Query 041407
Match_columns 241
No_of_seqs 146 out of 1160
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 06:44:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041407.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041407hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0703 Predicted GTPase-activ 100.0 9.8E-42 2.1E-46 308.7 6.7 109 1-109 15-127 (287)
2 PF01412 ArfGap: Putative GTPa 100.0 6.8E-40 1.5E-44 262.3 6.3 108 1-108 3-116 (116)
3 smart00105 ArfGap Putative GTP 100.0 3.1E-38 6.7E-43 251.5 10.0 102 9-110 1-109 (112)
4 COG5347 GTPase-activating prot 100.0 1.3E-34 2.9E-39 267.1 8.6 109 1-109 10-126 (319)
5 PLN03119 putative ADP-ribosyla 100.0 3E-33 6.6E-38 270.4 10.4 112 1-115 13-131 (648)
6 PLN03131 hypothetical protein; 100.0 8E-33 1.7E-37 269.3 10.3 113 1-116 13-132 (705)
7 PLN03114 ADP-ribosylation fact 100.0 7.1E-29 1.5E-33 230.0 9.3 110 1-110 12-130 (395)
8 KOG0704 ADP-ribosylation facto 100.0 6E-29 1.3E-33 229.3 7.2 105 3-107 11-126 (386)
9 KOG0706 Predicted GTPase-activ 99.9 9E-29 1.9E-33 233.8 6.4 82 1-82 13-94 (454)
10 KOG0705 GTPase-activating prot 99.9 3.7E-28 8E-33 235.2 7.8 112 2-113 504-621 (749)
11 KOG0521 Putative GTPase activa 99.9 2.6E-25 5.7E-30 225.2 2.9 112 2-113 417-536 (785)
12 KOG0818 GTPase-activating prot 99.8 5.2E-22 1.1E-26 190.3 5.4 106 5-110 2-121 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.8 2.6E-19 5.6E-24 179.7 3.9 103 7-109 294-404 (1186)
14 KOG0702 Predicted GTPase-activ 99.6 1E-15 2.3E-20 146.9 6.3 109 1-110 15-131 (524)
15 KOG0521 Putative GTPase activa 93.0 0.022 4.7E-07 59.3 -0.7 73 7-81 626-699 (785)
16 PF00643 zf-B_box: B-box zinc 81.3 1.6 3.4E-05 28.1 2.5 34 10-43 2-36 (42)
17 PRK00085 recO DNA repair prote 79.5 1.1 2.4E-05 39.3 1.8 36 3-38 141-177 (247)
18 TIGR00613 reco DNA repair prot 70.2 3.2 6.9E-05 36.3 2.2 38 3-40 139-177 (241)
19 PF08271 TF_Zn_Ribbon: TFIIB z 70.1 2.6 5.7E-05 27.7 1.3 27 13-40 2-28 (43)
20 PF01286 XPA_N: XPA protein N- 63.5 2.4 5.2E-05 27.4 0.1 27 12-38 4-31 (34)
21 PF11781 RRN7: RNA polymerase 63.4 6 0.00013 25.6 1.9 27 10-39 7-33 (36)
22 smart00401 ZnF_GATA zinc finge 55.5 13 0.00028 25.7 2.7 37 10-46 2-40 (52)
23 PF00320 GATA: GATA zinc finge 54.3 11 0.00023 24.1 1.9 32 14-45 1-34 (36)
24 cd01236 PH_outspread Outspread 53.3 5.3 0.00012 31.5 0.5 62 132-197 19-80 (104)
25 COG1381 RecO Recombinational D 52.3 6.7 0.00014 35.3 1.0 35 4-38 147-182 (251)
26 cd07171 NR_DBD_ER DNA-binding 51.3 11 0.00025 28.4 2.0 31 10-43 2-32 (82)
27 cd01264 PH_melted Melted pleck 49.8 6.5 0.00014 31.0 0.4 58 135-197 17-77 (101)
28 cd01251 PH_centaurin_alpha Cen 48.0 14 0.00031 28.5 2.1 36 135-176 14-49 (103)
29 cd07173 NR_DBD_AR DNA-binding 44.7 15 0.00033 27.8 1.7 31 10-43 2-32 (82)
30 cd06968 NR_DBD_ROR DNA-binding 43.0 18 0.00039 28.1 2.0 32 9-43 3-34 (95)
31 cd07160 NR_DBD_LXR DNA-binding 42.6 18 0.00039 28.5 2.0 31 10-43 17-47 (101)
32 cd07170 NR_DBD_ERR DNA-binding 41.8 18 0.00039 28.3 1.8 30 11-43 4-33 (97)
33 PF14803 Nudix_N_2: Nudix N-te 41.3 11 0.00024 24.2 0.4 30 12-42 1-33 (34)
34 PRK12495 hypothetical protein; 41.1 17 0.00038 32.8 1.8 30 7-40 38-67 (226)
35 cd01260 PH_CNK Connector enhan 39.2 11 0.00024 28.1 0.3 54 136-197 19-72 (96)
36 PRK00423 tfb transcription ini 38.4 23 0.0005 32.8 2.3 35 7-42 7-41 (310)
37 TIGR02419 C4_traR_proteo phage 38.3 9.2 0.0002 27.6 -0.3 35 7-41 27-62 (63)
38 cd06966 NR_DBD_CAR DNA-binding 35.5 19 0.00041 27.9 1.0 29 12-43 1-29 (94)
39 PF07282 OrfB_Zn_ribbon: Putat 34.0 26 0.00056 24.8 1.5 27 11-39 28-54 (69)
40 cd07161 NR_DBD_EcR DNA-binding 33.7 30 0.00065 26.6 1.9 29 12-43 2-30 (91)
41 cd07169 NR_DBD_GCNF_like DNA-b 32.7 31 0.00067 26.5 1.8 32 9-43 4-35 (90)
42 cd07172 NR_DBD_GR_PR DNA-bindi 32.6 31 0.00068 25.7 1.8 29 12-43 3-31 (78)
43 PF01258 zf-dskA_traR: Prokary 32.6 6.3 0.00014 25.0 -1.7 29 13-41 5-34 (36)
44 cd01238 PH_Tec Tec pleckstrin 32.5 20 0.00042 27.9 0.7 58 135-196 19-82 (106)
45 COG1997 RPL43A Ribosomal prote 32.0 34 0.00075 26.7 1.9 32 7-40 31-62 (89)
46 KOG3507 DNA-directed RNA polym 31.9 24 0.00052 25.6 1.0 23 12-37 21-43 (62)
47 cd07162 NR_DBD_PXR DNA-binding 31.8 33 0.00071 26.1 1.8 28 13-43 1-28 (87)
48 PF10764 Gin: Inhibitor of sig 30.1 30 0.00066 23.6 1.2 26 13-39 1-26 (46)
49 cd06956 NR_DBD_RXR DNA-binding 30.0 39 0.00084 25.0 1.9 28 13-43 2-29 (77)
50 cd07163 NR_DBD_TLX DNA-binding 29.9 23 0.00051 27.2 0.7 30 11-43 6-35 (92)
51 PF04189 Gcd10p: Gcd10p family 29.7 49 0.0011 31.0 2.9 46 57-103 106-151 (299)
52 cd01265 PH_PARIS-1 PARIS-1 ple 29.0 30 0.00064 26.2 1.2 55 135-196 15-69 (95)
53 cd03031 GRX_GRX_like Glutaredo 28.8 32 0.0007 28.7 1.4 28 8-44 96-123 (147)
54 PF12760 Zn_Tnp_IS1595: Transp 28.8 47 0.001 22.0 2.0 32 6-38 13-44 (46)
55 cd07158 NR_DBD_Ppar_like The D 28.4 33 0.00072 25.0 1.3 27 14-43 1-27 (73)
56 cd06965 NR_DBD_Ppar DNA-bindin 28.1 26 0.00057 26.5 0.7 27 14-43 2-28 (84)
57 cd07156 NR_DBD_VDR_like The DN 27.8 37 0.00081 24.7 1.5 27 14-43 1-27 (72)
58 cd06963 NR_DBD_GR_like The DNA 27.7 41 0.00089 24.7 1.7 27 14-43 1-27 (73)
59 PF14471 DUF4428: Domain of un 27.2 24 0.00052 24.4 0.3 30 13-43 1-32 (51)
60 cd07179 2DBD_NR_DBD2 The secon 27.2 43 0.00093 24.6 1.7 27 14-43 1-27 (74)
61 cd06955 NR_DBD_VDR DNA-binding 27.2 30 0.00065 27.6 0.9 30 11-43 6-35 (107)
62 cd07166 NR_DBD_REV_ERB DNA-bin 26.5 31 0.00066 26.4 0.8 30 11-43 3-32 (89)
63 smart00290 ZnF_UBP Ubiquitin C 26.3 44 0.00094 22.0 1.5 22 13-34 1-22 (50)
64 COG1734 DksA DnaK suppressor p 26.2 13 0.00029 30.3 -1.3 31 12-42 81-112 (120)
65 cd07165 NR_DBD_DmE78_like DNA- 26.1 37 0.00079 25.4 1.2 27 14-43 1-27 (81)
66 cd07168 NR_DBD_DHR4_like DNA-b 26.1 47 0.001 25.4 1.8 31 10-43 5-35 (90)
67 cd07155 NR_DBD_ER_like DNA-bin 26.1 36 0.00077 25.0 1.1 27 14-43 1-27 (75)
68 COG2174 RPL34A Ribosomal prote 25.8 45 0.00097 26.2 1.6 34 6-39 29-79 (93)
69 PRK11019 hypothetical protein; 25.4 18 0.00038 28.1 -0.7 37 10-47 35-73 (88)
70 PF00105 zf-C4: Zinc finger, C 25.3 48 0.001 23.6 1.6 28 12-42 1-28 (70)
71 PRK03681 hypA hydrogenase nick 25.2 29 0.00064 27.6 0.5 33 6-41 65-97 (114)
72 cd07157 2DBD_NR_DBD1 The first 24.8 32 0.0007 26.1 0.7 28 13-43 2-29 (86)
73 cd00202 ZnF_GATA Zinc finger D 24.7 48 0.001 23.1 1.5 33 13-45 1-35 (54)
74 PF06827 zf-FPG_IleRS: Zinc fi 24.7 36 0.00077 20.5 0.7 28 12-39 2-29 (30)
75 cd06958 NR_DBD_COUP_TF DNA-bin 24.3 41 0.0009 24.6 1.1 27 14-43 1-27 (73)
76 KOG1416 tRNA(1-methyladenosine 23.4 66 0.0014 32.0 2.6 43 59-102 115-157 (475)
77 PF09297 zf-NADH-PPase: NADH p 23.3 40 0.00086 20.7 0.8 25 10-40 2-30 (32)
78 cd06959 NR_DBD_EcR_like The DN 23.3 52 0.0011 24.0 1.5 27 14-43 2-28 (73)
79 cd06962 NR_DBD_FXR DNA-binding 22.3 38 0.00083 25.6 0.7 28 13-43 3-30 (84)
80 cd06960 NR_DBD_HNF4A DNA-bindi 22.3 43 0.00094 24.6 0.9 27 14-43 1-27 (76)
81 COG2158 Uncharacterized protei 21.7 55 0.0012 26.4 1.5 31 14-46 45-77 (112)
82 COG0675 Transposase and inacti 21.5 41 0.00089 29.7 0.8 22 12-40 310-331 (364)
83 cd01245 PH_RasGAP_CG5898 RAS G 21.4 43 0.00094 26.1 0.8 61 136-198 15-75 (98)
84 smart00399 ZnF_C4 c4 zinc fing 21.4 51 0.0011 23.7 1.1 27 14-43 2-28 (70)
85 smart00659 RPOLCX RNA polymera 21.3 44 0.00095 22.5 0.7 27 13-44 4-30 (44)
86 TIGR01384 TFS_arch transcripti 21.1 72 0.0016 24.4 2.0 28 11-38 62-97 (104)
87 cd06967 NR_DBD_TR2_like DNA-bi 21.0 42 0.00092 25.5 0.7 29 12-43 4-32 (87)
88 cd06961 NR_DBD_TR DNA-binding 21.0 48 0.001 25.1 0.9 27 14-43 2-28 (85)
89 PHA00080 DksA-like zinc finger 20.7 30 0.00065 25.6 -0.2 35 8-43 28-64 (72)
90 cd07164 NR_DBD_PNR_like_1 DNA- 20.3 57 0.0012 24.1 1.2 27 14-43 1-27 (78)
91 cd01266 PH_Gab Gab (Grb2-assoc 20.2 54 0.0012 25.2 1.1 43 135-179 17-62 (108)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=9.8e-42 Score=308.74 Aligned_cols=109 Identities=61% Similarity=1.119 Sum_probs=105.1
Q ss_pred ChHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHH
Q 041407 1 ILEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWE 80 (241)
Q Consensus 1 il~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wE 80 (241)
+|++|++.|+|+.|||||+++|+|||+|+|||||+.|+||||.||+|||+||||+||.|++|+|+.|+..||.+||++||
T Consensus 15 ~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~an~~~e 94 (287)
T KOG0703|consen 15 RLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNAKANSYYE 94 (287)
T ss_pred HHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcchhhhhhcc
Confidence 48899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCCCChHH----HHHHHHHHHhcCccccCC
Q 041407 81 AELPPNFDRSR----IEKFIRTKYEERKWVQKG 109 (241)
Q Consensus 81 a~lP~~~d~~~----re~fIraKYv~K~F~~~~ 109 (241)
+.+|..++++. +|+|||+|||+|+|+.++
T Consensus 95 a~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 95 AKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred ccCCccccCCChHHHHHHHHHHHHhhhhhccch
Confidence 99999887654 999999999999999875
No 2
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=6.8e-40 Score=262.32 Aligned_cols=108 Identities=55% Similarity=1.078 Sum_probs=89.4
Q ss_pred ChHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHH
Q 041407 1 ILEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWE 80 (241)
Q Consensus 1 il~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wE 80 (241)
+|+.|++.|+|++|||||+++|+|||++||||||+.|+|+||.||+|+|+||||+||+|++++|++|+.+||.++|++||
T Consensus 3 ~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~e 82 (116)
T PF01412_consen 3 ILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIWE 82 (116)
T ss_dssp HHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHHT
T ss_pred HHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHHH
Confidence 58899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCC------CCChHHHHHHHHHHHhcCccccC
Q 041407 81 AELPP------NFDRSRIEKFIRTKYEERKWVQK 108 (241)
Q Consensus 81 a~lP~------~~d~~~re~fIraKYv~K~F~~~ 108 (241)
++.+. ..+...+++||++||++++|+.+
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 83 ANSPPPKKPPPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp TTSTTTTTHCTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred cCCCCCCCCCCCCcHHHHHHHHHHHHHhhhhccC
Confidence 99422 23345699999999999999863
No 3
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=100.00 E-value=3.1e-38 Score=251.50 Aligned_cols=102 Identities=55% Similarity=1.036 Sum_probs=95.3
Q ss_pred CCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHHhcCCCCC-
Q 041407 9 PENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWEAELPPNF- 87 (241)
Q Consensus 9 pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wEa~lP~~~- 87 (241)
|+|++|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|++||+++|+..
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~ 80 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSL 80 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCcccc
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999999986432
Q ss_pred ------ChHHHHHHHHHHHhcCccccCCC
Q 041407 88 ------DRSRIEKFIRTKYEERKWVQKGA 110 (241)
Q Consensus 88 ------d~~~re~fIraKYv~K~F~~~~~ 110 (241)
+...+++||++||++|+|+.+.+
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhcccccc
Confidence 34569999999999999998754
No 4
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.3e-34 Score=267.08 Aligned_cols=109 Identities=49% Similarity=0.943 Sum_probs=100.4
Q ss_pred ChHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHH
Q 041407 1 ILEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWE 80 (241)
Q Consensus 1 il~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wE 80 (241)
++..|.+.++|+.|||||+++|+|||+|||||||++||||||+||+||++||||+||+|+++||++|..+||++||+|||
T Consensus 10 ~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~~~e 89 (319)
T COG5347 10 LLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANRFYE 89 (319)
T ss_pred HHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhhHhc
Confidence 36778899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCC--------CCChHHHHHHHHHHHhcCccccCC
Q 041407 81 AELPP--------NFDRSRIEKFIRTKYEERKWVQKG 109 (241)
Q Consensus 81 a~lP~--------~~d~~~re~fIraKYv~K~F~~~~ 109 (241)
.++-. ..+...+++||+.||++++|....
T Consensus 90 ~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~ 126 (319)
T COG5347 90 KNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDS 126 (319)
T ss_pred cCCCcccccccccccCHHHHHHHHHHHHHhhhccccc
Confidence 97422 235566999999999999999863
No 5
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=3e-33 Score=270.40 Aligned_cols=112 Identities=29% Similarity=0.689 Sum_probs=102.0
Q ss_pred ChHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHH
Q 041407 1 ILEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWE 80 (241)
Q Consensus 1 il~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wE 80 (241)
||++|++.|+|+.|+|||+.+|+|||+|||||||+.|+||||.|| +|||||+||+|+++||++|+.+||+++|++||
T Consensus 13 ILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~gGN~~AN~iye 89 (648)
T PLN03119 13 IIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNGGNQRAREIYL 89 (648)
T ss_pred HHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHhchHHHHHHHH
Confidence 689999999999999999999999999999999999999999998 49999999999999999999999999999999
Q ss_pred hcCCC-------CCChHHHHHHHHHHHhcCccccCCCCCCcc
Q 041407 81 AELPP-------NFDRSRIEKFIRTKYEERKWVQKGATQPTT 115 (241)
Q Consensus 81 a~lP~-------~~d~~~re~fIraKYv~K~F~~~~~~~~~~ 115 (241)
++++. ..+...+++|||+|||+|+|+.....+..+
T Consensus 90 anw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~ 131 (648)
T PLN03119 90 KNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPS 131 (648)
T ss_pred hhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCc
Confidence 98753 334556899999999999999987655443
No 6
>PLN03131 hypothetical protein; Provisional
Probab=99.98 E-value=8e-33 Score=269.30 Aligned_cols=113 Identities=31% Similarity=0.679 Sum_probs=102.0
Q ss_pred ChHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHH
Q 041407 1 ILEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWE 80 (241)
Q Consensus 1 il~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wE 80 (241)
||++|++.|+|+.|+|||+++|+|||++||||||++|+||||.|| +|||||+||+|++++|++|+.+||.+||++||
T Consensus 13 iLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~WtdeEV~~Mk~gGN~~AN~iye 89 (705)
T PLN03131 13 IIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKFTSQDVEALQNGGNQRAREIYL 89 (705)
T ss_pred HHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCCCCHHHHHHHHHhccHHHHHHHH
Confidence 689999999999999999999999999999999999999999998 39999999999999999999999999999999
Q ss_pred hcCC-------CCCChHHHHHHHHHHHhcCccccCCCCCCcch
Q 041407 81 AELP-------PNFDRSRIEKFIRTKYEERKWVQKGATQPTTK 116 (241)
Q Consensus 81 a~lP-------~~~d~~~re~fIraKYv~K~F~~~~~~~~~~~ 116 (241)
++++ .+.+...+++|||+|||+|+|+.....+..++
T Consensus 90 anwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~ppr 132 (705)
T PLN03131 90 KDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPR 132 (705)
T ss_pred hhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCch
Confidence 9874 23345568999999999999999875554444
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.95 E-value=7.1e-29 Score=230.00 Aligned_cols=110 Identities=39% Similarity=0.666 Sum_probs=95.5
Q ss_pred ChHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHH
Q 041407 1 ILEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWE 80 (241)
Q Consensus 1 il~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wE 80 (241)
||+.|+..|+|+.|+|||+++|+|+|++||||||+.|+|+||.||+||++|||++||.|++++|++|+.+||.++|+||+
T Consensus 12 vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~fF~ 91 (395)
T PLN03114 12 VFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVFFK 91 (395)
T ss_pred HHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred hcC-CCCCC-----hH---HHHHHHHHHHhcCccccCCC
Q 041407 81 AEL-PPNFD-----RS---RIEKFIRTKYEERKWVQKGA 110 (241)
Q Consensus 81 a~l-P~~~d-----~~---~re~fIraKYv~K~F~~~~~ 110 (241)
.+- ....+ .. .+-+-+.+|++.+.++.+..
T Consensus 92 qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 92 QYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 863 11111 11 13344888999998886653
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=6e-29 Score=229.28 Aligned_cols=105 Identities=40% Similarity=0.739 Sum_probs=86.5
Q ss_pred HhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHHhc
Q 041407 3 EGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWEAE 82 (241)
Q Consensus 3 ~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wEa~ 82 (241)
.+|+...+|++|+||++++|+|||++||||||++|||+||.||+|||+||||+||+|.+.||+.|+.+||+++++|++..
T Consensus 11 ~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~eFL~s~ 90 (386)
T KOG0704|consen 11 LELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFREFLSSQ 90 (386)
T ss_pred HhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHHHHhhC
Confidence 34444459999999999999999999999999999999999999999999999999999999999999999999999886
Q ss_pred C--CCCCC-hH--------HHHHHHHHHHhcCcccc
Q 041407 83 L--PPNFD-RS--------RIEKFIRTKYEERKWVQ 107 (241)
Q Consensus 83 l--P~~~d-~~--------~re~fIraKYv~K~F~~ 107 (241)
- .+..+ ++ ..++-|.+--+.+.|-+
T Consensus 91 ~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w~d 126 (386)
T KOG0704|consen 91 GIYKETWPIREKYNSRAAALYRDKIAALAEGREWND 126 (386)
T ss_pred ccccccccHHHhhccHHHHHHHHHHHHHhcCCcccc
Confidence 2 11111 11 14455666667777733
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.95 E-value=9e-29 Score=233.76 Aligned_cols=82 Identities=50% Similarity=0.925 Sum_probs=79.7
Q ss_pred ChHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHH
Q 041407 1 ILEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWE 80 (241)
Q Consensus 1 il~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wE 80 (241)
+++.|+.+++|++|||||+++|+|+|++||||||++||++||+|||||++|||+.||+|+..||++|+.|||++|+.|+.
T Consensus 13 vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~FFk 92 (454)
T KOG0706|consen 13 VFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARVFFK 92 (454)
T ss_pred HHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred hc
Q 041407 81 AE 82 (241)
Q Consensus 81 a~ 82 (241)
.+
T Consensus 93 qh 94 (454)
T KOG0706|consen 93 QH 94 (454)
T ss_pred Hc
Confidence 86
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.95 E-value=3.7e-28 Score=235.23 Aligned_cols=112 Identities=41% Similarity=0.899 Sum_probs=102.4
Q ss_pred hHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHHh
Q 041407 2 LEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWEA 81 (241)
Q Consensus 2 l~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wEa 81 (241)
|..+...+||..|+||+.++|.|||+|+|+.+|++|+||||.||.|+|+|||+.||.|..|.+..|..+||+.||++||.
T Consensus 504 ~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vWE~ 583 (749)
T KOG0705|consen 504 LQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVWEG 583 (749)
T ss_pred HHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHhhh
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cC-----C-CCCChHHHHHHHHHHHhcCccccCCCCCC
Q 041407 82 EL-----P-PNFDRSRIEKFIRTKYEERKWVQKGATQP 113 (241)
Q Consensus 82 ~l-----P-~~~d~~~re~fIraKYv~K~F~~~~~~~~ 113 (241)
.+ | +...|+.+|.||++||++|.|..+..-..
T Consensus 584 ~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~te 621 (749)
T KOG0705|consen 584 SSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPCTE 621 (749)
T ss_pred hccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCCCC
Confidence 54 2 23457779999999999999998865433
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.90 E-value=2.6e-25 Score=225.25 Aligned_cols=112 Identities=46% Similarity=0.910 Sum_probs=103.3
Q ss_pred hHhhhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHHh
Q 041407 2 LEGLLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWEA 81 (241)
Q Consensus 2 l~~L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wEa 81 (241)
+.++++.|||..|+|||++.|+|+|+|+|+.+|++|+|+||.||+|+|+|+|++||.|.++.+.+|+.+||..+|.+||+
T Consensus 417 ~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~ 496 (785)
T KOG0521|consen 417 IEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEA 496 (785)
T ss_pred hhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhc
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCC--------CChHHHHHHHHHHHhcCccccCCCCCC
Q 041407 82 ELPPN--------FDRSRIEKFIRTKYEERKWVQKGATQP 113 (241)
Q Consensus 82 ~lP~~--------~d~~~re~fIraKYv~K~F~~~~~~~~ 113 (241)
+++.- .++..|+.||++||++++|..+.....
T Consensus 497 ~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~~~ 536 (785)
T KOG0521|consen 497 LLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQIK 536 (785)
T ss_pred ccccccccCCCCccchhhhhHhhhcccceeeEeecccchh
Confidence 98632 235569999999999999998865444
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.85 E-value=5.2e-22 Score=190.30 Aligned_cols=106 Identities=37% Similarity=0.735 Sum_probs=94.2
Q ss_pred hhcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHHhcCC
Q 041407 5 LLKLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWEAELP 84 (241)
Q Consensus 5 L~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wEa~lP 84 (241)
+.+...-++|+|||+++|.|||++-|+|+|.+|..+||.||.|||.||++....|.++.|+++..+.|..+|.+||..|=
T Consensus 2 ~k~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Ll 81 (669)
T KOG0818|consen 2 SKRLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLL 81 (669)
T ss_pred cccchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhcc
Confidence 34566778999999999999999999999999999999999999999999999999999999999999999999999862
Q ss_pred CC------------CCh--HHHHHHHHHHHhcCccccCCC
Q 041407 85 PN------------FDR--SRIEKFIRTKYEERKWVQKGA 110 (241)
Q Consensus 85 ~~------------~d~--~~re~fIraKYv~K~F~~~~~ 110 (241)
+. .|. +.+++||++||+...|+.+..
T Consensus 82 d~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~~~ 121 (669)
T KOG0818|consen 82 DPATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHRLP 121 (669)
T ss_pred CchhhhcccCCCCCcCCCCccHHHHHHHHHHheeeeccCC
Confidence 21 111 249999999999999999543
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.76 E-value=2.6e-19 Score=179.69 Aligned_cols=103 Identities=48% Similarity=0.888 Sum_probs=95.1
Q ss_pred cCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcCCCccceeeecccCC--CChHHHHHHHhhCcHHHHHHHHhcCC
Q 041407 7 KLPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDT--WLPEQVAFMQSMGNEKSNKFWEAELP 84 (241)
Q Consensus 7 ~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~--Ws~~el~~mk~~GN~~aN~~wEa~lP 84 (241)
....|+.|+|||++.|.||++|+++.||-.|+|.||+||..+|+|+|++||. |+.+.++++..+||.++|+||-+++|
T Consensus 294 ~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~nl~ 373 (1186)
T KOG1117|consen 294 LNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAGNLP 373 (1186)
T ss_pred hccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccccCCC
Confidence 4678999999999999999999999999999999999999999999999995 99999999999999999999999998
Q ss_pred CCC------ChHHHHHHHHHHHhcCccccCC
Q 041407 85 PNF------DRSRIEKFIRTKYEERKWVQKG 109 (241)
Q Consensus 85 ~~~------d~~~re~fIraKYv~K~F~~~~ 109 (241)
++. ....|++||.+||.+.+|....
T Consensus 374 ~~e~lh~dssp~~r~~fi~~Kykeg~fRk~~ 404 (1186)
T KOG1117|consen 374 PNEHLHPDSSPSTRRQFIKEKYKEGKFRKEH 404 (1186)
T ss_pred CccccCCCCCcchhhhHHHHHhhcccccccc
Confidence 753 3446999999999999987653
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.59 E-value=1e-15 Score=146.89 Aligned_cols=109 Identities=29% Similarity=0.644 Sum_probs=100.5
Q ss_pred ChHhhhcCCCCCCCcCCCCCCC-CeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHH
Q 041407 1 ILEGLLKLPENRECADCGSKAP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFW 79 (241)
Q Consensus 1 il~~L~~~pgN~~CaDCgs~~P-~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~w 79 (241)
+||.|+++|+|++|++|.+..+ +|+++..|-|||..|+|.-|.|.. -+|||++.|..++..|+..++.+||+.+.++|
T Consensus 15 ~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQshgNq~~k~i~ 93 (524)
T KOG0702|consen 15 EIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSHGNQVCKEIW 93 (524)
T ss_pred HHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhcchhhhhhhh
Confidence 5899999999999999999887 999999999999999999999865 57999999999999999999999999999999
Q ss_pred Hhc-------CCCCCChHHHHHHHHHHHhcCccccCCC
Q 041407 80 EAE-------LPPNFDRSRIEKFIRTKYEERKWVQKGA 110 (241)
Q Consensus 80 Ea~-------lP~~~d~~~re~fIraKYv~K~F~~~~~ 110 (241)
.+. .|+..+....++||+.||+.|+|+.+..
T Consensus 94 fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n 131 (524)
T KOG0702|consen 94 FKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKN 131 (524)
T ss_pred hcchhhhhccCCCcccchhhHHHHhhhhccceeecCcc
Confidence 874 4677777889999999999999998754
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=93.03 E-value=0.022 Score=59.26 Aligned_cols=73 Identities=19% Similarity=0.228 Sum_probs=60.8
Q ss_pred cCCCCCCCcCCCCC-CCCeeEcccceeeehhchhhhhcCCCccceeeecccCCCChHHHHHHHhhCcHHHHHHHHh
Q 041407 7 KLPENRECADCGSK-APRWASVNLGIFICMQCSGIHRSLGVHISKVRSTTLDTWLPEQVAFMQSMGNEKSNKFWEA 81 (241)
Q Consensus 7 ~~pgN~~CaDCgs~-~P~was~n~GifvC~~CsgiHR~LG~hiSkVKSl~lD~Ws~~el~~mk~~GN~~aN~~wEa 81 (241)
..-.+..|++|++. ...|+++++.+-+|+.|+++|+.++.+.+...++.|++..+ +.+.-.-|+..++..+..
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~ 699 (785)
T KOG0521|consen 626 KASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATAS 699 (785)
T ss_pred HhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhh
Confidence 34457889999874 68899999999999999999999999999999999888776 777777777777766654
No 16
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=81.29 E-value=1.6 Score=28.15 Aligned_cols=34 Identities=12% Similarity=0.346 Sum_probs=29.2
Q ss_pred CCCCCcCCCCCCCCeeEcccceeeehhchhh-hhc
Q 041407 10 ENRECADCGSKAPRWASVNLGIFICMQCSGI-HRS 43 (241)
Q Consensus 10 gN~~CaDCgs~~P~was~n~GifvC~~Csgi-HR~ 43 (241)
.+..|..|+.....+-+.+-+.++|..|... |+.
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 3578999998888999999999999999998 876
No 17
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=79.54 E-value=1.1 Score=39.32 Aligned_cols=36 Identities=28% Similarity=0.470 Sum_probs=29.1
Q ss_pred HhhhcCCCCCCCcCCCCCCC-CeeEcccceeeehhch
Q 041407 3 EGLLKLPENRECADCGSKAP-RWASVNLGIFICMQCS 38 (241)
Q Consensus 3 ~~L~~~pgN~~CaDCgs~~P-~was~n~GifvC~~Cs 38 (241)
..+--.|.-..|+-||.+.. .|.+..-|.++|..|.
T Consensus 141 ~~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 141 AELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred HHcCCccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 33445667789999998754 7889999999999997
No 18
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=70.23 E-value=3.2 Score=36.29 Aligned_cols=38 Identities=32% Similarity=0.469 Sum_probs=29.7
Q ss_pred HhhhcCCCCCCCcCCCCCCC-CeeEcccceeeehhchhh
Q 041407 3 EGLLKLPENRECADCGSKAP-RWASVNLGIFICMQCSGI 40 (241)
Q Consensus 3 ~~L~~~pgN~~CaDCgs~~P-~was~n~GifvC~~Csgi 40 (241)
..+-=.|.-..|+.||..++ .+.+...|.++|..|...
T Consensus 139 ~~~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 139 QILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred HHcCCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 34445677789999998544 678999999999999764
No 19
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=70.12 E-value=2.6 Score=27.75 Aligned_cols=27 Identities=30% Similarity=0.719 Sum_probs=20.9
Q ss_pred CCcCCCCCCCCeeEcccceeeehhchhh
Q 041407 13 ECADCGSKAPRWASVNLGIFICMQCSGI 40 (241)
Q Consensus 13 ~CaDCgs~~P~was~n~GifvC~~Csgi 40 (241)
+|-.||+.. .-..-.-|-++|..|..|
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 689999977 455677899999999544
No 20
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=63.51 E-value=2.4 Score=27.35 Aligned_cols=27 Identities=22% Similarity=0.717 Sum_probs=16.7
Q ss_pred CCCcCCCCC-CCCeeEcccceeeehhch
Q 041407 12 RECADCGSK-APRWASVNLGIFICMQCS 38 (241)
Q Consensus 12 ~~CaDCgs~-~P~was~n~GifvC~~Cs 38 (241)
..|.+|+.+ .-+|..-+|+.-||..|.
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 479999987 677999999999999994
No 21
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=63.36 E-value=6 Score=25.58 Aligned_cols=27 Identities=33% Similarity=0.923 Sum_probs=22.8
Q ss_pred CCCCCcCCCCCCCCeeEcccceeeehhchh
Q 041407 10 ENRECADCGSKAPRWASVNLGIFICMQCSG 39 (241)
Q Consensus 10 gN~~CaDCgs~~P~was~n~GifvC~~Csg 39 (241)
.|..|..|++. |....=|-+.|..|..
T Consensus 7 ~~~~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 7 PNEPCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CCCcCCCCCCe---EeEccCCEEEhhhCce
Confidence 45679999997 8889999999999943
No 22
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=55.55 E-value=13 Score=25.69 Aligned_cols=37 Identities=27% Similarity=0.680 Sum_probs=30.2
Q ss_pred CCCCCcCCCCC-CCCeeEcccce-eeehhchhhhhcCCC
Q 041407 10 ENRECADCGSK-APRWASVNLGI-FICMQCSGIHRSLGV 46 (241)
Q Consensus 10 gN~~CaDCgs~-~P~was~n~Gi-fvC~~CsgiHR~LG~ 46 (241)
....|..|+.. .|.|=.-..|- ++|-.|.-..+..|.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 45789999975 68898888886 999999887777654
No 23
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=54.31 E-value=11 Score=24.10 Aligned_cols=32 Identities=28% Similarity=0.801 Sum_probs=23.2
Q ss_pred CcCCCCC-CCCeeEccccee-eehhchhhhhcCC
Q 041407 14 CADCGSK-APRWASVNLGIF-ICMQCSGIHRSLG 45 (241)
Q Consensus 14 CaDCgs~-~P~was~n~Gif-vC~~CsgiHR~LG 45 (241)
|..|+.. .|.|=....|-. ||-.|.-.+|..|
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8899976 799998888888 9999987776544
No 24
>cd01236 PH_outspread Outspread Pleckstrin homology (PH) domain. Outspread Pleckstrin homology (PH) domain. Outspread contains two PH domains and a C-terminal coiled-coil region. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=53.33 E-value=5.3 Score=31.53 Aligned_cols=62 Identities=16% Similarity=0.087 Sum_probs=39.8
Q ss_pred hcCCCCcccccchhHHHhhhhhhccCCCCCCCCCCCCCccccccCCCCCCCCCCCCceeEeeccCC
Q 041407 132 KRGIPRKTRTLSLEEEILTKHIAQIAPPPTVGRSRGGSLDMNEKAAAPIPPRVPPSVAEVQVPTNN 197 (241)
Q Consensus 132 k~~~~~k~r~l~~~~~~~~~~~~~~~p~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 (241)
.....+|.|+..|.+..+ + .+.........+-|+|||++...+.....+-+..++|.+.||.
T Consensus 19 ~~~K~WkrRWFvL~~~~~---L-~y~~d~~~~~~p~G~IdL~~~~~V~~~~~~~~~~~~f~I~tp~ 80 (104)
T cd01236 19 HRSKRWQRRWFILYDHGL---L-TYALDEMPTTLPQGTIDMNQCTDVVDAEARTGQKFSICILTPD 80 (104)
T ss_pred eeeccccceEEEEeCCCE---E-EEeeCCCCCcccceEEEccceEEEeecccccCCccEEEEECCC
Confidence 345678899999964322 2 3432221345666999999988776555555556778777664
No 25
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=52.30 E-value=6.7 Score=35.32 Aligned_cols=35 Identities=34% Similarity=0.696 Sum_probs=28.5
Q ss_pred hhhcCCCCCCCcCCCCCC-CCeeEcccceeeehhch
Q 041407 4 GLLKLPENRECADCGSKA-PRWASVNLGIFICMQCS 38 (241)
Q Consensus 4 ~L~~~pgN~~CaDCgs~~-P~was~n~GifvC~~Cs 38 (241)
.+-=.|.=..|+.||.+. |...+.-.|-++|..|+
T Consensus 147 ~~G~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 147 ELGIGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HcCCccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 333455567899999985 57999999999999998
No 26
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=51.33 E-value=11 Score=28.40 Aligned_cols=31 Identities=23% Similarity=0.645 Sum_probs=26.2
Q ss_pred CCCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 10 ENRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 10 gN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
+|..|.=||.+.. ...||+..|..|.+..|.
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 5778999998665 469999999999998875
No 27
>cd01264 PH_melted Melted pleckstrin homology (PH) domain. Melted pleckstrin homology (PH) domain. The melted protein has a C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=49.80 E-value=6.5 Score=31.01 Aligned_cols=58 Identities=14% Similarity=0.114 Sum_probs=36.8
Q ss_pred CCCcccccchhHHHhhhhhhccCCCCCCCCCCCCCccccccCCCCCCCCCC---CCceeEeeccCC
Q 041407 135 IPRKTRTLSLEEEILTKHIAQIAPPPTVGRSRGGSLDMNEKAAAPIPPRVP---PSVAEVQVPTNN 197 (241)
Q Consensus 135 ~~~k~r~l~~~~~~~~~~~~~~~p~~~~~~~~~~s~~~~~~~~~~~~~~~~---~~~~~~~~~~~~ 197 (241)
..++.|+..|....+ . +......+...-|+|||++...+.+..+.. +.+++|.+.||.
T Consensus 17 K~WkrRwF~L~~~~L----~-y~K~~~~~~~~~g~IdL~~~~sVk~~~~~~~~~~~~~~Fei~tp~ 77 (101)
T cd01264 17 KRWKTRYFTLSGAQL----L-FQKGKSKDDPDDCSIDLSKIRSVKAVAKKRRDRSLPKAFEIFTAD 77 (101)
T ss_pred ecceeEEEEEeCCEE----E-EEeccCccCCCCceEEcccceEEeeccccccccccCcEEEEEcCC
Confidence 356689999976533 3 333322333334899999999876554322 446899998764
No 28
>cd01251 PH_centaurin_alpha Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specifici
Probab=47.97 E-value=14 Score=28.47 Aligned_cols=36 Identities=14% Similarity=0.230 Sum_probs=24.8
Q ss_pred CCCcccccchhHHHhhhhhhccCCCCCCCCCCCCCccccccC
Q 041407 135 IPRKTRTLSLEEEILTKHIAQIAPPPTVGRSRGGSLDMNEKA 176 (241)
Q Consensus 135 ~~~k~r~l~~~~~~~~~~~~~~~p~~~~~~~~~~s~~~~~~~ 176 (241)
..+|.|+..|.+. .+.++.-+ ....+.|+|+|..+.
T Consensus 14 k~wkkRwFvL~~~----~L~Yyk~~--~d~~~~G~I~L~~~~ 49 (103)
T cd01251 14 EGFKKRWFTLDDR----RLMYFKDP--LDAFAKGEVFLGSQE 49 (103)
T ss_pred CCceeEEEEEeCC----EEEEECCC--CCcCcCcEEEeeccc
Confidence 3478999999754 34444444 456788999998764
No 29
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=44.65 E-value=15 Score=27.75 Aligned_cols=31 Identities=23% Similarity=0.652 Sum_probs=25.8
Q ss_pred CCCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 10 ENRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 10 gN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
..+.|.=||.+.. ...||+..|..|.+..|.
T Consensus 2 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 4567999998765 458999999999998875
No 30
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=43.01 E-value=18 Score=28.08 Aligned_cols=32 Identities=31% Similarity=0.750 Sum_probs=26.5
Q ss_pred CCCCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 9 PENRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 9 pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
..+..|.=||.+... ..||+..|..|.+..|.
T Consensus 3 ~~~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 3 IEVIPCKICGDKSSG---IHYGVITCEGCKGFFRR 34 (95)
T ss_pred ccccCCcccCCcCcc---eEECceeehhhHHhhHH
Confidence 356789999987654 58999999999999875
No 31
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=42.65 E-value=18 Score=28.48 Aligned_cols=31 Identities=32% Similarity=0.788 Sum_probs=26.1
Q ss_pred CCCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 10 ENRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 10 gN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
++..|.=||.+.. ...||+..|..|.+..|.
T Consensus 17 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKAS---GFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCc---ceEECcceehhhhhhhhh
Confidence 5678999998765 459999999999998875
No 32
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=41.78 E-value=18 Score=28.26 Aligned_cols=30 Identities=27% Similarity=0.670 Sum_probs=24.8
Q ss_pred CCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 11 NRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 11 N~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
+..|.=||.+.. ...||+..|..|.+..|.
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 357999998765 458999999999999875
No 33
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=41.25 E-value=11 Score=24.16 Aligned_cols=30 Identities=23% Similarity=0.527 Sum_probs=15.1
Q ss_pred CCCcCCCCCCCCeeEc---ccceeeehhchhhhh
Q 041407 12 RECADCGSKAPRWASV---NLGIFICMQCSGIHR 42 (241)
Q Consensus 12 ~~CaDCgs~~P~was~---n~GifvC~~CsgiHR 42 (241)
+.|-.||.+ .++... +.-=++|..|.-||-
T Consensus 1 kfC~~CG~~-l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGP-LERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccCh-hhhhcCCCCCccceECCCCCCEEe
Confidence 468889886 222222 445578999988883
No 34
>PRK12495 hypothetical protein; Provisional
Probab=41.08 E-value=17 Score=32.75 Aligned_cols=30 Identities=27% Similarity=0.507 Sum_probs=24.4
Q ss_pred cCCCCCCCcCCCCCCCCeeEcccceeeehhchhh
Q 041407 7 KLPENRECADCGSKAPRWASVNLGIFICMQCSGI 40 (241)
Q Consensus 7 ~~pgN~~CaDCgs~~P~was~n~GifvC~~Csgi 40 (241)
....+..|-+||.+=|.. -|+.+|..|..+
T Consensus 38 atmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 38 ATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred cccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 356789999999998832 699999999754
No 35
>cd01260 PH_CNK Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK is believed to regulate the activity and the subcellular localization of RAS activated RAF. CNK is composed of N-terminal SAM and PDZ domains along with a central or C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskelet
Probab=39.16 E-value=11 Score=28.11 Aligned_cols=54 Identities=11% Similarity=-0.025 Sum_probs=36.2
Q ss_pred CCcccccchhHHHhhhhhhccCCCCCCCCCCCCCccccccCCCCCCCCCCCCceeEeeccCC
Q 041407 136 PRKTRTLSLEEEILTKHIAQIAPPPTVGRSRGGSLDMNEKAAAPIPPRVPPSVAEVQVPTNN 197 (241)
Q Consensus 136 ~~k~r~l~~~~~~~~~~~~~~~p~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 (241)
.++.|+..|.+..+ .+...+ ....+.|.|+|.... +..+.+.. +.++|.+.+++
T Consensus 19 ~WkkrwfvL~~~~L-----~yyk~~-~~~~~~~~I~L~~~~-v~~~~~~~-k~~~F~I~~~~ 72 (96)
T cd01260 19 KWARRWFVLKGTTL-----YWYRSK-QDEKAEGLIFLSGFT-IESAKEVK-KKYAFKVCHPV 72 (96)
T ss_pred CceeEEEEEECCEE-----EEECCC-CCCccceEEEccCCE-EEEchhcC-CceEEEECCCC
Confidence 78899999976533 444443 556678999998753 32333333 77899997654
No 36
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=38.38 E-value=23 Score=32.82 Aligned_cols=35 Identities=23% Similarity=0.509 Sum_probs=24.9
Q ss_pred cCCCCCCCcCCCCCCCCeeEcccceeeehhchhhhh
Q 041407 7 KLPENRECADCGSKAPRWASVNLGIFICMQCSGIHR 42 (241)
Q Consensus 7 ~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR 42 (241)
.......|.+||+... =....-|-.||.+|.-|..
T Consensus 7 ~~~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 7 EEEEKLVCPECGSDKL-IYDYERGEIVCADCGLVIE 41 (310)
T ss_pred hcccCCcCcCCCCCCe-eEECCCCeEeecccCCccc
Confidence 3445578999997432 2345779999999988653
No 37
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=38.32 E-value=9.2 Score=27.56 Aligned_cols=35 Identities=34% Similarity=0.666 Sum_probs=23.2
Q ss_pred cCCCCCCCcCCCCCCCCee-Ecccceeeehhchhhh
Q 041407 7 KLPENRECADCGSKAPRWA-SVNLGIFICMQCSGIH 41 (241)
Q Consensus 7 ~~pgN~~CaDCgs~~P~wa-s~n~GifvC~~CsgiH 41 (241)
..++...|.|||.+=|.=- -.--|+..|+.|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREALPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhhcCCcCCcHHHHhhc
Confidence 4566789999998744211 1234778899997654
No 38
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=35.46 E-value=19 Score=27.88 Aligned_cols=29 Identities=31% Similarity=0.712 Sum_probs=23.7
Q ss_pred CCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 12 RECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 12 ~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
+.|.=||.+... ..||+..|..|.+..|.
T Consensus 1 ~~C~VCg~~a~g---~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 1 KICGVCGDKALG---YNFNAITCESCKAFFRR 29 (94)
T ss_pred CCCeeCCCcCcc---eEECcceeeeehheehh
Confidence 358889886654 48999999999998875
No 39
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=34.02 E-value=26 Score=24.80 Aligned_cols=27 Identities=22% Similarity=0.685 Sum_probs=22.4
Q ss_pred CCCCcCCCCCCCCeeEcccceeeehhchh
Q 041407 11 NRECADCGSKAPRWASVNLGIFICMQCSG 39 (241)
Q Consensus 11 N~~CaDCgs~~P~was~n~GifvC~~Csg 39 (241)
-+.|..||..... ..+-.+|.|..|.-
T Consensus 28 Sq~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 28 SQTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccCccccccc--ccccceEEcCCCCC
Confidence 4789999998877 77888999999844
No 40
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=33.74 E-value=30 Score=26.63 Aligned_cols=29 Identities=28% Similarity=0.721 Sum_probs=23.7
Q ss_pred CCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 12 RECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 12 ~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
..|.=||.+.. ...||++.|..|.+..|.
T Consensus 2 ~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 2 ELCLVCGDRAS---GYHYNALTCEGCKGFFRR 30 (91)
T ss_pred CCCeeCCCcCc---ceEECceeehhhHHHHHH
Confidence 35888998766 459999999999998875
No 41
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=32.66 E-value=31 Score=26.46 Aligned_cols=32 Identities=34% Similarity=0.862 Sum_probs=26.3
Q ss_pred CCCCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 9 PENRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 9 pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
.++..|.=||.+.. ...||+..|..|.+..|.
T Consensus 4 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRAT---GLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcCc---ceEECcceehhhHHHHHH
Confidence 45678999998665 458999999999998875
No 42
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=32.64 E-value=31 Score=25.70 Aligned_cols=29 Identities=21% Similarity=0.649 Sum_probs=23.9
Q ss_pred CCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 12 RECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 12 ~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
..|.=||.+.. ...||+..|..|.+..|.
T Consensus 3 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 3 KICLVCSDEAS---GCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 46888998665 459999999999998875
No 43
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=32.57 E-value=6.3 Score=24.98 Aligned_cols=29 Identities=28% Similarity=0.696 Sum_probs=16.0
Q ss_pred CCcCCCCCCCC-eeEcccceeeehhchhhh
Q 041407 13 ECADCGSKAPR-WASVNLGIFICMQCSGIH 41 (241)
Q Consensus 13 ~CaDCgs~~P~-was~n~GifvC~~CsgiH 41 (241)
.|.+||.+=|. =.-+--+..+|..|+..|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 48999975221 111223777899998765
No 44
>cd01238 PH_Tec Tec pleckstrin homology (PH) domain. Tec pleckstrin homology (PH) domain. Proteins in the Tec family of cytoplasmic protein tyrosine kinases that includes Bruton's tyrosine kinase (BTK), BMX, IL2-inducible T-cell kinase (Itk) and Tec. These proteins generally have an N-terminal PH domain, followed by a Tek homology (TH) domain, a SH3 domain, a SH2 domain and a kinase domain. Tec PH domains tether these proteins to membranes following the activation of PI3K and its subsequent phosphorylation of phosphoinositides. The importance of PH domain membrane anchoring is confirmed by the discovery of a mutation of a critical arginine residue in the BTK PH domain, which causes X-linked agammaglobulinemia (XLA) in humans and a related disorder is mice. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few dis
Probab=32.53 E-value=20 Score=27.87 Aligned_cols=58 Identities=16% Similarity=0.114 Sum_probs=34.2
Q ss_pred CCCcccccchhHHHhhhhhhccCCCCCCCCCCCCCccccccCCCCCCCCCC------CCceeEeeccC
Q 041407 135 IPRKTRTLSLEEEILTKHIAQIAPPPTVGRSRGGSLDMNEKAAAPIPPRVP------PSVAEVQVPTN 196 (241)
Q Consensus 135 ~~~k~r~l~~~~~~~~~~~~~~~p~~~~~~~~~~s~~~~~~~~~~~~~~~~------~~~~~~~~~~~ 196 (241)
..+|.|+..|++. .+.++...+.....+-|+|||.....+....+.. ...++|.+-|+
T Consensus 19 ~nwKkRwFvL~~~----~L~Yyk~~~~~~~~~kG~I~L~~~~~ve~~~~~~~~~~~~~~~~~F~i~t~ 82 (106)
T cd01238 19 LNYKERLFVLTKS----KLSYYEGDFEKRGSKKGSIDLSKIKCVETVKPEKNPPIPERFKYPFQVVHD 82 (106)
T ss_pred CCceeEEEEEcCC----EEEEECCCcccccCcceeEECCcceEEEEecCCcCcccccccCccEEEEeC
Confidence 3788999999754 3455555432234566999999875543222221 13466766553
No 45
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=32.00 E-value=34 Score=26.65 Aligned_cols=32 Identities=22% Similarity=0.580 Sum_probs=24.5
Q ss_pred cCCCCCCCcCCCCCCCCeeEcccceeeehhchhh
Q 041407 7 KLPENRECADCGSKAPRWASVNLGIFICMQCSGI 40 (241)
Q Consensus 7 ~~pgN~~CaDCgs~~P~was~n~GifvC~~Csgi 40 (241)
+...--.|-.|+.+ .---+..||+.|..|...
T Consensus 31 ~~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 31 QQRAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred HHhcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 33455689999998 455678999999999653
No 46
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=31.94 E-value=24 Score=25.64 Aligned_cols=23 Identities=26% Similarity=0.702 Sum_probs=14.3
Q ss_pred CCCcCCCCCCCCeeEcccceeeehhc
Q 041407 12 RECADCGSKAPRWASVNLGIFICMQC 37 (241)
Q Consensus 12 ~~CaDCgs~~P~was~n~GifvC~~C 37 (241)
-+|+|||+.+. --.--++-|-+|
T Consensus 21 YiCgdC~~en~---lk~~D~irCReC 43 (62)
T KOG3507|consen 21 YICGDCGQENT---LKRGDVIRCREC 43 (62)
T ss_pred EEecccccccc---ccCCCcEehhhc
Confidence 36888888754 112345677777
No 47
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=31.79 E-value=33 Score=26.06 Aligned_cols=28 Identities=29% Similarity=0.749 Sum_probs=22.8
Q ss_pred CCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 13 ECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 13 ~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
.|.=||.+... ..||+..|..|++..|.
T Consensus 1 ~C~VCg~~~~g---~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRATG---YHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCcc---eEECcceehhhHHHHHh
Confidence 37778877664 48999999999998875
No 48
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=30.06 E-value=30 Score=23.55 Aligned_cols=26 Identities=31% Similarity=0.744 Sum_probs=19.2
Q ss_pred CCcCCCCCCCCeeEcccceeeehhchh
Q 041407 13 ECADCGSKAPRWASVNLGIFICMQCSG 39 (241)
Q Consensus 13 ~CaDCgs~~P~was~n~GifvC~~Csg 39 (241)
.|.=|+...+. .-.=+|.|+|.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 47778887766 344579999999954
No 49
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=30.03 E-value=39 Score=25.00 Aligned_cols=28 Identities=32% Similarity=0.870 Sum_probs=23.1
Q ss_pred CCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 13 ECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 13 ~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
.|.=||.+... ..||+..|..|.+..|.
T Consensus 2 ~C~VC~~~~~g---~hygv~sC~aC~~FFRR 29 (77)
T cd06956 2 ICAICGDRASG---KHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCcccCCcCcc---eEECceeehhHHHHHHH
Confidence 47788876654 59999999999998875
No 50
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=29.89 E-value=23 Score=27.22 Aligned_cols=30 Identities=30% Similarity=0.832 Sum_probs=25.4
Q ss_pred CCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 11 NRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 11 N~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|..|.=||.+... ..||+..|..|.+..|.
T Consensus 6 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 6 DIPCKVCGDRSSG---KHYGIYACDGCSGFFKR 35 (92)
T ss_pred CCCCcccCCcCcc---cEECceeeeeeeeEEee
Confidence 7789999987664 59999999999998875
No 51
>PF04189 Gcd10p: Gcd10p family; InterPro: IPR007316 eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit of eIF3 [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation
Probab=29.69 E-value=49 Score=30.95 Aligned_cols=46 Identities=15% Similarity=0.231 Sum_probs=28.5
Q ss_pred CCCChHHHHHHHhhCcHHHHHHHHhcCCCCCChHHHHHHHHHHHhcC
Q 041407 57 DTWLPEQVAFMQSMGNEKSNKFWEAELPPNFDRSRIEKFIRTKYEER 103 (241)
Q Consensus 57 D~Ws~~el~~mk~~GN~~aN~~wEa~lP~~~d~~~re~fIraKYv~K 103 (241)
.+.+.+||+.|+.-|-. +.++-++-+-.+..-..|-+|=++||.+|
T Consensus 106 QkLt~eeIe~LK~~g~s-g~eII~kLiens~tF~~KT~FSqeKYlkr 151 (299)
T PF04189_consen 106 QKLTQEEIEELKKEGVS-GEEIIEKLIENSSTFDKKTEFSQEKYLKR 151 (299)
T ss_pred ccCCHHHHHHHHHcCCC-HHHHHHHHHHhccchhhhhHHHHHHHHHH
Confidence 34778999999987544 55555554433333344667777777653
No 52
>cd01265 PH_PARIS-1 PARIS-1 pleckstrin homology (PH) domain. PARIS-1 pleckstrin homology (PH) domain. PARIS-1 contains a PH domain and a TBC-type GTPase catalytic domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=28.99 E-value=30 Score=26.24 Aligned_cols=55 Identities=15% Similarity=0.175 Sum_probs=33.3
Q ss_pred CCCcccccchhHHHhhhhhhccCCCCCCCCCCCCCccccccCCCCCCCCCCCCceeEeeccC
Q 041407 135 IPRKTRTLSLEEEILTKHIAQIAPPPTVGRSRGGSLDMNEKAAAPIPPRVPPSVAEVQVPTN 196 (241)
Q Consensus 135 ~~~k~r~l~~~~~~~~~~~~~~~p~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (241)
..++.|+..|++.. ..+..+..+ .+..+-|+|||.....+..+.+ ....|.+.|+
T Consensus 15 K~WkkRWFvL~~~~--~~L~Yyk~~--~d~~p~G~I~L~~~~~~~~~~~---~~~~F~i~t~ 69 (95)
T cd01265 15 RGRRSRWFALDDRT--CYLYYYKDS--QDAKPLGRVDLSGAAFTYDPRE---EKGRFEIHSN 69 (95)
T ss_pred cCceeEEEEEcCCC--cEEEEECCC--CcccccceEECCccEEEcCCCC---CCCEEEEEcC
Confidence 46779999996431 124455444 5667889999998654422222 2356776654
No 53
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=28.84 E-value=32 Score=28.73 Aligned_cols=28 Identities=25% Similarity=0.743 Sum_probs=20.5
Q ss_pred CCCCCCCcCCCCCCCCeeEcccceeeehhchhhhhcC
Q 041407 8 LPENRECADCGSKAPRWASVNLGIFICMQCSGIHRSL 44 (241)
Q Consensus 8 ~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~L 44 (241)
..+...|.-||. .+|+ +|..|.|-|+.+
T Consensus 96 ~~~~~~C~~Cgg--~rfv-------~C~~C~Gs~k~~ 123 (147)
T cd03031 96 RAGGGVCEGCGG--ARFV-------PCSECNGSCKVF 123 (147)
T ss_pred ccCCCCCCCCCC--cCeE-------ECCCCCCcceEE
Confidence 345567888884 3454 999999999874
No 54
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=28.81 E-value=47 Score=22.01 Aligned_cols=32 Identities=25% Similarity=0.642 Sum_probs=24.1
Q ss_pred hcCCCCCCCcCCCCCCCCeeEcccceeeehhch
Q 041407 6 LKLPENRECADCGSKAPRWASVNLGIFICMQCS 38 (241)
Q Consensus 6 ~~~pgN~~CaDCgs~~P~was~n~GifvC~~Cs 38 (241)
++.|+.-+|.-||+....+. -+.+.+-|-.|.
T Consensus 13 ~RW~~g~~CP~Cg~~~~~~~-~~~~~~~C~~C~ 44 (46)
T PF12760_consen 13 IRWPDGFVCPHCGSTKHYRL-KTRGRYRCKACR 44 (46)
T ss_pred hcCCCCCCCCCCCCeeeEEe-CCCCeEECCCCC
Confidence 46777789999999855443 336999999884
No 55
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=28.42 E-value=33 Score=24.99 Aligned_cols=27 Identities=37% Similarity=0.901 Sum_probs=21.3
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+... ..||++.|..|.+..|.
T Consensus 1 C~VCg~~~~g---~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKASG---FHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCcc---eEECcchhhHHHHHHhh
Confidence 5557766553 58999999999999875
No 56
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=28.05 E-value=26 Score=26.46 Aligned_cols=27 Identities=37% Similarity=0.910 Sum_probs=22.2
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||..... ..||++.|..|.+..|.
T Consensus 2 C~VCg~~~~g---~hyGv~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKASG---FHYGVHACEGCKGFFRR 28 (84)
T ss_pred CcccCccCcc---eEEChhhhhhhhhheee
Confidence 7778876654 47999999999999875
No 57
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=27.84 E-value=37 Score=24.75 Aligned_cols=27 Identities=30% Similarity=0.823 Sum_probs=21.3
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+... ..||+..|..|.+..|.
T Consensus 1 C~VC~~~~~g---~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRATG---YHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCcc---cEECcceehhhhhhhch
Confidence 5557766654 48999999999998875
No 58
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=27.68 E-value=41 Score=24.67 Aligned_cols=27 Identities=26% Similarity=0.762 Sum_probs=21.1
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+.. ...||++.|..|.+..|.
T Consensus 1 C~VCg~~a~---~~hygv~sC~aCk~FFRR 27 (73)
T cd06963 1 CLICGDEAS---GCHYGVLTCGSCKVFFKR 27 (73)
T ss_pred CcccCccCc---ceEECceeehhhhHhHHH
Confidence 455776554 458999999999998875
No 59
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=27.24 E-value=24 Score=24.41 Aligned_cols=30 Identities=30% Similarity=0.695 Sum_probs=19.5
Q ss_pred CCcCCCCCCCCee--Ecccceeeehhchhhhhc
Q 041407 13 ECADCGSKAPRWA--SVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 13 ~CaDCgs~~P~wa--s~n~GifvC~~CsgiHR~ 43 (241)
.|+=||..-.-.- -+.=| +||.+|..--..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~ 32 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSG 32 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcC
Confidence 4788887644333 34557 899999864333
No 60
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=27.20 E-value=43 Score=24.59 Aligned_cols=27 Identities=33% Similarity=0.898 Sum_probs=21.2
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+... ..||+..|..|.+..|.
T Consensus 1 C~VCg~~~~g---~hygv~sC~aC~~FFRR 27 (74)
T cd07179 1 CRVCGGKSSG---FHFGALTCEGCKGFFRR 27 (74)
T ss_pred CcccCccCcc---eEECceeehhHHHHHHH
Confidence 5557766553 58999999999998875
No 61
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=27.18 E-value=30 Score=27.56 Aligned_cols=30 Identities=30% Similarity=0.767 Sum_probs=25.1
Q ss_pred CCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 11 NRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 11 N~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
...|.=||..... ..||+..|..|.+..|.
T Consensus 6 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 6 PRICGVCGDRATG---FHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCeecCCcCcc---cEECcceeeeecceecc
Confidence 3679999987664 59999999999998875
No 62
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=26.47 E-value=31 Score=26.41 Aligned_cols=30 Identities=33% Similarity=0.744 Sum_probs=24.6
Q ss_pred CCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 11 NRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 11 N~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
+..|.=||.+... ..||++.|..|.+..|.
T Consensus 3 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 32 (89)
T cd07166 3 VVLCKVCGDKASG---FHYGVHACEGCKGFFRR 32 (89)
T ss_pred CCCCcccCccCcc---eEEChhhhhhHhhEecc
Confidence 4569999987664 47999999999998875
No 63
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=26.32 E-value=44 Score=22.02 Aligned_cols=22 Identities=27% Similarity=0.760 Sum_probs=15.9
Q ss_pred CCcCCCCCCCCeeEcccceeee
Q 041407 13 ECADCGSKAPRWASVNLGIFIC 34 (241)
Q Consensus 13 ~CaDCgs~~P~was~n~GifvC 34 (241)
+|.+|+..+.-|+++.-|-..|
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcCCeEEecCCCCccc
Confidence 5999998877776666555555
No 64
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=26.17 E-value=13 Score=30.27 Aligned_cols=31 Identities=19% Similarity=0.553 Sum_probs=20.0
Q ss_pred CCCcCCCCCCC-CeeEcccceeeehhchhhhh
Q 041407 12 RECADCGSKAP-RWASVNLGIFICMQCSGIHR 42 (241)
Q Consensus 12 ~~CaDCgs~~P-~was~n~GifvC~~CsgiHR 42 (241)
..|.+||.+=| .=.-.--+..+|+.|...|-
T Consensus 81 G~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E 112 (120)
T COG1734 81 GICEECGEPIPEARLEARPTARLCIECQERAE 112 (120)
T ss_pred cchhccCCcCCHHHHhhCcchHHHHHHHHHHH
Confidence 37999998732 11122235678999988764
No 65
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=26.13 E-value=37 Score=25.40 Aligned_cols=27 Identities=37% Similarity=0.877 Sum_probs=21.4
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 1 C~VCg~~~~---g~hyG~~sC~aC~~FFRR 27 (81)
T cd07165 1 CKVCGDKAS---GYHYGVTSCEGCKGFFRR 27 (81)
T ss_pred CCccCccCc---ceEECchhhhhHHHHHHh
Confidence 555777655 359999999999998885
No 66
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=26.12 E-value=47 Score=25.44 Aligned_cols=31 Identities=29% Similarity=0.746 Sum_probs=25.2
Q ss_pred CCCCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 10 ENRECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 10 gN~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
....|.=||.+.. ...||+..|..|.+..|.
T Consensus 5 ~~~~C~VCg~~~~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 5 SPKLCSICEDKAT---GLHYGIITCEGCKGFFKR 35 (90)
T ss_pred cCCCCcccCCcCc---ceEECceehhhhhHhhhh
Confidence 3457889998665 459999999999998875
No 67
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=26.10 E-value=36 Score=25.04 Aligned_cols=27 Identities=26% Similarity=0.711 Sum_probs=21.3
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 1 C~VC~~~~~---g~hygv~sC~aCk~FFRR 27 (75)
T cd07155 1 CLVCGDIAS---GYHYGVASCEACKAFFKR 27 (75)
T ss_pred CcccCccCc---ceEEChhhhhhhHHHHHH
Confidence 556776655 459999999999998865
No 68
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=25.82 E-value=45 Score=26.20 Aligned_cols=34 Identities=26% Similarity=0.607 Sum_probs=23.8
Q ss_pred hcCCCCCCCcCCCCCC--------CCe---------eEcccceeeehhchh
Q 041407 6 LKLPENRECADCGSKA--------PRW---------ASVNLGIFICMQCSG 39 (241)
Q Consensus 6 ~~~pgN~~CaDCgs~~--------P~w---------as~n~GifvC~~Csg 39 (241)
.+.++--.|++||.+- .++ ++=.||-.+|..|..
T Consensus 29 kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 29 KKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 4667778999999751 111 234689999999964
No 69
>PRK11019 hypothetical protein; Provisional
Probab=25.44 E-value=18 Score=28.09 Aligned_cols=37 Identities=24% Similarity=0.569 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCC--CeeEcccceeeehhchhhhhcCCCc
Q 041407 10 ENRECADCGSKAP--RWASVNLGIFICMQCSGIHRSLGVH 47 (241)
Q Consensus 10 gN~~CaDCgs~~P--~was~n~GifvC~~CsgiHR~LG~h 47 (241)
.-..|.|||.+=| ++.- --++..|+.|...+-..+.+
T Consensus 35 syg~C~~CG~~Ip~~Rl~A-~P~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 35 SLTECEECGEPIPEARRKA-IPGVRLCVACQQEKDLQQAA 73 (88)
T ss_pred cCCeeCcCCCcCcHHHHhh-cCCccccHHHHHHHHHHHhH
Confidence 4579999999744 2322 23778999999987655443
No 70
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=25.31 E-value=48 Score=23.64 Aligned_cols=28 Identities=29% Similarity=0.787 Sum_probs=21.2
Q ss_pred CCCcCCCCCCCCeeEcccceeeehhchhhhh
Q 041407 12 RECADCGSKAPRWASVNLGIFICMQCSGIHR 42 (241)
Q Consensus 12 ~~CaDCgs~~P~was~n~GifvC~~CsgiHR 42 (241)
+.|.=||.+.. ...||+..|..|...=|
T Consensus 1 ~~C~VCg~~~~---~~~ygv~sC~~C~~FFr 28 (70)
T PF00105_consen 1 KKCKVCGDPAS---GYHYGVLSCNACKMFFR 28 (70)
T ss_dssp -BSTTTSSBES---EEETTEEEEHHHHHHHH
T ss_pred CCCeECCCccC---cccccccccccceeeee
Confidence 36888887554 56999999999998443
No 71
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.16 E-value=29 Score=27.65 Aligned_cols=33 Identities=18% Similarity=0.289 Sum_probs=23.3
Q ss_pred hcCCCCCCCcCCCCCCCCeeEcccceeeehhchhhh
Q 041407 6 LKLPENRECADCGSKAPRWASVNLGIFICMQCSGIH 41 (241)
Q Consensus 6 ~~~pgN~~CaDCgs~~P~was~n~GifvC~~CsgiH 41 (241)
...|..-.|.+||.. +....+..+.|..|.+..
T Consensus 65 ~~~p~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 65 EEQEAECWCETCQQY---VTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred EeeCcEEEcccCCCe---eecCCccCCcCcCcCCCC
Confidence 356788899999953 333345557899998754
No 72
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=24.79 E-value=32 Score=26.10 Aligned_cols=28 Identities=25% Similarity=0.730 Sum_probs=23.0
Q ss_pred CCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 13 ECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 13 ~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
.|.=||.+.. ...||+..|..|.+..|.
T Consensus 2 ~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPAA---GFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcCc---ccEECcceeeEeeeEEec
Confidence 4888887665 459999999999998875
No 73
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=24.73 E-value=48 Score=23.11 Aligned_cols=33 Identities=27% Similarity=0.740 Sum_probs=26.0
Q ss_pred CCcCCCCC-CCCeeEcc-cceeeehhchhhhhcCC
Q 041407 13 ECADCGSK-APRWASVN-LGIFICMQCSGIHRSLG 45 (241)
Q Consensus 13 ~CaDCgs~-~P~was~n-~GifvC~~CsgiHR~LG 45 (241)
.|..|+.. -|.|=.-. -+..+|-.|..-.+..|
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999975 57787665 78899999977666665
No 74
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=24.69 E-value=36 Score=20.50 Aligned_cols=28 Identities=14% Similarity=0.472 Sum_probs=17.6
Q ss_pred CCCcCCCCCCCCeeEcccceeeehhchh
Q 041407 12 RECADCGSKAPRWASVNLGIFICMQCSG 39 (241)
Q Consensus 12 ~~CaDCgs~~P~was~n~GifvC~~Csg 39 (241)
+.|.-|+..-+.-..-....++|..|..
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 4678888876666666778899999864
No 75
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=24.26 E-value=41 Score=24.56 Aligned_cols=27 Identities=30% Similarity=0.826 Sum_probs=21.2
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 1 C~VCg~~~~---g~hygv~sC~aC~~FFRR 27 (73)
T cd06958 1 CVVCGDKSS---GKHYGQFTCEGCKSFFKR 27 (73)
T ss_pred CCccCccCc---ceEEChhhhhhhhhhhhh
Confidence 555776655 358999999999998875
No 76
>KOG1416 consensus tRNA(1-methyladenosine) methyltransferase, subunit GCD10 [Translation, ribosomal structure and biogenesis]
Probab=23.37 E-value=66 Score=32.02 Aligned_cols=43 Identities=16% Similarity=0.135 Sum_probs=27.0
Q ss_pred CChHHHHHHHhhCcHHHHHHHHhcCCCCCChHHHHHHHHHHHhc
Q 041407 59 WLPEQVAFMQSMGNEKSNKFWEAELPPNFDRSRIEKFIRTKYEE 102 (241)
Q Consensus 59 Ws~~el~~mk~~GN~~aN~~wEa~lP~~~d~~~re~fIraKYv~ 102 (241)
.+.|||+.|+..|+. +.++-++-.-.+..-.+|-.|-+.||+.
T Consensus 115 Lt~EeI~~mr~eg~~-g~EiI~kLienSkTF~~KT~fSQeKYv~ 157 (475)
T KOG1416|consen 115 LTQEEIEEMRQEGLS-GEEIIEKLIENSKTFHNKTVFSQEKYVL 157 (475)
T ss_pred CCHHHHHHHHHhccC-HHHHHHHHHhcCcccccchhhhHHHHHH
Confidence 678999999998887 4555555332222223456666667754
No 77
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.34 E-value=40 Score=20.69 Aligned_cols=25 Identities=32% Similarity=0.786 Sum_probs=12.9
Q ss_pred CCCCCcCCCCC----CCCeeEcccceeeehhchhh
Q 041407 10 ENRECADCGSK----APRWASVNLGIFICMQCSGI 40 (241)
Q Consensus 10 gN~~CaDCgs~----~P~was~n~GifvC~~Csgi 40 (241)
.++.|.-||++ .-.|+ .+|..|...
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~------r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWA------RRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-------EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCE------eECCCCcCE
Confidence 37899999986 22343 577777543
No 78
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=23.30 E-value=52 Score=24.01 Aligned_cols=27 Identities=37% Similarity=0.950 Sum_probs=21.7
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 2 C~vCg~~~~---~~hygv~sC~aC~~FFRR 28 (73)
T cd06959 2 CVVCGDKAS---GFHYGVLSCEGCKGFFRR 28 (73)
T ss_pred CceeCCcCc---ceEECceeehhhHHHHHH
Confidence 666777655 459999999999998875
No 79
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=22.34 E-value=38 Score=25.62 Aligned_cols=28 Identities=32% Similarity=0.746 Sum_probs=23.1
Q ss_pred CCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 13 ECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 13 ~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
.|.=||.+... ..||+..|..|.+..|.
T Consensus 3 ~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 30 (84)
T cd06962 3 LCVVCGDKASG---YHYNALTCEGCKGFFRR 30 (84)
T ss_pred CCeecCCcCcc---eEECcceeecceeeeee
Confidence 48888876664 59999999999998874
No 80
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=22.31 E-value=43 Score=24.56 Aligned_cols=27 Identities=37% Similarity=0.944 Sum_probs=21.1
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+.. ...||+..|..|.+..|.
T Consensus 1 C~vCg~~~~---~~hygv~~C~aC~~FFrR 27 (76)
T cd06960 1 CAVCGDRAT---GKHYGVLSCNGCKGFFRR 27 (76)
T ss_pred CCccCccCc---ccEECcceeeeehheeCc
Confidence 556777654 458999999999998875
No 81
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=21.73 E-value=55 Score=26.45 Aligned_cols=31 Identities=32% Similarity=0.729 Sum_probs=24.5
Q ss_pred CcCCCCCCCCeeEcccc--eeeehhchhhhhcCCC
Q 041407 14 CADCGSKAPRWASVNLG--IFICMQCSGIHRSLGV 46 (241)
Q Consensus 14 CaDCgs~~P~was~n~G--ifvC~~CsgiHR~LG~ 46 (241)
|.||+. + .|++-.-| |.-|.+|-=|||.-++
T Consensus 45 c~~~~~-g-ewi~~~~G~~VwSC~dC~~iH~ke~~ 77 (112)
T COG2158 45 CENEEL-G-EWISDSNGRKVWSCSDCHWIHRKEGA 77 (112)
T ss_pred cccccc-C-ceeEcCCCCEEeeccccceecccchH
Confidence 445544 3 89999999 9999999999987553
No 82
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.54 E-value=41 Score=29.72 Aligned_cols=22 Identities=27% Similarity=0.825 Sum_probs=19.0
Q ss_pred CCCcCCCCCCCCeeEcccceeeehhchhh
Q 041407 12 RECADCGSKAPRWASVNLGIFICMQCSGI 40 (241)
Q Consensus 12 ~~CaDCgs~~P~was~n~GifvC~~Csgi 40 (241)
+.|.-||. +.-+.|.|..|...
T Consensus 310 ~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC-------ccceeEECCCCCCe
Confidence 78999999 67899999999763
No 83
>cd01245 PH_RasGAP_CG5898 RAS GTPase-activating protein (GAP) CG5898 Pleckstrin homology (PH) domain. RAS GTPase-activating protein (GAP) CG5898 Pleckstrin homology (PH) domain. This protein has a domain architecture of SH2-SH3-SH2-PH-C2-Ras_GAP. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=21.43 E-value=43 Score=26.13 Aligned_cols=61 Identities=15% Similarity=0.089 Sum_probs=33.7
Q ss_pred CCcccccchhHHHhhhhhhccCCCCCCCCCCCCCccccccCCCCCCCCCCCCceeEeeccCCC
Q 041407 136 PRKTRTLSLEEEILTKHIAQIAPPPTVGRSRGGSLDMNEKAAAPIPPRVPPSVAEVQVPTNNK 198 (241)
Q Consensus 136 ~~k~r~l~~~~~~~~~~~~~~~p~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 (241)
.+|.|+..|....-..++....++ ....+-|.||+....-.|....+-++++||.+.++..
T Consensus 15 ~wK~rwF~l~~~~s~~~l~yf~~~--~~~~p~gli~l~~~~V~~v~ds~~~r~~cFel~~~~~ 75 (98)
T cd01245 15 LWKTLYFALILDGSRSHESLLSSP--KKTKPIGLIDLSDAYLYPVHDSLFGRPNCFQIVERAL 75 (98)
T ss_pred ccceeEEEEecCCCCceEEEEcCC--CCCCccceeeccccEEEEccccccCCCeEEEEecCCC
Confidence 455777777421112344455544 3345557888888832222222235679999976544
No 84
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=21.39 E-value=51 Score=23.71 Aligned_cols=27 Identities=30% Similarity=0.877 Sum_probs=21.7
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.-||.+...+ .||+..|..|.+..|.
T Consensus 2 C~vC~~~~~~~---hygv~~C~aC~~FFRR 28 (70)
T smart00399 2 CCVCGDHASGF---HFGVCSCRACKAFFRR 28 (70)
T ss_pred CeEeCCcCccc---EeCCcEechhhhhhhh
Confidence 66787766544 8999999999998875
No 85
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=21.26 E-value=44 Score=22.46 Aligned_cols=27 Identities=26% Similarity=0.645 Sum_probs=18.7
Q ss_pred CCcCCCCCCCCeeEcccceeeehhchhhhhcC
Q 041407 13 ECADCGSKAPRWASVNLGIFICMQCSGIHRSL 44 (241)
Q Consensus 13 ~CaDCgs~~P~was~n~GifvC~~CsgiHR~L 44 (241)
.|.+||....-. ..+..-|..|. ||-|
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG--~rIl 30 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCRECG--YRIL 30 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCCC--ceEE
Confidence 699999864322 56788999994 4443
No 86
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=21.06 E-value=72 Score=24.40 Aligned_cols=28 Identities=25% Similarity=0.723 Sum_probs=22.0
Q ss_pred CCCCcCCCCCCCCeeEccc--------ceeeehhch
Q 041407 11 NRECADCGSKAPRWASVNL--------GIFICMQCS 38 (241)
Q Consensus 11 N~~CaDCgs~~P~was~n~--------GifvC~~Cs 38 (241)
+..|..||.....|..+-. -.|+|..|.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~ 97 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCG 97 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCC
Confidence 6899999999888875533 378898885
No 87
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=20.98 E-value=42 Score=25.51 Aligned_cols=29 Identities=31% Similarity=0.728 Sum_probs=23.7
Q ss_pred CCCcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 12 RECADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 12 ~~CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
..|.=||..... ..||+..|..|.+..|.
T Consensus 4 ~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 32 (87)
T cd06967 4 ELCVVCGDKASG---RHYGAVSCEGCKGFFKR 32 (87)
T ss_pred CCCeecCCcCCc---CEeCcceEeeeeeEeee
Confidence 458889987664 48999999999998864
No 88
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=20.97 E-value=48 Score=25.09 Aligned_cols=27 Identities=33% Similarity=0.771 Sum_probs=21.8
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||..... ..||+..|..|.+..|.
T Consensus 2 C~VCg~~~~g---~hygv~sC~aC~~FFRR 28 (85)
T cd06961 2 CVVCGDKATG---YHYRCITCEGCKGFFRR 28 (85)
T ss_pred CceeCCcCcc---eEEChhhhhhhhHhhHh
Confidence 6678876554 48999999999998875
No 89
>PHA00080 DksA-like zinc finger domain containing protein
Probab=20.65 E-value=30 Score=25.60 Aligned_cols=35 Identities=29% Similarity=0.681 Sum_probs=23.0
Q ss_pred CCCCCCCcCCCCCCC--CeeEcccceeeehhchhhhhc
Q 041407 8 LPENRECADCGSKAP--RWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 8 ~pgN~~CaDCgs~~P--~was~n~GifvC~~CsgiHR~ 43 (241)
.++...|.+||.+=| ++.- .-|+..|+.|...+-.
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a-~P~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 28 APSATHCEECGDPIPEARREA-VPGCRTCVSCQEILEL 64 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHh-CCCccCcHHHHHHHHH
Confidence 345568999998633 2222 2366789999887543
No 90
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=20.29 E-value=57 Score=24.13 Aligned_cols=27 Identities=30% Similarity=0.784 Sum_probs=21.1
Q ss_pred CcCCCCCCCCeeEcccceeeehhchhhhhc
Q 041407 14 CADCGSKAPRWASVNLGIFICMQCSGIHRS 43 (241)
Q Consensus 14 CaDCgs~~P~was~n~GifvC~~CsgiHR~ 43 (241)
|.=||.+... ..||+..|..|.+..|.
T Consensus 1 C~VCg~~~~g---~hyG~~~C~~C~~FFRR 27 (78)
T cd07164 1 CRVCGDRASG---KHYGVPSCDGCRGFFKR 27 (78)
T ss_pred CcccCccCcc---eEECcchhhhhhhhhhh
Confidence 5557766553 48999999999998875
No 91
>cd01266 PH_Gab Gab (Grb2-associated binder) pleckstrin homology (PH) domain. Gab (Grb2-associated binder) pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display str
Probab=20.22 E-value=54 Score=25.23 Aligned_cols=43 Identities=7% Similarity=-0.120 Sum_probs=27.8
Q ss_pred CCCcccccchhHHHh--h-hhhhccCCCCCCCCCCCCCccccccCCCC
Q 041407 135 IPRKTRTLSLEEEIL--T-KHIAQIAPPPTVGRSRGGSLDMNEKAAAP 179 (241)
Q Consensus 135 ~~~k~r~l~~~~~~~--~-~~~~~~~p~~~~~~~~~~s~~~~~~~~~~ 179 (241)
..++.|+..|.+..+ . -.+.++.-+ ....+-|+|||+....++
T Consensus 17 ~~WkrRwFvL~~~~l~~~~~~L~Yyk~~--~~~k~~g~I~L~~~~~v~ 62 (108)
T cd01266 17 TKWVRRYFVLHCGDRERNLFALEYYKTS--RKFKLEFVIDLESCSQVD 62 (108)
T ss_pred cCcEEEEEEEeccccCCCcceEEEECCC--CCCccceEEECCccEEEc
Confidence 467899999976432 1 123344433 567888999999976553
Done!