Query psy14580
Match_columns 149
No_of_seqs 111 out of 351
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 23:28:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14580.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14580hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00645 zf-PARP: Poly(ADP-rib 100.0 1.7E-29 3.7E-34 175.5 5.1 82 18-102 1-82 (82)
2 KOG4437|consensus 99.9 6.1E-27 1.3E-31 200.8 -2.8 132 10-146 1-165 (482)
3 PLN03123 poly [ADP-ribose] pol 99.9 6.5E-24 1.4E-28 201.3 8.8 88 11-105 4-91 (981)
4 PLN03123 poly [ADP-ribose] pol 99.8 3.1E-21 6.6E-26 183.2 7.7 86 9-104 101-186 (981)
5 KOG1037|consensus 95.2 0.0024 5.1E-08 58.5 -2.1 89 10-104 4-107 (531)
6 PF00412 LIM: LIM domain; Int 87.7 0.58 1.3E-05 29.2 2.6 28 27-64 1-28 (58)
7 smart00132 LIM Zinc-binding do 85.7 0.68 1.5E-05 26.2 1.9 29 26-64 1-29 (39)
8 PF10083 DUF2321: Uncharacteri 70.2 3.7 8E-05 32.4 2.3 28 83-110 92-119 (158)
9 COG1379 PHP family phosphoeste 64.5 2 4.4E-05 37.9 -0.2 50 13-62 254-305 (403)
10 PF06945 DUF1289: Protein of u 51.1 5 0.00011 25.5 -0.0 26 79-104 23-48 (51)
11 PF10367 Vps39_2: Vacuolar sor 46.3 22 0.00047 24.4 2.7 29 25-63 79-107 (109)
12 PF00628 PHD: PHD-finger; Int 45.8 10 0.00022 23.0 0.8 12 54-65 20-31 (51)
13 KOG1973|consensus 44.3 9.2 0.0002 32.1 0.6 9 55-63 242-250 (274)
14 PF09943 DUF2175: Uncharacteri 44.2 13 0.00028 27.3 1.2 32 25-66 3-34 (101)
15 PF11293 DUF3094: Protein of u 43.1 23 0.00049 23.4 2.1 19 88-106 3-21 (55)
16 cd07072 NR_LBD_DHR38_like Liga 34.1 32 0.00069 28.3 2.2 21 80-100 62-82 (239)
17 smart00249 PHD PHD zinc finger 34.1 11 0.00023 21.6 -0.4 10 54-63 20-29 (47)
18 cd06940 NR_LBD_REV_ERB The lig 32.4 34 0.00073 26.8 2.0 21 80-100 32-52 (189)
19 KOG0957|consensus 32.4 9 0.00019 35.8 -1.4 47 12-63 226-272 (707)
20 cd06945 NR_LBD_Nurr1_like The 31.8 36 0.00079 27.7 2.2 21 80-100 61-81 (239)
21 cd06941 NR_LBD_DmE78_like The 31.4 39 0.00085 26.2 2.2 20 80-99 22-41 (195)
22 COG4847 Uncharacterized protei 31.2 23 0.0005 26.0 0.8 30 26-65 8-37 (103)
23 cd06929 NR_LBD_F1 Ligand-bindi 31.2 36 0.00078 25.5 1.9 21 80-100 22-42 (174)
24 KOG3970|consensus 30.7 17 0.00037 30.7 0.1 31 25-66 51-82 (299)
25 cd06939 NR_LBD_ROR_like The li 30.5 40 0.00086 27.6 2.2 41 55-100 48-88 (241)
26 cd07071 NR_LBD_Nurr1 The ligan 29.6 45 0.00098 27.3 2.4 21 80-100 61-81 (238)
27 PF06750 DiS_P_DiS: Bacterial 28.5 29 0.00064 24.5 1.0 11 23-33 32-42 (92)
28 cd06942 NR_LBD_Sex_1_like The 27.2 48 0.001 25.8 2.1 20 80-99 22-41 (191)
29 cd07348 NR_LBD_NGFI-B The liga 27.1 50 0.0011 27.1 2.3 21 80-100 61-81 (238)
30 cd06933 NR_LBD_VDR The ligand 26.8 48 0.001 26.9 2.1 21 80-100 57-77 (238)
31 cd06930 NR_LBD_F2 Ligand-bindi 26.7 55 0.0012 24.0 2.2 21 80-100 19-39 (165)
32 cd06935 NR_LBD_TR The ligand b 26.3 50 0.0011 26.9 2.1 21 80-100 72-92 (243)
33 COG3478 Predicted nucleic-acid 26.0 35 0.00075 23.4 0.9 40 23-62 3-43 (68)
34 cd06937 NR_LBD_RAR The ligand 25.3 54 0.0012 26.5 2.1 21 80-100 58-78 (231)
35 cd06932 NR_LBD_PPAR The ligand 24.4 55 0.0012 27.1 2.0 43 53-100 61-103 (259)
36 PF02892 zf-BED: BED zinc fing 24.3 37 0.0008 20.1 0.7 18 20-37 12-29 (45)
37 cd06157 NR_LBD The ligand bind 24.0 62 0.0013 23.1 2.0 22 80-101 18-39 (168)
38 cd06934 NR_LBD_PXR_like The li 23.2 54 0.0012 26.4 1.7 21 80-100 55-75 (226)
39 cd06951 NR_LBD_Dax1_like The l 22.9 66 0.0014 25.9 2.2 21 80-100 39-59 (222)
40 cd06954 NR_LBD_LXR The ligand 21.7 72 0.0016 25.6 2.2 21 80-100 63-83 (236)
41 cd06949 NR_LBD_ER Ligand bindi 21.2 76 0.0016 25.7 2.2 21 80-100 52-72 (235)
42 cd07075 NR_LBD_MR Ligand bindi 21.1 75 0.0016 26.4 2.2 21 80-100 48-68 (248)
43 KOG3795|consensus 21.1 41 0.00088 27.5 0.6 11 21-31 12-22 (230)
44 KOG4217|consensus 21.0 52 0.0011 30.6 1.3 20 80-99 428-447 (605)
45 PF14446 Prok-RING_1: Prokaryo 20.9 48 0.001 21.7 0.8 32 24-64 5-37 (54)
46 cd07073 NR_LBD_AR Ligand bindi 20.7 80 0.0017 26.0 2.3 21 80-100 48-68 (246)
47 PF11571 Med27: Mediator compl 20.0 27 0.00058 24.5 -0.6 11 24-34 54-64 (90)
No 1
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=99.96 E-value=1.7e-29 Score=175.51 Aligned_cols=82 Identities=39% Similarity=0.775 Sum_probs=68.4
Q ss_pred EEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCCCCHHHHHHH
Q psy14580 18 DRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEV 97 (149)
Q Consensus 18 EyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~L~~eDQ~~I 97 (149)
||||||||+|++|+++|++|+||||.+++++.++|.++.|||+.||+......+..+ .++++|.||+.|+++||++|
T Consensus 1 EyAks~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~~~~~~~~~~~---~~~~~i~G~~~L~~~Dq~~i 77 (82)
T PF00645_consen 1 EYAKSGRAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFFKKQLRNRETT---GDIEEIKGFDELKPEDQEKI 77 (82)
T ss_dssp EE-SSSTEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHHHTTCCTTSST---SCGGGCETCCCS-HHHHHHH
T ss_pred CcCCCCCccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccccchhhhcccC---CCHHHCCChHHCCHHHHHHH
Confidence 899999999999999999999999999999988889999999999987432211111 47899999999999999999
Q ss_pred HHHch
Q psy14580 98 LSRFP 102 (149)
Q Consensus 98 ~~~~~ 102 (149)
+++|+
T Consensus 78 ~~~i~ 82 (82)
T PF00645_consen 78 RKLIE 82 (82)
T ss_dssp HHHHS
T ss_pred HHHhC
Confidence 99875
No 2
>KOG4437|consensus
Probab=99.92 E-value=6.1e-27 Score=200.83 Aligned_cols=132 Identities=33% Similarity=0.646 Sum_probs=110.1
Q ss_pred CCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCC--CCccceEEecCchhhHHHhhhhcccccCccCCCCCcC
Q psy14580 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWD 87 (149)
Q Consensus 10 ~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~--~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~ 87 (149)
|+..+|++.|||. .|+|++|+.+|.||.+|||.++++|+. .|.|..|||.+|+|+.+.++|+||+.|+++++|+||+
T Consensus 1 ~A~~RFC~DYAKR-~A~C~KCK~~i~KGV~R~GKi~P~~~S~~~~DMK~~~H~~C~FE~L~rAR~TTK~I~~~~EiEG~E 79 (482)
T KOG4437|consen 1 MAEQRFCVDYAKR-TAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWE 79 (482)
T ss_pred CCCchHHHHHHHH-hhhhHHHHHHHHHhhhhhccccCCCcccCCchHHHHHHHHHHHHHHHhccccccccccchhhcchh
Confidence 5678999999997 799999999999999999999999876 3689999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHchhhhccCCCCCCCCCcCCCCCCcccCC-------------------------------Cchhhhhh
Q psy14580 88 DLTPEDQEEVLSRFPESLRESNKDRDVPERKIPSSSEKKSK-------------------------------TPKKKAVA 136 (149)
Q Consensus 88 ~L~~eDQ~~I~~~~~~~~~~~~~kk~~~~~~~~~~~~~~~~-------------------------------~~~~~~~~ 136 (149)
+|.++||+.|.++|+++. ++..|+.+++ .|.+++++.+. +-++ =|
T Consensus 80 ~L~~~~~~~I~~~i~~Ls-~K~sK~~~~~-~K~T~~~~~T~~~~~~~~V~sT~~RK~~N~~~~rS~R~~~~~~~Sk--FN 155 (482)
T KOG4437|consen 80 ELEDNEKEQITQHIADLS-SKAAKKAVVQ-AKLTTTGQVTSPVKGASFVTSTNPRKFSNNSPKRSLRSSKCDPRSK--FN 155 (482)
T ss_pred hhchhhHHHHHHHHHHHH-HHhhhccccc-cccCccccccccccccCcccccCccccccccchhccccccCCcccc--ch
Confidence 999999999999998883 3334444333 44444443322 2233 68
Q ss_pred hhhhhhhhhc
Q psy14580 137 YFCLIRPLCF 146 (149)
Q Consensus 137 ~~~~~~~~~~ 146 (149)
.|++|+.||+
T Consensus 156 ~F~ef~kiCS 165 (482)
T KOG4437|consen 156 LFREFRKLCS 165 (482)
T ss_pred HHHHHHHHHH
Confidence 9999999997
No 3
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=99.90 E-value=6.5e-24 Score=201.32 Aligned_cols=88 Identities=34% Similarity=0.544 Sum_probs=80.0
Q ss_pred CCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCCCC
Q psy14580 11 DDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLT 90 (149)
Q Consensus 11 ~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~L~ 90 (149)
...+|.|||||||||+|++|+++|.||+||||.++++|+++|.++.|||++||+.. ...++++++|.||+.|+
T Consensus 4 ~~~~~~~EYAkS~Rs~Ck~C~~~I~K~~lRi~~~v~~~~~dg~~~~W~H~~Cf~~~-------~~~~~~~~~l~G~~~L~ 76 (981)
T PLN03123 4 PPKPWKAEYAKSSRSSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCILKK-------KNQIKSIDDVEGIDSLR 76 (981)
T ss_pred CCCCeeEEEecCCCccccccCCcccCCCeEEEEeecccccCCCCCeeecccccccc-------ccCCCChhhcCChhhCC
Confidence 34789999999999999999999999999999999999999999999999999852 22355789999999999
Q ss_pred HHHHHHHHHHchhhh
Q psy14580 91 PEDQEEVLSRFPESL 105 (149)
Q Consensus 91 ~eDQ~~I~~~~~~~~ 105 (149)
++||+.|++++++..
T Consensus 77 ~eDq~~i~~~i~~~~ 91 (981)
T PLN03123 77 WEDQQKIRKYVESGG 91 (981)
T ss_pred HHHHHHHHHHHhccC
Confidence 999999999998884
No 4
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=99.84 E-value=3.1e-21 Score=183.24 Aligned_cols=86 Identities=35% Similarity=0.618 Sum_probs=75.1
Q ss_pred CCCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCCcCC
Q psy14580 9 PEDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDD 88 (149)
Q Consensus 9 ~~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~ 88 (149)
+.....|.||||+||||+|++|+++|.||+||||..++++ +|.++.|||+.||++.+ . ..++++|.||++
T Consensus 101 ~~~~~~~~vEyAkS~Ra~Ck~C~~kI~KgelRig~~v~~~--~g~~~~W~H~~Cf~~~~----~----~~~~e~l~Gf~~ 170 (981)
T PLN03123 101 AASSFEYGIEVAKTSRATCRRCSEKILKGEVRISSKPEGQ--GYKGLAWHHAKCFLEMS----P----STPVEKLSGWDT 170 (981)
T ss_pred ccCCcceEEEEecCCCCccccCCceecCCceEEEeeecCC--CCCcccccccccccccC----C----CCChhhCCChhh
Confidence 4456899999999999999999999999999999998877 56779999999998632 1 126899999999
Q ss_pred CCHHHHHHHHHHchhh
Q psy14580 89 LTPEDQEEVLSRFPES 104 (149)
Q Consensus 89 L~~eDQ~~I~~~~~~~ 104 (149)
|+++||+.|++++.+.
T Consensus 171 L~~eDqe~v~~li~~~ 186 (981)
T PLN03123 171 LSDSDQEAVLPLVKKS 186 (981)
T ss_pred CCHHHHHHHHHHHhhc
Confidence 9999999999999644
No 5
>KOG1037|consensus
Probab=95.24 E-value=0.0024 Score=58.48 Aligned_cols=89 Identities=16% Similarity=0.185 Sum_probs=68.2
Q ss_pred CCCCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhHHHhhhhcccccCccCCCCC----
Q psy14580 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGG---- 85 (149)
Q Consensus 10 ~~~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G---- 85 (149)
........+|++++++.|+.|...|.+..+|.++......+++....|+|..||++.-...+. +..+.+|
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~~~~~~s~~~~~~~~~~~------~~v~~~~~~~~ 77 (531)
T KOG1037|consen 4 TPIALDNASVLKSEDLNSGTCEHVINKDEFRKGIKELKLIFDGDVDKWKHTSCFLKKDHLIRG------PEVKVPGLNQT 77 (531)
T ss_pred CCcccccchhhhhhchhccCCcccccchhhhhhhhhhhhccccccCcccccccccCccccccc------ccccccccccc
Confidence 345677889999999999999988999999999998888889999999999999763211111 2233445
Q ss_pred -----------cCCCCHHHHHHHHHHchhh
Q psy14580 86 -----------WDDLTPEDQEEVLSRFPES 104 (149)
Q Consensus 86 -----------~~~L~~eDQ~~I~~~~~~~ 104 (149)
...|.|++|+.+...++..
T Consensus 78 ~~~~~~~~~~~~~~l~~d~~~~~~~~~~~~ 107 (531)
T KOG1037|consen 78 NVENENNKEYTEEELEWDEQQKKRKTVEEG 107 (531)
T ss_pred cccccccchhhhhhhhcccccceeeeeeec
Confidence 7788888886666666554
No 6
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=87.66 E-value=0.58 Score=29.21 Aligned_cols=28 Identities=25% Similarity=0.623 Sum_probs=21.0
Q ss_pred ccccccCcCCCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580 27 CKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCIL 64 (149)
Q Consensus 27 Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~ 64 (149)
|.+|++.|..+++.|... ...||..||.
T Consensus 1 C~~C~~~I~~~~~~~~~~----------~~~~H~~Cf~ 28 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAM----------GKFWHPECFK 28 (58)
T ss_dssp BTTTSSBESSSSEEEEET----------TEEEETTTSB
T ss_pred CCCCCCCccCcEEEEEeC----------CcEEEccccc
Confidence 789999999888766331 2578999984
No 7
>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=85.66 E-value=0.68 Score=26.16 Aligned_cols=29 Identities=21% Similarity=0.543 Sum_probs=19.0
Q ss_pred cccccccCcCCCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580 26 GCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCIL 64 (149)
Q Consensus 26 ~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~ 64 (149)
.|.+|++.|..++..+... ..-||..||.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~----------~~~~H~~Cf~ 29 (39)
T smart00132 1 KCAGCGKPIRGGELVLRAL----------GKVWHPECFK 29 (39)
T ss_pred CccccCCcccCCcEEEEeC----------CccccccCCC
Confidence 4889999998774444321 2456888873
No 8
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=70.18 E-value=3.7 Score=32.41 Aligned_cols=28 Identities=18% Similarity=0.507 Sum_probs=22.8
Q ss_pred CCCcCCCCHHHHHHHHHHchhhhccCCC
Q psy14580 83 MGGWDDLTPEDQEEVLSRFPESLRESNK 110 (149)
Q Consensus 83 I~G~~~L~~eDQ~~I~~~~~~~~~~~~~ 110 (149)
++-.++|++++++.+.+.++++..++|+
T Consensus 92 ~ee~eeLs~deke~~~~sl~dL~~d~Pk 119 (158)
T PF10083_consen 92 IEEDEELSPDEKEQFKESLPDLTKDTPK 119 (158)
T ss_pred HHHhhcCCHHHHHHHHhhhHHHhhcCCc
Confidence 3347799999999999999999765554
No 9
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=64.47 E-value=2 Score=37.92 Aligned_cols=50 Identities=24% Similarity=0.392 Sum_probs=34.6
Q ss_pred CceEEEEccCCCccccccccCcCCCC-eEEEEE-eecCCCCCccceEEecCc
Q psy14580 13 KNFWVDRAKTGRSGCKKCKQKIDTGT-VRIAKM-GYNPFGSGKMKQWHHIDC 62 (149)
Q Consensus 13 ~~~~VEyAKS~RA~Ck~Ck~kI~KGe-LRIG~~-v~~~~~~g~~~~WyH~~C 62 (149)
..|..|=|+++|..|-+|+.+|.||. =||--. ..+|.+.-..+-++|.-=
T Consensus 254 t~y~le~A~~~~wrCpkCGg~ikKGV~dRv~ELad~~~~~p~~RPPYlhliP 305 (403)
T COG1379 254 TRYSLEEAKSLRWRCPKCGGKIKKGVSDRVLELADTEPEHPKHRPPYLHLIP 305 (403)
T ss_pred hccCcchhhhhcccCcccccchhhhHHHHHHHhhccCcccCCCCCCceeccc
Confidence 46889999999999999999999994 243211 122333344577888643
No 10
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=51.13 E-value=5 Score=25.51 Aligned_cols=26 Identities=15% Similarity=0.650 Sum_probs=23.0
Q ss_pred ccCCCCCcCCCCHHHHHHHHHHchhh
Q psy14580 79 VVDDMGGWDDLTPEDQEEVLSRFPES 104 (149)
Q Consensus 79 ~~edI~G~~~L~~eDQ~~I~~~~~~~ 104 (149)
++++|.+|..|+++.|..|...+..-
T Consensus 23 T~dEI~~W~~~s~~er~~i~~~l~~R 48 (51)
T PF06945_consen 23 TLDEIRDWKSMSDDERRAILARLRAR 48 (51)
T ss_pred cHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence 57889999999999999999888654
No 11
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=46.34 E-value=22 Score=24.42 Aligned_cols=29 Identities=24% Similarity=0.650 Sum_probs=19.9
Q ss_pred ccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580 25 SGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI 63 (149)
Q Consensus 25 A~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf 63 (149)
..|..|++.|..+.+-+- | +| +-+|..|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~-----p--~~---~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVF-----P--CG---HVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEe-----C--CC---eEEecccc
Confidence 459999999988643221 2 23 66799996
No 12
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=45.80 E-value=10 Score=23.05 Aligned_cols=12 Identities=25% Similarity=0.830 Sum_probs=9.6
Q ss_pred cceEEecCchhh
Q psy14580 54 MKQWHHIDCILE 65 (149)
Q Consensus 54 ~~~WyH~~Cf~~ 65 (149)
-..|||..|+-.
T Consensus 20 C~~~~H~~C~~~ 31 (51)
T PF00628_consen 20 CNRWYHQECVGP 31 (51)
T ss_dssp TSCEEETTTSTS
T ss_pred CChhhCcccCCC
Confidence 468999999743
No 13
>KOG1973|consensus
Probab=44.35 E-value=9.2 Score=32.14 Aligned_cols=9 Identities=33% Similarity=1.305 Sum_probs=8.0
Q ss_pred ceEEecCch
Q psy14580 55 KQWHHIDCI 63 (149)
Q Consensus 55 ~~WyH~~Cf 63 (149)
..|||+.|+
T Consensus 242 ~eWFH~~CV 250 (274)
T KOG1973|consen 242 IEWFHFTCV 250 (274)
T ss_pred cceEEEecc
Confidence 389999997
No 14
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=44.19 E-value=13 Score=27.32 Aligned_cols=32 Identities=25% Similarity=0.409 Sum_probs=20.6
Q ss_pred ccccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhhH
Q psy14580 25 SGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEV 66 (149)
Q Consensus 25 A~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~~ 66 (149)
=+|--|++.|--|++== ... .|. -||.||...
T Consensus 3 WkC~iCg~~I~~gqlFT-F~~-----kG~----VH~~C~~~~ 34 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFT-FTK-----KGP----VHYECFREK 34 (101)
T ss_pred eEEEecCCeeeecceEE-Eec-----CCc----EeHHHHHHH
Confidence 37889999998887421 111 132 399999764
No 15
>PF11293 DUF3094: Protein of unknown function (DUF3094); InterPro: IPR021444 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=43.09 E-value=23 Score=23.36 Aligned_cols=19 Identities=32% Similarity=0.475 Sum_probs=16.2
Q ss_pred CCCHHHHHHHHHHchhhhc
Q psy14580 88 DLTPEDQEEVLSRFPESLR 106 (149)
Q Consensus 88 ~L~~eDQ~~I~~~~~~~~~ 106 (149)
.|.+|||++|.+.+.....
T Consensus 3 rL~pEDQ~~Vd~yL~a~~~ 21 (55)
T PF11293_consen 3 RLNPEDQQRVDEYLQAGVN 21 (55)
T ss_pred CCCHHHHHHHHHHHhCCCC
Confidence 6899999999999877753
No 16
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 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=34.15 E-value=32 Score=28.29 Aligned_cols=21 Identities=33% Similarity=0.586 Sum_probs=18.0
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...|+||.+|+.+||..+.+.
T Consensus 62 AK~IPgF~~L~~~DQi~LLk~ 82 (239)
T cd07072 62 AEKIPGFPDLCKEDQELLFQS 82 (239)
T ss_pred hccCCCccCCCHHHHHHHHHH
Confidence 467999999999999988654
No 17
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs 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. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of
Probab=32.42 E-value=34 Score=26.78 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=17.7
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
.-.|+||.+|+.+||..+.+.
T Consensus 32 aK~iPgF~~L~~~DQi~LLk~ 52 (189)
T cd06940 32 AKRIPGFRDLSQHDQVTLLKA 52 (189)
T ss_pred HhcCCCcccCChhhHHHHHHH
Confidence 456999999999999988643
No 19
>KOG0957|consensus
Probab=32.41 E-value=9 Score=35.78 Aligned_cols=47 Identities=26% Similarity=0.386 Sum_probs=34.5
Q ss_pred CCceEEEEccCCCccccccccCcCCCCeEEEEEeecCCCCCccceEEecCch
Q psy14580 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCI 63 (149)
Q Consensus 12 ~~~~~VEyAKS~RA~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf 63 (149)
.+.+.+.||+=|+-.|..|..+|. .|.|+-+. -..|....|+|+-|.
T Consensus 226 Vtl~em~ysk~Gak~Cs~Ced~~f---ARtGvci~--CdaGMCk~YfHVTCA 272 (707)
T KOG0957|consen 226 VTLEEMDYSKFGAKTCSACEDKIF---ARTGVCIR--CDAGMCKEYFHVTCA 272 (707)
T ss_pred ccHHHhhhhhhccchhccccchhh---hhcceeee--ccchhhhhhhhhhHH
Confidence 345667899999999999988873 35554332 124667899999994
No 20
>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. 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
Probab=31.76 E-value=36 Score=27.74 Aligned_cols=21 Identities=33% Similarity=0.621 Sum_probs=17.6
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
..-|+||.+|..+||..+.+.
T Consensus 61 AK~IPgF~~L~~~DQi~LLk~ 81 (239)
T cd06945 61 AEKIPGFKDLHREDQDLLLES 81 (239)
T ss_pred HHhCCCcccCCHHHHHHHHHH
Confidence 356999999999999988653
No 21
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: 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. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. 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. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=31.36 E-value=39 Score=26.24 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=17.2
Q ss_pred cCCCCCcCCCCHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLS 99 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~ 99 (149)
...|+||.+|+.+||-.+.+
T Consensus 22 aK~iP~F~~L~~~DQi~LLk 41 (195)
T cd06941 22 AKRIPGFCDLSQDDQLLLIK 41 (195)
T ss_pred HHcCCCcccCCHHHHHHHHH
Confidence 45699999999999998854
No 22
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.18 E-value=23 Score=26.00 Aligned_cols=30 Identities=27% Similarity=0.550 Sum_probs=19.7
Q ss_pred cccccccCcCCCCeEEEEEeecCCCCCccceEEecCchhh
Q psy14580 26 GCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILE 65 (149)
Q Consensus 26 ~Ck~Ck~kI~KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~~ 65 (149)
+|.-|+..|-.|+ ++-.... |. -|++|+..
T Consensus 8 kC~VCg~~iieGq-kFTF~~k-----Gs----VH~eCl~~ 37 (103)
T COG4847 8 KCYVCGGTIIEGQ-KFTFTKK-----GS----VHYECLAE 37 (103)
T ss_pred eEeeeCCEeeecc-EEEEeeC-----Cc----chHHHHHH
Confidence 6889999998886 2222111 22 39999865
No 23
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. 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).
Probab=31.16 E-value=36 Score=25.45 Aligned_cols=21 Identities=29% Similarity=0.514 Sum_probs=17.9
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...|+||..|+.+||..+.+.
T Consensus 22 ak~ip~F~~L~~~Dq~~Llk~ 42 (174)
T cd06929 22 AKRIPGFRELSQEDQIALLKG 42 (174)
T ss_pred ccCCcCcccCChhHHHHHHHh
Confidence 467999999999999988653
No 24
>KOG3970|consensus
Probab=30.65 E-value=17 Score=30.72 Aligned_cols=31 Identities=26% Similarity=0.628 Sum_probs=23.3
Q ss_pred ccccccccCcCCC-CeEEEEEeecCCCCCccceEEecCchhhH
Q psy14580 25 SGCKKCKQKIDTG-TVRIAKMGYNPFGSGKMKQWHHIDCILEV 66 (149)
Q Consensus 25 A~Ck~Ck~kI~KG-eLRIG~~v~~~~~~g~~~~WyH~~Cf~~~ 66 (149)
..|+-|+..++.| .+|+-. .+-+||+|+-+.
T Consensus 51 pNC~LC~t~La~gdt~RLvC-----------yhlfHW~Clner 82 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVC-----------YHLFHWKCLNER 82 (299)
T ss_pred CCCceeCCccccCcceeehh-----------hhhHHHHHhhHH
Confidence 5799999999887 566632 466799998763
No 25
>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. 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. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that 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. RORbeta expression is largely r
Probab=30.55 E-value=40 Score=27.59 Aligned_cols=41 Identities=17% Similarity=0.261 Sum_probs=27.0
Q ss_pred ceEEecCchhhHHHhhhhcccccCccCCCCCcCCCCHHHHHHHHHH
Q psy14580 55 KQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 55 ~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~L~~eDQ~~I~~~ 100 (149)
.-|.|+.+.+..... . .|+=.-.|+||.+|+.+||-.+.+.
T Consensus 48 ~~~~~~~~~~t~~i~--~---vVefAK~IPgF~~L~~~DQi~LLk~ 88 (241)
T cd06939 48 EMWQLCAEKITEAIQ--Y---VVEFAKRIPGFMELCQNDQIVLLKA 88 (241)
T ss_pred HHHHHHHHHHHHHHH--H---HHHHHhcCCCcccCCHHHHHHHHHH
Confidence 568888886542111 1 1111356999999999999988643
No 26
>cd07071 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 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=29.65 E-value=45 Score=27.32 Aligned_cols=21 Identities=24% Similarity=0.536 Sum_probs=17.9
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...|+||.+|..+||..+.+.
T Consensus 61 AK~iPgF~~L~~~DQi~LLk~ 81 (238)
T cd07071 61 AEKIPGFTDLPKADQDLLFES 81 (238)
T ss_pred hccCCCccCCCHHHHHHHHHH
Confidence 456999999999999988654
No 27
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=28.47 E-value=29 Score=24.52 Aligned_cols=11 Identities=36% Similarity=0.800 Sum_probs=6.3
Q ss_pred CCccccccccC
Q psy14580 23 GRSGCKKCKQK 33 (149)
Q Consensus 23 ~RA~Ck~Ck~k 33 (149)
.||.|-.|+..
T Consensus 32 ~rS~C~~C~~~ 42 (92)
T PF06750_consen 32 PRSHCPHCGHP 42 (92)
T ss_pred CCCcCcCCCCc
Confidence 35666666644
No 28
>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 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=27.20 E-value=48 Score=25.76 Aligned_cols=20 Identities=30% Similarity=0.665 Sum_probs=17.1
Q ss_pred cCCCCCcCCCCHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLS 99 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~ 99 (149)
.-.|+||..|+.+||..+.+
T Consensus 22 aK~iPgF~~L~~~DQi~LLk 41 (191)
T cd06942 22 VKSIPGFNQLSGEDRAQLLK 41 (191)
T ss_pred HhcCCCcccCChhHHHHHHH
Confidence 35699999999999998854
No 29
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): 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 the 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 transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=27.08 E-value=50 Score=27.08 Aligned_cols=21 Identities=33% Similarity=0.605 Sum_probs=17.8
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...|+||.+|+.+||..+.+.
T Consensus 61 AK~iPgF~~L~~~DQi~LLk~ 81 (238)
T cd07348 61 AEKIPGFSDFCKEDQELLLES 81 (238)
T ss_pred HccCCCccCCChHHHHHHHHH
Confidence 457999999999999988654
No 30
>cd06933 NR_LBD_VDR The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily. The ligand binding domain of vitamin D receptors (VDR): 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 corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and
Probab=26.79 E-value=48 Score=26.95 Aligned_cols=21 Identities=38% Similarity=0.539 Sum_probs=17.9
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...|+||.+|.-+||..+.+.
T Consensus 57 AK~iPgF~~L~~~DQi~LLk~ 77 (238)
T cd06933 57 AKMIPGFRDLTAEDQIALLKS 77 (238)
T ss_pred HcCCCccccCChHHHHHHHHH
Confidence 456999999999999998654
No 31
>cd06930 NR_LBD_F2 Ligand-binding domain of nuclear receptor family 2. Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. 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 non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=26.73 E-value=55 Score=24.03 Aligned_cols=21 Identities=19% Similarity=0.403 Sum_probs=17.8
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...++||.+|+.+||..+.+.
T Consensus 19 ak~~p~F~~L~~~Dq~~Llk~ 39 (165)
T cd06930 19 AKNLPAFRNLPLDDQLTLLQN 39 (165)
T ss_pred HHcCCccccCChHHHHHHHHH
Confidence 456999999999999988655
No 32
>cd06935 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors. The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate 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 heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), a
Probab=26.33 E-value=50 Score=26.92 Aligned_cols=21 Identities=24% Similarity=0.265 Sum_probs=17.8
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
.-.|+||.+|+.+||-.+.+.
T Consensus 72 AK~iPgF~~L~~~DQi~LLk~ 92 (243)
T cd06935 72 AKKLPMFTELPCEDQIILLKG 92 (243)
T ss_pred HhcCCccccCChHHHHHHHHH
Confidence 457999999999999988653
No 33
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=25.95 E-value=35 Score=23.35 Aligned_cols=40 Identities=15% Similarity=0.307 Sum_probs=24.2
Q ss_pred CCcccccccc-CcCCCCeEEEEEeecCCCCCccceEEecCc
Q psy14580 23 GRSGCKKCKQ-KIDTGTVRIAKMGYNPFGSGKMKQWHHIDC 62 (149)
Q Consensus 23 ~RA~Ck~Ck~-kI~KGeLRIG~~v~~~~~~g~~~~WyH~~C 62 (149)
++.+|-+|+. ....++|+.--.-.+-.+|-.-..++|..|
T Consensus 3 ~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itC 43 (68)
T COG3478 3 NAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITC 43 (68)
T ss_pred ccccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEe
Confidence 4667999984 567777776311111122333467999988
No 34
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally 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. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=25.26 E-value=54 Score=26.55 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=17.6
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
.-.|+||.+|+.+||-.+.+.
T Consensus 58 AK~iPgF~~L~~~DQi~LLk~ 78 (231)
T cd06937 58 AKRLPGFTTLTIADQITLLKA 78 (231)
T ss_pred HhcCCccccCCHHHHHHHHHH
Confidence 456999999999999988643
No 35
>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): 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 element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, P
Probab=24.45 E-value=55 Score=27.10 Aligned_cols=43 Identities=14% Similarity=0.241 Sum_probs=26.9
Q ss_pred ccceEEecCchhhHHHhhhhcccccCccCCCCCcCCCCHHHHHHHHHH
Q psy14580 53 KMKQWHHIDCILEVFKKQRQTTAKIEVVDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 53 ~~~~WyH~~Cf~~~~~k~r~t~k~i~~~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...-|+|..|....-.+ . .|+=.-.|+||.+|+.+||-.+++.
T Consensus 61 ~~~~~~~~~~~~~~~i~--~---vVewAK~IPgF~~L~~~DQi~LLk~ 103 (259)
T cd06932 61 RIRLFQRCQVRSVETIR--E---LTEFAKSLPGFRNLDLNDQVTLLKY 103 (259)
T ss_pred HHHHHHHHHHHHHHHHH--H---HHHHHhcCCCcccCChhHHHHHHHH
Confidence 34568887665431111 0 1111356999999999999988643
No 36
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=24.26 E-value=37 Score=20.08 Aligned_cols=18 Identities=22% Similarity=0.529 Sum_probs=10.9
Q ss_pred ccCCCccccccccCcCCC
Q psy14580 20 AKTGRSGCKKCKQKIDTG 37 (149)
Q Consensus 20 AKS~RA~Ck~Ck~kI~KG 37 (149)
....+|.|+-|++.|.-+
T Consensus 12 ~~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 12 GDKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp GCSS-EEETTTTEE----
T ss_pred CCcCeEEeCCCCeEEeeC
Confidence 467899999998776543
No 37
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with 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=23.97 E-value=62 Score=23.10 Aligned_cols=22 Identities=32% Similarity=0.539 Sum_probs=18.5
Q ss_pred cCCCCCcCCCCHHHHHHHHHHc
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSRF 101 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~~ 101 (149)
+..++||..|+.+||..+.+..
T Consensus 18 ~~~~~~f~~L~~~dq~~Llk~~ 39 (168)
T cd06157 18 AKSIPGFRELPLEDQIVLLKSF 39 (168)
T ss_pred HHcCCchhcCChHHHHHHHHHH
Confidence 4579999999999999986654
No 38
>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor 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. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of
Probab=23.20 E-value=54 Score=26.44 Aligned_cols=21 Identities=29% Similarity=0.338 Sum_probs=17.6
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
.-.|+||.+|+.+||-.+.+.
T Consensus 55 AK~iPgF~~L~~~DQi~LLk~ 75 (226)
T cd06934 55 AKDLPYFRSLPIEDQISLLKG 75 (226)
T ss_pred hcCCcccccCCcchHHHHHHH
Confidence 456999999999999988643
No 39
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=22.85 E-value=66 Score=25.90 Aligned_cols=21 Identities=33% Similarity=0.556 Sum_probs=17.3
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...|+||.+|+.+||..+.+.
T Consensus 39 AK~iP~F~~L~~~DQi~LLk~ 59 (222)
T cd06951 39 VRNLPCFTYLPPDDQLRLLRR 59 (222)
T ss_pred HHhCCCcccCChHHHHHHHHH
Confidence 356999999999999887543
No 40
>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect 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. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee
Probab=21.67 E-value=72 Score=25.57 Aligned_cols=21 Identities=33% Similarity=0.447 Sum_probs=17.9
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...|+||..|+.+||..+.+.
T Consensus 63 aK~lP~F~~L~~~DQi~LLK~ 83 (236)
T cd06954 63 AKQLPGFLTLTREDQIALLKA 83 (236)
T ss_pred HcCCCCcccCChHHHHHHHHH
Confidence 457999999999999988654
No 41
>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. 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 doma
Probab=21.22 E-value=76 Score=25.75 Aligned_cols=21 Identities=29% Similarity=0.466 Sum_probs=17.6
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
.-.|+||.+|+.+||-.+.+.
T Consensus 52 AK~iP~F~~L~~~DQi~LLk~ 72 (235)
T cd06949 52 AKKIPGFVDLSLHDQVHLLES 72 (235)
T ss_pred HHhCCCcccCCHHHHHHHHHH
Confidence 346999999999999988654
No 42
>cd07075 NR_LBD_MR Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR h
Probab=21.12 E-value=75 Score=26.41 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=17.9
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
...|+||.+|..+||-.+.+.
T Consensus 48 AK~IPgF~~L~~~DQi~LLk~ 68 (248)
T cd07075 48 AKVLPGFRNLPLEDQITLIQY 68 (248)
T ss_pred HHcCCCcccCCHHHHHHHHHH
Confidence 346999999999999988654
No 43
>KOG3795|consensus
Probab=21.11 E-value=41 Score=27.52 Aligned_cols=11 Identities=55% Similarity=1.050 Sum_probs=9.3
Q ss_pred cCCCccccccc
Q psy14580 21 KTGRSGCKKCK 31 (149)
Q Consensus 21 KS~RA~Ck~Ck 31 (149)
-+||++|.+|+
T Consensus 12 ieGRs~C~~C~ 22 (230)
T KOG3795|consen 12 IEGRSTCPGCK 22 (230)
T ss_pred ccccccCCCCC
Confidence 36999999995
No 44
>KOG4217|consensus
Probab=20.95 E-value=52 Score=30.65 Aligned_cols=20 Identities=30% Similarity=0.697 Sum_probs=17.4
Q ss_pred cCCCCCcCCCCHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLS 99 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~ 99 (149)
.+.|+||.+|.++||+.+.+
T Consensus 428 aekiPgf~el~paDq~lLle 447 (605)
T KOG4217|consen 428 AEKIPGFAELPPADQDLLLE 447 (605)
T ss_pred HHhCcCcccCChhhHHHHHH
Confidence 47899999999999998754
No 45
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=20.94 E-value=48 Score=21.68 Aligned_cols=32 Identities=19% Similarity=0.310 Sum_probs=20.9
Q ss_pred CccccccccCcC-CCCeEEEEEeecCCCCCccceEEecCchh
Q psy14580 24 RSGCKKCKQKID-TGTVRIAKMGYNPFGSGKMKQWHHIDCIL 64 (149)
Q Consensus 24 RA~Ck~Ck~kI~-KGeLRIG~~v~~~~~~g~~~~WyH~~Cf~ 64 (149)
...|..|++.|. ++.+-+--.- ..=||-.|.-
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~C---------gapyHR~C~~ 37 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPEC---------GAPYHRDCWE 37 (54)
T ss_pred CccChhhCCcccCCCCEEECCCC---------CCcccHHHHh
Confidence 468999999996 5665554322 2346888863
No 46
>cd07073 NR_LBD_AR Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator. The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an 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 modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell funct
Probab=20.71 E-value=80 Score=26.04 Aligned_cols=21 Identities=24% Similarity=0.449 Sum_probs=17.6
Q ss_pred cCCCCCcCCCCHHHHHHHHHH
Q psy14580 80 VDDMGGWDDLTPEDQEEVLSR 100 (149)
Q Consensus 80 ~edI~G~~~L~~eDQ~~I~~~ 100 (149)
.-.|+||.+|..+||-.+.+.
T Consensus 48 AK~iP~F~~L~~~DQi~LLk~ 68 (246)
T cd07073 48 AKALPGFRNLHVDDQMAVIQY 68 (246)
T ss_pred HHcCCCccCCCHHHHHHHHHH
Confidence 346999999999999988654
No 47
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=20.01 E-value=27 Score=24.47 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=9.5
Q ss_pred CccccccccCc
Q psy14580 24 RSGCKKCKQKI 34 (149)
Q Consensus 24 RA~Ck~Ck~kI 34 (149)
...|++|++-+
T Consensus 54 s~pC~~C~klL 64 (90)
T PF11571_consen 54 STPCKKCGKLL 64 (90)
T ss_pred cchhhHHHhHh
Confidence 47899999888
Done!