Query psy719
Match_columns 45
No_of_seqs 100 out of 342
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 20:26:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy719.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/719hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0614|consensus 99.2 5E-12 1.1E-16 83.1 2.4 45 1-45 260-304 (732)
2 KOG1113|consensus 99.1 3.1E-11 6.7E-16 75.7 1.6 45 1-45 228-272 (368)
3 PLN02868 acyl-CoA thioesterase 96.8 0.0019 4.1E-08 40.7 3.8 37 9-45 4-40 (413)
4 PRK09392 ftrB transcriptional 96.8 0.0015 3.2E-08 37.7 3.1 37 9-45 3-39 (236)
5 KOG0498|consensus 96.7 0.002 4.3E-08 44.0 3.2 39 7-45 413-451 (727)
6 KOG1113|consensus 96.4 0.0069 1.5E-07 38.7 4.1 41 5-45 114-154 (368)
7 PLN03192 Voltage-dependent pot 96.4 0.0061 1.3E-07 41.3 4.0 38 8-45 369-406 (823)
8 COG2905 Predicted signal-trans 96.2 0.0046 1E-07 41.6 2.8 35 11-45 5-39 (610)
9 cd00038 CAP_ED effector domain 93.7 0.087 1.9E-06 25.9 2.5 26 20-45 1-26 (115)
10 smart00100 cNMP Cyclic nucleot 93.4 0.12 2.5E-06 25.4 2.6 26 20-45 1-26 (120)
11 KOG0500|consensus 93.2 0.095 2.1E-06 35.0 2.6 37 9-45 303-339 (536)
12 KOG0614|consensus 90.1 0.26 5.6E-06 33.8 2.1 40 6-45 147-186 (732)
13 PRK11753 DNA-binding transcrip 86.7 0.82 1.8E-05 25.6 2.5 26 20-45 4-29 (211)
14 PRK11161 fumarate/nitrate redu 80.3 2.3 4.9E-05 24.4 2.6 31 15-45 15-46 (235)
15 PF06167 Peptidase_M90: Glucos 72.0 4.5 9.8E-05 24.7 2.4 27 9-35 26-52 (253)
16 PF13099 DUF3944: Domain of un 71.5 2.3 4.9E-05 18.9 0.8 22 18-39 7-28 (35)
17 cd06929 NR_LBD_F1 Ligand-bindi 65.9 7.1 0.00015 21.4 2.3 25 8-32 15-39 (174)
18 smart00430 HOLI Ligand binding 64.0 6.7 0.00015 20.6 1.9 25 9-33 6-30 (163)
19 PF14749 Acyl-CoA_ox_N: Acyl-c 62.7 11 0.00024 20.0 2.5 26 4-29 15-41 (125)
20 cd06930 NR_LBD_F2 Ligand-bindi 62.4 16 0.00036 19.6 3.3 25 8-32 12-36 (165)
21 COG5111 RPC34 DNA-directed RNA 59.8 11 0.00024 23.5 2.5 29 8-36 211-240 (301)
22 cd06938 NR_LBD_EcR The ligand 58.8 12 0.00027 21.9 2.5 24 9-32 53-76 (231)
23 cd06954 NR_LBD_LXR The ligand 58.7 13 0.00028 21.8 2.6 24 9-32 57-80 (236)
24 cd06942 NR_LBD_Sex_1_like The 58.4 15 0.00032 20.9 2.7 27 6-32 13-39 (191)
25 cd06157 NR_LBD The ligand bind 58.0 14 0.0003 19.4 2.4 25 9-33 12-36 (168)
26 cd06940 NR_LBD_REV_ERB The lig 58.0 13 0.00029 21.2 2.5 24 9-32 26-49 (189)
27 cd07068 NR_LBD_ER_like The lig 57.1 22 0.00048 20.6 3.4 27 7-33 39-65 (221)
28 cd07070 NR_LBD_SF-1 The ligand 56.9 18 0.0004 21.4 3.0 25 8-32 51-75 (237)
29 cd06953 NR_LBD_DHR4_like The l 55.7 20 0.00044 20.8 3.1 25 8-32 40-64 (213)
30 PF09119 SicP-binding: SicP bi 54.2 2 4.3E-05 22.4 -1.2 16 12-27 10-25 (81)
31 cd06936 NR_LBD_Fxr The ligand 53.7 15 0.00032 21.6 2.2 25 8-32 49-73 (221)
32 PRK02289 4-oxalocrotonate taut 51.6 13 0.00029 17.4 1.6 22 17-38 5-26 (60)
33 PF02944 BESS: BESS motif; In 50.4 7 0.00015 16.9 0.4 19 14-32 8-26 (37)
34 PF00104 Hormone_recep: Ligand 49.7 21 0.00044 19.4 2.3 25 9-33 31-55 (203)
35 cd02638 R3H_unknown_1 R3H doma 49.6 23 0.0005 17.5 2.2 23 15-37 17-39 (62)
36 cd06943 NR_LBD_RXR_like The li 49.3 26 0.00056 20.0 2.8 25 8-32 43-67 (207)
37 cd06944 NR_LBD_Ftz-F1_like The 47.9 34 0.00073 20.2 3.2 24 9-32 52-75 (237)
38 PF10003 DUF2244: Integral mem 47.8 13 0.00029 20.5 1.3 23 16-38 116-138 (140)
39 cd06948 NR_LBD_COUP-TF Ligand 47.3 35 0.00076 20.1 3.2 25 8-32 43-67 (236)
40 COG3228 Uncharacterized protei 47.2 19 0.00041 22.5 2.0 24 11-34 23-46 (266)
41 PF12550 GCR1_C: Transcription 47.0 32 0.0007 17.2 2.6 33 4-36 48-80 (81)
42 COG0664 Crp cAMP-binding prote 46.9 22 0.00047 19.3 2.1 31 15-45 2-32 (214)
43 KOG0499|consensus 46.5 11 0.00025 26.5 1.1 35 11-45 525-559 (815)
44 cd06949 NR_LBD_ER Ligand bindi 46.2 41 0.0009 19.9 3.4 25 8-32 45-69 (235)
45 cd06946 NR_LBD_ERR The ligand 46.0 22 0.00048 20.6 2.2 24 9-32 41-64 (221)
46 PF09796 QCR10: Ubiquinol-cyto 45.2 13 0.00028 18.4 1.0 13 11-23 39-51 (64)
47 cd02641 R3H_Smubp-2_like R3H d 44.6 38 0.00081 16.2 3.6 28 8-35 5-37 (60)
48 PRK15410 DgsA anti-repressor M 44.2 19 0.0004 22.3 1.7 24 11-35 19-42 (260)
49 cd06952 NR_LBD_TR2_like The li 44.0 41 0.00088 19.5 3.1 25 8-32 34-58 (222)
50 cd06941 NR_LBD_DmE78_like The 43.4 34 0.00074 19.4 2.6 25 8-32 15-39 (195)
51 cd07350 NR_LBD_Dax1 The ligand 42.9 45 0.00099 19.8 3.2 25 8-32 32-56 (232)
52 PF14842 FliG_N: FliG N-termin 40.9 9.3 0.0002 20.1 0.0 20 18-37 24-43 (108)
53 COG0399 WecE Predicted pyridox 40.7 23 0.00049 22.9 1.7 23 17-39 348-370 (374)
54 PF10660 MitoNEET_N: Iron-cont 40.6 9.2 0.0002 19.0 0.0 32 10-41 11-42 (64)
55 PF07498 Rho_N: Rho terminatio 40.2 14 0.0003 16.5 0.5 21 21-41 2-22 (43)
56 cd06931 NR_LBD_HNF4_like The l 40.2 35 0.00076 19.7 2.4 24 9-32 46-69 (222)
57 PF04282 DUF438: Family of unk 39.6 51 0.0011 16.6 2.6 28 8-35 19-57 (71)
58 PF10330 Stb3: Putative Sin3 b 39.1 63 0.0014 17.2 3.4 26 12-37 28-54 (92)
59 cd07069 NR_LBD_Lrh-1 The ligan 38.8 56 0.0012 19.5 3.2 25 8-32 53-77 (241)
60 PF08385 DHC_N1: Dynein heavy 38.6 16 0.00035 23.6 0.9 35 4-38 91-126 (579)
61 cd06935 NR_LBD_TR The ligand b 37.8 42 0.0009 20.0 2.5 25 8-32 65-89 (243)
62 PF11460 DUF3007: Protein of u 37.2 48 0.001 18.0 2.5 33 4-36 64-102 (104)
63 cd02644 R3H_jag R3H domain fou 37.0 49 0.0011 16.1 2.3 19 19-37 26-44 (67)
64 PF02276 CytoC_RC: Photosynthe 37.0 27 0.00058 22.4 1.6 25 13-37 52-76 (314)
65 cd06933 NR_LBD_VDR The ligand 35.6 48 0.0011 19.6 2.5 25 8-32 50-74 (238)
66 PF03281 Mab-21: Mab-21 protei 34.8 32 0.00069 20.6 1.7 26 12-37 263-288 (292)
67 cd07073 NR_LBD_AR Ligand bindi 34.2 83 0.0018 18.9 3.4 25 8-32 41-65 (246)
68 PRK15407 lipopolysaccharide bi 34.1 31 0.00067 22.2 1.6 22 17-38 411-432 (438)
69 cd07349 NR_LBD_SHP The ligand 34.0 78 0.0017 18.7 3.2 25 6-30 30-54 (222)
70 cd06939 NR_LBD_ROR_like The li 33.8 57 0.0012 19.5 2.6 24 9-32 62-85 (241)
71 cd06937 NR_LBD_RAR The ligand 33.5 80 0.0017 18.6 3.2 25 8-32 51-75 (231)
72 cd07072 NR_LBD_DHR38_like Liga 33.2 60 0.0013 19.5 2.7 25 8-32 55-79 (239)
73 PF04369 Lactococcin: Lactococ 32.8 24 0.00053 17.4 0.8 13 21-33 7-19 (60)
74 cd06932 NR_LBD_PPAR The ligand 32.6 58 0.0013 19.6 2.6 25 8-32 76-100 (259)
75 PRK10119 putative hydrolase; P 32.3 72 0.0016 19.2 2.9 33 10-44 80-112 (231)
76 cd06945 NR_LBD_Nurr1_like The 32.3 64 0.0014 19.2 2.7 25 8-32 54-78 (239)
77 cd06951 NR_LBD_Dax1_like The l 32.2 85 0.0018 18.4 3.2 25 8-32 32-56 (222)
78 cd06950 NR_LBD_Tlx_PNR_like Th 31.6 93 0.002 17.9 3.2 24 9-32 40-63 (206)
79 PF08479 POTRA_2: POTRA domain 31.4 20 0.00043 17.4 0.4 24 21-44 28-51 (76)
80 COG0099 RpsM Ribosomal protein 31.2 34 0.00073 19.1 1.3 20 21-40 45-64 (121)
81 PHA02994 hypothetical protein; 30.5 32 0.00069 21.0 1.2 31 9-39 186-216 (218)
82 cd01277 HINT_subgroup HINT (hi 30.0 42 0.00091 16.7 1.5 21 17-37 44-64 (103)
83 PF05397 Med15_fungi: Mediator 29.3 1E+02 0.0022 16.6 3.0 32 7-38 8-43 (115)
84 PRK02220 4-oxalocrotonate taut 29.0 50 0.0011 15.0 1.5 22 17-38 5-26 (61)
85 PF15100 TMEM187: TMEM187 prot 29.0 21 0.00045 22.1 0.2 25 13-37 208-232 (242)
86 PF00511 PPV_E2_C: E2 (early) 28.8 39 0.00085 17.3 1.2 16 9-24 58-73 (81)
87 PF03250 Tropomodulin: Tropomo 28.6 28 0.0006 20.0 0.7 19 18-36 18-36 (147)
88 smart00315 RGS Regulator of G 28.6 25 0.00055 17.5 0.5 32 10-41 26-58 (118)
89 PF00645 zf-PARP: Poly(ADP-rib 28.5 74 0.0016 15.5 2.2 23 15-37 60-82 (82)
90 PF12646 DUF3783: Domain of un 28.2 48 0.001 15.6 1.4 21 19-39 4-24 (58)
91 cd00491 4Oxalocrotonate_Tautom 28.1 53 0.0012 14.6 1.5 21 17-37 4-24 (58)
92 TIGR01847 bacteriocin_sig bact 28.0 43 0.00094 13.8 1.1 13 21-33 1-13 (26)
93 PRK15375 pathogenicity island 27.9 44 0.00096 22.9 1.6 20 8-27 38-57 (535)
94 PLN02806 complex I subunit 27.9 48 0.0011 17.2 1.4 16 8-23 16-31 (81)
95 cd08795 Death_IRAK2 Death doma 27.7 49 0.0011 17.3 1.5 20 19-38 1-20 (88)
96 PF09228 Prok-TraM: Prokaryoti 27.7 31 0.00068 18.6 0.7 20 18-37 18-38 (102)
97 TIGR02379 ECA_wecE TDP-4-keto- 27.5 57 0.0012 20.5 2.0 22 17-38 352-373 (376)
98 PF14841 FliG_M: FliG middle d 27.3 69 0.0015 15.8 2.0 31 10-40 40-70 (79)
99 COG4840 Uncharacterized protei 27.3 57 0.0012 16.5 1.6 16 22-37 52-67 (71)
100 PF06518 DUF1104: Protein of u 27.0 32 0.00069 18.1 0.7 22 20-41 2-23 (93)
101 PF04708 Pox_F16: Poxvirus F16 26.4 47 0.001 20.2 1.4 31 9-39 186-216 (218)
102 PF13443 HTH_26: Cro/C1-type H 26.2 50 0.0011 15.0 1.3 17 22-38 36-52 (63)
103 TIGR01358 DAHP_synth_II 3-deox 26.0 87 0.0019 21.0 2.7 30 11-40 271-306 (443)
104 PF07894 DUF1669: Protein of u 25.9 1.3E+02 0.0029 18.9 3.4 33 8-40 35-67 (284)
105 PF08597 eIF3_subunit: Transla 25.8 46 0.001 19.9 1.3 29 10-38 162-192 (245)
106 cd06934 NR_LBD_PXR_like The li 25.8 75 0.0016 18.7 2.2 24 9-32 49-72 (226)
107 PF09720 Unstab_antitox: Putat 25.6 63 0.0014 14.7 1.5 14 23-36 1-14 (54)
108 cd00616 AHBA_syn 3-amino-5-hyd 25.6 66 0.0014 19.1 2.0 22 16-37 331-352 (352)
109 PF02330 MAM33: Mitochondrial 25.6 38 0.00082 19.5 0.9 15 5-19 187-201 (204)
110 PF09187 DUF1950: Domain of un 25.6 77 0.0017 17.5 2.0 19 5-23 2-20 (119)
111 TIGR02929 anfG_nitrog Fe-only 25.3 58 0.0013 17.8 1.5 27 12-38 63-89 (109)
112 PF04803 Cor1: Cor1/Xlr/Xmr co 25.1 29 0.00062 19.3 0.3 30 8-37 95-124 (130)
113 KOG3808|consensus 24.9 23 0.00051 17.9 -0.1 15 13-27 22-36 (74)
114 PF03047 ComC: COMC family; I 24.9 24 0.00053 15.2 0.0 18 16-33 6-23 (32)
115 PF03255 ACCA: Acetyl co-enzym 24.7 47 0.001 19.0 1.1 17 19-35 47-63 (145)
116 PF10439 Bacteriocin_IIc: Bact 24.3 32 0.0007 16.6 0.4 13 20-32 4-16 (65)
117 PLN02291 phospho-2-dehydro-3-d 24.3 97 0.0021 21.0 2.7 30 11-40 291-326 (474)
118 PF14418 OHA: OST-HTH Associat 24.3 1.1E+02 0.0023 15.3 2.8 29 8-36 12-42 (75)
119 PF10945 DUF2629: Protein of u 24.1 51 0.0011 15.3 1.0 21 4-24 22-42 (44)
120 PF08752 COP-gamma_platf: Coat 24.0 76 0.0017 18.1 1.9 21 7-27 1-21 (151)
121 cd02640 R3H_NRF R3H domain of 24.0 1E+02 0.0022 14.8 3.9 28 8-35 5-37 (60)
122 TIGR02930 vnfG_nitrog V-contai 23.9 64 0.0014 17.7 1.5 27 12-38 63-89 (109)
123 PRK11706 TDP-4-oxo-6-deoxy-D-g 23.6 74 0.0016 19.7 2.0 23 16-38 350-372 (375)
124 PF06989 BAALC_N: BAALC N-term 23.5 20 0.00043 17.1 -0.5 11 33-43 8-18 (53)
125 cd07348 NR_LBD_NGFI-B The liga 23.1 1.1E+02 0.0025 18.3 2.6 25 8-32 54-78 (238)
126 PF04472 DUF552: Protein of un 22.9 41 0.00089 16.4 0.6 21 21-41 29-49 (73)
127 cd06875 PX_IRAS The phosphoino 22.7 70 0.0015 17.0 1.5 35 5-41 73-107 (116)
128 cd08304 DD_superfamily The Dea 22.5 36 0.00078 16.6 0.3 21 18-38 2-22 (69)
129 cd07071 NR_LBD_Nurr1 The ligan 22.0 1.3E+02 0.0028 18.0 2.7 25 8-32 54-78 (238)
130 PF14285 DUF4367: Domain of un 21.9 67 0.0014 17.3 1.4 15 22-36 154-168 (168)
131 PRK15348 type III secretion sy 21.8 57 0.0012 20.0 1.2 25 17-41 20-44 (249)
132 COG4103 Uncharacterized protei 21.8 33 0.00071 19.7 0.1 26 20-45 92-117 (148)
133 PF01041 DegT_DnrJ_EryC1: DegT 21.6 63 0.0014 19.9 1.4 22 16-37 342-363 (363)
134 PRK11658 UDP-4-amino-4-deoxy-L 21.5 87 0.0019 19.5 2.0 22 17-38 354-375 (379)
135 TIGR00013 taut 4-oxalocrotonat 21.3 85 0.0018 14.3 1.5 21 17-37 4-25 (63)
136 PF05415 Peptidase_C36: Beet n 21.3 1.5E+02 0.0033 15.9 3.4 34 4-41 32-66 (104)
137 PF08369 PCP_red: Proto-chloro 21.2 39 0.00085 15.3 0.3 11 12-22 6-16 (45)
138 cd06947 NR_LBD_GR_Like Ligand 21.1 1.9E+02 0.0042 17.4 3.3 25 8-32 41-65 (246)
139 PF05119 Terminase_4: Phage te 20.8 1.2E+02 0.0025 15.1 2.1 28 9-36 6-33 (100)
140 cd08309 Death_IRAK Death domai 20.6 83 0.0018 16.2 1.5 18 21-38 3-20 (95)
141 COG5432 RAD18 RING-finger-cont 20.6 58 0.0013 21.2 1.1 21 16-36 14-34 (391)
142 PF14515 HOASN: Haem-oxygenase 20.6 24 0.00053 18.6 -0.5 22 17-38 7-28 (93)
143 PF15563 Imm11: Immunity prote 20.5 84 0.0018 19.2 1.7 23 8-30 151-173 (224)
144 PF06881 Elongin_A: RNA polyme 20.5 62 0.0013 16.9 1.0 17 19-35 14-30 (109)
145 COG1342 Predicted DNA-binding 20.4 24 0.00051 19.1 -0.6 19 20-38 65-83 (99)
146 cd01275 FHIT FHIT (fragile his 20.3 89 0.0019 16.4 1.6 21 17-37 44-64 (126)
147 PF07914 DUF1679: Protein of u 20.3 82 0.0018 20.4 1.7 21 16-36 161-181 (414)
148 PF08006 DUF1700: Protein of u 20.1 61 0.0013 18.2 1.0 29 8-38 3-31 (181)
149 cd08307 Death_Pelle Death doma 20.1 85 0.0018 16.6 1.5 18 22-39 4-21 (97)
No 1
>KOG0614|consensus
Probab=99.22 E-value=5e-12 Score=83.15 Aligned_cols=45 Identities=18% Similarity=0.307 Sum_probs=43.1
Q ss_pred CchHHHHHHHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 1 MGSTIRKRKLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 1 ~~~~~~kr~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
|.++.+++++|..||++||+|++|+++-|.||||+|++++|++|+
T Consensus 260 ~~tg~~r~~~~~~fLrsv~~~q~l~Ee~L~KiaD~le~~~Yd~g~ 304 (732)
T KOG0614|consen 260 MRTGLERHEQYMNFLRSVPLFQNLPEELLLKIADVLEEEYYDAGE 304 (732)
T ss_pred HHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHHHHHHHhhcCCc
Confidence 468999999999999999999999999999999999999999986
No 2
>KOG1113|consensus
Probab=99.10 E-value=3.1e-11 Score=75.73 Aligned_cols=45 Identities=38% Similarity=0.488 Sum_probs=43.1
Q ss_pred CchHHHHHHHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 1 MGSTIRKRKLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 1 ~~~~~~kr~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
|.++.++|.+|+.||++||+|++|..+++.+|||+|.++.|++|+
T Consensus 228 ~~s~~kkrkMy~~~l~s~pil~~l~k~er~kv~dal~~k~y~~G~ 272 (368)
T KOG1113|consen 228 MKSCIKKRKMYEPFLESVPILESLEKLERAKVADALGTKSYKDGE 272 (368)
T ss_pred eccchhhhhhhhhhhhcchhhHHHHHHHHHhhhcccceeeccCCc
Confidence 567899999999999999999999999999999999999999995
No 3
>PLN02868 acyl-CoA thioesterase family protein
Probab=96.85 E-value=0.0019 Score=40.74 Aligned_cols=37 Identities=30% Similarity=0.315 Sum_probs=33.9
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
+....+|+++|+|+.|++.++.+|+..++..+|.+|+
T Consensus 4 ~~~~~~L~~~~~F~~L~~~~l~~l~~~~~~~~~~~Ge 40 (413)
T PLN02868 4 ESVVEFLGSVPLLQRLPSSSLKKIAEVVVPKRYGKGE 40 (413)
T ss_pred HHHHHHHhcCcccccCCHHHHHHHHHhceEEEECCCC
Confidence 3466889999999999999999999999999999986
No 4
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=96.84 E-value=0.0015 Score=37.72 Aligned_cols=37 Identities=5% Similarity=0.012 Sum_probs=33.9
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
.....+|+.+|+|+.|++.++..++.......|++|+
T Consensus 3 ~~~~~~l~~~~~f~~L~~~~~~~l~~~~~~~~~~~ge 39 (236)
T PRK09392 3 REDLIRLRNLPLFADMADATFERLMRGAFLQRFPPGT 39 (236)
T ss_pred chHHHHHhcCccccCCCHHHHHHHHhhcceeecCCCC
Confidence 3456799999999999999999999999999999996
No 5
>KOG0498|consensus
Probab=96.70 E-value=0.002 Score=43.99 Aligned_cols=39 Identities=15% Similarity=0.307 Sum_probs=35.9
Q ss_pred HHHHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 7 KRKLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 7 kr~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
+|-.+.+++++||+|+.+++.-|..|++-|++++|.+||
T Consensus 413 ~~hL~~~lv~~vpLF~~md~~~L~al~~rlk~~~f~pge 451 (727)
T KOG0498|consen 413 KRHLCLDLVRKVPLFAGMDDGLLDALCSRLKPEYFTPGE 451 (727)
T ss_pred HHHHhHHHHhhCchhhcCCHHHHHHHHHHhhhhccCCCC
Confidence 355678999999999999999999999999999999986
No 6
>KOG1113|consensus
Probab=96.39 E-value=0.0069 Score=38.74 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 5 IRKRKLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 5 ~~kr~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
.+.++...+++++.-+|++|+++++..+.||+.++.+.+|+
T Consensus 114 ~e~~~~L~~a~r~~~LF~~Ld~eq~~~v~dam~~~~v~~G~ 154 (368)
T KOG1113|consen 114 DETRRRLEEAFRKNLLFANLDDEQLSQVLDAMFEKRVKAGE 154 (368)
T ss_pred HHHHHHHHHHHHhccccccCCHHHHHHHHHhhceeeecCCc
Confidence 34566678999999999999999999999999999999985
No 7
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=96.38 E-value=0.0061 Score=41.29 Aligned_cols=38 Identities=8% Similarity=0.230 Sum_probs=34.7
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
++.+..++++||+|+++++..+..|+..+++++|.+||
T Consensus 369 ~~l~~~~l~~~~lF~~~s~~~l~~L~~~~~~~~~~pge 406 (823)
T PLN03192 369 QHLFLPVVEKVYLFKGVSREILLLLVTKMKAEYIPPRE 406 (823)
T ss_pred HHHHHHHHhhCcchhcCCHHHHHHHHHhhheeeeCCCC
Confidence 45567889999999999999999999999999999986
No 8
>COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]
Probab=96.24 E-value=0.0046 Score=41.56 Aligned_cols=35 Identities=17% Similarity=0.259 Sum_probs=33.2
Q ss_pred HHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 11 YEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 11 ~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
..+||...|-|..|+++++.+|.++|+..+|.+||
T Consensus 5 ~~~Fl~~~pPF~~L~~eel~~L~~~l~v~yy~kge 39 (610)
T COG2905 5 PDQFLQQHPPFSQLPAEELEQLMGALEVKYYRKGE 39 (610)
T ss_pred HHHHHhcCCCcccCCHHHHHHHHhhhccccccCCC
Confidence 46899999999999999999999999999999996
No 9
>cd00038 CAP_ED effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of
Probab=93.68 E-value=0.087 Score=25.87 Aligned_cols=26 Identities=12% Similarity=0.172 Sum_probs=23.8
Q ss_pred ccCCCChHHHhhHhhhhheeeecCCC
Q psy719 20 ILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 20 ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
+|+.|++..+..+++.+....|.+|+
T Consensus 1 ~f~~l~~~~~~~l~~~~~~~~~~~g~ 26 (115)
T cd00038 1 LFSGLDDEELEELADALEERRFPAGE 26 (115)
T ss_pred CcccCCHHHHHHHHhhceeeeeCCCC
Confidence 57899999999999999999999886
No 10
>smart00100 cNMP Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
Probab=93.35 E-value=0.12 Score=25.44 Aligned_cols=26 Identities=12% Similarity=0.183 Sum_probs=23.8
Q ss_pred ccCCCChHHHhhHhhhhheeeecCCC
Q psy719 20 ILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 20 ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
+|.+|++..+..++..+....|.+|+
T Consensus 1 ~f~~l~~~~~~~l~~~~~~~~~~~g~ 26 (120)
T smart00100 1 LFKNLDAEELRELADALEPVRYPAGE 26 (120)
T ss_pred CcCCCCHHHHHHHHHhceEEEeCCCC
Confidence 47889999999999999999999986
No 11
>KOG0500|consensus
Probab=93.16 E-value=0.095 Score=35.03 Aligned_cols=37 Identities=14% Similarity=0.258 Sum_probs=34.6
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
+-+.+-|++|+||++..+.-|.-+.--|++..|.+||
T Consensus 303 nvh~dTLkkV~iF~~ce~~lL~elVLklk~qvfSPgD 339 (536)
T KOG0500|consen 303 NVHLDTLKKVRIFQDCEAGLLVELVLKLKPQVFSPGD 339 (536)
T ss_pred HHHHHHHHhhhHHHhcchhHHHHHHHHhcceeeCCCC
Confidence 4578899999999999999999999999999999997
No 12
>KOG0614|consensus
Probab=90.11 E-value=0.26 Score=33.77 Aligned_cols=40 Identities=8% Similarity=0.139 Sum_probs=35.3
Q ss_pred HHHHHHHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 6 RKRKLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 6 ~kr~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
.-++.+.+.+..=.+|++|+..++..|.+||-+..|.+|.
T Consensus 147 ~~k~lI~dAi~~NdFLknLd~~Qi~e~v~~Myp~~~~~gs 186 (732)
T KOG0614|consen 147 GAKQLIRDAIQKNDFLKNLDASQIKELVDCMYPVEYRAGS 186 (732)
T ss_pred cHHHHHHHHHHhhHHHHhhhHHHHHHHHHhhCcccccCCc
Confidence 3466778888888999999999999999999999999884
No 13
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=86.66 E-value=0.82 Score=25.64 Aligned_cols=26 Identities=4% Similarity=-0.103 Sum_probs=23.5
Q ss_pred ccCCCChHHHhhHhhhhheeeecCCC
Q psy719 20 ILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 20 ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
+-+.|++.++..+++.+...+|++|+
T Consensus 4 ~~~~~~~~~~~~l~~~~~~~~~~kg~ 29 (211)
T PRK11753 4 LGKPQTDPTLEWFLSHCHIHKYPAKS 29 (211)
T ss_pred ccCCCCHHHHHHHHhhCeEEEeCCCC
Confidence 34789999999999999999999986
No 14
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=80.30 E-value=2.3 Score=24.38 Aligned_cols=31 Identities=13% Similarity=0.287 Sum_probs=24.2
Q ss_pred hhcCcccCCCChHHHhhHhhhhhe-eeecCCC
Q psy719 15 LSRVSILVQCGSKKMGIVAKHVTC-AMVEKGE 45 (45)
Q Consensus 15 L~~V~ilk~L~~~~l~kiad~l~~-~~y~~Ge 45 (45)
+++-+.+-+|++.++..|+..... ..|.+|+
T Consensus 15 ~~~~~~~~~l~~~~l~~L~~~~~~~~~~~kge 46 (235)
T PRK11161 15 ISQLCIPFTLNEHELDQLDNIIERKKPIQKGQ 46 (235)
T ss_pred ccccccccCCCHHHHHHHHHhhhhceeecCCC
Confidence 444555557999999999998864 6799886
No 15
>PF06167 Peptidase_M90: Glucose-regulated metallo-peptidase M90; InterPro: IPR010384 MtfA (earlier known as YeeI) is a transcription factor that binds Mlc (make large colonies), itself a repressor of glucose and hence a protein important in regulation of the phosphoenolpyruvate:glucose-phosphotransferase (PtsG) system, the major glucose transporter in Escherichia coli. Mlc is a repressor of ptsG, and MtfA is found to bind and inactivate Mlc with high affinity []. The membrane-bound protein EIICBGlc encoded by the ptsG gene is the major glucose transporter in E. coli. ; PDB: 3DL1_A 3KHI_A.
Probab=71.97 E-value=4.5 Score=24.66 Aligned_cols=27 Identities=7% Similarity=0.192 Sum_probs=18.0
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHhhh
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVAKH 35 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kiad~ 35 (45)
.....+|.++|+++.|++.++.++...
T Consensus 26 ~~w~~~l~~~p~y~~L~~~~~~~l~~~ 52 (253)
T PF06167_consen 26 EEWRAILAQVPFYRRLSPEEQRRLRQR 52 (253)
T ss_dssp --HHHHC--SGGGTT--HHHHHHHHHH
T ss_pred HHHHHHHHhCHHhhcCCHHHHHHHHHH
Confidence 456789999999999999999888554
No 16
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=71.48 E-value=2.3 Score=18.91 Aligned_cols=22 Identities=14% Similarity=0.367 Sum_probs=18.1
Q ss_pred CcccCCCChHHHhhHhhhhhee
Q psy719 18 VSILVQCGSKKMGIVAKHVTCA 39 (45)
Q Consensus 18 V~ilk~L~~~~l~kiad~l~~~ 39 (45)
..+|+.+++.+|.-++++|.-.
T Consensus 7 LeFL~~cs~edL~~L~~~Lt~d 28 (35)
T PF13099_consen 7 LEFLAECSNEDLKDLVDILTHD 28 (35)
T ss_pred hHHHHHCCHHHHHHHHHHHhcC
Confidence 4567889999999999999643
No 17
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=65.95 E-value=7.1 Score=21.40 Aligned_cols=25 Identities=12% Similarity=0.086 Sum_probs=20.9
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|.+++|.|..|+..+...+
T Consensus 15 l~~~v~~ak~ip~F~~L~~~Dq~~L 39 (174)
T cd06929 15 IRRVVEFAKRIPGFRELSQEDQIAL 39 (174)
T ss_pred HHHHHhhccCCcCcccCChhHHHHH
Confidence 4557899999999999999886655
No 18
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=63.97 E-value=6.7 Score=20.55 Aligned_cols=25 Identities=12% Similarity=0.089 Sum_probs=21.1
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHh
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVA 33 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kia 33 (45)
....+|++++|.|..|+..+...+.
T Consensus 6 ~~~~~~~~~~~~f~~L~~~dq~~Ll 30 (163)
T smart00430 6 LLAVEWAKTFPFFRELSQEDKLILL 30 (163)
T ss_pred HHHHHHHHhChhHhhCCHHHHHHHH
Confidence 3467899999999999998877764
No 19
>PF14749 Acyl-CoA_ox_N: Acyl-coenzyme A oxidase N-terminal; PDB: 2FON_A 1W07_B 1IS2_B 2DDH_A.
Probab=62.74 E-value=11 Score=19.97 Aligned_cols=26 Identities=12% Similarity=0.216 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHhhcCcccCC-CChHHH
Q psy719 4 TIRKRKLYEEFLSRVSILVQ-CGSKKM 29 (45)
Q Consensus 4 ~~~kr~~~~~fL~~V~ilk~-L~~~~l 29 (45)
..++|+...+++.+-|+|.. .+.+.+
T Consensus 15 ~~~~rr~i~~~i~~dP~f~~~~~~~~l 41 (125)
T PF14749_consen 15 KLERRREIESLIESDPIFSKPPDRYFL 41 (125)
T ss_dssp HHHHHHHHHHHHHT-GGG---TTGGGS
T ss_pred HHHHHHHHHHHHhhChhhhcCCCcccC
Confidence 45778889999999999998 554443
No 20
>cd06930 NR_LBD_F2 Ligand-binding domain of nuclear receptor family 2. Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=62.43 E-value=16 Score=19.62 Aligned_cols=25 Identities=0% Similarity=-0.160 Sum_probs=20.6
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|.+++|.|..|+..+...+
T Consensus 12 l~~~ie~ak~~p~F~~L~~~Dq~~L 36 (165)
T cd06930 12 LFKTVDWAKNLPAFRNLPLDDQLTL 36 (165)
T ss_pred HHHHHHHHHcCCccccCChHHHHHH
Confidence 3456899999999999999886655
No 21
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=59.84 E-value=11 Score=23.54 Aligned_cols=29 Identities=14% Similarity=0.148 Sum_probs=25.8
Q ss_pred HHHHHHHhhcCcccC-CCChHHHhhHhhhh
Q psy719 8 RKLYEEFLSRVSILV-QCGSKKMGIVAKHV 36 (45)
Q Consensus 8 r~~~~~fL~~V~ilk-~L~~~~l~kiad~l 36 (45)
-++...|++++.|++ .|....+..+||+|
T Consensus 211 ~~~I~n~vr~~ni~~v~L~l~n~~sL~dvL 240 (301)
T COG5111 211 LEDIMNYVRNVNILSVPLRLDNLESLADVL 240 (301)
T ss_pred HHHHHHHHHhceeeeccccHHHHHHHhHhe
Confidence 356889999999998 69999999999998
No 22
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=58.77 E-value=12 Score=21.91 Aligned_cols=24 Identities=17% Similarity=0.162 Sum_probs=19.8
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
....+|.+++|.|.+|+..+-..+
T Consensus 53 ~~iIefaK~lp~F~~L~~~DQi~L 76 (231)
T cd06938 53 QLIVEFAKRLPGFDKLSREDQITL 76 (231)
T ss_pred HHHHHHHhcCCccccCChhHHHHH
Confidence 446899999999999998775555
No 23
>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee
Probab=58.71 E-value=13 Score=21.81 Aligned_cols=24 Identities=4% Similarity=0.032 Sum_probs=20.1
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
....+|.+++|.|..|+..+...+
T Consensus 57 ~~~VefaK~lP~F~~L~~~DQi~L 80 (236)
T cd06954 57 QEIVDFAKQLPGFLTLTREDQIAL 80 (236)
T ss_pred HHHHHHHcCCCCcccCChHHHHHH
Confidence 347899999999999998876555
No 24
>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=58.38 E-value=15 Score=20.91 Aligned_cols=27 Identities=7% Similarity=0.054 Sum_probs=21.4
Q ss_pred HHHHHHHHHhhcCcccCCCChHHHhhH
Q psy719 6 RKRKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 6 ~kr~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
..-....+|.+++|.|.+|+..+...+
T Consensus 13 ~~i~~~IefaK~iPgF~~L~~~DQi~L 39 (191)
T cd06942 13 MHIQEIVQFVKSIPGFNQLSGEDRAQL 39 (191)
T ss_pred HHHHHHHHHHhcCCCcccCChhHHHHH
Confidence 334567899999999999998875554
No 25
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=58.00 E-value=14 Score=19.43 Aligned_cols=25 Identities=8% Similarity=0.010 Sum_probs=20.7
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHh
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVA 33 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kia 33 (45)
....+|.+++|.|..|+..+...+.
T Consensus 12 ~~~i~~~~~~~~f~~L~~~dq~~Ll 36 (168)
T cd06157 12 LLIVEWAKSIPGFRELPLEDQIVLL 36 (168)
T ss_pred HHHHHHHHcCCchhcCChHHHHHHH
Confidence 4568999999999999998866653
No 26
>cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of
Probab=57.96 E-value=13 Score=21.22 Aligned_cols=24 Identities=13% Similarity=0.115 Sum_probs=19.5
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
....+|.|+||-|.+|+..+-..+
T Consensus 26 ~~~V~waK~iPgF~~L~~~DQi~L 49 (189)
T cd06940 26 REVVEFAKRIPGFRDLSQHDQVTL 49 (189)
T ss_pred HHHHHHHhcCCCcccCChhhHHHH
Confidence 457899999999999988765444
No 27
>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin
Probab=57.06 E-value=22 Score=20.62 Aligned_cols=27 Identities=0% Similarity=-0.143 Sum_probs=21.7
Q ss_pred HHHHHHHHhhcCcccCCCChHHHhhHh
Q psy719 7 KRKLYEEFLSRVSILVQCGSKKMGIVA 33 (45)
Q Consensus 7 kr~~~~~fL~~V~ilk~L~~~~l~kia 33 (45)
.-....+|.+++|.|+.|+..+...+.
T Consensus 39 ~l~~~vewaK~lp~F~~L~~~DQi~LL 65 (221)
T cd07068 39 ELVHIISWAKHIPGFSDLSLNDQMHLL 65 (221)
T ss_pred HHHHHHHHHHhCCCcccCCHHHHHHHH
Confidence 344578999999999999998866653
No 28
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=56.88 E-value=18 Score=21.44 Aligned_cols=25 Identities=4% Similarity=-0.040 Sum_probs=20.2
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
--...+|.|++|.|++|+..+-..+
T Consensus 51 L~~~VeWaK~lP~F~~L~~~DQi~L 75 (237)
T cd07070 51 FISIVDWARRCMVFKELEVADQMTL 75 (237)
T ss_pred HHHHHHHHHhCCChhhCCHHHHHHH
Confidence 3456899999999999998776555
No 29
>cd06953 NR_LBD_DHR4_like The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4. The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=55.74 E-value=20 Score=20.81 Aligned_cols=25 Identities=4% Similarity=-0.003 Sum_probs=20.1
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|.+++|.|++|+..+...+
T Consensus 40 l~~~I~waK~lp~F~~L~~~DQi~L 64 (213)
T cd06953 40 LFRQIQWTKKLPFFTELSIKDHTHL 64 (213)
T ss_pred HHHHHHHHhcCCchhhCCHHHHHHH
Confidence 3456899999999999998876554
No 30
>PF09119 SicP-binding: SicP binding; InterPro: IPR015203 Members of this family bind the chaperone SicP, which is required both to maintain the stability of SptP, as well as to ensure the eventual secretion of the protein. The domain is found in the Salmonella effector protein SptP, which interacts with SicP chaperone dimers mainly through four regions of its chaperone-binding domain. The structure of the SptP-SicP complex contains four molecules of SicP, aligned in a linear fashion and arranged in two sets of tightly bound homodimers that bind two SptP molecules. The SicP homodimers do not interact with each other, but are held together by a molecular interface formed between two SptP molecules. Each SptP molecule is wrapped around by three SicP chaperones (two chaperones from one homodimer and a third one from the opposite homodimer pair) []. ; GO: 0005615 extracellular space; PDB: 1JYO_F.
Probab=54.18 E-value=2 Score=22.41 Aligned_cols=16 Identities=13% Similarity=0.343 Sum_probs=8.0
Q ss_pred HHHhhcCcccCCCChH
Q psy719 12 EEFLSRVSILVQCGSK 27 (45)
Q Consensus 12 ~~fL~~V~ilk~L~~~ 27 (45)
..||.++|+|++++.-
T Consensus 10 lt~L~~~PLlkN~~AV 25 (81)
T PF09119_consen 10 LTWLGKIPLLKNTNAV 25 (81)
T ss_dssp EEEEE----TT-HHHH
T ss_pred HHHHHcCcccccHHHH
Confidence 4689999999997654
No 31
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=53.71 E-value=15 Score=21.57 Aligned_cols=25 Identities=8% Similarity=0.018 Sum_probs=20.1
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|.+++|.|..|+..+...+
T Consensus 49 l~~~IefaK~iP~F~~L~~~DQi~L 73 (221)
T cd06936 49 VQVLVEFTKGLPGFETLDHEDQIAL 73 (221)
T ss_pred HHHHHHHHhCCCchhhCChhHHHHH
Confidence 3457899999999999988776554
No 32
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=51.62 E-value=13 Score=17.36 Aligned_cols=22 Identities=18% Similarity=0.300 Sum_probs=17.7
Q ss_pred cCcccCCCChHHHhhHhhhhhe
Q psy719 17 RVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~~ 38 (45)
.|.++++.+++++.+|++++..
T Consensus 5 ~i~~~~Grs~EqK~~L~~~it~ 26 (60)
T PRK02289 5 RIDLFEGRSQEQKNALAREVTE 26 (60)
T ss_pred EEEECCCCCHHHHHHHHHHHHH
Confidence 4677888999999999888753
No 33
>PF02944 BESS: BESS motif; InterPro: IPR004210 The BESS domain has been named after the three proteins that originally defined the domain: BEAF (Boundary element associated factor 32) [], Suvar(3)7 [] and Stonewall []). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain. The BESS domain directs a variety of protein-protein interactions, including interactions with itself, with Dorsal, and with a TBP-associated factor. It is found in a single copy in Drosophila proteins and is often associated with the MADF domain [, , ]. Proteins known to contain a BESS domain include: Drosophila Boundary element associated factor 32 (BEAF-32). Drosophila Suppressor of variegation protein 3-7 (Su(var)3-7), which could play a role in chromosome condensation. Drosophila Ravus, which is homologous to the C-terminal part of Su(var)3-7 []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation. Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3). It functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. ; GO: 0003677 DNA binding
Probab=50.39 E-value=7 Score=16.93 Aligned_cols=19 Identities=16% Similarity=0.051 Sum_probs=13.5
Q ss_pred HhhcCcccCCCChHHHhhH
Q psy719 14 FLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 14 fL~~V~ilk~L~~~~l~ki 32 (45)
|++=+|.++.|++....++
T Consensus 8 l~Sl~p~~k~L~~~~k~~~ 26 (37)
T PF02944_consen 8 LLSLLPHMKRLPPKQKLKF 26 (37)
T ss_pred HHHhHHHHHhCCHHHHHHH
Confidence 3444699999999876543
No 34
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 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 (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=49.73 E-value=21 Score=19.42 Aligned_cols=25 Identities=4% Similarity=0.038 Sum_probs=20.3
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHh
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVA 33 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kia 33 (45)
....+|.+++|-|..|+..+...+.
T Consensus 31 ~~~v~~~k~~p~f~~L~~~dk~~Ll 55 (203)
T PF00104_consen 31 RLIVDWAKSFPEFSELSMEDKIALL 55 (203)
T ss_dssp HHHHHHHHTSTTGGGS-HHHHHHHH
T ss_pred HHHHHHHHhCcCHHhhhhhhhhhHH
Confidence 4578999999999999998877764
No 35
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=49.62 E-value=23 Score=17.54 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=19.3
Q ss_pred hhcCcccCCCChHHHhhHhhhhh
Q psy719 15 LSRVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 15 L~~V~ilk~L~~~~l~kiad~l~ 37 (45)
++++=.|..++++++.-|=.+|.
T Consensus 17 ~~r~v~LePM~~~ERkIIH~~Lq 39 (62)
T cd02638 17 RYRVLLFPPLNSRRRYLIHQTVE 39 (62)
T ss_pred cCCeEecCCCChHHHHHHHHHHh
Confidence 56777899999999998877776
No 36
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=49.32 E-value=26 Score=19.95 Aligned_cols=25 Identities=12% Similarity=0.044 Sum_probs=20.4
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|.+++|.|..|+..+...+
T Consensus 43 l~~~Iewak~lp~F~~L~~~DQ~~L 67 (207)
T cd06943 43 LFQLVEWAKRIPHFSELPLDDQVIL 67 (207)
T ss_pred HHHHHHHHHhCchhhccChhhhHHH
Confidence 3456899999999999998876655
No 37
>cd06944 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors. The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not
Probab=47.95 E-value=34 Score=20.24 Aligned_cols=24 Identities=4% Similarity=-0.112 Sum_probs=19.9
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-...+|.+++|.|++|+..+...+
T Consensus 52 ~~~VewaK~lp~F~~L~~~DQi~L 75 (237)
T cd06944 52 FSIVEWARNSVFFKELKVDDQMKL 75 (237)
T ss_pred HHHHHHHHhCCChhcCCHHHHHHH
Confidence 346899999999999998876655
No 38
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=47.75 E-value=13 Score=20.46 Aligned_cols=23 Identities=13% Similarity=0.031 Sum_probs=19.4
Q ss_pred hcCcccCCCChHHHhhHhhhhhe
Q psy719 16 SRVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 16 ~~V~ilk~L~~~~l~kiad~l~~ 38 (45)
++|.+-.-|+++|+..+|+.|..
T Consensus 116 ~~veiG~fL~~~eR~~la~~L~~ 138 (140)
T PF10003_consen 116 REVEIGRFLNPEEREELARELRR 138 (140)
T ss_pred EEEEEccCCCHHHHHHHHHHHHh
Confidence 46778888999999999998863
No 39
>cd06948 NR_LBD_COUP-TF Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family. The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): 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. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone
Probab=47.33 E-value=35 Score=20.10 Aligned_cols=25 Identities=4% Similarity=-0.080 Sum_probs=19.9
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
--...+|.|++|.|.+|+..+...+
T Consensus 43 L~~~VewaK~lp~F~~L~~~DQi~L 67 (236)
T cd06948 43 LFSAVEWARNIPFFPDLQVTDQVAL 67 (236)
T ss_pred HHHHHHHHHhCcCcccCCHHHHHHH
Confidence 3446899999999999998775544
No 40
>COG3228 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.20 E-value=19 Score=22.48 Aligned_cols=24 Identities=13% Similarity=0.267 Sum_probs=20.3
Q ss_pred HHHHhhcCcccCCCChHHHhhHhh
Q psy719 11 YEEFLSRVSILVQCGSKKMGIVAK 34 (45)
Q Consensus 11 ~~~fL~~V~ilk~L~~~~l~kiad 34 (45)
....|+.+|+|-.|++.++.++..
T Consensus 23 W~~~l~~lP~l~~L~~~e~~RL~~ 46 (266)
T COG3228 23 WQAALSNLPLLLCLSPQEQRRLVE 46 (266)
T ss_pred HHHHHhcCCcccCCCHHHHHHHHH
Confidence 356788899999999999999844
No 41
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=47.05 E-value=32 Score=17.16 Aligned_cols=33 Identities=15% Similarity=0.233 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhhcCcccCCCChHHHhhHhhhh
Q psy719 4 TIRKRKLYEEFLSRVSILVQCGSKKMGIVAKHV 36 (45)
Q Consensus 4 ~~~kr~~~~~fL~~V~ilk~L~~~~l~kiad~l 36 (45)
...+|....+|+..+..-.+++..+-..++|.+
T Consensus 48 ~y~rRK~Ii~~I~~l~~~~g~~~~~ai~~le~~ 80 (81)
T PF12550_consen 48 TYSRRKVIIDFIERLANERGISEEEAIEILEEI 80 (81)
T ss_pred hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 567889999999998888999999888777653
No 42
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=46.91 E-value=22 Score=19.27 Aligned_cols=31 Identities=23% Similarity=0.279 Sum_probs=24.3
Q ss_pred hhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 15 LSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 15 L~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
+...+.|..++...+..++.......|.+|+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ 32 (214)
T COG0664 2 LKENPLLNLLPSELLELLALKLEVRKLPKGE 32 (214)
T ss_pred cccccccccCCHHHHHHHhhhceeEeeCCCC
Confidence 4567778878888888888888888888874
No 43
>KOG0499|consensus
Probab=46.48 E-value=11 Score=26.46 Aligned_cols=35 Identities=14% Similarity=0.282 Sum_probs=30.8
Q ss_pred HHHHhhcCcccCCCChHHHhhHhhhhheeeecCCC
Q psy719 11 YEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 11 ~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
+-+.|++|.+|++.+..-+.-+.--|.++.|=+||
T Consensus 525 ~y~~lSKVqLFq~Cdr~mirDmllrLRsV~yLPgD 559 (815)
T KOG0499|consen 525 NYSILSKVQLFQGCDRQMIRDMLLRLRSVLYLPGD 559 (815)
T ss_pred ehhhhhHHHHhhhhHHHHHHHHHHHhhceeecCCc
Confidence 34679999999999999999999999999998886
No 44
>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal doma
Probab=46.17 E-value=41 Score=19.90 Aligned_cols=25 Identities=4% Similarity=-0.052 Sum_probs=20.4
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||.|.+|+..+-..+
T Consensus 45 l~~~VewAK~iP~F~~L~~~DQi~L 69 (235)
T cd06949 45 LVHMINWAKKIPGFVDLSLHDQVHL 69 (235)
T ss_pred HHHHHHHHHhCCCcccCCHHHHHHH
Confidence 3456899999999999998776555
No 45
>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-
Probab=46.00 E-value=22 Score=20.59 Aligned_cols=24 Identities=0% Similarity=-0.097 Sum_probs=19.6
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
....+|.+++|.|..|+..+...+
T Consensus 41 ~~~Ve~aK~lp~F~~L~~~DQi~L 64 (221)
T cd06946 41 VVIIGWAKHIPGFSSLSLNDQMSL 64 (221)
T ss_pred HHHHHHHHhCCCcccCCHHHHHHH
Confidence 345899999999999998876554
No 46
>PF09796 QCR10: Ubiquinol-cytochrome-c reductase complex subunit (QCR10); InterPro: IPR019182 This entry represents subunit 10 of the cytochrome b-c1 complex (also known as the ubiquinol-cytochrome c reductase complex or complex III). This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome. Subunit 10 is required for stable association of the iron-sulphur protein with the complex [].
Probab=45.24 E-value=13 Score=18.43 Aligned_cols=13 Identities=8% Similarity=0.381 Sum_probs=10.5
Q ss_pred HHHHhhcCcccCC
Q psy719 11 YEEFLSRVSILVQ 23 (45)
Q Consensus 11 ~~~fL~~V~ilk~ 23 (45)
..++|++||++.+
T Consensus 39 q~dil~KIP~~G~ 51 (64)
T PF09796_consen 39 QRDILQKIPVFGS 51 (64)
T ss_pred HHHHHHhCCcccc
Confidence 3589999999875
No 47
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=44.63 E-value=38 Score=16.19 Aligned_cols=28 Identities=11% Similarity=0.135 Sum_probs=20.8
Q ss_pred HHHHHHHhhcCc----ccCC-CChHHHhhHhhh
Q psy719 8 RKLYEEFLSRVS----ILVQ-CGSKKMGIVAKH 35 (45)
Q Consensus 8 r~~~~~fL~~V~----ilk~-L~~~~l~kiad~ 35 (45)
++....|+.+-+ .|.. |+..++.-|-++
T Consensus 5 ~~~i~~F~~~~~~~~l~F~p~ls~~eR~~vH~l 37 (60)
T cd02641 5 KAMVKAFMKDPKATELEFPPTLSSHDRLLVHEL 37 (60)
T ss_pred HHHHHHHHcCCCcCcEECCCCCCHHHHHHHHHH
Confidence 566788888766 6777 999888776444
No 48
>PRK15410 DgsA anti-repressor MtfA; Provisional
Probab=44.25 E-value=19 Score=22.30 Aligned_cols=24 Identities=17% Similarity=0.268 Sum_probs=19.2
Q ss_pred HHHHhhcCcccCCCChHHHhhHhhh
Q psy719 11 YEEFLSRVSILVQCGSKKMGIVAKH 35 (45)
Q Consensus 11 ~~~fL~~V~ilk~L~~~~l~kiad~ 35 (45)
..++|+ +|+++.|++.++.++...
T Consensus 19 W~~~l~-~pfy~~Ls~~~~~~L~~~ 42 (260)
T PRK15410 19 WQEALS-IPLLTPLTEQEQQKLVAL 42 (260)
T ss_pred HHHHHh-hHHHhcCCHHHHHHHHHH
Confidence 456777 899999999998887544
No 49
>cd06952 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2. The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D
Probab=44.02 E-value=41 Score=19.46 Aligned_cols=25 Identities=8% Similarity=0.065 Sum_probs=19.7
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|.+++|-|.+|+..+-..+
T Consensus 34 l~~~v~wak~iP~F~~L~~~DQ~~L 58 (222)
T cd06952 34 LFLSIHWARSIPAFQALGAETQTSL 58 (222)
T ss_pred HHHHHHHHHhCCchhhCChHHHHHH
Confidence 4456899999999999988774444
No 50
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=43.40 E-value=34 Score=19.38 Aligned_cols=25 Identities=12% Similarity=0.131 Sum_probs=20.4
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||-|.+|+..+-..+
T Consensus 15 l~~iI~waK~iP~F~~L~~~DQi~L 39 (195)
T cd06941 15 VQRVVEFAKRIPGFCDLSQDDQLLL 39 (195)
T ss_pred HHHHHHHHHcCCCcccCCHHHHHHH
Confidence 4557899999999999988776555
No 51
>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.
Probab=42.92 E-value=45 Score=19.85 Aligned_cols=25 Identities=8% Similarity=-0.027 Sum_probs=19.5
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
--...+|-|+||.|.+|+..+-..+
T Consensus 32 L~~~VeWAK~iP~F~~L~~~DQi~L 56 (232)
T cd07350 32 LVKTLRFVKGVPCFQELPLDDQLVL 56 (232)
T ss_pred HHHHHHHHHhCcCcccCChHHHHHH
Confidence 3456899999999999987764444
No 52
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=40.86 E-value=9.3 Score=20.13 Aligned_cols=20 Identities=5% Similarity=0.283 Sum_probs=14.6
Q ss_pred CcccCCCChHHHhhHhhhhh
Q psy719 18 VSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 18 V~ilk~L~~~~l~kiad~l~ 37 (45)
.++|+.|++.++.+|+.++.
T Consensus 24 a~vlk~l~~~ei~~i~~~ma 43 (108)
T PF14842_consen 24 AEVLKHLDEEEIERISREMA 43 (108)
T ss_dssp HHHHHHS-HHHHHHHHHHHH
T ss_pred HHHHccCCHHHHHHHHHHHH
Confidence 36788888888888877654
No 53
>COG0399 WecE Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]
Probab=40.68 E-value=23 Score=22.92 Aligned_cols=23 Identities=4% Similarity=0.059 Sum_probs=20.6
Q ss_pred cCcccCCCChHHHhhHhhhhhee
Q psy719 17 RVSILVQCGSKKMGIVAKHVTCA 39 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~~~ 39 (45)
++|+..+|++.+..+|++++...
T Consensus 348 ~LP~~p~l~~~~~~~V~~~l~~~ 370 (374)
T COG0399 348 SLPLHPNLSEEDVDRVIEALKEV 370 (374)
T ss_pred EccCCCCCCHHHHHHHHHHHHHH
Confidence 68999999999999999998653
No 54
>PF10660 MitoNEET_N: Iron-containing outer mitochondrial membrane protein N-terminus ; InterPro: IPR019610 The CDGSH iron sulphur domain are a group of iron-sulphur (Fe-S) clusters and a unique 39 amino acid CDGSH domain [C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H]. The CDGSH iron sulphur domain protein (also referred to as mitoNEET) is an integral membrane protein located in the outer mitochondrial membrane and whose function may be to transport iron into the mitochondria []. Iron in turn is essential for the function of several mitochondrial enzymes. This entry represents the N-terminal of the mitoNEET and Miner-type proteins that carry a CDGSH-type cluster-binding domain (IPR018967 from INTERPRO) that coordinate a redox-active 2Fe-2S cluster. In the outer mitochondrian membrane (OMM), the CDGSH 2Fe-2S-containing domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by the N-terminal domain found in higher vertebrates [, , ]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM.; GO: 0051537 2 iron, 2 sulfur cluster binding, 0043231 intracellular membrane-bounded organelle; PDB: 2R13_A 3REE_A 2QD0_B.
Probab=40.56 E-value=9.2 Score=19.01 Aligned_cols=32 Identities=13% Similarity=0.022 Sum_probs=0.0
Q ss_pred HHHHHhhcCcccCCCChHHHhhHhhhhheeee
Q psy719 10 LYEEFLSRVSILVQCGSKKMGIVAKHVTCAMV 41 (45)
Q Consensus 10 ~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y 41 (45)
.--++|+++||=+++..+-+..+-|.+....+
T Consensus 11 ~lP~YL~~lPiP~s~gg~f~Ls~kdWl~Lvp~ 42 (64)
T PF10660_consen 11 SLPNYLKSLPIPDSFGGFFKLSVKDWLALVPF 42 (64)
T ss_dssp --------------------------------
T ss_pred ccccccccccccccccccccccHHHHHHHHhH
Confidence 35678999999999888888777777655444
No 55
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=40.20 E-value=14 Score=16.54 Aligned_cols=21 Identities=14% Similarity=0.048 Sum_probs=13.1
Q ss_pred cCCCChHHHhhHhhhhheeee
Q psy719 21 LVQCGSKKMGIVAKHVTCAMV 41 (45)
Q Consensus 21 lk~L~~~~l~kiad~l~~~~y 41 (45)
|++++..+|..||.-+....|
T Consensus 2 L~~~~~~eL~~iAk~lgI~~~ 22 (43)
T PF07498_consen 2 LKSMTLSELREIAKELGIEGY 22 (43)
T ss_dssp HHCS-HHHHHHHHHCTT-TTG
T ss_pred cccCCHHHHHHHHHHcCCCCC
Confidence 456777788888877765543
No 56
>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal lig
Probab=40.20 E-value=35 Score=19.65 Aligned_cols=24 Identities=4% Similarity=0.016 Sum_probs=19.6
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
....+|.+.+|.|+.|+..+...+
T Consensus 46 ~~~vewak~~p~F~~L~~~Dq~~L 69 (222)
T cd06931 46 LVLVEWAKYIPAFCELPLDDQVAL 69 (222)
T ss_pred HHHHHHHHhCCccccCChHHHHHH
Confidence 346789999999999998876655
No 57
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=39.63 E-value=51 Score=16.58 Aligned_cols=28 Identities=11% Similarity=0.161 Sum_probs=20.2
Q ss_pred HHHHHHHhhcCccc-----------CCCChHHHhhHhhh
Q psy719 8 RKLYEEFLSRVSIL-----------VQCGSKKMGIVAKH 35 (45)
Q Consensus 8 r~~~~~fL~~V~il-----------k~L~~~~l~kiad~ 35 (45)
|+.+.+.+++|+-. .+++..+..++||.
T Consensus 19 k~~F~~~~~~Vs~~EI~~~Eq~Li~eG~~~eeiq~LCdv 57 (71)
T PF04282_consen 19 KEEFKKLFSDVSASEISAAEQELIQEGMPVEEIQKLCDV 57 (71)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHcCCCHHHHHHHhHH
Confidence 56677777777532 45888888888875
No 58
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=39.08 E-value=63 Score=17.20 Aligned_cols=26 Identities=8% Similarity=-0.004 Sum_probs=18.7
Q ss_pred HHHhhcCcccCCCChHHHhhH-hhhhh
Q psy719 12 EEFLSRVSILVQCGSKKMGIV-AKHVT 37 (45)
Q Consensus 12 ~~fL~~V~ilk~L~~~~l~ki-ad~l~ 37 (45)
-..-.+||-|+.|++..-.++ ..||+
T Consensus 28 ~~Lt~~vPgF~~ls~sKqRRLi~~ALE 54 (92)
T PF10330_consen 28 GYLTTSVPGFSDLSPSKQRRLIMAALE 54 (92)
T ss_pred HHHhccCCCcccCCHHHHHHHHHHHHh
Confidence 334468999999988655554 67776
No 59
>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=38.84 E-value=56 Score=19.47 Aligned_cols=25 Identities=4% Similarity=-0.158 Sum_probs=19.8
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|++|.|.+|+-.+-..+
T Consensus 53 L~~~VeWAK~iP~F~~L~~~DQi~L 77 (241)
T cd07069 53 LFSIVEWARSSIFFRELKVDDQMKL 77 (241)
T ss_pred HHHHHHHHhhCCCcccCCHHHHHHH
Confidence 3456899999999999998775554
No 60
>PF08385 DHC_N1: Dynein heavy chain, N-terminal region 1; InterPro: IPR013594 Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit []. The region featured in this family includes the sequences implicated in mediating these interactions []. It is thought to be flexible and not to adopt a rigid conformation [].
Probab=38.57 E-value=16 Score=23.63 Aligned_cols=35 Identities=9% Similarity=0.158 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhhcC-cccCCCChHHHhhHhhhhhe
Q psy719 4 TIRKRKLYEEFLSRV-SILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 4 ~~~kr~~~~~fL~~V-~ilk~L~~~~l~kiad~l~~ 38 (45)
+...-+.+..||+.+ |+++.|....+..|.+++.+
T Consensus 91 ~~~ea~d~~~fL~~l~~~~~~l~~~~~~~i~~~i~~ 126 (579)
T PF08385_consen 91 ALNEAKDNNKFLKPLEPPFELLEASDLSEIQESIPP 126 (579)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHH
Confidence 445566799999999 99999988888888887654
No 61
>cd06935 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors. The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), a
Probab=37.82 E-value=42 Score=19.99 Aligned_cols=25 Identities=8% Similarity=0.151 Sum_probs=19.7
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|++|-|.+|+..+-..+
T Consensus 65 l~~iVefAK~iPgF~~L~~~DQi~L 89 (243)
T cd06935 65 ITRVVDFAKKLPMFTELPCEDQIIL 89 (243)
T ss_pred HHHHHHHHhcCCccccCChHHHHHH
Confidence 3457899999999999988764443
No 62
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=37.18 E-value=48 Score=17.98 Aligned_cols=33 Identities=18% Similarity=0.354 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHhhcC------cccCCCChHHHhhHhhhh
Q psy719 4 TIRKRKLYEEFLSRV------SILVQCGSKKMGIVAKHV 36 (45)
Q Consensus 4 ~~~kr~~~~~fL~~V------~ilk~L~~~~l~kiad~l 36 (45)
-.++|+.|++-...+ .-|.+|+++|+.++-.-+
T Consensus 64 y~~Q~k~Ye~a~~~~~~~~lqkRle~l~~eE~~~L~~ei 102 (104)
T PF11460_consen 64 YMQQRKDYEEAVDQLTNEELQKRLEELSPEELEALQAEI 102 (104)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHhCCHHHHHHHHHHh
Confidence 345556666544222 457889999988885544
No 63
>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=37.05 E-value=49 Score=16.12 Aligned_cols=19 Identities=11% Similarity=0.076 Sum_probs=15.8
Q ss_pred cccCCCChHHHhhHhhhhh
Q psy719 19 SILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 19 ~ilk~L~~~~l~kiad~l~ 37 (45)
-.|..|+++++.-|-+++.
T Consensus 26 ~~l~PM~~~eRrivH~~~~ 44 (67)
T cd02644 26 VKLEPMNAYERRIIHDALA 44 (67)
T ss_pred eEeCCCCHHHHHHHHHHHH
Confidence 4578899999999888876
No 64
>PF02276 CytoC_RC: Photosynthetic reaction centre cytochrome C subunit; InterPro: IPR003158 The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors []. LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) []. Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP [, , ]. The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits []. RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain []. In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface. In the purple bacterium Rhodocyclus gelatinosus (Rhodopseudomonas gelatinosa), a high potential Fe-S protein (HiPIP) acts as an electron donor to reaction centre-bound cyt bc1 under anaerobic conditions in the light, while cyt c acts as a soluble electron carrier under aerobic conditions in the dark in order to re-reduce the oxidized electron donor [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0019684 photosynthesis, light reaction, 0030077 plasma membrane light-harvesting complex; PDB: 7PRC_C 6PRC_C 2X5V_C 2X5U_C 2WJM_C 2JBL_C 3T6D_C 3D38_C 2WJN_C 1VRN_C ....
Probab=36.97 E-value=27 Score=22.37 Aligned_cols=25 Identities=16% Similarity=0.193 Sum_probs=19.5
Q ss_pred HHhhcCcccCCCChHHHhhHhhhhh
Q psy719 13 EFLSRVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 13 ~fL~~V~ilk~L~~~~l~kiad~l~ 37 (45)
+.-++|..|++|+..+..+|-.++.
T Consensus 52 e~ykNv~VL~dls~~ef~rlM~amt 76 (314)
T PF02276_consen 52 EVYKNVKVLGDLSVAEFDRLMAAMT 76 (314)
T ss_dssp HHSSS-SSSTTSBHHHHHHHHHHHH
T ss_pred HHHhcchhhcCCCHHHHHHHHHHHH
Confidence 4557899999999999998876653
No 65
>cd06933 NR_LBD_VDR The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily. The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and
Probab=35.57 E-value=48 Score=19.64 Aligned_cols=25 Identities=4% Similarity=-0.101 Sum_probs=19.8
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||-|.+|+..+-..+
T Consensus 50 l~~iI~wAK~iPgF~~L~~~DQi~L 74 (238)
T cd06933 50 IQKVIGFAKMIPGFRDLTAEDQIAL 74 (238)
T ss_pred HHHHHHHHcCCCccccCChHHHHHH
Confidence 3557899999999999988665444
No 66
>PF03281 Mab-21: Mab-21 protein
Probab=34.81 E-value=32 Score=20.59 Aligned_cols=26 Identities=8% Similarity=0.326 Sum_probs=21.7
Q ss_pred HHHhhcCcccCCCChHHHhhHhhhhh
Q psy719 12 EEFLSRVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 12 ~~fL~~V~ilk~L~~~~l~kiad~l~ 37 (45)
.=|+.++-+|.++++.++..++..+.
T Consensus 263 hff~~~~NLf~~~~~~~~~~~~~~~~ 288 (292)
T PF03281_consen 263 HFFIPNLNLFQHLSPEELDELARKLE 288 (292)
T ss_pred ccCCCCcccCCCCCHHHHHHHHHHHH
Confidence 34778899999999999999987764
No 67
>cd07073 NR_LBD_AR Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator. The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell funct
Probab=34.20 E-value=83 Score=18.93 Aligned_cols=25 Identities=4% Similarity=-0.158 Sum_probs=19.6
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
--...+|-|+||-|.+|+-.+-..+
T Consensus 41 L~~~VeWAK~iP~F~~L~~~DQi~L 65 (246)
T cd07073 41 LVHVVKWAKALPGFRNLHVDDQMAV 65 (246)
T ss_pred HHHHHHHHHcCCCccCCCHHHHHHH
Confidence 4456899999999999987665444
No 68
>PRK15407 lipopolysaccharide biosynthesis protein RfbH; Provisional
Probab=34.12 E-value=31 Score=22.23 Aligned_cols=22 Identities=5% Similarity=0.096 Sum_probs=19.8
Q ss_pred cCcccCCCChHHHhhHhhhhhe
Q psy719 17 RVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~~ 38 (45)
.+|+..+|++.++..|++++..
T Consensus 411 ~LP~~~~l~~~~v~~i~~~i~~ 432 (438)
T PRK15407 411 WIGVYPGLTEEMLDYVIEKIEE 432 (438)
T ss_pred EecCCCCCCHHHHHHHHHHHHH
Confidence 6799999999999999999864
No 69
>cd07349 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.
Probab=33.96 E-value=78 Score=18.68 Aligned_cols=25 Identities=8% Similarity=-0.071 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhcCcccCCCChHHHh
Q psy719 6 RKRKLYEEFLSRVSILVQCGSKKMG 30 (45)
Q Consensus 6 ~kr~~~~~fL~~V~ilk~L~~~~l~ 30 (45)
+.--...+|-|+||-|.+|+-.+-.
T Consensus 30 ~~L~~~V~WAK~iP~F~~L~~~DQi 54 (222)
T cd07349 30 DVLVKTVAFMRNLPSFWQLPPQDQL 54 (222)
T ss_pred HHHHHHHHHHhcCCCcccCChHHHH
Confidence 3344568999999999999876644
No 70
>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely r
Probab=33.83 E-value=57 Score=19.46 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=19.4
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
....+|-|+||-|.+|+..+-..+
T Consensus 62 ~~vVefAK~IPgF~~L~~~DQi~L 85 (241)
T cd06939 62 QYVVEFAKRIPGFMELCQNDQIVL 85 (241)
T ss_pred HHHHHHHhcCCCcccCCHHHHHHH
Confidence 457899999999999988765444
No 71
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=33.52 E-value=80 Score=18.63 Aligned_cols=25 Identities=12% Similarity=-0.049 Sum_probs=19.6
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||-|.+|+..+-..+
T Consensus 51 l~~~V~wAK~iPgF~~L~~~DQi~L 75 (231)
T cd06937 51 IIKIVEFAKRLPGFTTLTIADQITL 75 (231)
T ss_pred HHHHHHHHhcCCccccCCHHHHHHH
Confidence 4457899999999999988664443
No 72
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=33.16 E-value=60 Score=19.45 Aligned_cols=25 Identities=4% Similarity=0.138 Sum_probs=19.7
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||-|.+|+..+-..+
T Consensus 55 i~~iv~wAK~IPgF~~L~~~DQi~L 79 (239)
T cd07072 55 IDVIKTFAEKIPGFPDLCKEDQELL 79 (239)
T ss_pred HHHHHHHhccCCCccCCCHHHHHHH
Confidence 3457899999999999988764444
No 73
>PF04369 Lactococcin: Lactococcin-like family; InterPro: IPR007464 Bacteriocins are produced by bacteria to inhibit the growth of similar or closely related bacterial strains. The class II bacteriocins are small heat-stable proteins for which disulphide bonds are the only modification to the peptide. Lactococcin A and B are class-IId bacteriocins (one-peptide non-pediocin-like bacteriocin) [, ].; GO: 0042742 defense response to bacterium, 0005576 extracellular region
Probab=32.77 E-value=24 Score=17.38 Aligned_cols=13 Identities=0% Similarity=0.094 Sum_probs=10.8
Q ss_pred cCCCChHHHhhHh
Q psy719 21 LVQCGSKKMGIVA 33 (45)
Q Consensus 21 lk~L~~~~l~kia 33 (45)
|+.|+++||.+|.
T Consensus 7 f~~~sdeeL~~i~ 19 (60)
T PF04369_consen 7 FNILSDEELSKIN 19 (60)
T ss_pred ceecCHHHHhhcc
Confidence 6778999999885
No 74
>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, P
Probab=32.60 E-value=58 Score=19.65 Aligned_cols=25 Identities=8% Similarity=-0.000 Sum_probs=19.3
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||-|.+|+..+-..+
T Consensus 76 i~~vVewAK~IPgF~~L~~~DQi~L 100 (259)
T cd06932 76 IRELTEFAKSLPGFRNLDLNDQVTL 100 (259)
T ss_pred HHHHHHHHhcCCCcccCChhHHHHH
Confidence 3457899999999999987664433
No 75
>PRK10119 putative hydrolase; Provisional
Probab=32.29 E-value=72 Score=19.24 Aligned_cols=33 Identities=9% Similarity=0.077 Sum_probs=25.6
Q ss_pred HHHHHhhcCcccCCCChHHHhhHhhhhheeeecCC
Q psy719 10 LYEEFLSRVSILVQCGSKKMGIVAKHVTCAMVEKG 44 (45)
Q Consensus 10 ~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y~~G 44 (45)
....||++. +.++++..+..|..++....|..|
T Consensus 80 ~a~~~L~~~--~~g~~~~~i~~V~~iI~~~sfs~~ 112 (231)
T PRK10119 80 ETRRILRED--FPDFPAEKIEAVCHAIEAHSFSAQ 112 (231)
T ss_pred HHHHHHHHc--ccCcCHHHHHHHHHHHHHcCCCCC
Confidence 355677664 456899999999999999998764
No 76
>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as
Probab=32.26 E-value=64 Score=19.18 Aligned_cols=25 Identities=0% Similarity=0.129 Sum_probs=19.9
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||-|.+|+..+-..+
T Consensus 54 l~~iv~wAK~IPgF~~L~~~DQi~L 78 (239)
T cd06945 54 VDVIRQWAEKIPGFKDLHREDQDLL 78 (239)
T ss_pred HHHHHHHHHhCCCcccCCHHHHHHH
Confidence 3456899999999999988775544
No 77
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=32.15 E-value=85 Score=18.44 Aligned_cols=25 Identities=4% Similarity=-0.104 Sum_probs=19.2
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|++|-|.+|+..+-..+
T Consensus 32 L~~~V~wAK~iP~F~~L~~~DQi~L 56 (222)
T cd06951 32 LLKTIRFVRNLPCFTYLPPDDQLRL 56 (222)
T ss_pred HHHHHHHHHhCCCcccCChHHHHHH
Confidence 3456889999999999988764433
No 78
>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge
Probab=31.64 E-value=93 Score=17.92 Aligned_cols=24 Identities=4% Similarity=0.007 Sum_probs=19.5
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-...+|-|++|.|.+|+..+-..+
T Consensus 40 ~~~VewaK~ip~F~~L~~~DQi~L 63 (206)
T cd06950 40 FMAVKWAKSIPAFSTLPFRDQLIL 63 (206)
T ss_pred HHHHHHHHhCCccccCCHHHHHHH
Confidence 446889999999999998875554
No 79
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=31.43 E-value=20 Score=17.36 Aligned_cols=24 Identities=21% Similarity=0.029 Sum_probs=17.2
Q ss_pred cCCCChHHHhhHhhhhheeeecCC
Q psy719 21 LVQCGSKKMGIVAKHVTCAMVEKG 44 (45)
Q Consensus 21 lk~L~~~~l~kiad~l~~~~y~~G 44 (45)
-+.++..++..+++.+...+.++|
T Consensus 28 g~~l~~~~l~~~~~~l~~~y~~~G 51 (76)
T PF08479_consen 28 GRCLTLADLQQLADALTNYYREKG 51 (76)
T ss_dssp TSBB-HHHHHHHHHHHHHHHHHTT
T ss_pred CCCcCHHHHHHHHHHHHHHHHHcC
Confidence 456788888999988877666555
No 80
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=31.19 E-value=34 Score=19.07 Aligned_cols=20 Identities=0% Similarity=0.021 Sum_probs=16.3
Q ss_pred cCCCChHHHhhHhhhhheee
Q psy719 21 LVQCGSKKMGIVAKHVTCAM 40 (45)
Q Consensus 21 lk~L~~~~l~kiad~l~~~~ 40 (45)
..+|+++|+.+|.+++...+
T Consensus 45 ~~eLteeei~~ir~~i~~~~ 64 (121)
T COG0099 45 VGELTEEEIERLRDAIQNKY 64 (121)
T ss_pred hccCCHHHHHHHHHHHHhcC
Confidence 46799999999999987533
No 81
>PHA02994 hypothetical protein; Provisional
Probab=30.47 E-value=32 Score=20.97 Aligned_cols=31 Identities=6% Similarity=0.242 Sum_probs=26.9
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHhhhhhee
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVAKHVTCA 39 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~ 39 (45)
-.|..|..+|..++.+....+..||+.+...
T Consensus 186 ~~f~~Fv~kik~l~~~~~~~id~iC~~~~~i 216 (218)
T PHA02994 186 ISFRKFVNKIKKLKTLKNSSIDNICNDMKSI 216 (218)
T ss_pred hHHHHHHHHHHHhcccccchHHHHHHhhhcc
Confidence 5688999999999999887799999998654
No 82
>cd01277 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression.
Probab=30.01 E-value=42 Score=16.67 Aligned_cols=21 Identities=5% Similarity=0.064 Sum_probs=15.5
Q ss_pred cCcccCCCChHHHhhHhhhhh
Q psy719 17 RVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~ 37 (45)
-|+-|.+|+++++..+++++.
T Consensus 44 H~~~~~~l~~~e~~~l~~~~~ 64 (103)
T cd01277 44 HYENLLDLDPEELAELILAAK 64 (103)
T ss_pred ccCChhhCCHHHHHHHHHHHH
Confidence 355677889988888877664
No 83
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=29.34 E-value=1e+02 Score=16.62 Aligned_cols=32 Identities=16% Similarity=0.223 Sum_probs=25.0
Q ss_pred HHHHHHHHhhcCcccC----CCChHHHhhHhhhhhe
Q psy719 7 KRKLYEEFLSRVSILV----QCGSKKMGIVAKHVTC 38 (45)
Q Consensus 7 kr~~~~~fL~~V~ilk----~L~~~~l~kiad~l~~ 38 (45)
=|+.|.+.-++.+-++ +|++.+...|.+.|..
T Consensus 8 ik~l~~e~~~~~~~l~~v~~~ls~eeK~~i~~~l~~ 43 (115)
T PF05397_consen 8 IKQLYEEVSRNPVRLSPVTNSLSPEEKAAIRQQLQE 43 (115)
T ss_pred HHHHHHHHHhcCCCCCcccccCCHHHHHHHHHHHHH
Confidence 3677888888877774 5789999888887754
No 84
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=29.01 E-value=50 Score=15.01 Aligned_cols=22 Identities=14% Similarity=0.288 Sum_probs=15.3
Q ss_pred cCcccCCCChHHHhhHhhhhhe
Q psy719 17 RVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~~ 38 (45)
+|.+++..++.++.+|+.++..
T Consensus 5 ~i~~~~Grs~eqk~~l~~~it~ 26 (61)
T PRK02220 5 HIKLIEGRTEEQLKALVKDVTA 26 (61)
T ss_pred EEEEcCCCCHHHHHHHHHHHHH
Confidence 3556677788888888776643
No 85
>PF15100 TMEM187: TMEM187 protein family
Probab=28.95 E-value=21 Score=22.07 Aligned_cols=25 Identities=12% Similarity=0.068 Sum_probs=21.4
Q ss_pred HHhhcCcccCCCChHHHhhHhhhhh
Q psy719 13 EFLSRVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 13 ~fL~~V~ilk~L~~~~l~kiad~l~ 37 (45)
--|.+-++|+.|+-.--+||||+|.
T Consensus 208 ~~La~~~lFq~lTGhFWSKvcdvlq 232 (242)
T PF15100_consen 208 HELARWRLFQRLTGHFWSKVCDVLQ 232 (242)
T ss_pred HHHHhhHHHHHhcccHHHHHHHHHH
Confidence 3466779999999999999999985
No 86
>PF00511 PPV_E2_C: E2 (early) protein, C terminal; InterPro: IPR000427 E2 is an early regulatory protein found in the dsDNA papillomaviruses. The viral genome is a 7.9-kb circular DNA that codes for at least eight early and two late (capsid) proteins. The products of the early genes E6 and E7 are oncoproteins that destabilise the cellular tumour suppressors p53 and pRB. The product of the E1 gene is a helicase necessary for viral DNA replication. The products of the E2 gene play key roles in the regulation of viral gene transcription and DNA replication. During early stages of viral infection, the E2 protein represses the transcription of the oncogenes E6 and E7, reintroduction of E2 into cervical cancer cell-lines leads to repression of E6/E7 transcription, stabilisation of the tumour suppressor p53, and cell-cycle arrest at the G1 phase of the cell cycle. E2 can also induce apoptosis by a p53-independent mechanism. E2 proteins from all papillomavirus strains bind a consensus palindromic sequence ACCgNNNNcGGT present in multiple copies in the regulatory region. It can either activate or repress transcription, depending on E2RE's position with regard to proximal promoter elements. Repression occurs by sterically hindering the assembly of the transcription initiation complex. The E2 protein is composed of a C-terminal DNA-binding domain and an N-terminal trans-activation domain. E2 exists in solution and binds to DNA as a dimer The E2-DNA binding domain forms a dimeric beta-barrel, with each subunit contributing an anti-parallel 4-stranded beta-sheet "half-barrel" [, ]. The topology of each subunit is beta1-1-beta2-beta3-2-beta4. Helix 1 is the recognition helix housing all of the amino acid residues involved in direct DNA sequence specification. Upon dimerisation, strands beta2 and beta4 at the edges of each subunit participate in a continuous hydrogen-bonding network, which results in an 8-stranded beta-barrel. The dimer interface is extensive, made up of hydrogen bonds between subunits and a substantial hydrophobic beta-barrel core. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006275 regulation of DNA replication, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1JJH_C 1DBD_B 2BOP_A 1DHM_B 1A7G_E 1JJ4_B 1F9F_D 2AYG_A 2AYE_E 2AYB_A ....
Probab=28.84 E-value=39 Score=17.28 Aligned_cols=16 Identities=25% Similarity=0.320 Sum_probs=9.5
Q ss_pred HHHHHHhhcCcccCCC
Q psy719 9 KLYEEFLSRVSILVQC 24 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L 24 (45)
++...||+.|++=++.
T Consensus 58 ~QR~~FL~~V~lPkgv 73 (81)
T PF00511_consen 58 EQREQFLKTVKLPKGV 73 (81)
T ss_dssp HHHHHHHHHS---TTS
T ss_pred HHHHHHHhcCcCCCCE
Confidence 4567899999986554
No 87
>PF03250 Tropomodulin: Tropomodulin; InterPro: IPR004934 Actin filaments have an intrinsic polarity, each with a fast-growing (barbed) end and a slow-growing (pointed) end. To regulate the dynamics at these ends, capping proteins have evolved that specifically bind to either the barbed or the pointed ends of the filament, where they block the association and dissociation of monomers. Pointed ends, for which actin monomers have significantly lower association and dissociation rate-constants than for barbed, are capped by either the Arp2/3 complex or tropomodulins []. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments []. Limited proteolysis shows this protein is composed of two domains. The unstructured tropomyosin-binding region at the N terminus has an actin pointed-end-capping activity that is dramatically up-regulated by tropomyosin coating of the actin filament[]. The second region is found near the C terminus. This tropomyosin-independent capping-domain caps pure actin. ; GO: 0005523 tropomyosin binding, 0005856 cytoskeleton
Probab=28.63 E-value=28 Score=20.01 Aligned_cols=19 Identities=5% Similarity=0.204 Sum_probs=15.8
Q ss_pred CcccCCCChHHHhhHhhhh
Q psy719 18 VSILVQCGSKKMGIVAKHV 36 (45)
Q Consensus 18 V~ilk~L~~~~l~kiad~l 36 (45)
=.||..|++.||..+...|
T Consensus 18 DelL~~LS~EEL~~L~~el 36 (147)
T PF03250_consen 18 DELLAKLSPEELEELENEL 36 (147)
T ss_pred HHHHHhCCHHHHHHHHHHH
Confidence 3689999999999998554
No 88
>smart00315 RGS Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
Probab=28.61 E-value=25 Score=17.53 Aligned_cols=32 Identities=13% Similarity=0.037 Sum_probs=15.5
Q ss_pred HHHHHhhcCcccCCCCh-HHHhhHhhhhheeee
Q psy719 10 LYEEFLSRVSILVQCGS-KKMGIVAKHVTCAMV 41 (45)
Q Consensus 10 ~~~~fL~~V~ilk~L~~-~~l~kiad~l~~~~y 41 (45)
++..|+..|.-++.+.. .++.+.|.-+-..++
T Consensus 26 e~l~F~~~v~~~~~~~~~~~~~~~a~~I~~~yi 58 (118)
T smart00315 26 ENLEFWLAVEEFKKAEDDEERIAKAREIYDKFL 58 (118)
T ss_pred HhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHh
Confidence 34555555555555544 455555544433333
No 89
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=28.55 E-value=74 Score=15.53 Aligned_cols=23 Identities=4% Similarity=0.079 Sum_probs=17.4
Q ss_pred hhcCcccCCCChHHHhhHhhhhh
Q psy719 15 LSRVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 15 L~~V~ilk~L~~~~l~kiad~l~ 37 (45)
...++=|.+|.+.+..+|.+.++
T Consensus 60 ~~~i~G~~~L~~~Dq~~i~~~i~ 82 (82)
T PF00645_consen 60 IEEIKGFDELKPEDQEKIRKLIE 82 (82)
T ss_dssp GGGCETCCCS-HHHHHHHHHHHS
T ss_pred HHHCCChHHCCHHHHHHHHHHhC
Confidence 45667788899999999988774
No 90
>PF12646 DUF3783: Domain of unknown function (DUF3783); InterPro: IPR016621 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.22 E-value=48 Score=15.60 Aligned_cols=21 Identities=5% Similarity=0.061 Sum_probs=17.1
Q ss_pred cccCCCChHHHhhHhhhhhee
Q psy719 19 SILVQCGSKKMGIVAKHVTCA 39 (45)
Q Consensus 19 ~ilk~L~~~~l~kiad~l~~~ 39 (45)
=+|.+++..++.++.+++...
T Consensus 4 ll~~g~~~~el~~~l~~~r~~ 24 (58)
T PF12646_consen 4 LLFSGFSGEELDKFLDALRKA 24 (58)
T ss_pred EEECCCCHHHHHHHHHHHHHc
Confidence 468889999999998887655
No 91
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=28.13 E-value=53 Score=14.63 Aligned_cols=21 Identities=19% Similarity=0.181 Sum_probs=14.8
Q ss_pred cCcccCCCChHHHhhHhhhhh
Q psy719 17 RVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~ 37 (45)
+|.+++.-+.++..+++.++.
T Consensus 4 ~i~~~~grt~eqk~~l~~~i~ 24 (58)
T cd00491 4 QIYILEGRTDEQKRELIERVT 24 (58)
T ss_pred EEEEcCCCCHHHHHHHHHHHH
Confidence 355667777888888877764
No 92
>TIGR01847 bacteriocin_sig bacteriocin-type signal sequence. Bacteriocins are bacterial peptide products toxic to closely related bacteria. This model represents the N-terminal region up to the GG cleavage motif. Processing to remove this bacteriocin leader peptide occurs together with export by an ABC transporter. Note: because this model is so small (15 amino acids), it may have many spurious high-scoring matches to unrelated proteins, even with fairly stringent cutoff scores. The most likely true positives are small proteins of Gram-positive bacteria, matching regions that start within the first 15 amino acids, and encoded near bacteriocin transport family proteins (TIGR01000, TIGR01193).
Probab=27.99 E-value=43 Score=13.81 Aligned_cols=13 Identities=8% Similarity=0.238 Sum_probs=9.6
Q ss_pred cCCCChHHHhhHh
Q psy719 21 LVQCGSKKMGIVA 33 (45)
Q Consensus 21 lk~L~~~~l~kia 33 (45)
|+.|+..+|..|.
T Consensus 1 fk~Ls~kEL~~I~ 13 (26)
T TIGR01847 1 FKELSEKELAQII 13 (26)
T ss_pred CccCCHHHHhhcc
Confidence 4678888888774
No 93
>PRK15375 pathogenicity island 1 effector protein StpP; Provisional
Probab=27.91 E-value=44 Score=22.88 Aligned_cols=20 Identities=5% Similarity=0.107 Sum_probs=16.1
Q ss_pred HHHHHHHhhcCcccCCCChH
Q psy719 8 RKLYEEFLSRVSILVQCGSK 27 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~ 27 (45)
-+....+|.+||+|+++..-
T Consensus 38 ~~k~~~~l~~~pl~~~~~~v 57 (535)
T PRK15375 38 SSKVLTWLGKMPLFKNTEVV 57 (535)
T ss_pred HHHHHHHHhcCccccchHHH
Confidence 35578999999999997653
No 94
>PLN02806 complex I subunit
Probab=27.87 E-value=48 Score=17.24 Aligned_cols=16 Identities=19% Similarity=0.530 Sum_probs=13.3
Q ss_pred HHHHHHHhhcCcccCC
Q psy719 8 RKLYEEFLSRVSILVQ 23 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~ 23 (45)
-+.|.+-|+++|++..
T Consensus 16 ~qlysNalRKLP~mrh 31 (81)
T PLN02806 16 TQLYSNALRKLPLMRH 31 (81)
T ss_pred HHHHHhHHhhCccccC
Confidence 3568899999999984
No 95
>cd08795 Death_IRAK2 Death domain of Interleukin 1 Receptor Associated Kinase-2. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 1 (IRAK1). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors (TLRs), nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK2 is an essential component of several signaling pathways, including NF-kappaB and the IL-1 signaling pathways. It is an inactive kinase that participates in septic shock mediated by TLR4 and TLR9. It plays a redundant role with IRAK1 in early NF-kB and MAPK responses, and remains present at later stages whereas IRAK1 disappears. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-as
Probab=27.74 E-value=49 Score=17.34 Aligned_cols=20 Identities=5% Similarity=0.029 Sum_probs=13.7
Q ss_pred cccCCCChHHHhhHhhhhhe
Q psy719 19 SILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 19 ~ilk~L~~~~l~kiad~l~~ 38 (45)
|.+-+||..++.++|..|..
T Consensus 1 ~~iy~lP~~v~~~lc~~lDs 20 (88)
T cd08795 1 PYVYQLPAWVLDDFCRNMDA 20 (88)
T ss_pred CchhhCCHHHHHHHHHHHcc
Confidence 45566777777777777653
No 96
>PF09228 Prok-TraM: Prokaryotic Transcriptional repressor TraM; InterPro: IPR015309 Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a globular head and an elongated tail, and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation []. ; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Q0O_D 2HJD_D 1UPG_A 1US6_B 1RFY_B.
Probab=27.66 E-value=31 Score=18.63 Aligned_cols=20 Identities=0% Similarity=0.096 Sum_probs=15.1
Q ss_pred CcccCCCChHHHhhHh-hhhh
Q psy719 18 VSILVQCGSKKMGIVA-KHVT 37 (45)
Q Consensus 18 V~ilk~L~~~~l~kia-d~l~ 37 (45)
++++.+|++.+|-.|+ +|+.
T Consensus 18 ~~l~~~l~~seLE~Ltv~AIR 38 (102)
T PF09228_consen 18 EGLFSGLPKSELETLTVSAIR 38 (102)
T ss_dssp HHHCTTS-HHHHHHHHHHHHH
T ss_pred HHHhcCCCHHHHHHHHHHHHH
Confidence 4678899999999997 6653
No 97
>TIGR02379 ECA_wecE TDP-4-keto-6-deoxy-D-glucose transaminase. This family consists of TDP-4-keto-6-deoxy-D-glucose transaminases, the WecE (formerly RffA) protein of enterobacterial common antigen (ECA) biosynthesis, from enterobacteria. It also includes closely matching sequence from species not expected to make ECA, but which contain other genes for the biosynthesis of TDP-4-keto-6-deoxy-D-Glc, an intermediate in the biosynthesis of other compounds as well and the substrate of WecA. This family belongs to the DegT/DnrJ/EryC1/StrS aminotransferase family (pfam01041).
Probab=27.48 E-value=57 Score=20.48 Aligned_cols=22 Identities=9% Similarity=0.132 Sum_probs=19.8
Q ss_pred cCcccCCCChHHHhhHhhhhhe
Q psy719 17 RVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~~ 38 (45)
++|+...|++.+...|++++..
T Consensus 352 ~LP~~~~l~~~~~~~i~~~i~~ 373 (376)
T TIGR02379 352 RLPLYYGLSKEDQARVIQTICD 373 (376)
T ss_pred EccCCCCCCHHHHHHHHHHHHH
Confidence 6899999999999999999864
No 98
>PF14841 FliG_M: FliG middle domain; PDB: 3HJL_A 3AJC_A 1LKV_X 3SOH_D 3USY_B 3USW_A.
Probab=27.34 E-value=69 Score=15.84 Aligned_cols=31 Identities=13% Similarity=0.206 Sum_probs=24.3
Q ss_pred HHHHHhhcCcccCCCChHHHhhHhhhhheee
Q psy719 10 LYEEFLSRVSILVQCGSKKMGIVAKHVTCAM 40 (45)
Q Consensus 10 ~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~ 40 (45)
...+.+..+--+..+++..+..|.+.|..+.
T Consensus 40 ~r~~v~~Ria~~~~v~~~~i~~ie~~L~~~l 70 (79)
T PF14841_consen 40 LRAEVVRRIARLESVSPEVIEEIEEVLEEKL 70 (79)
T ss_dssp HHHHHHHHHHTCCCCSHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 3456777888888999999999988887543
No 99
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.29 E-value=57 Score=16.52 Aligned_cols=16 Identities=13% Similarity=0.204 Sum_probs=13.4
Q ss_pred CCCChHHHhhHhhhhh
Q psy719 22 VQCGSKKMGIVAKHVT 37 (45)
Q Consensus 22 k~L~~~~l~kiad~l~ 37 (45)
.++++.|..-||+.|.
T Consensus 52 enfSpsEmqaiA~eL~ 67 (71)
T COG4840 52 ENFSPSEMQAIADELG 67 (71)
T ss_pred ccCCHHHHHHHHHHHH
Confidence 4688999999999875
No 100
>PF06518 DUF1104: Protein of unknown function (DUF1104); InterPro: IPR009488 This family consists of several hypothetical proteins of unknown function which appear to be found exclusively in Helicobacter pylori.; PDB: 2XRH_A.
Probab=27.03 E-value=32 Score=18.14 Aligned_cols=22 Identities=14% Similarity=-0.004 Sum_probs=15.2
Q ss_pred ccCCCChHHHhhHhhhhheeee
Q psy719 20 ILVQCGSKKMGIVAKHVTCAMV 41 (45)
Q Consensus 20 ilk~L~~~~l~kiad~l~~~~y 41 (45)
-|+.+++.+|.++|--+.+..+
T Consensus 2 DFsk~sn~EL~kmaG~v~~k~~ 23 (93)
T PF06518_consen 2 DFSKKSNEELIKMAGKVDPKDV 23 (93)
T ss_dssp SSTTS-HHHHHHTTTTS-GGGH
T ss_pred cchhcChHHHHHHHCCCCHHHH
Confidence 3778899999999877766544
No 101
>PF04708 Pox_F16: Poxvirus F16 protein; InterPro: IPR006798 This entry represents the Poxvirus F16 proteins.
Probab=26.38 E-value=47 Score=20.24 Aligned_cols=31 Identities=6% Similarity=0.273 Sum_probs=27.6
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHhhhhhee
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVAKHVTCA 39 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~ 39 (45)
..|..|..+|.-++....+++..||+.+...
T Consensus 186 ~~fk~Fi~kik~l~~~~~~~i~~IC~~~~~i 216 (218)
T PF04708_consen 186 ISFKRFINKIKKLKKKENSDIDEICNNMKSI 216 (218)
T ss_pred HHHHHHHHHHHHhcccchhhHHHHHhhhhhc
Confidence 5689999999999999999999999988653
No 102
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=26.19 E-value=50 Score=14.98 Aligned_cols=17 Identities=18% Similarity=0.337 Sum_probs=10.8
Q ss_pred CCCChHHHhhHhhhhhe
Q psy719 22 VQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 22 k~L~~~~l~kiad~l~~ 38 (45)
..++-..+.+||++|..
T Consensus 36 ~~~~~~~l~~ia~~l~~ 52 (63)
T PF13443_consen 36 SNPSLDTLEKIAKALNC 52 (63)
T ss_dssp ----HHHHHHHHHHHT-
T ss_pred ccccHHHHHHHHHHcCC
Confidence 46888999999999864
No 103
>TIGR01358 DAHP_synth_II 3-deoxy-7-phosphoheptulonate synthase, class II. Homologs scoring between trusted and noise cutoff include proteins involved in antibiotic biosynthesis; one example is active as this enzyme, while another acts on an amino analog.
Probab=26.01 E-value=87 Score=21.03 Aligned_cols=30 Identities=13% Similarity=0.067 Sum_probs=25.2
Q ss_pred HHHHhhcC------cccCCCChHHHhhHhhhhheee
Q psy719 11 YEEFLSRV------SILVQCGSKKMGIVAKHVTCAM 40 (45)
Q Consensus 11 ~~~fL~~V------~ilk~L~~~~l~kiad~l~~~~ 40 (45)
+.+|++.| .+-.+++++++..++|.|.+..
T Consensus 271 HVef~rgI~NPIGvKvGP~~~p~~l~~L~~~LnP~~ 306 (443)
T TIGR01358 271 HVEFLRGVRNPIGIKVGPSMTPDELLRLIERLNPEN 306 (443)
T ss_pred HHHHHhcCCCCeeEEECCCCCHHHHHHHHHHhCCCC
Confidence 56788774 7888999999999999998764
No 104
>PF07894 DUF1669: Protein of unknown function (DUF1669); InterPro: IPR012461 This family is composed of sequences derived from hypothetical eukaryotic proteins of unknown function. Some members of this family are annotated as being potential phospholipases but no literature was found to support this.
Probab=25.94 E-value=1.3e+02 Score=18.92 Aligned_cols=33 Identities=15% Similarity=0.104 Sum_probs=27.8
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhHhhhhheee
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIVAKHVTCAM 40 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~ 40 (45)
.+.|..||++=-+..=|++.|+..|....+.-.
T Consensus 35 ~eAy~~~L~~E~~~~FLS~~Ei~~I~~~~~~~~ 67 (284)
T PF07894_consen 35 PEAYYEFLKEEGERDFLSSEEIQYILENAEDPD 67 (284)
T ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHhccCCC
Confidence 467899999999999999999999988875533
No 105
>PF08597 eIF3_subunit: Translation initiation factor eIF3 subunit; InterPro: IPR013906 This shows protein subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae (Baker's yeast) protein Q05775 from SWISSPROT has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p []. ; PDB: 3BPJ_D 2KRB_B.
Probab=25.85 E-value=46 Score=19.86 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=19.7
Q ss_pred HHHHHhhcC--cccCCCChHHHhhHhhhhhe
Q psy719 10 LYEEFLSRV--SILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 10 ~~~~fL~~V--~ilk~L~~~~l~kiad~l~~ 38 (45)
.|..||..+ .+..+|+..++.+|+..|..
T Consensus 162 ~y~~fl~~l~r~l~~~L~~~~ikki~s~l~~ 192 (245)
T PF08597_consen 162 HYPSFLKELIRDLCKNLTSEDIKKISSSLTV 192 (245)
T ss_dssp THHHHHHHHHHHHHTTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 355566555 56678999999999877653
No 106
>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of
Probab=25.84 E-value=75 Score=18.68 Aligned_cols=24 Identities=8% Similarity=-0.025 Sum_probs=18.8
Q ss_pred HHHHHHhhcCcccCCCChHHHhhH
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
....+|-|+||-|.+|+..+-..+
T Consensus 49 ~~iV~wAK~iPgF~~L~~~DQi~L 72 (226)
T cd06934 49 KQIIKFAKDLPYFRSLPIEDQISL 72 (226)
T ss_pred HHHHHHhcCCcccccCCcchHHHH
Confidence 457899999999999987664433
No 107
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=25.64 E-value=63 Score=14.71 Aligned_cols=14 Identities=14% Similarity=0.147 Sum_probs=10.1
Q ss_pred CCChHHHhhHhhhh
Q psy719 23 QCGSKKMGIVAKHV 36 (45)
Q Consensus 23 ~L~~~~l~kiad~l 36 (45)
.|+..++..+++.|
T Consensus 1 ~L~~~er~~L~e~L 14 (54)
T PF09720_consen 1 QLPPEERAELAEEL 14 (54)
T ss_pred CcCHHHHHHHHHHH
Confidence 36777877777765
No 108
>cd00616 AHBA_syn 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT, Arnb aminotransferase and pilin glycosylation protein. The prototype of this family, the AHBA_synthase, is a dimeric PLP dependent enzyme. AHBA_syn is the terminal enzyme of 3-amino-5-hydroxybenzoic acid (AHBA) formation which is involved in the biosynthesis of ansamycin antibiotics, including rifamycin B. Some members of this CD are involved in 4-amino-6-deoxy-monosaccharide D-perosamine synthesis. Perosamine is an important element in the glycosylation of several cell products, such as antibiotics and lipopolysaccharides of gram-positive and gram-negative bacteria. The pilin glycosylation protein
Probab=25.62 E-value=66 Score=19.15 Aligned_cols=22 Identities=5% Similarity=0.063 Sum_probs=18.7
Q ss_pred hcCcccCCCChHHHhhHhhhhh
Q psy719 16 SRVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 16 ~~V~ilk~L~~~~l~kiad~l~ 37 (45)
=.+|+-..+++.++..|+++|+
T Consensus 331 l~l~~~~~~t~~di~~i~~~l~ 352 (352)
T cd00616 331 LSLPLHPSLTEEEIDRVIEALR 352 (352)
T ss_pred EEccCCCCCCHHHHHHHHHHhC
Confidence 3678888899999999999874
No 109
>PF02330 MAM33: Mitochondrial glycoprotein; InterPro: IPR003428 This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.; GO: 0005759 mitochondrial matrix; PDB: 3QV0_A 1YQF_F 3JV1_A 1P32_A 3RPX_A.
Probab=25.60 E-value=38 Score=19.53 Aligned_cols=15 Identities=13% Similarity=0.377 Sum_probs=11.8
Q ss_pred HHHHHHHHHHhhcCc
Q psy719 5 IRKRKLYEEFLSRVS 19 (45)
Q Consensus 5 ~~kr~~~~~fL~~V~ 19 (45)
.+.+++|..||++|.
T Consensus 187 ~kEq~eYi~wL~~l~ 201 (204)
T PF02330_consen 187 DKEQREYIRWLKNLK 201 (204)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 456778999999875
No 110
>PF09187 DUF1950: Domain of unknown function(DUF1950); InterPro: IPR015270 Members of this family are a set of functionally uncharacterised hypothetical eukaryotic proteins []. ; PDB: 2Q3T_A 1VK5_A 3GAN_A.
Probab=25.57 E-value=77 Score=17.53 Aligned_cols=19 Identities=21% Similarity=0.718 Sum_probs=13.4
Q ss_pred HHHHHHHHHHhhcCcccCC
Q psy719 5 IRKRKLYEEFLSRVSILVQ 23 (45)
Q Consensus 5 ~~kr~~~~~fL~~V~ilk~ 23 (45)
+++-++|.++.+.+||-.+
T Consensus 2 iRrAemYQ~yMk~iPIP~~ 20 (119)
T PF09187_consen 2 IRRAEMYQDYMKQIPIPSS 20 (119)
T ss_dssp HHHHHHHHHHHHTS---SS
T ss_pred cchHHHHHHHHHcCCCCCC
Confidence 4678899999999999765
No 111
>TIGR02929 anfG_nitrog Fe-only nitrogenase, delta subunit. Nitrogenase, also called dinitrogenase, is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, AnfG, represents the delta subunit of the Fe-only alternative nitrogenase. It is homologous to VnfG, the delta subunit of the V-containing (vanadium) nitrogenase.
Probab=25.26 E-value=58 Score=17.84 Aligned_cols=27 Identities=7% Similarity=0.117 Sum_probs=21.9
Q ss_pred HHHhhcCcccCCCChHHHhhHhhhhhe
Q psy719 12 EEFLSRVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 12 ~~fL~~V~ilk~L~~~~l~kiad~l~~ 38 (45)
.+|-++.|.+..|+..++..+-+.|.+
T Consensus 63 ~~~k~rfpW~~~~~kdei~~l~~~lk~ 89 (109)
T TIGR02929 63 GAYKRRFPWLEDMTKDEIKTLMQALHE 89 (109)
T ss_pred HHHHHhCcHHHhCCHHHHHHHHHHHHH
Confidence 466778899999999999888877754
No 112
>PF04803 Cor1: Cor1/Xlr/Xmr conserved region; InterPro: IPR006888 Cor1 is a component of the chromosome core in the meiotic prophase chromosomes []. Xlr is a lymphoid cell specific protein []. Xmr is abundantly transcribed in testis in a tissue-specific and developmentally regulated manner. The protein is located in the nuclei of spermatocytes, early in the prophase of the first meiotic division, and later becomes concentrated in the XY nuclear subregion where it is in particular associated with the axes of sex chromosomes [].
Probab=25.08 E-value=29 Score=19.31 Aligned_cols=30 Identities=17% Similarity=0.356 Sum_probs=22.2
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhHhhhhh
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~kiad~l~ 37 (45)
++.++.||+++.-|..-.+..+..+.+-|+
T Consensus 95 K~l~eqflK~le~le~~~~~~l~~~q~Elk 124 (130)
T PF04803_consen 95 KELHEQFLKSLEDLEKSHDNQLSSIQSELK 124 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 677899999998888776666666655543
No 113
>KOG3808|consensus
Probab=24.92 E-value=23 Score=17.92 Aligned_cols=15 Identities=13% Similarity=0.078 Sum_probs=11.1
Q ss_pred HHhhcCcccCCCChH
Q psy719 13 EFLSRVSILVQCGSK 27 (45)
Q Consensus 13 ~fL~~V~ilk~L~~~ 27 (45)
.+|++||-++++-..
T Consensus 22 AYlk~vpr~~swlls 36 (74)
T KOG3808|consen 22 AYLKSVPRFPSWLLS 36 (74)
T ss_pred HHHhhcccchHHHHh
Confidence 478999999885443
No 114
>PF03047 ComC: COMC family; InterPro: IPR004288 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family consists of streptococcal competence stimulating peptide precursors, which are generally up to 50 amino acid residues long. In all the members of this family, the leader sequence is cleaved after two conserved glycine residues; thus the leader sequence is of the double- glycine type []. Competence stimulating peptides (CSP) are small (less than 25 amino acid residues) cationic peptides. The N-terminal amino acid residue is negatively charged, either glutamate or aspartate. The C-terminal end is positively charged. The third residue is also positively charged: a highly conserved arginine []. Some COMC proteins and their precursors (not included in this family) do not fully follow the above description. Functionally, CSP act as pheromones, stimulating competence for genetic transformation in streptococci. In streptococci, the (CSP mediated) competence response requires exponential cell growth at a critical density, a relatively simple requirement when compared to the stationary-phase requirement of Haemophilus, or the late-logarithmic- phase of Bacillus []. All bacteria induced to competence by a particular CSP are said to belong to the same pherotype, because each CSP is recognised by a specific receptor (the signalling domain of a histidine kinase ComD). Pherotypes are not necessarily species-specific. In addition, an organism may change pherotype. There are two possible mechanisms for pherotype switching: horizontal gene transfer, and accumulation of point mutations. The biological significance of pherotypes and pherotype switching is not definitively determined. Pherotype switching occurs frequently enough in naturally competent streptococci to suggest that it may be an important contributor to genetic exchange between different bacterial species []. This entry also includes proteins that form bacteriocin-like propetides with a glycine-glycine cleavage site. The bacteriocin is initially formed as a pre-propeptide and upon cleavage at the glycine-glycine cleavage site, a leader peptide and the propeptide would be formed. The propeptide then undergoes posttranslational modification before becoming functional [].; GO: 0005186 pheromone activity; PDB: 2I2J_A 2I2H_A 2A1C_A.
Probab=24.85 E-value=24 Score=15.16 Aligned_cols=18 Identities=0% Similarity=0.073 Sum_probs=0.0
Q ss_pred hcCcccCCCChHHHhhHh
Q psy719 16 SRVSILVQCGSKKMGIVA 33 (45)
Q Consensus 16 ~~V~ilk~L~~~~l~kia 33 (45)
+++.-|+.|++.+|..|.
T Consensus 6 ~~L~~F~~lt~~eL~~I~ 23 (32)
T PF03047_consen 6 KTLEQFEELTEEELQEIQ 23 (32)
T ss_dssp ------------------
T ss_pred hhHHHHhcCCHHHHhhcc
Confidence 355667888888888773
No 115
>PF03255 ACCA: Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; InterPro: IPR001095 This entry contains the alpha subunit the acetyl coenzyme A carboxylase complex (6.4.1.2 from EC). It catalyses the first step in the synthesis of long-chain fatty acids which involves the carboxylation of acetyl-CoA to malonyl-CoA. The acetyl-CoA carboxylase complex is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association []. The reaction involves two steps: Biotin carrier protein + ATP + HCO3 - -> Carboxybiotin carrier protein + ADP + Pi Carboxybiotin carrier protein + Acetyl-CoA -> Malonyl-CoA + Biotin carrier protein ; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex; PDB: 2F9I_A 2F9Y_A.
Probab=24.69 E-value=47 Score=19.01 Aligned_cols=17 Identities=18% Similarity=0.114 Sum_probs=12.3
Q ss_pred cccCCCChHHHhhHhhh
Q psy719 19 SILVQCGSKKMGIVAKH 35 (45)
Q Consensus 19 ~ilk~L~~~~l~kiad~ 35 (45)
.+.++|++|++.++|-.
T Consensus 47 eiy~~lt~w~~V~~aRh 63 (145)
T PF03255_consen 47 EIYSNLTPWQRVQLARH 63 (145)
T ss_dssp HHHHT--HHHHHHHHTB
T ss_pred hccCCCCHHHHHHHhhC
Confidence 56788999999999854
No 116
>PF10439 Bacteriocin_IIc: Bacteriocin class II with double-glycine leader peptide; InterPro: IPR019493 Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related strains. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, e.g. IPR015046 from INTERPRO. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein []. The ABC transporter is thought to recognise the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter []. It seems likely that the whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins, and the same bacteriocins can be produced by different species. The proteins in this entry include amylovorin-L, lactacin-F and salivaricin CRL 1328, all of them class IIb two-peptide bacteriocins.
Probab=24.35 E-value=32 Score=16.60 Aligned_cols=13 Identities=0% Similarity=0.041 Sum_probs=9.9
Q ss_pred ccCCCChHHHhhH
Q psy719 20 ILVQCGSKKMGIV 32 (45)
Q Consensus 20 ilk~L~~~~l~ki 32 (45)
-|+.|++++|..|
T Consensus 4 ~f~~L~~eeL~~I 16 (65)
T PF10439_consen 4 NFEVLDEEELSSI 16 (65)
T ss_pred HHHhcCHHHHHHh
Confidence 4667888888876
No 117
>PLN02291 phospho-2-dehydro-3-deoxyheptonate aldolase
Probab=24.33 E-value=97 Score=21.00 Aligned_cols=30 Identities=13% Similarity=0.098 Sum_probs=25.1
Q ss_pred HHHHhhcC------cccCCCChHHHhhHhhhhheee
Q psy719 11 YEEFLSRV------SILVQCGSKKMGIVAKHVTCAM 40 (45)
Q Consensus 11 ~~~fL~~V------~ilk~L~~~~l~kiad~l~~~~ 40 (45)
+.+|++.| .+-.+.+++++.+++|.|.+..
T Consensus 291 HVef~rgI~NPIGvKvGPs~~pdel~~L~~~LnP~~ 326 (474)
T PLN02291 291 HVEFLRGVANPLGIKVSDKMDPEELVKLIEILNPQN 326 (474)
T ss_pred HHHHHhcCCCCeeEEECCCCCHHHHHHHHHHhCCCC
Confidence 56777774 7788999999999999998764
No 118
>PF14418 OHA: OST-HTH Associated domain
Probab=24.32 E-value=1.1e+02 Score=15.29 Aligned_cols=29 Identities=14% Similarity=0.106 Sum_probs=21.1
Q ss_pred HHHHHHHhh--cCcccCCCChHHHhhHhhhh
Q psy719 8 RKLYEEFLS--RVSILVQCGSKKMGIVAKHV 36 (45)
Q Consensus 8 r~~~~~fL~--~V~ilk~L~~~~l~kiad~l 36 (45)
|-....+|+ ..|.|++|+...+..|....
T Consensus 12 RY~~A~~Lk~~gp~~lr~l~Lg~i~~iVqla 42 (75)
T PF14418_consen 12 RYGMAQFLKKRGPPFLRSLSLGDICHIVQLA 42 (75)
T ss_pred HHHHHHHHHhcCchhhcCCcHHHHHHHHHHH
Confidence 444555665 47999999999988886654
No 119
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=24.14 E-value=51 Score=15.25 Aligned_cols=21 Identities=19% Similarity=0.319 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHhhcCcccCCC
Q psy719 4 TIRKRKLYEEFLSRVSILVQC 24 (45)
Q Consensus 4 ~~~kr~~~~~fL~~V~ilk~L 24 (45)
.+.+++...+.+.+.|+|..|
T Consensus 22 DIsr~e~l~~~~~RWPLLaEl 42 (44)
T PF10945_consen 22 DISREERLNQALQRWPLLAEL 42 (44)
T ss_pred HHHHHHHHHHHHHHChhHHHH
Confidence 456777788888999988654
No 120
>PF08752 COP-gamma_platf: Coatomer gamma subunit appendage platform subdomain; InterPro: IPR014863 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal appendage domain of the gamma subunit of coatomer complexes. The appendage domain of the gamma coatomer subunit has a similar overall structural fold to the appendage domain of clathrin adaptors, and can also share the same motif-based cargo recognition and accessory factor recruitment mechanisms. The coatomer gamma subunit appendage domain contains a protein-protein interaction site and a second proposed binding site that interacts with the alpha, beta, epsilon COPI subcomplex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0005798 Golgi-associated vesicle; PDB: 1PZD_A 1R4X_A.
Probab=23.96 E-value=76 Score=18.07 Aligned_cols=21 Identities=29% Similarity=0.442 Sum_probs=15.6
Q ss_pred HHHHHHHHhhcCcccCCCChH
Q psy719 7 KRKLYEEFLSRVSILVQCGSK 27 (45)
Q Consensus 7 kr~~~~~fL~~V~ilk~L~~~ 27 (45)
|.+.|.+=|.+||-|.+|.+-
T Consensus 1 ~~~~y~~~l~~ipe~~~lG~l 21 (151)
T PF08752_consen 1 KQEEYAEQLSKIPEFANLGPL 21 (151)
T ss_dssp -HHHHHHHHHTSGGGTTS-S-
T ss_pred ChHHHHHHHHcChhHhhcCcc
Confidence 457789999999999987653
No 121
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=23.95 E-value=1e+02 Score=14.79 Aligned_cols=28 Identities=4% Similarity=0.232 Sum_probs=19.4
Q ss_pred HHHHHHHhhcC----cccCC-CChHHHhhHhhh
Q psy719 8 RKLYEEFLSRV----SILVQ-CGSKKMGIVAKH 35 (45)
Q Consensus 8 r~~~~~fL~~V----~ilk~-L~~~~l~kiad~ 35 (45)
++...+|+.+- =.|.. |++.++.-|-++
T Consensus 5 ~~~i~~F~~s~~~~~l~f~p~lt~~eR~~vH~~ 37 (60)
T cd02640 5 RQIIQNYAHSDDIRDMVFSPEFSKEERALIHQI 37 (60)
T ss_pred HHHHHHHHcCCccceEEcCCCCCHHHHHHHHHH
Confidence 56678888664 35665 999888776443
No 122
>TIGR02930 vnfG_nitrog V-containing nitrogenase, delta subunit. Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfG, represents the delta subunit of the V-containing (vanadium) alternative nitrogenase. It is homologous to AnfG, the delta subunit of the Fe-only nitrogenase.
Probab=23.91 E-value=64 Score=17.68 Aligned_cols=27 Identities=7% Similarity=0.108 Sum_probs=21.9
Q ss_pred HHHhhcCcccCCCChHHHhhHhhhhhe
Q psy719 12 EEFLSRVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 12 ~~fL~~V~ilk~L~~~~l~kiad~l~~ 38 (45)
.+|-++.|.+..|+..++..+-+.|.+
T Consensus 63 ~~~k~rfpW~~~~~kdei~~l~~~lk~ 89 (109)
T TIGR02930 63 SDIKERFPWISELDKDQILELVESVKK 89 (109)
T ss_pred HHHHHhCcHHHhCCHHHHHHHHHHHHH
Confidence 466778899999999999888877754
No 123
>PRK11706 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional
Probab=23.58 E-value=74 Score=19.69 Aligned_cols=23 Identities=9% Similarity=0.083 Sum_probs=20.0
Q ss_pred hcCcccCCCChHHHhhHhhhhhe
Q psy719 16 SRVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 16 ~~V~ilk~L~~~~l~kiad~l~~ 38 (45)
=++|+...|++.++..|++++..
T Consensus 350 l~lP~~~~l~~~~~~~i~~~i~~ 372 (375)
T PRK11706 350 LRLPLFYNLTDVEQRTVIDTILE 372 (375)
T ss_pred EeccCCCCCCHHHHHHHHHHHHH
Confidence 37899999999999999999864
No 124
>PF06989 BAALC_N: BAALC N-terminus; InterPro: IPR009728 This entry represents the mammalian BAALC proteins. BAALC (brain and acute leukaemia, cytoplasmic) is highly conserved among mammals, but is absent from lower organisms. Two isoforms are specifically expressed in neuroectoderm-derived tissues, but not in tumours or cancer cell lines of non-neural tissue origin. It has been shown that blasts from a subset of patients with acute leukaemia greatly overexpress eight different BAALC transcripts, resulting in five protein isoforms. Among patients with acute myeloid leukaemia, those overexpressing BAALC show distinctly poor prognosis, pointing to a key role of the BAALC products in leukaemia. It has been suggested that BAALC is a gene implicated in both neuroectodermal and hematopoietic cell functions [].; GO: 0005737 cytoplasm
Probab=23.48 E-value=20 Score=17.10 Aligned_cols=11 Identities=18% Similarity=0.117 Sum_probs=8.4
Q ss_pred hhhhheeeecC
Q psy719 33 AKHVTCAMVEK 43 (45)
Q Consensus 33 ad~l~~~~y~~ 43 (45)
||++++.+|+.
T Consensus 8 adaiepry~es 18 (53)
T PF06989_consen 8 ADAIEPRYYES 18 (53)
T ss_pred cccccchhhhh
Confidence 68888888753
No 125
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=23.15 E-value=1.1e+02 Score=18.26 Aligned_cols=25 Identities=0% Similarity=0.131 Sum_probs=19.4
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||-|.+|+..+-..+
T Consensus 54 l~~iVewAK~iPgF~~L~~~DQi~L 78 (238)
T cd07348 54 LEVIRKWAEKIPGFSDFCKEDQELL 78 (238)
T ss_pred HHHHHHHHccCCCccCCChHHHHHH
Confidence 3457899999999999987664443
No 126
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=22.93 E-value=41 Score=16.36 Aligned_cols=21 Identities=10% Similarity=0.109 Sum_probs=14.0
Q ss_pred cCCCChHHHhhHhhhhheeee
Q psy719 21 LVQCGSKKMGIVAKHVTCAMV 41 (45)
Q Consensus 21 lk~L~~~~l~kiad~l~~~~y 41 (45)
|..|+..+..++.|.|....|
T Consensus 29 l~~l~~~~~~Ri~Dfl~G~~~ 49 (73)
T PF04472_consen 29 LENLDDEEAQRILDFLSGAVY 49 (73)
T ss_dssp -TTS-HHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHhchhe
Confidence 466788888888888765555
No 127
>cd06875 PX_IRAS The phosphoinositide binding Phox Homology domain of the Imidazoline Receptor Antisera-Selected. The PX domain is a phosphoinositide binding (PI) module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Imidazoline Receptor Antisera-Selected (IRAS), also called nischarin, contains an N-terminal PX domain, leucine rich repeats, and a predicted coiled coil domain. The PX domain of IRAS binds to phosphatidylinositol-3-phosphate in membranes. Together with the coiled coil domain, it is essential for the localization of IRAS to endosomes. IRAS has been shown to interact with integrin and inhibit cell migration. Its interaction with alpha5 integrin causes a redistribution of the receptor from the cell surface to endosomal structures, suggesting that IRAS may function as a sorting nexin (SNX) which regulates the endosomal trafficking of integrin. SNXs make up the largest group a
Probab=22.73 E-value=70 Score=17.01 Aligned_cols=35 Identities=17% Similarity=0.129 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhhcCcccCCCChHHHhhHhhhhheeee
Q psy719 5 IRKRKLYEEFLSRVSILVQCGSKKMGIVAKHVTCAMV 41 (45)
Q Consensus 5 ~~kr~~~~~fL~~V~ilk~L~~~~l~kiad~l~~~~y 41 (45)
.+||.....||++| ++......-.-+.+.|+...|
T Consensus 73 e~Rr~~Le~yL~~l--l~~~~~~~s~~l~~FL~~~~~ 107 (116)
T cd06875 73 EKRRKELEIYLQTL--LSFFQKTMPRELAHFLDFHKY 107 (116)
T ss_pred HHHHHHHHHHHHHH--HhhhcccCCHHHHHHhCCCce
Confidence 46677778888875 333322222345666655544
No 128
>cd08304 DD_superfamily The Death Domain Superfamily of protein-protein interaction domains. The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer.
Probab=22.51 E-value=36 Score=16.56 Aligned_cols=21 Identities=0% Similarity=-0.001 Sum_probs=15.3
Q ss_pred CcccCCCChHHHhhHhhhhhe
Q psy719 18 VSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 18 V~ilk~L~~~~l~kiad~l~~ 38 (45)
+.++++|+..+..++++++.+
T Consensus 2 ~~L~~~L~~~~~~~l~~~l~~ 22 (69)
T cd08304 2 LDLCENLTLEVLQQLKTALKS 22 (69)
T ss_pred hHHHHHhhHhHHHHHHHHHHc
Confidence 345667778888888888764
No 129
>cd07071 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=22.02 E-value=1.3e+02 Score=17.96 Aligned_cols=25 Identities=0% Similarity=0.125 Sum_probs=19.6
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|+||-|.+|+..+-..+
T Consensus 54 i~~iVewAK~iPgF~~L~~~DQi~L 78 (238)
T cd07071 54 MEIIRGWAEKIPGFTDLPKADQDLL 78 (238)
T ss_pred HHHHHHHhccCCCccCCCHHHHHHH
Confidence 3557899999999999988764443
No 130
>PF14285 DUF4367: Domain of unknown function (DUF4367)
Probab=21.93 E-value=67 Score=17.27 Aligned_cols=15 Identities=7% Similarity=0.113 Sum_probs=12.2
Q ss_pred CCCChHHHhhHhhhh
Q psy719 22 VQCGSKKMGIVAKHV 36 (45)
Q Consensus 22 k~L~~~~l~kiad~l 36 (45)
.+|+.+|+.|||..+
T Consensus 154 g~i~~eElikIaesi 168 (168)
T PF14285_consen 154 GNISKEELIKIAESI 168 (168)
T ss_pred CCCCHHHHHHHHhcC
Confidence 678999999998753
No 131
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=21.84 E-value=57 Score=20.03 Aligned_cols=25 Identities=4% Similarity=-0.009 Sum_probs=21.2
Q ss_pred cCcccCCCChHHHhhHhhhhheeee
Q psy719 17 RVSILVQCGSKKMGIVAKHVTCAMV 41 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~~~~y 41 (45)
+++++.+|++.+-..|...|+....
T Consensus 20 ~~~LysgL~~~dA~~I~a~L~~~gI 44 (249)
T PRK15348 20 DVDLYRSLPEDEANQMLALLMQHHI 44 (249)
T ss_pred ChHHHcCCCHHHHHHHHHHHHHcCC
Confidence 5789999999999999999976544
No 132
>COG4103 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.82 E-value=33 Score=19.74 Aligned_cols=26 Identities=8% Similarity=-0.077 Sum_probs=16.9
Q ss_pred ccCCCChHHHhhHhhhhheeeecCCC
Q psy719 20 ILVQCGSKKMGIVAKHVTCAMVEKGE 45 (45)
Q Consensus 20 ilk~L~~~~l~kiad~l~~~~y~~Ge 45 (45)
++.+|+...+..++-.|-+..|.+|+
T Consensus 92 l~r~Ld~e~R~eli~~mweIa~ADg~ 117 (148)
T COG4103 92 LKRHLDEEQRLELIGLMWEIAYADGE 117 (148)
T ss_pred HHHhcCHHHHHHHHHHHHHHHHcccc
Confidence 34467777777777776666666664
No 133
>PF01041 DegT_DnrJ_EryC1: DegT/DnrJ/EryC1/StrS aminotransferase family; InterPro: IPR000653 This entry represents a family that are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA P72454 from SWISSPROT, StsC P77952 from SWISSPROT and StsS []. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase 2.6.1.50 from EC, which catalyses the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin [].; PDB: 2FNI_A 2FNU_A 2FN6_A 2PO3_A 3UWC_A 1O61_B 1O62_B 1O69_B 1B9I_A 1B9H_A ....
Probab=21.61 E-value=63 Score=19.91 Aligned_cols=22 Identities=9% Similarity=0.166 Sum_probs=18.9
Q ss_pred hcCcccCCCChHHHhhHhhhhh
Q psy719 16 SRVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 16 ~~V~ilk~L~~~~l~kiad~l~ 37 (45)
=.+|+...|++.++..||+++.
T Consensus 342 l~LP~~~~lt~edv~~I~~~ir 363 (363)
T PF01041_consen 342 LSLPIHPRLTEEDVDYIAEAIR 363 (363)
T ss_dssp EEEEHSTTSCHHHHHHHHHHHH
T ss_pred EECcCCCCCCHHHHHHHhhccC
Confidence 3789999999999999999863
No 134
>PRK11658 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase; Provisional
Probab=21.52 E-value=87 Score=19.51 Aligned_cols=22 Identities=5% Similarity=0.080 Sum_probs=19.3
Q ss_pred cCcccCCCChHHHhhHhhhhhe
Q psy719 17 RVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~~ 38 (45)
.+|+...|++.+...|++++..
T Consensus 354 ~lP~~~~l~~~~~~~i~~~i~~ 375 (379)
T PRK11658 354 SLPLFPDMTDADVDRVITALQQ 375 (379)
T ss_pred EccCCCCCCHHHHHHHHHHHHH
Confidence 6788899999999999998864
No 135
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=21.34 E-value=85 Score=14.26 Aligned_cols=21 Identities=19% Similarity=0.143 Sum_probs=14.7
Q ss_pred cCccc-CCCChHHHhhHhhhhh
Q psy719 17 RVSIL-VQCGSKKMGIVAKHVT 37 (45)
Q Consensus 17 ~V~il-k~L~~~~l~kiad~l~ 37 (45)
.|.++ +..+..+...|+.++.
T Consensus 4 ~i~i~~~grt~eqK~~l~~~it 25 (63)
T TIGR00013 4 NIYILKEGRTDEQKRQLIEGVT 25 (63)
T ss_pred EEEECCCCCCHHHHHHHHHHHH
Confidence 45667 6778888888776654
No 136
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=21.32 E-value=1.5e+02 Score=15.91 Aligned_cols=34 Identities=15% Similarity=0.179 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhhcCcccCCCChHHHhhH-hhhhheeee
Q psy719 4 TIRKRKLYEEFLSRVSILVQCGSKKMGIV-AKHVTCAMV 41 (45)
Q Consensus 4 ~~~kr~~~~~fL~~V~ilk~L~~~~l~ki-ad~l~~~~y 41 (45)
+......|-.+|++ +..+.|+=.++ ||+|....|
T Consensus 32 n~~~i~~y~~W~r~----~~~STW~DC~mFA~~LkVsm~ 66 (104)
T PF05415_consen 32 NVSTIKKYHTWLRK----KRPSTWDDCRMFADALKVSMQ 66 (104)
T ss_pred hHHHHHHHHHHHhc----CCCCcHHHHHHHHHhheeEEE
Confidence 33444557777776 56778887777 888876544
No 137
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=21.24 E-value=39 Score=15.31 Aligned_cols=11 Identities=36% Similarity=0.591 Sum_probs=6.2
Q ss_pred HHHhhcCcccC
Q psy719 12 EEFLSRVSILV 22 (45)
Q Consensus 12 ~~fL~~V~ilk 22 (45)
...|++||.|-
T Consensus 6 ~~~L~~iP~fv 16 (45)
T PF08369_consen 6 EARLDRIPFFV 16 (45)
T ss_dssp HHHHCTS-HHH
T ss_pred HHHHHHCCHHH
Confidence 45677776653
No 138
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=21.10 E-value=1.9e+02 Score=17.37 Aligned_cols=25 Identities=0% Similarity=-0.194 Sum_probs=19.2
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhH
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIV 32 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ki 32 (45)
-....+|-|++|-|.+|+..+-..+
T Consensus 41 L~~~VeWAK~iPgF~~L~~~DQi~L 65 (246)
T cd06947 41 LVSVVKWAKALPGFRNLHLDDQMTL 65 (246)
T ss_pred HHHHHHHHHcCCCcccCCHHHHHHH
Confidence 3456899999999999987664433
No 139
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=20.79 E-value=1.2e+02 Score=15.09 Aligned_cols=28 Identities=14% Similarity=0.021 Sum_probs=22.5
Q ss_pred HHHHHHhhcCcccCCCChHHHhhHhhhh
Q psy719 9 KLYEEFLSRVSILVQCGSKKMGIVAKHV 36 (45)
Q Consensus 9 ~~~~~fL~~V~ilk~L~~~~l~kiad~l 36 (45)
+.....|....++..++...+...|.+.
T Consensus 6 ~~i~~~L~~~~~l~~~D~~~l~~yc~~~ 33 (100)
T PF05119_consen 6 KRIVPELKELGILSNLDVPLLERYCEAY 33 (100)
T ss_pred HHHHHHHHHcCCCcHhHHHHHHHHHHHH
Confidence 3466778888999999998888888775
No 140
>cd08309 Death_IRAK Death domain of Interleukin-1 Receptor-Associated Kinases. Death Domains (DDs) found in Interleukin-1 (IL-1) Receptor-Associated Kinases (IRAK1-4) and similar proteins. IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. All four types are involved in signal transduction involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinase pathways. IRAK1 and IRAK4 are active kinases while IRAK2 and IRAK-M (also called IRAK3) are inactive. In general, IRAKs are expressed ubiquitously, except for IRAK-M which is detected only in macrophages. The insect homologs, Pelle and Tube, are important components of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in the innate immune response. Most members have an N-terminal DD followed by a kinase domain. In general, DDs are protein-protein interaction domains found in a variety of domain a
Probab=20.63 E-value=83 Score=16.19 Aligned_cols=18 Identities=11% Similarity=0.002 Sum_probs=14.5
Q ss_pred cCCCChHHHhhHhhhhhe
Q psy719 21 LVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 21 lk~L~~~~l~kiad~l~~ 38 (45)
+-+|+...+.++|+.|.+
T Consensus 3 i~~Lp~~~~~~L~~~LD~ 20 (95)
T cd08309 3 IRQLPYSVLARLCKVLDP 20 (95)
T ss_pred ceeCCHHHHHHHHHHhCC
Confidence 346888889999998876
No 141
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=20.63 E-value=58 Score=21.16 Aligned_cols=21 Identities=10% Similarity=-0.010 Sum_probs=18.7
Q ss_pred hcCcccCCCChHHHhhHhhhh
Q psy719 16 SRVSILVQCGSKKMGIVAKHV 36 (45)
Q Consensus 16 ~~V~ilk~L~~~~l~kiad~l 36 (45)
.+||-|+.|+.--+..||++-
T Consensus 14 T~IPSL~~LDs~lrC~IC~~~ 34 (391)
T COG5432 14 TKIPSLKGLDSMLRCRICDCR 34 (391)
T ss_pred ccCcchhcchhHHHhhhhhhe
Confidence 479999999999999999873
No 142
>PF14515 HOASN: Haem-oxygenase-associated N-terminal helices; PDB: 3BJD_B.
Probab=20.59 E-value=24 Score=18.56 Aligned_cols=22 Identities=18% Similarity=0.119 Sum_probs=14.9
Q ss_pred cCcccCCCChHHHhhHhhhhhe
Q psy719 17 RVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~~ 38 (45)
+.|-+++|+-.+-.-+||+|.+
T Consensus 7 S~p~~qnl~~~~a~i~AdAL~~ 28 (93)
T PF14515_consen 7 SLPQLQNLHINEARIVADALAP 28 (93)
T ss_dssp HHHHHHT--SHHHHHHHHHTST
T ss_pred chHhhhcccchHHHHHHHHHcc
Confidence 3466777887887788998865
No 143
>PF15563 Imm11: Immunity protein 11
Probab=20.52 E-value=84 Score=19.19 Aligned_cols=23 Identities=13% Similarity=0.112 Sum_probs=18.2
Q ss_pred HHHHHHHhhcCcccCCCChHHHh
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMG 30 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~ 30 (45)
+......|.+||++++.+++...
T Consensus 151 ~~~I~~~L~~i~~fk~~~~~i~d 173 (224)
T PF15563_consen 151 RNEIIQHLQQISFFKSHSDYIHD 173 (224)
T ss_pred HHHHHHHHHhccchhHHHHHHHH
Confidence 45567889999999999887543
No 144
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=20.49 E-value=62 Score=16.93 Aligned_cols=17 Identities=18% Similarity=0.534 Sum_probs=14.2
Q ss_pred cccCCCChHHHhhHhhh
Q psy719 19 SILVQCGSKKMGIVAKH 35 (45)
Q Consensus 19 ~ilk~L~~~~l~kiad~ 35 (45)
|+|..+++.+|..|-+.
T Consensus 14 piL~~~~~~QL~~iE~~ 30 (109)
T PF06881_consen 14 PILEKCSPEQLRRIEDN 30 (109)
T ss_pred HHHccCCHHHHHHHHHh
Confidence 78888999999988664
No 145
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=20.37 E-value=24 Score=19.06 Aligned_cols=19 Identities=11% Similarity=-0.085 Sum_probs=13.2
Q ss_pred ccCCCChHHHhhHhhhhhe
Q psy719 20 ILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 20 ilk~L~~~~l~kiad~l~~ 38 (45)
.|.++-..-+.||||||.+
T Consensus 65 Tfwr~l~sAR~KvA~aLve 83 (99)
T COG1342 65 TFWRLLTSARKKVADALVE 83 (99)
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 3444556678899999864
No 146
>cd01275 FHIT FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into three branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Fhit plays a very important role in the development of tumours. Infact, Fhit deletions are among the earliest and most frequent genetic alterations in the development of tumours.
Probab=20.31 E-value=89 Score=16.35 Aligned_cols=21 Identities=19% Similarity=0.139 Sum_probs=15.8
Q ss_pred cCcccCCCChHHHhhHhhhhh
Q psy719 17 RVSILVQCGSKKMGIVAKHVT 37 (45)
Q Consensus 17 ~V~ilk~L~~~~l~kiad~l~ 37 (45)
-|+-+.+|++.++..+++++.
T Consensus 44 H~~~~~~L~~~e~~~l~~~~~ 64 (126)
T cd01275 44 HVPRLEDLTPEEIADLFKLVQ 64 (126)
T ss_pred ccCChhhCCHHHHHHHHHHHH
Confidence 456678899988888777654
No 147
>PF07914 DUF1679: Protein of unknown function (DUF1679); InterPro: IPR012877 This region is found in a number of Caenorhabditis elegans and Caenorhabditis briggsae proteins, in one case (Q19034 from SWISSPROT) as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in zinc finger-C4 and HLH domain-containing kinases. In fact, one member of this family (Q9GUC1 from SWISSPROT) is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins (IPR000536 from INTERPRO, IPR008946 from INTERPRO, and IPR001628 from INTERPRO).
Probab=20.31 E-value=82 Score=20.42 Aligned_cols=21 Identities=0% Similarity=0.113 Sum_probs=18.2
Q ss_pred hcCcccCCCChHHHhhHhhhh
Q psy719 16 SRVSILVQCGSKKMGIVAKHV 36 (45)
Q Consensus 16 ~~V~ilk~L~~~~l~kiad~l 36 (45)
..+++..+++.+++.+|+++|
T Consensus 161 ~~~~~~e~~~~eql~~iv~aL 181 (414)
T PF07914_consen 161 HSMDMYENLSVEQLLQIVRAL 181 (414)
T ss_pred eeecccCCCCHHHHHHHHHHH
Confidence 456888899999999999987
No 148
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=20.12 E-value=61 Score=18.23 Aligned_cols=29 Identities=7% Similarity=0.014 Sum_probs=17.6
Q ss_pred HHHHHHHhhcCcccCCCChHHHhhHhhhhhe
Q psy719 8 RKLYEEFLSRVSILVQCGSKKMGIVAKHVTC 38 (45)
Q Consensus 8 r~~~~~fL~~V~ilk~L~~~~l~kiad~l~~ 38 (45)
|++|.+-|++ .|+.||+.++..+.+--++
T Consensus 3 k~efL~~L~~--~L~~lp~~e~~e~l~~Y~e 31 (181)
T PF08006_consen 3 KNEFLNELEK--YLKKLPEEEREEILEYYEE 31 (181)
T ss_pred HHHHHHHHHH--HHHcCCHHHHHHHHHHHHH
Confidence 3445544443 5677888888877655443
No 149
>cd08307 Death_Pelle Death domain of the protein kinase Pelle. Death domain (DD) of the protein kinase Pelle from Drosophila melanogaster and simlar proteins. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and in mediating innate immune responses to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Pelle also functions in photoreceptor axon targeting. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.11 E-value=85 Score=16.57 Aligned_cols=18 Identities=0% Similarity=-0.147 Sum_probs=14.5
Q ss_pred CCCChHHHhhHhhhhhee
Q psy719 22 VQCGSKKMGIVAKHVTCA 39 (45)
Q Consensus 22 k~L~~~~l~kiad~l~~~ 39 (45)
.+||...+.++|+.|.+.
T Consensus 4 r~Lp~~~~~~Lc~lLD~~ 21 (97)
T cd08307 4 YDIPFTERKQLCALLDTD 21 (97)
T ss_pred ccCCHHHHHHHHHHhCCc
Confidence 468888999999988764
Done!