done!