Query psy6818
Match_columns 162
No_of_seqs 129 out of 350
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 19:10:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6818.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6818hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03123 poly [ADP-ribose] pol 100.0 2.8E-36 6E-41 287.6 10.5 127 1-136 40-185 (981)
2 PF00645 zf-PARP: Poly(ADP-rib 99.9 1.1E-27 2.3E-32 168.0 5.2 81 52-135 1-82 (82)
3 PLN03123 poly [ADP-ribose] pol 99.9 4.9E-22 1.1E-26 190.3 7.9 85 50-140 9-93 (981)
4 KOG4437|consensus 99.6 5.1E-17 1.1E-21 140.4 -5.0 101 50-152 7-111 (482)
5 PF00645 zf-PARP: Poly(ADP-rib 99.4 1.2E-13 2.6E-18 96.6 0.5 47 2-48 31-82 (82)
6 KOG4437|consensus 97.6 7E-06 1.5E-10 71.9 -2.0 44 5-48 43-94 (482)
7 KOG1037|consensus 94.9 0.007 1.5E-07 55.9 -0.0 70 2-71 42-153 (531)
8 KOG1037|consensus 93.3 0.019 4.2E-07 53.1 -0.5 92 50-146 10-116 (531)
9 PF00412 LIM: LIM domain; Int 87.5 0.52 1.1E-05 29.7 2.3 29 61-102 1-29 (58)
10 smart00132 LIM Zinc-binding do 84.6 0.7 1.5E-05 26.3 1.7 30 60-102 1-30 (39)
11 PF11293 DUF3094: Protein of u 69.2 6.1 0.00013 26.0 2.8 26 120-145 2-27 (55)
12 COG1379 PHP family phosphoeste 63.8 3.7 8E-05 36.5 1.3 23 50-72 257-279 (403)
13 PF06945 DUF1289: Protein of u 53.3 4.7 0.0001 25.7 0.1 26 112-137 23-48 (51)
14 cd07072 NR_LBD_DHR38_like Liga 50.5 13 0.00027 30.9 2.3 21 112-132 61-81 (239)
15 KOG3795|consensus 49.6 8.4 0.00018 31.5 1.0 69 55-159 12-80 (230)
16 cd06929 NR_LBD_F1 Ligand-bindi 45.3 17 0.00036 27.6 2.1 21 112-132 21-41 (174)
17 cd06940 NR_LBD_REV_ERB The lig 43.1 15 0.00034 29.0 1.7 21 112-132 31-51 (189)
18 cd07348 NR_LBD_NGFI-B The liga 42.0 19 0.00041 29.8 2.1 21 112-132 60-80 (238)
19 cd07071 NR_LBD_Nurr1 The ligan 41.7 22 0.00048 29.4 2.5 22 112-133 60-81 (238)
20 cd06945 NR_LBD_Nurr1_like The 40.0 22 0.00048 29.3 2.2 21 112-132 60-80 (239)
21 cd06939 NR_LBD_ROR_like The li 39.3 20 0.00043 29.6 1.8 38 92-132 48-87 (241)
22 cd06935 NR_LBD_TR The ligand b 38.7 21 0.00046 29.4 1.9 37 93-132 53-91 (243)
23 PF00628 PHD: PHD-finger; Int 38.3 19 0.00041 22.0 1.2 13 7-19 19-31 (51)
24 cd06941 NR_LBD_DmE78_like The 38.2 25 0.00054 27.7 2.1 21 112-132 21-41 (195)
25 PF10367 Vps39_2: Vacuolar sor 37.7 42 0.0009 23.2 3.1 30 59-101 79-108 (109)
26 PF09986 DUF2225: Uncharacteri 37.4 1E+02 0.0023 25.0 5.7 68 59-139 6-83 (214)
27 KOG4217|consensus 36.4 18 0.00039 33.7 1.2 20 113-132 428-447 (605)
28 cd06933 NR_LBD_VDR The ligand 36.2 26 0.00057 28.8 2.1 21 112-132 56-76 (238)
29 smart00249 PHD PHD zinc finger 35.0 13 0.00028 21.5 -0.0 12 7-18 19-30 (47)
30 cd06930 NR_LBD_F2 Ligand-bindi 34.2 26 0.00057 26.1 1.6 21 113-133 19-39 (165)
31 cd06937 NR_LBD_RAR The ligand 33.8 28 0.00061 28.5 1.9 21 112-132 57-77 (231)
32 PF06750 DiS_P_DiS: Bacterial 33.5 21 0.00045 25.5 0.9 11 58-68 58-68 (92)
33 cd06934 NR_LBD_PXR_like The li 32.8 29 0.00063 28.3 1.8 21 112-132 54-74 (226)
34 cd06942 NR_LBD_Sex_1_like The 32.3 32 0.0007 27.0 1.9 21 112-132 21-41 (191)
35 cd06932 NR_LBD_PPAR The ligand 32.0 32 0.00069 28.8 1.9 39 91-132 62-102 (259)
36 cd06954 NR_LBD_LXR The ligand 32.0 33 0.00072 27.8 2.0 21 112-132 62-82 (236)
37 cd06951 NR_LBD_Dax1_like The l 31.1 37 0.00081 27.6 2.2 20 113-132 39-58 (222)
38 cd06938 NR_LBD_EcR The ligand 29.0 37 0.00081 27.6 1.8 38 92-132 39-78 (231)
39 cd07073 NR_LBD_AR Ligand bindi 28.7 39 0.00085 28.1 1.9 20 113-132 48-67 (246)
40 cd06157 NR_LBD The ligand bind 28.7 37 0.0008 24.6 1.6 22 113-134 18-39 (168)
41 cd06949 NR_LBD_ER Ligand bindi 27.7 48 0.001 27.2 2.2 21 112-132 51-71 (235)
42 cd07075 NR_LBD_MR Ligand bindi 26.3 51 0.0011 27.6 2.2 21 113-133 48-68 (248)
43 cd07349 NR_LBD_SHP The ligand 25.4 56 0.0012 26.7 2.2 20 113-132 39-58 (222)
44 cd06950 NR_LBD_Tlx_PNR_like Th 25.2 55 0.0012 26.1 2.1 21 112-132 45-65 (206)
45 cd06952 NR_LBD_TR2_like The li 24.9 51 0.0011 26.4 1.9 21 113-133 41-61 (222)
46 cd07076 NR_LBD_GR Ligand bindi 24.7 54 0.0012 27.4 2.1 20 113-132 48-67 (247)
47 cd06947 NR_LBD_GR_Like Ligand 24.5 61 0.0013 26.9 2.3 20 113-132 48-67 (246)
48 cd06953 NR_LBD_DHR4_like The l 24.4 54 0.0012 26.4 1.9 21 112-132 46-66 (213)
49 PF13240 zinc_ribbon_2: zinc-r 24.4 44 0.00095 17.8 1.0 13 60-72 1-13 (23)
50 cd07350 NR_LBD_Dax1 The ligand 24.0 61 0.0013 26.7 2.2 20 113-132 39-58 (232)
51 cd07069 NR_LBD_Lrh-1 The ligan 24.0 52 0.0011 27.1 1.8 20 113-132 60-79 (241)
52 cd06936 NR_LBD_Fxr The ligand 23.8 49 0.0011 26.8 1.6 21 112-132 55-75 (221)
53 cd07070 NR_LBD_SF-1 The ligand 23.6 55 0.0012 26.8 1.9 20 113-132 58-77 (237)
54 cd06943 NR_LBD_RXR_like The li 22.8 52 0.0011 25.9 1.5 22 112-133 49-70 (207)
55 KOG1973|consensus 22.4 35 0.00076 28.9 0.5 12 91-102 240-252 (274)
56 cd06946 NR_LBD_ERR The ligand 22.2 69 0.0015 25.7 2.2 22 112-133 46-67 (221)
57 PF11460 DUF3007: Protein of u 20.9 59 0.0013 24.1 1.4 19 118-136 86-104 (104)
58 KOG1701|consensus 20.9 21 0.00045 32.7 -1.2 30 60-102 276-305 (468)
59 cd07068 NR_LBD_ER_like The lig 20.9 79 0.0017 25.4 2.3 40 91-133 26-67 (221)
60 PF05810 NinF: NinF protein; 20.6 24 0.00052 23.4 -0.6 20 57-76 16-35 (58)
61 PF10330 Stb3: Putative Sin3 b 20.5 81 0.0018 22.9 2.0 23 113-135 31-54 (92)
62 cd06931 NR_LBD_HNF4_like The l 20.4 76 0.0016 25.3 2.1 22 113-134 52-73 (222)
63 KOG3970|consensus 20.3 34 0.00074 29.0 0.0 32 58-103 50-82 (299)
64 PF02892 zf-BED: BED zinc fing 20.2 37 0.00081 20.2 0.2 17 55-71 13-29 (45)
No 1
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=100.00 E-value=2.8e-36 Score=287.57 Aligned_cols=127 Identities=35% Similarity=0.592 Sum_probs=113.5
Q ss_pred CCCCCCCCCceeeeccccCCCC-CCCCCCcCCCcCCChhhHHHHHHhhc-c-----------------ceeeecCCCccc
Q psy6818 1 SPFFDGKTPKWFHEECFWKKNR-PKALLDIHNVTSLRHQDQEMIKSKIL-G-----------------NIEYAKSNRSTC 61 (162)
Q Consensus 1 s~~fdG~~~~W~H~~Cff~k~~-~~~~~~i~g~~~Lrw~DQ~~i~~~i~-~-----------------~vEYAkS~Ra~C 61 (162)
||+|||.||.|||++|||++.. +.++++|+||++|||+||++|+++|+ + .|||||||||+|
T Consensus 40 ~~~~dg~~~~W~H~~Cf~~~~~~~~~~~~l~G~~~L~~eDq~~i~~~i~~~~~~~~~~~~~~~~~~~~~vEyAkS~Ra~C 119 (981)
T PLN03123 40 STQFDGFMPMWNHASCILKKKNQIKSIDDVEGIDSLRWEDQQKIRKYVESGGTGTGTASDAAASSFEYGIEVAKTSRATC 119 (981)
T ss_pred ccccCCCCCeeeccccccccccCCCChhhcCChhhCCHHHHHHHHHHHhccCCCCCcccccccCCcceEEEEecCCCCcc
Confidence 6899999999999999998764 45788999999999999999999994 0 899999999999
Q ss_pred ccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccccccccccCCCCCCCCCCcCCCHHHHHHHHHHhhc
Q psy6818 62 RGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSASGKQIPGFGSLEKKDQKIVEATLPS 136 (162)
Q Consensus 62 k~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~~~~~~~~~~~~e~I~Gf~~L~~eDQ~~Ik~~~~~ 136 (162)
++|+++|.||+||||+.++++. |.++.|||++||++..... ++++|+||++|+++||+.|++++.+
T Consensus 120 k~C~~kI~KgelRig~~v~~~~-----g~~~~W~H~~Cf~~~~~~~----~~e~l~Gf~~L~~eDqe~v~~li~~ 185 (981)
T PLN03123 120 RRCSEKILKGEVRISSKPEGQG-----YKGLAWHHAKCFLEMSPST----PVEKLSGWDTLSDSDQEAVLPLVKK 185 (981)
T ss_pred ccCCceecCCceEEEeeecCCC-----CCcccccccccccccCCCC----ChhhCCChhhCCHHHHHHHHHHHhh
Confidence 9999999999999999887652 4579999999999876532 6789999999999999999999954
No 2
>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=99.94 E-value=1.1e-27 Score=168.03 Aligned_cols=81 Identities=40% Similarity=0.764 Sum_probs=67.4
Q ss_pred eeecCCCcccccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccccccccccC-CCCCCCCCCcCCCHHHHHHH
Q psy6818 52 EYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFS-ASGKQIPGFGSLEKKDQKIV 130 (162)
Q Consensus 52 EYAkS~Ra~Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~~~~~~~~~-~~~e~I~Gf~~L~~eDQ~~I 130 (162)
||||||||+|++|+++|+||+||||+++.++.. +|.++.|||++||+......... .++++|+||+.|+++||++|
T Consensus 1 EyAks~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~---~~~~~~W~H~~C~~~~~~~~~~~~~~~~~i~G~~~L~~~Dq~~i 77 (82)
T PF00645_consen 1 EYAKSGRAKCKGCKKKIAKGELRIGKIVPSPEG---DGDIPKWYHWDCFFKKQLRNRETTGDIEEIKGFDELKPEDQEKI 77 (82)
T ss_dssp EE-SSSTEBETTTSCBE-TTSEEEEEEEEETTS---SCEEEEEEEHHHHHHTTCCTTSSTSCGGGCETCCCS-HHHHHHH
T ss_pred CcCCCCCccCcccCCcCCCCCEEEEEEeccccc---CCCCCceECccccccchhhhcccCCCHHHCCChHHCCHHHHHHH
Confidence 899999999999999999999999999987753 46789999999999876443211 37899999999999999999
Q ss_pred HHHhh
Q psy6818 131 EATLP 135 (162)
Q Consensus 131 k~~~~ 135 (162)
+++|+
T Consensus 78 ~~~i~ 82 (82)
T PF00645_consen 78 RKLIE 82 (82)
T ss_dssp HHHHS
T ss_pred HHHhC
Confidence 99885
No 3
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=99.86 E-value=4.9e-22 Score=190.29 Aligned_cols=85 Identities=34% Similarity=0.583 Sum_probs=76.3
Q ss_pred ceeeecCCCcccccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccccccccccCCCCCCCCCCcCCCHHHHHH
Q psy6818 50 NIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSASGKQIPGFGSLEKKDQKI 129 (162)
Q Consensus 50 ~vEYAkS~Ra~Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~~~~~~~~~~~~e~I~Gf~~L~~eDQ~~ 129 (162)
.|||||||||+|++|+++|+||+||||+++++++ +.|.++.|||++||++.+..++ ++++|+||+.|+++||+.
T Consensus 9 ~~EYAkS~Rs~Ck~C~~~I~K~~lRi~~~v~~~~---~dg~~~~W~H~~Cf~~~~~~~~---~~~~l~G~~~L~~eDq~~ 82 (981)
T PLN03123 9 KAEYAKSSRSSCKTCKSPIDKDELRLGKMVQSTQ---FDGFMPMWNHASCILKKKNQIK---SIDDVEGIDSLRWEDQQK 82 (981)
T ss_pred eEEEecCCCccccccCCcccCCCeEEEEeecccc---cCCCCCeeeccccccccccCCC---ChhhcCChhhCCHHHHHH
Confidence 7999999999999999999999999999998774 2477899999999998766554 688999999999999999
Q ss_pred HHHHhhccCCC
Q psy6818 130 VEATLPSLSDG 140 (162)
Q Consensus 130 Ik~~~~~~~~~ 140 (162)
|+++++....+
T Consensus 83 i~~~i~~~~~~ 93 (981)
T PLN03123 83 IRKYVESGGTG 93 (981)
T ss_pred HHHHHhccCCC
Confidence 99999888754
No 4
>KOG4437|consensus
Probab=99.57 E-value=5.1e-17 Score=140.38 Aligned_cols=101 Identities=25% Similarity=0.495 Sum_probs=85.6
Q ss_pred ceeeecCCCcccccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccc----cccccccCCCCCCCCCCcCCCHH
Q psy6818 50 NIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNA----VRLDLEFSASGKQIPGFGSLEKK 125 (162)
Q Consensus 50 ~vEYAkS~Ra~Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~----~~~~~~~~~~~e~I~Gf~~L~~e 125 (162)
+++||| ..|+|++|+++|.||.+|||+++++++..+ -|.|..|||..|+|. .|.+++.++..++|+||++|..+
T Consensus 7 C~DYAK-R~A~C~KCK~~i~KGV~R~GKi~P~~~S~~-~~DMK~~~H~~C~FE~L~rAR~TTK~I~~~~EiEG~E~L~~~ 84 (482)
T KOG4437|consen 7 CVDYAK-RTAGCKKCKEKIVKGVCRIGKVVPNPFSES-GGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWEELEDN 84 (482)
T ss_pred HHHHHH-HhhhhHHHHHHHHHhhhhhccccCCCcccC-CchHHHHHHHHHHHHHHHhccccccccccchhhcchhhhchh
Confidence 578998 479999999999999999999998876522 245899999999875 46778888889999999999999
Q ss_pred HHHHHHHHhhccCCCCCCcccccccee
Q psy6818 126 DQKIVEATLPSLSDGVSKTDAISHFLL 152 (162)
Q Consensus 126 DQ~~Ik~~~~~~~~~~~~~~~~~~~~~ 152 (162)
||+.|++.+.++....+|.+..+.++|
T Consensus 85 ~~~~I~~~i~~Ls~K~sK~~~~~~K~T 111 (482)
T KOG4437|consen 85 EKEQITQHIADLSSKAAKKAVVQAKLT 111 (482)
T ss_pred hHHHHHHHHHHHHHHhhhccccccccC
Confidence 999999999998776666666666665
No 5
>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=99.36 E-value=1.2e-13 Score=96.64 Aligned_cols=47 Identities=38% Similarity=0.707 Sum_probs=39.7
Q ss_pred CCCCCCCCceeeeccccCCCCC-----CCCCCcCCCcCCChhhHHHHHHhhc
Q psy6818 2 PFFDGKTPKWFHEECFWKKNRP-----KALLDIHNVTSLRHQDQEMIKSKIL 48 (162)
Q Consensus 2 ~~fdG~~~~W~H~~Cff~k~~~-----~~~~~i~g~~~Lrw~DQ~~i~~~i~ 48 (162)
+.++|.++.|||+.||+..... .++++|.||++|+|+||++|++.|+
T Consensus 31 ~~~~~~~~~W~H~~C~~~~~~~~~~~~~~~~~i~G~~~L~~~Dq~~i~~~i~ 82 (82)
T PF00645_consen 31 PEGDGDIPKWYHWDCFFKKQLRNRETTGDIEEIKGFDELKPEDQEKIRKLIE 82 (82)
T ss_dssp TTSSCEEEEEEEHHHHHHTTCCTTSSTSCGGGCETCCCS-HHHHHHHHHHHS
T ss_pred cccCCCCCceECccccccchhhhcccCCCHHHCCChHHCCHHHHHHHHHHhC
Confidence 4557899999999999986532 5789999999999999999999874
No 6
>KOG4437|consensus
Probab=97.59 E-value=7e-06 Score=71.86 Aligned_cols=44 Identities=25% Similarity=0.618 Sum_probs=37.5
Q ss_pred CCCCCceeeeccccCCC---CC-----CCCCCcCCCcCCChhhHHHHHHhhc
Q psy6818 5 DGKTPKWFHEECFWKKN---RP-----KALLDIHNVTSLRHQDQEMIKSKIL 48 (162)
Q Consensus 5 dG~~~~W~H~~Cff~k~---~~-----~~~~~i~g~~~Lrw~DQ~~i~~~i~ 48 (162)
-|+|..|||..|+|.+. ++ ...++|+||+.|.-+||+.|++.|.
T Consensus 43 ~~DMK~~~H~~C~FE~L~rAR~TTK~I~~~~EiEG~E~L~~~~~~~I~~~i~ 94 (482)
T KOG4437|consen 43 GGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWEELEDNEKEQITQHIA 94 (482)
T ss_pred CchHHHHHHHHHHHHHHHhccccccccccchhhcchhhhchhhHHHHHHHHH
Confidence 57899999999999743 33 3457999999999999999999994
No 7
>KOG1037|consensus
Probab=94.92 E-value=0.007 Score=55.92 Aligned_cols=70 Identities=26% Similarity=0.395 Sum_probs=52.4
Q ss_pred CCCCCCCCceeeeccccCCCC-CC-CCCCcCC---------------CcCCChhhHHHHHHhhc----------c-----
Q psy6818 2 PFFDGKTPKWFHEECFWKKNR-PK-ALLDIHN---------------VTSLRHQDQEMIKSKIL----------G----- 49 (162)
Q Consensus 2 ~~fdG~~~~W~H~~Cff~k~~-~~-~~~~i~g---------------~~~Lrw~DQ~~i~~~i~----------~----- 49 (162)
.+|++.++.|+|.+||+++.. +. +..+.+| +..|+|++|++++.... |
T Consensus 42 ~~~~~~~~~~~~~s~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~l~~d~~~~~~~~~~~~~v~~~~~s~~~~~~ 121 (531)
T KOG1037|consen 42 LIFDGDVDKWKHTSCFLKKDHLIRGPEVKVPGLNQTNVENENNKEYTEEELEWDEQQKKRKTVEEGGVTGKGQSGIVKKS 121 (531)
T ss_pred hccccccCcccccccccCcccccccccccccccccccccccccchhhhhhhhcccccceeeeeeecccccccccccchhh
Confidence 579999999999999998763 33 4457788 99999999999998884 1
Q ss_pred -------ceeeecCCCcccc---cccccccCC
Q psy6818 50 -------NIEYAKSNRSTCR---GCEAKIAKG 71 (162)
Q Consensus 50 -------~vEYAkS~Ra~Ck---~C~~kI~Kg 71 (162)
..++.++++.++. .|.+.|.++
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 153 (531)
T KOG1037|consen 122 KSLDKAKKPFEIKSYKLTKNGMETRDEFIPLG 153 (531)
T ss_pred hhhhhccchhhhhcchhhhhhhhhhhhhhccc
Confidence 4445555554444 466777777
No 8
>KOG1037|consensus
Probab=93.35 E-value=0.019 Score=53.07 Aligned_cols=92 Identities=23% Similarity=0.268 Sum_probs=67.3
Q ss_pred ceeeecCCCcccccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccccccccccCCCCCCCCC-----------
Q psy6818 50 NIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSASGKQIPG----------- 118 (162)
Q Consensus 50 ~vEYAkS~Ra~Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~~~~~~~~~~~~e~I~G----------- 118 (162)
..+|+++.++.|+.|...|.+..+|.++.....- +.+..+.|+|..||.+...... +...+.+|
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~~~~---~~~~~~~~~~~s~~~~~~~~~~--~~~v~~~~~~~~~~~~~~~ 84 (531)
T KOG1037|consen 10 NASVLKSEDLNSGTCEHVINKDEFRKGIKELKLI---FDGDVDKWKHTSCFLKKDHLIR--GPEVKVPGLNQTNVENENN 84 (531)
T ss_pred cchhhhhhchhccCCcccccchhhhhhhhhhhhc---cccccCcccccccccCcccccc--ccccccccccccccccccc
Confidence 4578899999999999889999999998764432 1345788999999987643322 23445566
Q ss_pred ----CcCCCHHHHHHHHHHhhccCCCCCCccc
Q psy6818 119 ----FGSLEKKDQKIVEATLPSLSDGVSKTDA 146 (162)
Q Consensus 119 ----f~~L~~eDQ~~Ik~~~~~~~~~~~~~~~ 146 (162)
.+.|.+++|+.++..++.........+-
T Consensus 85 ~~~~~~~l~~d~~~~~~~~~~~~~v~~~~~s~ 116 (531)
T KOG1037|consen 85 KEYTEEELEWDEQQKKRKTVEEGGVTGKGQSG 116 (531)
T ss_pred chhhhhhhhcccccceeeeeeecccccccccc
Confidence 8999999998887777666554444443
No 9
>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=87.50 E-value=0.52 Score=29.69 Aligned_cols=29 Identities=28% Similarity=0.702 Sum_probs=21.8
Q ss_pred cccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccc
Q psy6818 61 CRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNA 102 (162)
Q Consensus 61 Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~ 102 (162)
|.+|++.|..+++.+.. ...-||.+||.=
T Consensus 1 C~~C~~~I~~~~~~~~~-------------~~~~~H~~Cf~C 29 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKA-------------MGKFWHPECFKC 29 (58)
T ss_dssp BTTTSSBESSSSEEEEE-------------TTEEEETTTSBE
T ss_pred CCCCCCCccCcEEEEEe-------------CCcEEEcccccc
Confidence 78999999988876621 134789999973
No 10
>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=84.64 E-value=0.7 Score=26.31 Aligned_cols=30 Identities=30% Similarity=0.771 Sum_probs=20.1
Q ss_pred ccccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccc
Q psy6818 60 TCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNA 102 (162)
Q Consensus 60 ~Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~ 102 (162)
.|.+|++.|..++..+.. ...-||..||.=
T Consensus 1 ~C~~C~~~i~~~~~~~~~-------------~~~~~H~~Cf~C 30 (39)
T smart00132 1 KCAGCGKPIRGGELVLRA-------------LGKVWHPECFKC 30 (39)
T ss_pred CccccCCcccCCcEEEEe-------------CCccccccCCCC
Confidence 488999999877444421 134678888864
No 11
>PF11293 DUF3094: Protein of unknown function (DUF3094); InterPro: IPR021444 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=69.20 E-value=6.1 Score=26.00 Aligned_cols=26 Identities=23% Similarity=0.294 Sum_probs=21.4
Q ss_pred cCCCHHHHHHHHHHhhccCCCCCCcc
Q psy6818 120 GSLEKKDQKIVEATLPSLSDGVSKTD 145 (162)
Q Consensus 120 ~~L~~eDQ~~Ik~~~~~~~~~~~~~~ 145 (162)
..|.+|||++|.+-+...-..+++.-
T Consensus 2 ~rL~pEDQ~~Vd~yL~a~~~~VER~P 27 (55)
T PF11293_consen 2 SRLNPEDQQRVDEYLQAGVNQVERKP 27 (55)
T ss_pred CCCCHHHHHHHHHHHhCCCCccccCC
Confidence 36999999999999988877776643
No 12
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=63.81 E-value=3.7 Score=36.45 Aligned_cols=23 Identities=48% Similarity=0.667 Sum_probs=20.9
Q ss_pred ceeeecCCCcccccccccccCCC
Q psy6818 50 NIEYAKSNRSTCRGCEAKIAKGE 72 (162)
Q Consensus 50 ~vEYAkS~Ra~Ck~C~~kI~Kge 72 (162)
..|-|+++|..|.+|+.+|.||.
T Consensus 257 ~le~A~~~~wrCpkCGg~ikKGV 279 (403)
T COG1379 257 SLEEAKSLRWRCPKCGGKIKKGV 279 (403)
T ss_pred CcchhhhhcccCcccccchhhhH
Confidence 56889999999999999999993
No 13
>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=53.26 E-value=4.7 Score=25.73 Aligned_cols=26 Identities=15% Similarity=0.281 Sum_probs=22.6
Q ss_pred CCCCCCCCcCCCHHHHHHHHHHhhcc
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEATLPSL 137 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~~~~~~ 137 (162)
+.++|.+|..|+++.|..|.+.+.+-
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 46799999999999999999888654
No 14
>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=50.50 E-value=13 Score=30.94 Aligned_cols=21 Identities=38% Similarity=0.619 Sum_probs=18.5
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||..+.+
T Consensus 61 wAK~IPgF~~L~~~DQi~LLk 81 (239)
T cd07072 61 FAEKIPGFPDLCKEDQELLFQ 81 (239)
T ss_pred HhccCCCccCCCHHHHHHHHH
Confidence 467999999999999998854
No 15
>KOG3795|consensus
Probab=49.58 E-value=8.4 Score=31.47 Aligned_cols=69 Identities=22% Similarity=0.388 Sum_probs=39.4
Q ss_pred cCCCcccccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccccccccccCCCCCCCCCCcCCCHHHHHHHHHHh
Q psy6818 55 KSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSASGKQIPGFGSLEKKDQKIVEATL 134 (162)
Q Consensus 55 kS~Ra~Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~~~~~~~~~~~~e~I~Gf~~L~~eDQ~~Ik~~~ 134 (162)
.++|++|.+|+ ..-.+|-.+|.+...- ..|.+|-.+ |+- | -+.+
T Consensus 12 ieGRs~C~~C~------------------------~SRkFfCY~C~VPV~v------p~E~~P~vk-LPL--~---vDII 55 (230)
T KOG3795|consen 12 IEGRSTCPGCK------------------------SSRKFFCYDCRVPVPV------PGEFTPTVK-LPL--A---VDII 55 (230)
T ss_pred ccccccCCCCC------------------------CcceEEEEeeccccCc------chhcccccc-cce--e---eeee
Confidence 36999999992 1234777888775421 223333221 111 0 1223
Q ss_pred hccCCCCCCccccccceeeeEEEEe
Q psy6818 135 PSLSDGVSKTDAISHFLLIPLYLTL 159 (162)
Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (162)
+--+...-|.+|+-+++|-|..+.+
T Consensus 56 KHp~E~DGKSsAiHAkiLAP~~VrI 80 (230)
T KOG3795|consen 56 KHPMEKDGKSSALHAKILAPDQVRI 80 (230)
T ss_pred cCccccCCchhhhhhhhcCcceeee
Confidence 3334455678899999999987643
No 16
>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=45.34 E-value=17 Score=27.62 Aligned_cols=21 Identities=38% Similarity=0.585 Sum_probs=18.3
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||..|+.+||..+.+
T Consensus 21 ~ak~ip~F~~L~~~Dq~~Llk 41 (174)
T cd06929 21 FAKRIPGFRELSQEDQIALLK 41 (174)
T ss_pred hccCCcCcccCChhHHHHHHH
Confidence 467999999999999998854
No 17
>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=43.14 E-value=15 Score=28.98 Aligned_cols=21 Identities=38% Similarity=0.589 Sum_probs=18.2
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||..+.+
T Consensus 31 waK~iPgF~~L~~~DQi~LLk 51 (189)
T cd06940 31 FAKRIPGFRDLSQHDQVTLLK 51 (189)
T ss_pred HHhcCCCcccCChhhHHHHHH
Confidence 367999999999999998854
No 18
>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=41.97 E-value=19 Score=29.82 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=18.3
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||..+.+
T Consensus 60 wAK~iPgF~~L~~~DQi~LLk 80 (238)
T cd07348 60 WAEKIPGFSDFCKEDQELLLE 80 (238)
T ss_pred HHccCCCccCCChHHHHHHHH
Confidence 367999999999999998864
No 19
>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=41.71 E-value=22 Score=29.38 Aligned_cols=22 Identities=36% Similarity=0.620 Sum_probs=18.8
Q ss_pred CCCCCCCCcCCCHHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEAT 133 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~~ 133 (162)
-+..||||.+|+.+||..+.+.
T Consensus 60 wAK~iPgF~~L~~~DQi~LLk~ 81 (238)
T cd07071 60 WAEKIPGFTDLPKADQDLLFES 81 (238)
T ss_pred HhccCCCccCCCHHHHHHHHHH
Confidence 3679999999999999988553
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=39.96 E-value=22 Score=29.29 Aligned_cols=21 Identities=33% Similarity=0.675 Sum_probs=18.3
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||..+.+
T Consensus 60 wAK~IPgF~~L~~~DQi~LLk 80 (239)
T cd06945 60 WAEKIPGFKDLHREDQDLLLE 80 (239)
T ss_pred HHHhCCCcccCCHHHHHHHHH
Confidence 357999999999999998864
No 21
>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=39.26 E-value=20 Score=29.63 Aligned_cols=38 Identities=26% Similarity=0.316 Sum_probs=27.2
Q ss_pred CeeeecCCcccc--ccccccCCCCCCCCCCcCCCHHHHHHHHH
Q psy6818 92 PEWYHLSCFNAV--RLDLEFSASGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 92 ~~WyH~~Cf~~~--~~~~~~~~~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
..|.|..+.+.. +..++ -+..||||.+|+.+||-.+.+
T Consensus 48 ~~~~~~~~~~t~~i~~vVe---fAK~IPgF~~L~~~DQi~LLk 87 (241)
T cd06939 48 EMWQLCAEKITEAIQYVVE---FAKRIPGFMELCQNDQIVLLK 87 (241)
T ss_pred HHHHHHHHHHHHHHHHHHH---HHhcCCCcccCCHHHHHHHHH
Confidence 458888775432 22233 367999999999999998754
No 22
>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=38.65 E-value=21 Score=29.41 Aligned_cols=37 Identities=22% Similarity=0.270 Sum_probs=25.4
Q ss_pred eeeecCCcccc--ccccccCCCCCCCCCCcCCCHHHHHHHHH
Q psy6818 93 EWYHLSCFNAV--RLDLEFSASGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 93 ~WyH~~Cf~~~--~~~~~~~~~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
.|.|+...... ...++ -+..||||.+|+.+||-.+.+
T Consensus 53 ~~~~~~~~~~~~l~~iVe---fAK~iPgF~~L~~~DQi~LLk 91 (243)
T cd06935 53 AFSHFTKIITPAITRVVD---FAKKLPMFTELPCEDQIILLK 91 (243)
T ss_pred HHHHHHHHHHHHHHHHHH---HHhcCCccccCChHHHHHHHH
Confidence 46676554432 12223 467999999999999998754
No 23
>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=38.26 E-value=19 Score=21.97 Aligned_cols=13 Identities=31% Similarity=0.999 Sum_probs=10.3
Q ss_pred CCCceeeeccccC
Q psy6818 7 KTPKWFHEECFWK 19 (162)
Q Consensus 7 ~~~~W~H~~Cff~ 19 (162)
...+|||..|.-.
T Consensus 19 ~C~~~~H~~C~~~ 31 (51)
T PF00628_consen 19 SCNRWYHQECVGP 31 (51)
T ss_dssp TTSCEEETTTSTS
T ss_pred CCChhhCcccCCC
Confidence 3579999999854
No 24
>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=38.23 E-value=25 Score=27.67 Aligned_cols=21 Identities=38% Similarity=0.621 Sum_probs=18.0
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||..|+.+||-.+.+
T Consensus 21 waK~iP~F~~L~~~DQi~LLk 41 (195)
T cd06941 21 FAKRIPGFCDLSQDDQLLLIK 41 (195)
T ss_pred HHHcCCCcccCCHHHHHHHHH
Confidence 357899999999999998754
No 25
>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=37.74 E-value=42 Score=23.22 Aligned_cols=30 Identities=20% Similarity=0.398 Sum_probs=20.4
Q ss_pred cccccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCcc
Q psy6818 59 STCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFN 101 (162)
Q Consensus 59 a~Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~ 101 (162)
..|..|++.|..+.+-+ .| ...=+|..|+-
T Consensus 79 ~~C~vC~k~l~~~~f~~-----~p--------~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVV-----FP--------CGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEE-----eC--------CCeEEeccccc
Confidence 56999999998864333 12 12578999963
No 26
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=37.40 E-value=1e+02 Score=24.99 Aligned_cols=68 Identities=24% Similarity=0.349 Sum_probs=42.0
Q ss_pred cccccccccccC-----CCeEEEEEeecCCCCcccCC-cCeeee----cCCccccccccccCCCCCCCCCCcCCCHHHHH
Q psy6818 59 STCRGCEAKIAK-----GEIRVSKMNYDSDQGKMIGG-IPEWYH----LSCFNAVRLDLEFSASGKQIPGFGSLEKKDQK 128 (162)
Q Consensus 59 a~Ck~C~~kI~K-----geLRig~~~~~~~~~~~~g~-~~~WyH----~~Cf~~~~~~~~~~~~~e~I~Gf~~L~~eDQ~ 128 (162)
-+|.-|++.... |.+|+.....+.. +.|++ .|-+|. +.|.+... -..|+.|++..++
T Consensus 6 ~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~--~~Y~~vnP~~Y~V~vCP~CgyA~~-----------~~~F~~l~~~~~~ 72 (214)
T PF09986_consen 6 ITCPVCGKEFKTKKVRSGKIRVIRRDSDFC--PRYKGVNPLFYEVWVCPHCGYAAF-----------EEDFEKLSPEQKE 72 (214)
T ss_pred eECCCCCCeeeeeEEEcCCceEeeecCCCc--cccCCCCCeeeeEEECCCCCCccc-----------ccccccCCHHHHH
Confidence 479999976654 4555543333322 34543 566776 45655321 1227799999999
Q ss_pred HHHHHhhccCC
Q psy6818 129 IVEATLPSLSD 139 (162)
Q Consensus 129 ~Ik~~~~~~~~ 139 (162)
.|++.+.+...
T Consensus 73 ~i~~~i~~~~~ 83 (214)
T PF09986_consen 73 KIKENISSRWK 83 (214)
T ss_pred HHHHHHHhhcc
Confidence 99998876654
No 27
>KOG4217|consensus
Probab=36.40 E-value=18 Score=33.68 Aligned_cols=20 Identities=35% Similarity=0.689 Sum_probs=17.8
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
++.|+||.+|.++||+.+.+
T Consensus 428 aekiPgf~el~paDq~lLle 447 (605)
T KOG4217|consen 428 AEKIPGFAELPPADQDLLLE 447 (605)
T ss_pred HHhCcCcccCChhhHHHHHH
Confidence 57899999999999998854
No 28
>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=36.24 E-value=26 Score=28.77 Aligned_cols=21 Identities=38% Similarity=0.515 Sum_probs=18.3
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||..+.+
T Consensus 56 wAK~iPgF~~L~~~DQi~LLk 76 (238)
T cd06933 56 FAKMIPGFRDLTAEDQIALLK 76 (238)
T ss_pred HHcCCCccccCChHHHHHHHH
Confidence 367999999999999998864
No 29
>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 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=34.24 E-value=26 Score=26.08 Aligned_cols=21 Identities=29% Similarity=0.447 Sum_probs=18.0
Q ss_pred CCCCCCCcCCCHHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEAT 133 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~~ 133 (162)
+..+|||..|+.+||..+.+.
T Consensus 19 ak~~p~F~~L~~~Dq~~Llk~ 39 (165)
T cd06930 19 AKNLPAFRNLPLDDQLTLLQN 39 (165)
T ss_pred HHcCCccccCChHHHHHHHHH
Confidence 568999999999999887554
No 31
>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=33.83 E-value=28 Score=28.47 Aligned_cols=21 Identities=33% Similarity=0.501 Sum_probs=18.2
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||-.+.+
T Consensus 57 wAK~iPgF~~L~~~DQi~LLk 77 (231)
T cd06937 57 FAKRLPGFTTLTIADQITLLK 77 (231)
T ss_pred HHhcCCccccCCHHHHHHHHH
Confidence 367999999999999998854
No 32
>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=33.51 E-value=21 Score=25.45 Aligned_cols=11 Identities=55% Similarity=1.017 Sum_probs=5.2
Q ss_pred Ccccccccccc
Q psy6818 58 RSTCRGCEAKI 68 (162)
Q Consensus 58 Ra~Ck~C~~kI 68 (162)
|.+|+.|+++|
T Consensus 58 rGrCr~C~~~I 68 (92)
T PF06750_consen 58 RGRCRYCGAPI 68 (92)
T ss_pred CCCCcccCCCC
Confidence 44444444444
No 33
>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=32.79 E-value=29 Score=28.27 Aligned_cols=21 Identities=33% Similarity=0.336 Sum_probs=18.2
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||-.+.+
T Consensus 54 wAK~iPgF~~L~~~DQi~LLk 74 (226)
T cd06934 54 FAKDLPYFRSLPIEDQISLLK 74 (226)
T ss_pred HhcCCcccccCCcchHHHHHH
Confidence 367999999999999998754
No 34
>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=32.33 E-value=32 Score=26.99 Aligned_cols=21 Identities=33% Similarity=0.476 Sum_probs=18.0
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||..|+.+||..+.+
T Consensus 21 faK~iPgF~~L~~~DQi~LLk 41 (191)
T cd06942 21 FVKSIPGFNQLSGEDRAQLLK 41 (191)
T ss_pred HHhcCCCcccCChhHHHHHHH
Confidence 357899999999999998754
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=32.03 E-value=32 Score=28.77 Aligned_cols=39 Identities=26% Similarity=0.273 Sum_probs=26.4
Q ss_pred cCeeeecCCcccc--ccccccCCCCCCCCCCcCCCHHHHHHHHH
Q psy6818 91 IPEWYHLSCFNAV--RLDLEFSASGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 91 ~~~WyH~~Cf~~~--~~~~~~~~~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
...|++..|.... +.-++ -+..||||.+|+.+||-.+.+
T Consensus 62 ~~~~~~~~~~~~~~i~~vVe---wAK~IPgF~~L~~~DQi~LLk 102 (259)
T cd06932 62 IRLFQRCQVRSVETIRELTE---FAKSLPGFRNLDLNDQVTLLK 102 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHhcCCCcccCChhHHHHHHH
Confidence 3458876554321 12223 367999999999999998854
No 36
>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=32.00 E-value=33 Score=27.82 Aligned_cols=21 Identities=38% Similarity=0.566 Sum_probs=18.3
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||..|+.+||..+.+
T Consensus 62 faK~lP~F~~L~~~DQi~LLK 82 (236)
T cd06954 62 FAKQLPGFLTLTREDQIALLK 82 (236)
T ss_pred HHcCCCCcccCChHHHHHHHH
Confidence 367999999999999998854
No 37
>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=31.13 E-value=37 Score=27.60 Aligned_cols=20 Identities=25% Similarity=0.288 Sum_probs=17.2
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
+..||||..|+.+||..+.+
T Consensus 39 AK~iP~F~~L~~~DQi~LLk 58 (222)
T cd06951 39 VRNLPCFTYLPPDDQLRLLR 58 (222)
T ss_pred HHhCCCcccCChHHHHHHHH
Confidence 57899999999999977644
No 38
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=29.00 E-value=37 Score=27.58 Aligned_cols=38 Identities=26% Similarity=0.486 Sum_probs=25.2
Q ss_pred CeeeecCCcccc--ccccccCCCCCCCCCCcCCCHHHHHHHHH
Q psy6818 92 PEWYHLSCFNAV--RLDLEFSASGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 92 ~~WyH~~Cf~~~--~~~~~~~~~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
..|.|+.-.... +..+. -+..||||..|+.+||..+.+
T Consensus 39 ~~~~~~~~~~~~~i~~iIe---faK~lp~F~~L~~~DQi~LLK 78 (231)
T cd06938 39 MRFRHITEMTILTVQLIVE---FAKRLPGFDKLSREDQITLLK 78 (231)
T ss_pred hHHHHHHHHHHHHHHHHHH---HHhcCCccccCChhHHHHHHH
Confidence 456776543321 12223 367999999999999998754
No 39
>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=28.75 E-value=39 Score=28.10 Aligned_cols=20 Identities=40% Similarity=0.605 Sum_probs=17.8
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
+..||||.+|+.+||-.+.+
T Consensus 48 AK~iP~F~~L~~~DQi~LLk 67 (246)
T cd07073 48 AKALPGFRNLHVDDQMAVIQ 67 (246)
T ss_pred HHcCCCccCCCHHHHHHHHH
Confidence 57899999999999998854
No 40
>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=28.68 E-value=37 Score=24.64 Aligned_cols=22 Identities=36% Similarity=0.628 Sum_probs=18.4
Q ss_pred CCCCCCCcCCCHHHHHHHHHHh
Q psy6818 113 GKQIPGFGSLEKKDQKIVEATL 134 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~~~ 134 (162)
+..++||..|+.+||..+.+..
T Consensus 18 ~~~~~~f~~L~~~dq~~Llk~~ 39 (168)
T cd06157 18 AKSIPGFRELPLEDQIVLLKSF 39 (168)
T ss_pred HHcCCchhcCChHHHHHHHHHH
Confidence 4689999999999999886543
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=27.66 E-value=48 Score=27.17 Aligned_cols=21 Identities=38% Similarity=0.469 Sum_probs=18.1
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||-.+.+
T Consensus 51 wAK~iP~F~~L~~~DQi~LLk 71 (235)
T cd06949 51 WAKKIPGFVDLSLHDQVHLLE 71 (235)
T ss_pred HHHhCCCcccCCHHHHHHHHH
Confidence 357899999999999998854
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=26.32 E-value=51 Score=27.59 Aligned_cols=21 Identities=33% Similarity=0.483 Sum_probs=18.3
Q ss_pred CCCCCCCcCCCHHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEAT 133 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~~ 133 (162)
+..||||.+|+.+||-.+.+.
T Consensus 48 AK~IPgF~~L~~~DQi~LLk~ 68 (248)
T cd07075 48 AKVLPGFRNLPLEDQITLIQY 68 (248)
T ss_pred HHcCCCcccCCHHHHHHHHHH
Confidence 578999999999999988654
No 43
>cd07349 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.
Probab=25.39 E-value=56 Score=26.69 Aligned_cols=20 Identities=25% Similarity=0.421 Sum_probs=17.3
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
+..||||.+|+-+||-.+.+
T Consensus 39 AK~iP~F~~L~~~DQi~LLk 58 (222)
T cd07349 39 MRNLPSFWQLPPQDQLLLLQ 58 (222)
T ss_pred HhcCCCcccCChHHHHHHHH
Confidence 56999999999999997644
No 44
>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. 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. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge
Probab=25.18 E-value=55 Score=26.14 Aligned_cols=21 Identities=38% Similarity=0.521 Sum_probs=17.6
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||-.+.+
T Consensus 45 waK~ip~F~~L~~~DQi~LLk 65 (206)
T cd06950 45 WAKSIPAFSTLPFRDQLILLE 65 (206)
T ss_pred HHHhCCccccCCHHHHHHHHH
Confidence 357899999999999977644
No 45
>cd06952 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2. The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D
Probab=24.88 E-value=51 Score=26.40 Aligned_cols=21 Identities=24% Similarity=0.438 Sum_probs=17.7
Q ss_pred CCCCCCCcCCCHHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEAT 133 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~~ 133 (162)
+..||||..|+.+||..+.+.
T Consensus 41 ak~iP~F~~L~~~DQ~~LLk~ 61 (222)
T cd06952 41 ARSIPAFQALGAETQTSLVRA 61 (222)
T ss_pred HHhCCchhhCChHHHHHHHHH
Confidence 457999999999999988553
No 46
>cd07076 NR_LBD_GR Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription
Probab=24.73 E-value=54 Score=27.44 Aligned_cols=20 Identities=40% Similarity=0.594 Sum_probs=17.8
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
+..||||.+|+-+||-.+.+
T Consensus 48 AK~IPgF~~L~l~DQi~LLk 67 (247)
T cd07076 48 AKAIPGFRNLHLDDQMTLLQ 67 (247)
T ss_pred HhcCCCcccCCHHHHHHHHH
Confidence 57899999999999998855
No 47
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in 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 use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=24.52 E-value=61 Score=26.94 Aligned_cols=20 Identities=35% Similarity=0.576 Sum_probs=17.7
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
+..||||.+|+.+||..+.+
T Consensus 48 AK~iPgF~~L~~~DQi~LLk 67 (246)
T cd06947 48 AKALPGFRNLHLDDQMTLIQ 67 (246)
T ss_pred HHcCCCcccCCHHHHHHHHH
Confidence 57899999999999998754
No 48
>cd06953 NR_LBD_DHR4_like The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4. The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 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=24.37 E-value=54 Score=26.37 Aligned_cols=21 Identities=29% Similarity=0.324 Sum_probs=18.1
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||..+.+
T Consensus 46 waK~lp~F~~L~~~DQi~LLk 66 (213)
T cd06953 46 WTKKLPFFTELSIKDHTHLLT 66 (213)
T ss_pred HHhcCCchhhCCHHHHHHHHH
Confidence 357999999999999998754
No 49
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=24.35 E-value=44 Score=17.81 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=9.9
Q ss_pred ccccccccccCCC
Q psy6818 60 TCRGCEAKIAKGE 72 (162)
Q Consensus 60 ~Ck~C~~kI~Kge 72 (162)
.|..|+..|..+.
T Consensus 1 ~Cp~CG~~~~~~~ 13 (23)
T PF13240_consen 1 YCPNCGAEIEDDA 13 (23)
T ss_pred CCcccCCCCCCcC
Confidence 4888998887663
No 50
>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.
Probab=24.03 E-value=61 Score=26.69 Aligned_cols=20 Identities=30% Similarity=0.391 Sum_probs=17.7
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
+..||||.+|+-+||..+.+
T Consensus 39 AK~iP~F~~L~~~DQi~LLk 58 (232)
T cd07350 39 VKGVPCFQELPLDDQLVLVR 58 (232)
T ss_pred HHhCcCcccCChHHHHHHHH
Confidence 57899999999999998754
No 51
>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 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=24.03 E-value=52 Score=27.15 Aligned_cols=20 Identities=20% Similarity=0.114 Sum_probs=17.7
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
+..||||.+|+-+||-.+.+
T Consensus 60 AK~iP~F~~L~~~DQi~LLk 79 (241)
T cd07069 60 ARSSIFFRELKVDDQMKLLQ 79 (241)
T ss_pred HhhCCCcccCCHHHHHHHHH
Confidence 57999999999999998754
No 52
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=23.82 E-value=49 Score=26.79 Aligned_cols=21 Identities=33% Similarity=0.550 Sum_probs=18.1
Q ss_pred CCCCCCCCcCCCHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
-+..||||.+|+.+||..+.+
T Consensus 55 faK~iP~F~~L~~~DQi~LLk 75 (221)
T cd06936 55 FTKGLPGFETLDHEDQIALLK 75 (221)
T ss_pred HHhCCCchhhCChhHHHHHHH
Confidence 367999999999999998754
No 53
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 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=23.57 E-value=55 Score=26.84 Aligned_cols=20 Identities=25% Similarity=0.230 Sum_probs=17.7
Q ss_pred CCCCCCCcCCCHHHHHHHHH
Q psy6818 113 GKQIPGFGSLEKKDQKIVEA 132 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~ 132 (162)
+..||||.+|+.+||..+.+
T Consensus 58 aK~lP~F~~L~~~DQi~LLk 77 (237)
T cd07070 58 ARRCMVFKELEVADQMTLLQ 77 (237)
T ss_pred HHhCCChhhCCHHHHHHHHH
Confidence 57899999999999998854
No 54
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=22.75 E-value=52 Score=25.91 Aligned_cols=22 Identities=36% Similarity=0.460 Sum_probs=18.8
Q ss_pred CCCCCCCCcCCCHHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEAT 133 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~~ 133 (162)
-+..+|||..|+.+||..+.+.
T Consensus 49 wak~lp~F~~L~~~DQ~~LLk~ 70 (207)
T cd06943 49 WAKRIPHFSELPLDDQVILLRA 70 (207)
T ss_pred HHHhCchhhccChhhhHHHHHH
Confidence 3578999999999999988654
No 55
>KOG1973|consensus
Probab=22.44 E-value=35 Score=28.90 Aligned_cols=12 Identities=42% Similarity=1.378 Sum_probs=9.4
Q ss_pred cC-eeeecCCccc
Q psy6818 91 IP-EWYHLSCFNA 102 (162)
Q Consensus 91 ~~-~WyH~~Cf~~ 102 (162)
.+ .|||+.|+=-
T Consensus 240 C~~eWFH~~CVGL 252 (274)
T KOG1973|consen 240 CPIEWFHFTCVGL 252 (274)
T ss_pred CCcceEEEecccc
Confidence 55 8999999743
No 56
>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-
Probab=22.17 E-value=69 Score=25.66 Aligned_cols=22 Identities=41% Similarity=0.558 Sum_probs=18.5
Q ss_pred CCCCCCCCcCCCHHHHHHHHHH
Q psy6818 112 SGKQIPGFGSLEKKDQKIVEAT 133 (162)
Q Consensus 112 ~~e~I~Gf~~L~~eDQ~~Ik~~ 133 (162)
-+..+|||..|+.+||..+.+.
T Consensus 46 ~aK~lp~F~~L~~~DQi~LLk~ 67 (221)
T cd06946 46 WAKHIPGFSSLSLNDQMSLLQS 67 (221)
T ss_pred HHHhCCCcccCCHHHHHHHHHH
Confidence 3578999999999999987543
No 57
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=20.92 E-value=59 Score=24.08 Aligned_cols=19 Identities=11% Similarity=0.265 Sum_probs=16.1
Q ss_pred CCcCCCHHHHHHHHHHhhc
Q psy6818 118 GFGSLEKKDQKIVEATLPS 136 (162)
Q Consensus 118 Gf~~L~~eDQ~~Ik~~~~~ 136 (162)
-|++|++|+++++.+.+++
T Consensus 86 Rle~l~~eE~~~L~~eiee 104 (104)
T PF11460_consen 86 RLEELSPEELEALQAEIEE 104 (104)
T ss_pred HHHhCCHHHHHHHHHHhcC
Confidence 5789999999999887764
No 58
>KOG1701|consensus
Probab=20.91 E-value=21 Score=32.72 Aligned_cols=30 Identities=20% Similarity=0.652 Sum_probs=21.9
Q ss_pred ccccccccccCCCeEEEEEeecCCCCcccCCcCeeeecCCccc
Q psy6818 60 TCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNA 102 (162)
Q Consensus 60 ~Ck~C~~kI~KgeLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~ 102 (162)
.|-+|++.|.-.++-+ ..|.+-||+.||+=
T Consensus 276 iC~~C~K~V~g~~~ac-------------~Am~~~fHv~CFtC 305 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAV-------------EAMDQLFHVQCFTC 305 (468)
T ss_pred hhhhcCCcccCcchHH-------------HHhhhhhcccceeh
Confidence 8999998886554222 23678999999984
No 59
>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are 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. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin
Probab=20.91 E-value=79 Score=25.37 Aligned_cols=40 Identities=25% Similarity=0.271 Sum_probs=27.1
Q ss_pred cCeeeecCCccccc--cccccCCCCCCCCCCcCCCHHHHHHHHHH
Q psy6818 91 IPEWYHLSCFNAVR--LDLEFSASGKQIPGFGSLEKKDQKIVEAT 133 (162)
Q Consensus 91 ~~~WyH~~Cf~~~~--~~~~~~~~~e~I~Gf~~L~~eDQ~~Ik~~ 133 (162)
...|.|+....... ..+. -+..+|||..|+.+||..+.+.
T Consensus 26 ~~~~~~~~~~a~~~l~~~ve---waK~lp~F~~L~~~DQi~LLk~ 67 (221)
T cd07068 26 VSLLATLSDLADRELVHIIS---WAKHIPGFSDLSLNDQMHLLQS 67 (221)
T ss_pred hHHHHHHHHHHHHHHHHHHH---HHHhCCCcccCCHHHHHHHHHH
Confidence 34577776655431 1122 3578999999999999988643
No 60
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=20.64 E-value=24 Score=23.39 Aligned_cols=20 Identities=30% Similarity=0.650 Sum_probs=16.3
Q ss_pred CCcccccccccccCCCeEEE
Q psy6818 57 NRSTCRGCEAKIAKGEIRVS 76 (162)
Q Consensus 57 ~Ra~Ck~C~~kI~KgeLRig 76 (162)
.||-|.+|++++.-.++.+.
T Consensus 16 ~RAlCa~C~~~L~~~E~h~C 35 (58)
T PF05810_consen 16 ERALCANCGQKLHPDETHVC 35 (58)
T ss_pred HHHHHhccCcccccchhhHH
Confidence 47779999999988887664
No 61
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=20.54 E-value=81 Score=22.87 Aligned_cols=23 Identities=30% Similarity=0.550 Sum_probs=17.5
Q ss_pred CCCCCCCcCCCHHHHHHH-HHHhh
Q psy6818 113 GKQIPGFGSLEKKDQKIV-EATLP 135 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~I-k~~~~ 135 (162)
..++|||+.|++.-|.++ ..+++
T Consensus 31 t~~vPgF~~ls~sKqRRLi~~ALE 54 (92)
T PF10330_consen 31 TTSVPGFSDLSPSKQRRLIMAALE 54 (92)
T ss_pred hccCCCcccCCHHHHHHHHHHHHh
Confidence 469999999998776665 55555
No 62
>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal lig
Probab=20.43 E-value=76 Score=25.31 Aligned_cols=22 Identities=32% Similarity=0.353 Sum_probs=18.5
Q ss_pred CCCCCCCcCCCHHHHHHHHHHh
Q psy6818 113 GKQIPGFGSLEKKDQKIVEATL 134 (162)
Q Consensus 113 ~e~I~Gf~~L~~eDQ~~Ik~~~ 134 (162)
+..+|||..|+.+||..+.+..
T Consensus 52 ak~~p~F~~L~~~Dq~~Llk~~ 73 (222)
T cd06931 52 AKYIPAFCELPLDDQVALLRAH 73 (222)
T ss_pred HHhCCccccCChHHHHHHHHHH
Confidence 4689999999999999886543
No 63
>KOG3970|consensus
Probab=20.25 E-value=34 Score=29.03 Aligned_cols=32 Identities=28% Similarity=0.661 Sum_probs=23.2
Q ss_pred CcccccccccccCC-CeEEEEEeecCCCCcccCCcCeeeecCCcccc
Q psy6818 58 RSTCRGCEAKIAKG-EIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAV 103 (162)
Q Consensus 58 Ra~Ck~C~~kI~Kg-eLRig~~~~~~~~~~~~g~~~~WyH~~Cf~~~ 103 (162)
-..|+-|+.+++.| .+|+- ...-+||+||-..
T Consensus 50 ~pNC~LC~t~La~gdt~RLv--------------CyhlfHW~Clner 82 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRLV--------------CYHLFHWKCLNER 82 (299)
T ss_pred CCCCceeCCccccCcceeeh--------------hhhhHHHHHhhHH
Confidence 36799999999886 56661 2346799998764
No 64
>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=20.23 E-value=37 Score=20.18 Aligned_cols=17 Identities=18% Similarity=0.511 Sum_probs=10.1
Q ss_pred cCCCcccccccccccCC
Q psy6818 55 KSNRSTCRGCEAKIAKG 71 (162)
Q Consensus 55 kS~Ra~Ck~C~~kI~Kg 71 (162)
...+|.|+-|++.|.-+
T Consensus 13 ~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CSS-EEETTTTEE----
T ss_pred CcCeEEeCCCCeEEeeC
Confidence 46889999998776543
Done!