Query psy12247
Match_columns 119
No_of_seqs 110 out of 355
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 22:31:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12247.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12247hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1654|consensus 100.0 1E-54 2.2E-59 300.7 11.9 116 1-117 1-116 (116)
2 cd01611 GABARAP Ubiquitin doma 100.0 1.3E-52 2.9E-57 293.3 13.6 112 5-117 1-112 (112)
3 PTZ00380 microtubule-associate 100.0 3.5E-50 7.6E-55 283.7 12.1 110 3-118 2-112 (121)
4 PF02991 Atg8: Autophagy prote 100.0 2.4E-49 5.2E-54 273.7 12.2 104 13-117 1-104 (104)
5 cd01612 APG12_C Ubiquitin-like 100.0 3.2E-35 6.9E-40 197.5 10.1 86 31-117 2-87 (87)
6 PF04110 APG12: Ubiquitin-like 99.9 6.5E-27 1.4E-31 157.1 7.2 86 31-117 2-87 (87)
7 KOG3439|consensus 99.9 2E-25 4.4E-30 154.7 9.6 86 31-117 31-116 (116)
8 PF04106 APG5: Autophagy prote 96.8 0.0034 7.5E-08 47.6 5.9 100 9-111 88-195 (197)
9 PF11816 DUF3337: Domain of un 95.3 0.23 5E-06 40.3 9.9 87 25-112 211-328 (331)
10 PF11976 Rad60-SLD: Ubiquitin- 93.6 0.28 6E-06 30.5 5.3 50 45-95 11-60 (72)
11 cd06406 PB1_P67 A PB1 domain i 93.0 0.51 1.1E-05 31.3 5.9 57 50-109 16-76 (80)
12 KOG2660|consensus 90.9 0.47 1E-05 38.9 4.8 73 40-114 159-235 (331)
13 PF13019 Telomere_Sde2: Telome 90.7 2 4.3E-05 32.0 7.6 79 29-110 1-81 (162)
14 cd00196 UBQ Ubiquitin-like pro 88.9 2.5 5.4E-05 23.0 5.9 44 44-88 7-50 (69)
15 smart00213 UBQ Ubiquitin homol 88.6 2 4.4E-05 25.2 5.3 46 47-94 12-57 (64)
16 PF00240 ubiquitin: Ubiquitin 87.3 1.1 2.4E-05 27.3 3.6 46 48-95 9-54 (69)
17 KOG2976|consensus 82.8 19 0.00041 28.9 9.4 79 23-110 178-273 (278)
18 cd01790 Herp_N Homocysteine-re 80.7 13 0.00029 24.3 7.5 62 48-111 15-79 (79)
19 PF03671 Ufm1: Ubiquitin fold 80.5 9.9 0.00021 24.9 5.9 60 41-101 12-71 (76)
20 PF10302 DUF2407: DUF2407 ubiq 79.4 10 0.00022 25.7 6.1 71 40-112 10-94 (97)
21 cd01763 Sumo Small ubiquitin-r 79.3 10 0.00022 24.6 5.9 62 26-95 9-70 (87)
22 cd01807 GDX_N ubiquitin-like d 78.1 5.3 0.00012 24.9 4.2 44 49-94 15-58 (74)
23 cd01813 UBP_N UBP ubiquitin pr 77.5 3.9 8.5E-05 26.0 3.4 45 50-95 15-61 (74)
24 cd01798 parkin_N amino-termina 77.2 6.2 0.00013 24.3 4.2 56 49-109 13-68 (70)
25 cd01769 UBL Ubiquitin-like dom 77.1 7.6 0.00016 22.9 4.5 57 48-110 11-68 (69)
26 PF09358 UBA_e1_C: Ubiquitin-a 76.7 8.3 0.00018 27.1 5.2 51 46-99 34-94 (125)
27 cd01806 Nedd8 Nebb8-like ubiq 76.3 10 0.00022 23.2 5.0 58 48-111 14-72 (76)
28 PF08154 NLE: NLE (NUC135) dom 74.7 18 0.00038 22.5 6.6 42 43-84 14-56 (65)
29 cd01805 RAD23_N Ubiquitin-like 74.5 9 0.0002 23.7 4.5 56 48-109 14-72 (77)
30 cd01803 Ubiquitin Ubiquitin. U 72.7 14 0.0003 22.6 5.0 58 48-111 14-72 (76)
31 COG3343 RpoE DNA-directed RNA 71.9 4.9 0.00011 30.3 3.1 47 54-117 30-77 (175)
32 cd05992 PB1 The PB1 domain is 71.3 22 0.00047 22.0 7.6 65 45-109 10-79 (81)
33 smart00666 PB1 PB1 domain. Pho 70.7 23 0.0005 22.1 6.8 64 45-108 11-78 (81)
34 cd01808 hPLIC_N Ubiquitin-like 70.2 22 0.00049 21.8 5.7 57 48-110 13-70 (71)
35 cd01812 BAG1_N Ubiquitin-like 68.7 10 0.00022 23.0 3.7 44 49-94 14-57 (71)
36 cd01810 ISG15_repeat2 ISG15 ub 67.2 27 0.00059 21.6 5.7 58 49-111 13-70 (74)
37 cd01809 Scythe_N Ubiquitin-lik 65.9 24 0.00052 21.2 5.0 46 47-94 13-58 (72)
38 cd01793 Fubi Fubi ubiquitin-li 64.6 27 0.00058 21.7 5.1 60 45-109 9-68 (74)
39 cd01776 Rin1_RA Ubiquitin doma 64.6 13 0.00028 25.0 3.7 34 49-82 18-53 (87)
40 PF00564 PB1: PB1 domain; Int 62.8 30 0.00064 21.6 5.2 53 49-101 16-71 (84)
41 PF12436 USP7_ICP0_bdg: ICP0-b 62.0 11 0.00024 29.3 3.6 46 49-94 89-138 (249)
42 PTZ00044 ubiquitin; Provisiona 61.1 22 0.00047 21.9 4.2 46 47-94 13-58 (76)
43 cd01800 SF3a120_C Ubiquitin-li 60.7 22 0.00047 22.3 4.2 58 49-111 12-69 (76)
44 cd06411 PB1_p51 The PB1 domain 59.9 47 0.001 21.8 6.0 58 50-107 12-74 (78)
45 PF11543 UN_NPL4: Nuclear pore 59.0 4.3 9.4E-05 26.4 0.7 57 48-108 17-77 (80)
46 PF12752 SUZ: SUZ domain; Int 58.3 10 0.00022 23.2 2.2 19 6-24 35-53 (59)
47 cd06407 PB1_NLP A PB1 domain i 57.5 23 0.0005 23.1 4.0 55 45-99 10-68 (82)
48 cd01796 DDI1_N DNA damage indu 55.6 27 0.00058 21.6 3.9 55 49-108 14-69 (71)
49 cd01794 DC_UbP_C dendritic cel 54.7 43 0.00094 20.8 4.8 46 47-94 11-56 (70)
50 cd01791 Ubl5 UBL5 ubiquitin-li 54.4 28 0.0006 22.0 3.9 56 50-110 17-72 (73)
51 PF00837 T4_deiodinase: Iodoth 54.2 17 0.00036 28.7 3.3 33 3-36 158-190 (237)
52 PRK06437 hypothetical protein; 53.6 24 0.00052 21.9 3.4 33 49-86 15-47 (67)
53 TIGR01683 thiS thiamine biosyn 52.9 31 0.00068 20.9 3.8 38 45-87 4-41 (64)
54 PF00788 RA: Ras association ( 51.2 59 0.0013 20.3 7.1 64 45-109 17-89 (93)
55 PF14533 USP7_C2: Ubiquitin-sp 51.2 12 0.00027 28.3 2.2 51 45-95 34-90 (213)
56 cd06396 PB1_NBR1 The PB1 domai 51.1 69 0.0015 21.1 6.4 63 45-110 10-78 (81)
57 cd01760 RBD Ubiquitin-like dom 49.6 63 0.0014 20.6 5.0 55 41-95 6-62 (72)
58 cd01799 Hoil1_N Ubiquitin-like 48.5 58 0.0013 20.6 4.7 45 48-94 16-60 (75)
59 cd01792 ISG15_repeat1 ISG15 ub 47.1 27 0.00059 22.1 3.0 58 50-112 18-77 (80)
60 PF00789 UBX: UBX domain; Int 47.0 30 0.00064 21.7 3.2 54 42-95 14-70 (82)
61 cd01804 midnolin_N Ubiquitin-l 47.0 71 0.0015 20.1 5.8 58 49-112 16-73 (78)
62 TIGR01682 moaD molybdopterin c 44.8 30 0.00065 21.8 2.9 39 48-86 19-60 (80)
63 cd00754 MoaD Ubiquitin domain 44.6 24 0.00051 21.8 2.4 39 48-86 19-60 (80)
64 PF02597 ThiS: ThiS family; I 44.4 44 0.00096 20.3 3.6 42 46-87 13-55 (77)
65 cd06398 PB1_Joka2 The PB1 doma 43.5 49 0.0011 22.0 3.9 54 45-98 10-72 (91)
66 cd01815 BMSC_UbP_N Ubiquitin-l 43.5 52 0.0011 21.3 3.9 55 50-108 16-72 (75)
67 cd01802 AN1_N ubiquitin-like d 42.3 63 0.0014 21.8 4.4 59 48-111 41-99 (103)
68 PRK13964 coaD phosphopantethei 41.7 82 0.0018 22.6 5.1 85 8-97 44-137 (140)
69 PRK13669 hypothetical protein; 41.7 24 0.00051 23.3 2.1 27 74-100 45-73 (78)
70 cd01795 USP48_C USP ubiquitin- 41.1 63 0.0014 22.5 4.2 43 50-94 20-63 (107)
71 PRK10953 cysJ sulfite reductas 41.0 2.6E+02 0.0055 24.7 9.1 87 26-114 433-523 (600)
72 TIGR00601 rad23 UV excision re 40.7 1.7E+02 0.0036 24.5 7.4 64 44-112 8-76 (378)
73 PF05717 TnpB_IS66: IS66 Orf2 40.3 44 0.00094 22.9 3.4 27 56-82 16-43 (107)
74 COG0669 CoaD Phosphopantethein 39.8 68 0.0015 23.9 4.5 98 6-106 43-146 (159)
75 KOG1209|consensus 39.0 61 0.0013 25.9 4.3 53 44-100 54-110 (289)
76 PF11470 TUG-UBL1: GLUT4 regul 37.3 91 0.002 19.5 4.2 41 43-84 5-45 (65)
77 cd01797 NIRF_N amino-terminal 37.2 77 0.0017 20.1 4.0 56 51-111 19-74 (78)
78 cd01768 RA RA (Ras-associating 37.1 93 0.002 19.5 4.4 55 44-99 12-73 (87)
79 PF09379 FERM_N: FERM N-termin 36.6 65 0.0014 19.8 3.5 35 46-80 8-42 (80)
80 PF06970 RepA_N: Replication i 36.5 18 0.00039 23.3 0.9 17 99-115 42-58 (76)
81 PF14560 Ubiquitin_2: Ubiquiti 36.3 50 0.0011 21.1 3.0 33 47-79 16-49 (87)
82 cd01775 CYR1_RA Ubiquitin doma 35.3 87 0.0019 21.4 4.1 35 48-82 16-52 (97)
83 TIGR02609 doc_partner putative 35.2 64 0.0014 20.4 3.3 20 63-82 17-36 (74)
84 cd06408 PB1_NoxR The PB1 domai 34.9 62 0.0014 21.6 3.3 28 49-78 16-43 (86)
85 PF00255 GSHPx: Glutathione pe 34.9 48 0.001 22.7 2.9 40 75-117 22-65 (108)
86 cd00565 ThiS ThiaminS ubiquiti 34.5 80 0.0017 19.0 3.6 39 45-88 5-43 (65)
87 COG1019 Predicted nucleotidylt 33.3 2E+02 0.0044 21.3 7.1 66 9-74 54-122 (158)
88 PRK08364 sulfur carrier protei 32.9 56 0.0012 20.2 2.8 34 48-86 17-50 (70)
89 PF03568 Peptidase_C50: Peptid 32.8 2.6E+02 0.0056 23.0 7.3 72 26-100 203-287 (383)
90 PF01704 UDPGP: UTP--glucose-1 32.4 1.3E+02 0.0027 25.5 5.5 57 11-87 88-144 (420)
91 smart00314 RA Ras association 32.1 1.3E+02 0.0029 18.9 4.9 39 42-80 13-54 (90)
92 KOG4147|consensus 31.7 55 0.0012 23.2 2.7 57 53-116 32-88 (127)
93 cd01766 Ufm1 Urm1-like ubiquit 31.5 71 0.0015 21.0 3.1 59 42-101 13-71 (82)
94 PF10137 TIR-like: Predicted n 31.5 79 0.0017 22.2 3.6 16 101-116 110-125 (125)
95 smart00148 PLCXc Phospholipase 31.4 57 0.0012 22.9 2.9 43 52-94 66-108 (135)
96 PF12436 USP7_ICP0_bdg: ICP0-b 30.8 1.2E+02 0.0027 23.4 4.9 53 27-82 175-227 (249)
97 cd01777 SNX27_RA Ubiquitin dom 30.8 1.2E+02 0.0026 20.3 4.2 43 42-84 9-55 (87)
98 PRK04115 hypothetical protein; 30.7 2.1E+02 0.0045 20.8 5.7 54 17-79 51-113 (137)
99 COG0386 BtuE Glutathione perox 30.7 76 0.0016 23.7 3.5 38 75-114 26-67 (162)
100 PRK02363 DNA-directed RNA poly 30.4 55 0.0012 23.3 2.6 50 52-117 17-66 (129)
101 PF01886 DUF61: Protein of unk 30.4 1.2E+02 0.0027 21.5 4.5 56 15-79 46-111 (132)
102 KOG0010|consensus 30.2 1.3E+02 0.0029 26.2 5.3 54 45-104 25-78 (493)
103 PF08825 E2_bind: E2 binding d 29.7 57 0.0012 21.4 2.5 46 50-95 2-59 (84)
104 COG2002 AbrB Regulators of sta 29.1 65 0.0014 21.0 2.7 21 62-82 20-40 (89)
105 smart00295 B41 Band 4.1 homolo 28.9 1.5E+02 0.0034 21.0 4.9 52 45-96 14-70 (207)
106 PRK13125 trpA tryptophan synth 28.3 62 0.0014 24.8 2.8 17 100-118 150-166 (244)
107 cd01617 DCX Ubiquitin-like dom 28.1 1.6E+02 0.0036 18.6 4.9 61 44-114 13-77 (80)
108 PF07929 PRiA4_ORF3: Plasmid p 27.7 1.3E+02 0.0028 21.8 4.3 29 46-74 19-47 (179)
109 PF11767 SET_assoc: Histone ly 27.4 1.6E+02 0.0036 18.4 4.2 56 48-112 5-63 (66)
110 PF12251 zf-SNAP50_C: snRNA-ac 27.3 70 0.0015 24.2 2.9 39 47-85 2-47 (196)
111 PF04014 Antitoxin-MazE: Antid 26.9 90 0.002 17.7 2.7 20 63-82 14-33 (47)
112 cd00137 PI-PLCc Catalytic doma 26.7 80 0.0017 24.8 3.3 53 54-108 73-127 (274)
113 cd00952 CHBPH_aldolase Trans-o 26.6 71 0.0015 25.5 3.0 29 9-37 58-86 (309)
114 PF07293 DUF1450: Protein of u 26.3 65 0.0014 21.0 2.2 28 74-101 45-74 (78)
115 cd01782 AF6_RA_repeat1 Ubiquit 26.1 1.4E+02 0.003 21.0 3.9 34 49-82 40-79 (112)
116 PF10336 DUF2420: Protein of u 25.8 2.3E+02 0.0049 19.5 5.4 62 54-116 10-97 (113)
117 KOG3483|consensus 25.7 1.1E+02 0.0023 20.4 3.2 61 41-102 23-83 (94)
118 KOG3218|consensus 25.5 1.1E+02 0.0024 23.6 3.7 29 54-84 36-64 (208)
119 cd01767 UBX UBX (ubiquitin reg 25.2 1.7E+02 0.0038 18.0 5.3 52 42-95 10-65 (77)
120 PF14060 DUF4252: Domain of un 25.2 93 0.002 21.7 3.1 25 88-112 20-44 (155)
121 PF02196 RBD: Raf-like Ras-bin 25.1 1.1E+02 0.0024 19.2 3.1 38 41-79 7-44 (71)
122 PRK08577 hypothetical protein; 24.9 77 0.0017 22.0 2.6 21 63-83 20-40 (136)
123 TIGR01408 Ube1 ubiquitin-activ 24.6 1.6E+02 0.0035 27.8 5.2 58 49-109 916-985 (1008)
124 TIGR02313 HpaI-NOT-DapA 2,4-di 24.6 85 0.0018 24.8 3.0 102 9-113 50-166 (294)
125 cd01818 TIAM1_RBD Ubiquitin do 24.5 1.3E+02 0.0027 19.8 3.3 34 41-74 6-39 (77)
126 cd01789 Alp11_N Ubiquitin-like 24.2 1.8E+02 0.0038 18.6 4.1 33 50-82 18-51 (84)
127 PF00388 PI-PLC-X: Phosphatidy 24.2 56 0.0012 22.8 1.8 32 53-84 65-96 (146)
128 cd00408 DHDPS-like Dihydrodipi 24.1 91 0.002 24.0 3.1 100 9-113 47-161 (281)
129 PRK11130 moaD molybdopterin sy 24.0 1.1E+02 0.0023 19.3 3.0 35 54-90 25-64 (81)
130 cd00951 KDGDH 5-dehydro-4-deox 23.7 84 0.0018 24.7 2.9 99 9-113 50-161 (289)
131 cd03483 MutL_Trans_MLH1 MutL_T 23.6 89 0.0019 21.6 2.7 27 73-99 47-75 (127)
132 PF12108 SF3a60_bindingd: Spli 23.3 99 0.0022 16.4 2.2 17 11-27 12-28 (28)
133 PRK08053 sulfur carrier protei 23.3 1.8E+02 0.0038 17.6 3.8 37 46-87 7-43 (66)
134 PF04663 Phenol_monoox: Phenol 22.8 79 0.0017 20.2 2.1 41 22-64 5-45 (67)
135 cd00329 TopoII_MutL_Trans MutL 22.7 94 0.002 19.6 2.5 27 73-99 43-72 (107)
136 PRK07440 hypothetical protein; 22.7 1.8E+02 0.004 18.0 3.8 36 47-87 12-47 (70)
137 PF01650 Peptidase_C13: Peptid 22.7 1E+02 0.0022 24.1 3.2 31 52-82 77-115 (256)
138 PLN02799 Molybdopterin synthas 22.0 55 0.0012 20.6 1.3 39 47-85 21-61 (82)
139 TIGR00683 nanA N-acetylneurami 21.9 98 0.0021 24.4 2.9 101 9-113 51-166 (290)
140 PF14836 Ubiquitin_3: Ubiquiti 21.7 1.6E+02 0.0034 19.7 3.5 45 50-94 19-66 (88)
141 PF01119 DNA_mis_repair: DNA m 21.4 94 0.002 21.0 2.4 28 70-97 36-65 (119)
142 cd09001 GH43_XYL_2 Glycosyl hy 21.4 44 0.00096 25.7 0.9 15 99-113 126-140 (269)
143 PRK02261 methylaspartate mutas 21.0 3.1E+02 0.0066 19.3 6.1 62 8-69 65-135 (137)
144 PRK03170 dihydrodipicolinate s 20.9 1.1E+02 0.0023 23.9 2.9 101 8-113 50-165 (292)
145 KOG1651|consensus 20.8 2.1E+02 0.0046 21.5 4.3 41 75-117 35-79 (171)
146 PRK06083 sulfur carrier protei 20.8 1.7E+02 0.0037 19.1 3.5 38 45-87 24-61 (84)
147 PRK03620 5-dehydro-4-deoxygluc 20.7 1.1E+02 0.0024 24.2 3.0 28 9-36 57-84 (303)
148 PF08216 CTNNBL: Catenin-beta- 20.5 92 0.002 21.7 2.2 20 9-28 33-52 (108)
149 PRK04147 N-acetylneuraminate l 20.1 1.1E+02 0.0023 24.0 2.8 29 9-37 54-82 (293)
No 1
>KOG1654|consensus
Probab=100.00 E-value=1e-54 Score=300.66 Aligned_cols=116 Identities=33% Similarity=0.605 Sum_probs=114.2
Q ss_pred CCCcccccCCHHHHHHHHHHHHhcCCCcceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEE
Q psy12247 1 MKFQYTEKYSLEERIKIGENLARNHPNCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFI 80 (119)
Q Consensus 1 m~~~fk~~~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~V 80 (119)
|+++||++|||++|+.|+++||+|||+|||||||+++++++|.|||+|||||+++|||||+.+|||||+|+|++|+||||
T Consensus 1 ~~~~FK~~~~fe~R~~E~~~Ir~kyP~riPVIvEk~~~~~lp~lDK~KyLVP~dltvgqfi~iIRkRiqL~~~kA~flfV 80 (116)
T KOG1654|consen 1 MKSSFKERHPFEKRKAEVRRIREKYPDRIPVIVEKAGKSQLPDLDKKKYLVPDDLTVGQFIKIIRKRIQLSPEKAFFLFV 80 (116)
T ss_pred CcchhhccCCHHHHHHHHHHHHHHCCCCCcEEEEecccccCcccccceeeccccccHHHHHHHHHHHhccChhHeEEEEE
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCeecCCcCchHHHHHhHhcCCCCeEEEEeccccccc
Q psy12247 81 ESMIVPADSTRMETLSQRFADKDGLIYMVYSDVNIFV 117 (119)
Q Consensus 81 n~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~~fG 117 (119)
||.+ |+++++|++||+.+||+||||||+||+|+|||
T Consensus 81 n~~~-p~ts~~ms~~Ye~~kdeDgFLYm~Ys~e~tfG 116 (116)
T KOG1654|consen 81 NNTS-PPTSATMSALYEEEKDEDGFLYMTYSGENTFG 116 (116)
T ss_pred cCcC-CcchhhHHHHHHhhcccCcEEEEEeccccccC
Confidence 9999 77799999999999999999999999999999
No 2
>cd01611 GABARAP Ubiquitin domain of GABA-receptor-associated protein. GABARAP (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion. GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1. Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like protein that is conjugated to the membrane phospholipid, phosphatidylethanolamine as part of a ubiquitin-like conjugation system essential for autophagosome-formation.
Probab=100.00 E-value=1.3e-52 Score=293.32 Aligned_cols=112 Identities=36% Similarity=0.688 Sum_probs=110.3
Q ss_pred ccccCCHHHHHHHHHHHHhcCCCcceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCee
Q psy12247 5 YTEKYSLEERIKIGENLARNHPNCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMI 84 (119)
Q Consensus 5 fk~~~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~ 84 (119)
||++||||+|++|+++||+|||++||||||+++++++|+|+++||+||+++||+||+.+||++|+|++++||||||||+
T Consensus 1 fk~~~s~e~R~~e~~~ir~kyp~~iPVIvE~~~~~~~p~l~k~KflVp~~~tv~~f~~~irk~l~l~~~~slfl~Vn~~- 79 (112)
T cd01611 1 FKERHPFEKRKAEVERIRAKYPDRIPVIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNS- 79 (112)
T ss_pred CccccCHHHHHHHHHHHHHHCCCceEEEEEEcCCCCcccccCceEEecCCCCHHHHHHHHHHHhCCCccceEEEEECCc-
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999996
Q ss_pred cCCcCchHHHHHhHhcCCCCeEEEEeccccccc
Q psy12247 85 VPADSTRMETLSQRFADKDGLIYMVYSDVNIFV 117 (119)
Q Consensus 85 ~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~~fG 117 (119)
+|++|++||+||++|||+||||||+||+++|||
T Consensus 80 ~p~~~~~~~~lY~~~kd~DGfLyl~Ys~~~tfG 112 (112)
T cd01611 80 LPPTSATMSQLYEEHKDEDGFLYMTYSSEETFG 112 (112)
T ss_pred cCCchhHHHHHHHHhCCCCCEEEEEEeccccCC
Confidence 599999999999999999999999999999999
No 3
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=100.00 E-value=3.5e-50 Score=283.66 Aligned_cols=110 Identities=16% Similarity=0.253 Sum_probs=106.3
Q ss_pred CcccccCCHHHHHHHHHHHHhcCCCcceEEEEcCCCCCCCCCCcceE-EecCCcchHhHHHHHHHhhcCCCCCeEEEEEc
Q psy12247 3 FQYTEKYSLEERIKIGENLARNHPNCAFVILERSPSALLPQMPRSNY-VVAYEMTVGHFFYLLRKKMALRPEEACFFFIE 81 (119)
Q Consensus 3 ~~fk~~~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~~~p~L~k~Kf-lvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn 81 (119)
++||++||||+|++|+++||+|||++||||||++++++ +|+|| |||+|+||+||+++||+||+|++++ +|||||
T Consensus 2 ~~fK~~~s~e~R~~e~~~Ir~kyPdrIPVIvEk~~~s~----dK~KfllVP~d~tV~qF~~iIRkrl~l~~~k-~flfVn 76 (121)
T PTZ00380 2 SAYHSSNPVEARRAECARLQAKYPGHVAVVVEAAEKAG----SKVHFLALPRDATVAELEAAVRQALGTSAKK-VTLAIE 76 (121)
T ss_pred cchhhcCCHHHHHHHHHHHHHHCCCccEEEEeecCCCC----CceEEEEcCCCCcHHHHHHHHHHHcCCChhH-EEEEEC
Confidence 47999999999999999999999999999999999887 89999 6999999999999999999999999 999999
Q ss_pred CeecCCcCchHHHHHhHhcCCCCeEEEEecccccccC
Q psy12247 82 SMIVPADSTRMETLSQRFADKDGLIYMVYSDVNIFVD 118 (119)
Q Consensus 82 ~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~~fG~ 118 (119)
|.+ |+++++||+||++|||+||||||+||+++|||+
T Consensus 77 n~l-p~~s~~mg~lYe~~KDeDGFLYi~Ys~e~tFG~ 112 (121)
T PTZ00380 77 GST-PAVTATVGDIADACKRDDGFLYVSVRTEQAMGA 112 (121)
T ss_pred Ccc-CCccchHHHHHHHhcCCCCeEEEEEcccccccc
Confidence 987 999999999999999999999999999999994
No 4
>PF02991 Atg8: Autophagy protein Atg8 ubiquitin like; InterPro: IPR004241 Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N terminus and the C terminus of Atg19. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [] Related proteins that belong to this group include the human ganglioside expression factor and a symbiosis-related fungal protein.; PDB: 3ECI_A 3D32_B 1GNU_A 1KM7_A 1KLV_A 1KOT_A 3DOW_A 1KJT_A 1V49_A 2ZJD_C ....
Probab=100.00 E-value=2.4e-49 Score=273.73 Aligned_cols=104 Identities=36% Similarity=0.733 Sum_probs=94.4
Q ss_pred HHHHHHHHHHhcCCCcceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchH
Q psy12247 13 ERIKIGENLARNHPNCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRM 92 (119)
Q Consensus 13 ~R~~e~~~ir~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m 92 (119)
+|++|+++||+|||++||||||+++++++|.||++|||||.++||+||+.+||++|++++++||||||||.+ |+++++|
T Consensus 1 ~R~~e~~~ir~kyP~~IPVIvEr~~~s~lp~ldk~KfLvp~~~tv~qf~~~ir~rl~l~~~~alfl~Vn~~l-p~~s~tm 79 (104)
T PF02991_consen 1 ERKEESERIREKYPDKIPVIVERYPKSKLPDLDKKKFLVPKDLTVGQFVYIIRKRLQLSPEQALFLFVNNTL-PSTSSTM 79 (104)
T ss_dssp HHHHHHHHHHHHSTTEEEEEEEE-TTSSS---SSSEEEEETTSBHHHHHHHHHHHTT--TTS-EEEEBTTBE-SSTTSBH
T ss_pred CcHHHHHHHHHHCCCccEEEEEEccCCChhhcCccEEEEcCCCchhhHHHHhhhhhcCCCCceEEEEEcCcc-cchhhHH
Confidence 699999999999999999999999999999999999999999999999999999999999999999999966 9999999
Q ss_pred HHHHhHhcCCCCeEEEEeccccccc
Q psy12247 93 ETLSQRFADKDGLIYMVYSDVNIFV 117 (119)
Q Consensus 93 ~~lY~~~kd~DGfLyl~Ys~~~~fG 117 (119)
|+||++|||+||||||+||++++||
T Consensus 80 ~elY~~~kdeDGFLY~~Ys~e~tFG 104 (104)
T PF02991_consen 80 GELYEKYKDEDGFLYMTYSSEETFG 104 (104)
T ss_dssp HHHHHHHB-TTSSEEEEEESSSSBC
T ss_pred HHHHHHhCCCCCeEEEEeccccccC
Confidence 9999999999999999999999999
No 5
>cd01612 APG12_C Ubiquitin-like domain of APG12. APG12_C The carboxy-terminal ubiquitin-like domain of APG12. Autophagy is a process in which cytoplasmic components are delivered to the lysosome/vacuole for degradation. Autophagy requires a ubiquitin-like protein conjugation system, in which APG12 is covalently bound to APG5.
Probab=100.00 E-value=3.2e-35 Score=197.49 Aligned_cols=86 Identities=17% Similarity=0.389 Sum_probs=81.5
Q ss_pred EEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEe
Q psy12247 31 VILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVY 110 (119)
Q Consensus 31 VIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Y 110 (119)
|.|.-.+.+++|+|+++||+||+++||++|+.+||++|++++++|+||||||+++|++|++||+||++| |+||||||+|
T Consensus 2 v~i~~~~~g~~p~l~k~kflv~~~~tv~~~~~~lrk~L~l~~~~slflyvnn~f~p~~d~~~g~LY~~~-~~dGfLyi~Y 80 (87)
T cd01612 2 VTIRFKPIGSAPILKQKVFKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPDENVGNLYRCF-GTNGELIVSY 80 (87)
T ss_pred eEEEEEECCCCccccccEEEeCCCCCHHHHHHHHHHHhCCCccCeEEEEECCccCCCchhHHHHHHHhc-CCCCEEEEEE
Confidence 455555678999999999999999999999999999999999999999999999899999999999999 8999999999
Q ss_pred ccccccc
Q psy12247 111 SDVNIFV 117 (119)
Q Consensus 111 s~~~~fG 117 (119)
|+++|||
T Consensus 81 s~~~afG 87 (87)
T cd01612 81 CKTVAFG 87 (87)
T ss_pred eCccccC
Confidence 9999999
No 6
>PF04110 APG12: Ubiquitin-like autophagy protein Apg12 ; InterPro: IPR007242 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents Apg12, which is covalently bound to Apg5 [].; GO: 0000045 autophagic vacuole assembly, 0005737 cytoplasm; PDB: 1WZ3_B.
Probab=99.94 E-value=6.5e-27 Score=157.07 Aligned_cols=86 Identities=20% Similarity=0.412 Sum_probs=62.9
Q ss_pred EEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEe
Q psy12247 31 VILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVY 110 (119)
Q Consensus 31 VIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Y 110 (119)
|.|--.+.+++|.|+++||.|.++.|++.++.+|||+|+++++++||+|||++|+|++|+++|+||+||+ .||-|.|+|
T Consensus 2 V~v~fk~iG~aPilk~~k~kI~~~~~f~~vi~fLrk~Lk~~~~~slFlYin~sFaPspDe~vg~L~~~f~-~~~~Liv~Y 80 (87)
T PF04110_consen 2 VTVRFKAIGSAPILKQKKFKISASQTFATVIAFLRKKLKLKPSDSLFLYINNSFAPSPDETVGDLYRCFG-TNGELIVSY 80 (87)
T ss_dssp EEEEEEEETT----S--EEEEETTSBTHHHHHHHHHHCT----SS-EEEEEEEE---TTSBHHHHHHHH--BTTBEEEEE
T ss_pred EEEEEEecCCCccccCcEEEECCCCchHHHHHHHHHHhCCccCCeEEEEEcCccCCCchhHHHHHHHHhC-CCCEEEEEE
Confidence 3343445578999999999999999999999999999999999999999999999999999999999998 899999999
Q ss_pred ccccccc
Q psy12247 111 SDVNIFV 117 (119)
Q Consensus 111 s~~~~fG 117 (119)
|.++|||
T Consensus 81 s~t~A~G 87 (87)
T PF04110_consen 81 SKTPAWG 87 (87)
T ss_dssp ESSS---
T ss_pred ecccccC
Confidence 9999999
No 7
>KOG3439|consensus
Probab=99.93 E-value=2e-25 Score=154.73 Aligned_cols=86 Identities=16% Similarity=0.323 Sum_probs=81.1
Q ss_pred EEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEe
Q psy12247 31 VILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVY 110 (119)
Q Consensus 31 VIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Y 110 (119)
|.|.-.+-+++|.|+++||.|+.+.||+.++.+|||.|+|++.++|||||||+|+|++|+.+|+||+||+ .||.|.++|
T Consensus 31 V~i~l~aiG~~PilK~~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sFAPsPDq~v~~Ly~cf~-~d~~Lvl~Y 109 (116)
T KOG3439|consen 31 VQIRLRAIGDAPILKKSKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFG-TDGKLVLNY 109 (116)
T ss_pred EEEEEeccCCCcceecceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCccCCCchhHHHHHHHhcC-CCCEEEEEE
Confidence 4444455689999999999999999999999999999999999999999999999999999999999997 899999999
Q ss_pred ccccccc
Q psy12247 111 SDVNIFV 117 (119)
Q Consensus 111 s~~~~fG 117 (119)
|...|||
T Consensus 110 c~s~A~G 116 (116)
T KOG3439|consen 110 CISVAWG 116 (116)
T ss_pred eeecccC
Confidence 9999999
No 8
>PF04106 APG5: Autophagy protein Apg5 ; InterPro: IPR007239 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents autophagy protein 5 (Apg5).; GO: 0006914 autophagy, 0005737 cytoplasm; PDB: 2DYM_G 2DYO_A.
Probab=96.82 E-value=0.0034 Score=47.56 Aligned_cols=100 Identities=14% Similarity=0.117 Sum_probs=49.6
Q ss_pred CCHHHHHHHHHHHH---hcCCCcceEEEEcCCCCCCCCCCcceEEec---CCcchHhHHHHHHHhh--cCCCCCeEEEEE
Q psy12247 9 YSLEERIKIGENLA---RNHPNCAFVILERSPSALLPQMPRSNYVVA---YEMTVGHFFYLLRKKM--ALRPEEACFFFI 80 (119)
Q Consensus 9 ~~~e~R~~e~~~ir---~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp---~~~tv~~~~~~lRk~l--~l~~~~slfl~V 80 (119)
+.|++=..-..++. ..-..+|||.|-.... .|.++..--.+. ...|+++++..+=-.+ .-+......+++
T Consensus 88 ~~~~~f~~i~~kl~~~~~~~~r~IPiRiy~~~~--~~~iQ~~i~~~~~~g~~~TL~d~L~~~lp~~f~s~~~~~~~~~ii 165 (197)
T PF04106_consen 88 HDFDQFWSINSKLMPPDPSKFRHIPIRIYLPGS--VPVIQPPIPPIKEDGQPQTLGDALSELLPELFPSSDEPELARVII 165 (197)
T ss_dssp T-HHHHHHHHHHHS----SS-SB--EEEEE-SS----EE----B----TT---BTGGGHHHHHTTT--T------EEEEE
T ss_pred hCHHHHHHHHHHHHhhcCCCcceeEEEEEeCCC--cceEecccccccCCCCcCcHHHHHHHhChhhcccccCccccEEEE
Confidence 33444444455565 6667899999977543 223322211111 2347777654432211 112345678889
Q ss_pred cCeecCCcCchHHHHHhHhcCCCCeEEEEec
Q psy12247 81 ESMIVPADSTRMETLSQRFADKDGLIYMVYS 111 (119)
Q Consensus 81 n~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys 111 (119)
+|.- ++.|+.|..||+.+.-.||||||.-.
T Consensus 166 hGI~-ipldtpl~~l~~~l~~~D~FLhivv~ 195 (197)
T PF04106_consen 166 HGIE-IPLDTPLQWLYENLSYPDGFLHIVVR 195 (197)
T ss_dssp TTEE-E-TTSBHHHHHHHH--TTS-EEEEEE
T ss_pred eCee-CCCCCcHHHHHHHccCCCCeEEEEEE
Confidence 9988 77799999999999999999999753
No 9
>PF11816 DUF3337: Domain of unknown function (DUF3337); InterPro: IPR021772 This family of proteins are functionally uncharacterised. This family is only found in eukaryotes. This presumed domain is typically between 285 to 342 amino acids in length.
Probab=95.32 E-value=0.23 Score=40.31 Aligned_cols=87 Identities=16% Similarity=0.224 Sum_probs=70.3
Q ss_pred CCCcceEEEEcCCCCCCCCCCcc-----------------eEEecCCcchHhHHHHHHHhh--------------cCCCC
Q psy12247 25 HPNCAFVILERSPSALLPQMPRS-----------------NYVVAYEMTVGHFFYLLRKKM--------------ALRPE 73 (119)
Q Consensus 25 yp~~ipVIvE~~~~~~~p~L~k~-----------------Kflvp~~~tv~~~~~~lRk~l--------------~l~~~ 73 (119)
-+.+|+-++.+...+..|.+... |.-.|.-+.|..+...|-.|+ .+.++
T Consensus 211 e~~Ki~F~L~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rL~A~~mLrvkKI~~yV~ek~~~~~~~~~~~~~~~~~~p~ 290 (331)
T PF11816_consen 211 EPPKISFVLQPWDGSLPPNLKPDGKSQKKIKLPPLSEGNSRLNAPRMLRVKKILEYVAEKLEKTPESKTPEMKPKKLKPE 290 (331)
T ss_pred CCCeeEEEEeecCCCCccccCCCccccccccccccccccceecccchhhhHHHHHHHHHHhccCccccCccccccCCCCC
Confidence 45677888888875555555554 888888899999999999999 45788
Q ss_pred CeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEecc
Q psy12247 74 EACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSD 112 (119)
Q Consensus 74 ~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~ 112 (119)
+.|=|+||+.+ .++++||+.+=..+=-..|-|.|.|..
T Consensus 291 e~lEl~C~gqv-L~~~mtLaTVr~~~WK~~~di~L~YR~ 328 (331)
T PF11816_consen 291 EWLELLCNGQV-LPPDMTLATVRTFIWKSSGDIVLHYRR 328 (331)
T ss_pred ceEEEEeCCeE-cCCcCCHHHHHHhhccCCCeEEEEEEe
Confidence 99999999999 556999999988844468899999964
No 10
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=93.59 E-value=0.28 Score=30.46 Aligned_cols=50 Identities=18% Similarity=0.183 Sum_probs=39.8
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHH
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETL 95 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~l 95 (119)
+...|.|..+.+++.++...+++.++++.+++-|+.++.- ..++.|++++
T Consensus 11 ~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~-L~~~~T~~~~ 60 (72)
T PF11976_consen 11 KEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKR-LDPNDTPEDL 60 (72)
T ss_dssp EEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEE-E-TTSCHHHH
T ss_pred CEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEE-cCCCCCHHHC
Confidence 4567889999999999999999999999667778888877 4445677665
No 11
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=92.95 E-value=0.51 Score=31.28 Aligned_cols=57 Identities=19% Similarity=0.183 Sum_probs=44.6
Q ss_pred EecCCcchHhHHHHHHHhhcCCCCCeEEEEEc----CeecCCcCchHHHHHhHhcCCCCeEEEE
Q psy12247 50 VVAYEMTVGHFFYLLRKKMALRPEEACFFFIE----SMIVPADSTRMETLSQRFADKDGLIYMV 109 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn----~~~~p~~~~~m~~lY~~~kd~DGfLyl~ 109 (119)
-||.+.+++++...|++||++++ +.+.|.-. +.+.|-.|+.|...+.+=+ ||-|-+-
T Consensus 16 rvp~~~~y~~L~~ki~~kLkl~~-e~i~LsYkde~s~~~v~l~d~dle~aws~~~--~~~lTLw 76 (80)
T cd06406 16 QVARGLSYATLLQKISSKLELPA-EHITLSYKSEASGEDVILSDTNMEDVWSQAK--DGCLTLW 76 (80)
T ss_pred EcCCCCCHHHHHHHHHHHhCCCc-hhcEEEeccCCCCCccCcChHHHHHHHHhhc--CCeEEEE
Confidence 58999999999999999999985 45666544 3554668889999998886 7766543
No 12
>KOG2660|consensus
Probab=90.89 E-value=0.47 Score=38.92 Aligned_cols=73 Identities=19% Similarity=0.250 Sum_probs=59.4
Q ss_pred CCCCCCcceEE-ecCCcchHhHHHHHHHhhc-CCCCCeEEEEEcCeecCCcCchHHHHHhHhcC--CCCeEEEEecccc
Q psy12247 40 LLPQMPRSNYV-VAYEMTVGHFFYLLRKKMA-LRPEEACFFFIESMIVPADSTRMETLSQRFAD--KDGLIYMVYSDVN 114 (119)
Q Consensus 40 ~~p~L~k~Kfl-vp~~~tv~~~~~~lRk~l~-l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd--~DGfLyl~Ys~~~ 114 (119)
.++.|. .+|+ ++...|+.++..++|+++. +.+.-.+=+++|+.+ ...+.||.++.-.+.+ -||-|-+.|+..+
T Consensus 159 ~~k~l~-~~fvrcsa~~Tv~hlkkfl~~k~~~~~~~~~idi~~~d~~-l~~~~TLk~i~~~~~~~~r~~pL~l~y~v~p 235 (331)
T KOG2660|consen 159 TLKDLV-RRFLRCSAAATVNHLKKFLRKKMDNLSNKSEIDILCEEEL-LGDYYTLKDIAYAYRWRSRDPPLPLRYRVKP 235 (331)
T ss_pred cccccc-cceEeccHHHHHHHHHHHHHHHhccccchhhheeecCCcc-ccchhhhhhhhhhhcccccCCcceeEecccc
Confidence 455555 5775 8999999999999999998 777667778888877 7778999988877766 4999999998543
No 13
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=90.73 E-value=2 Score=32.02 Aligned_cols=79 Identities=14% Similarity=0.235 Sum_probs=55.4
Q ss_pred ceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEc-C-eecCCcCchHHHHHhHhcCCCCeE
Q psy12247 29 AFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIE-S-MIVPADSTRMETLSQRFADKDGLI 106 (119)
Q Consensus 29 ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn-~-~~~p~~~~~m~~lY~~~kd~DGfL 106 (119)
|-|+|...+.-.+| ..-.+-+|.+.|++++...|..++.......++|+++ | .+.+..+..++.+...-.|. +|+
T Consensus 1 i~Vlvss~~g~~lp--~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~-~~~ 77 (162)
T PF13019_consen 1 INVLVSSFDGLTLP--PTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDS-DFI 77 (162)
T ss_pred CeEEEecCCCCCCC--CeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhccCcCCC-Cce
Confidence 34666543321221 3345679999999999999999999988877778776 4 55467788889888776533 676
Q ss_pred EEEe
Q psy12247 107 YMVY 110 (119)
Q Consensus 107 yl~Y 110 (119)
.+..
T Consensus 78 ~l~l 81 (162)
T PF13019_consen 78 TLRL 81 (162)
T ss_pred EEEE
Confidence 6654
No 14
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=88.87 E-value=2.5 Score=23.04 Aligned_cols=44 Identities=23% Similarity=0.249 Sum_probs=34.1
Q ss_pred CCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCc
Q psy12247 44 MPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPAD 88 (119)
Q Consensus 44 L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~ 88 (119)
.....+.++.+.|++++...|..+.+.. .+...|++++..++..
T Consensus 7 ~~~~~~~~~~~~tv~~l~~~i~~~~~~~-~~~~~l~~~~~~~~~~ 50 (69)
T cd00196 7 GKTVELLVPSGTTVADLKEKLAKKLGLP-PEQQRLLVNGKILPDS 50 (69)
T ss_pred CCEEEEEcCCCCcHHHHHHHHHHHHCcC-hHHeEEEECCeECCCC
Confidence 4556678889999999999999998854 4467788888774443
No 15
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=88.60 E-value=2 Score=25.23 Aligned_cols=46 Identities=11% Similarity=0.035 Sum_probs=35.3
Q ss_pred ceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHH
Q psy12247 47 SNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 47 ~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~ 94 (119)
..+-|+.+.|++++...|..+.+++++ .+=|+.++.. ...+.++++
T Consensus 12 ~~~~v~~~~tv~~lk~~i~~~~~~~~~-~~~L~~~g~~-L~d~~tL~~ 57 (64)
T smart00213 12 ITLEVKPSDTVSELKEKIAELTGIPVE-QQRLIYKGKV-LEDDRTLAD 57 (64)
T ss_pred EEEEECCCCcHHHHHHHHHHHHCCCHH-HEEEEECCEE-CCCCCCHHH
Confidence 346799999999999999999999766 3556667877 445666654
No 16
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=87.34 E-value=1.1 Score=27.35 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=38.4
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHH
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETL 95 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~l 95 (119)
.+-|+.+.||+++...|-.+.+++++ .+-|+.++..+ ..+.+|+++
T Consensus 9 ~~~v~~~~tV~~lK~~i~~~~~~~~~-~~~L~~~G~~L-~d~~tL~~~ 54 (69)
T PF00240_consen 9 TLEVDPDDTVADLKQKIAEETGIPPE-QQRLIYNGKEL-DDDKTLSDY 54 (69)
T ss_dssp EEEEETTSBHHHHHHHHHHHHTSTGG-GEEEEETTEEE-STTSBTGGG
T ss_pred EEEECCCCCHHHhhhhcccccccccc-cceeeeeeecc-cCcCcHHHc
Confidence 45699999999999999999998876 46677799984 778888765
No 17
>KOG2976|consensus
Probab=82.76 E-value=19 Score=28.91 Aligned_cols=79 Identities=14% Similarity=0.164 Sum_probs=48.2
Q ss_pred hcCCCcceEEEEcC--C-------CCCCCCCCcceEEecCCcchHhHHHHHHHhhc--------CCCCCeEEEEEcCeec
Q psy12247 23 RNHPNCAFVILERS--P-------SALLPQMPRSNYVVAYEMTVGHFFYLLRKKMA--------LRPEEACFFFIESMIV 85 (119)
Q Consensus 23 ~kyp~~ipVIvE~~--~-------~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~--------l~~~~slfl~Vn~~~~ 85 (119)
...+-+||+.+--+ + +...|. +. .++-..+-+=.+|.+++. .+..+. +.+.+.=
T Consensus 178 ~n~~r~IPL~iy~sq~~t~r~f~~~~~~P~-----~~-~~d~~~stlge~l~d~~~~s~~s~d~~~~~~~--viihGIe- 248 (278)
T KOG2976|consen 178 DNRSRHIPLRIYTSQVKTARDFRTSLTFPC-----IS-QPDGSLSTLGEFLKDRLPDSLDSKDDINGNDP--VIIHGIE- 248 (278)
T ss_pred ccccccceeEeeccccccccchhhccccce-----ee-cCchhhhhhhHHHHhhcccccCccccccccCc--eEEeccc-
Confidence 34789999999743 1 123331 11 123223333334556653 222233 5556655
Q ss_pred CCcCchHHHHHhHhcCCCCeEEEEe
Q psy12247 86 PADSTRMETLSQRFADKDGLIYMVY 110 (119)
Q Consensus 86 p~~~~~m~~lY~~~kd~DGfLyl~Y 110 (119)
++..+.+..||......||||||+-
T Consensus 249 i~l~tpL~~l~~~L~ypD~FLHI~l 273 (278)
T KOG2976|consen 249 IPLHTPLYWLYSNLSYPDGFLHIVL 273 (278)
T ss_pred ccccchHHHHHhhccCCCcceEEEE
Confidence 7778999999999999999999975
No 18
>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein. Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.
Probab=80.74 E-value=13 Score=24.28 Aligned_cols=62 Identities=13% Similarity=0.154 Sum_probs=44.7
Q ss_pred eEEe--cCCcchHhHHHHHHHhhc-CCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEec
Q psy12247 48 NYVV--AYEMTVGHFFYLLRKKMA-LRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYS 111 (119)
Q Consensus 48 Kflv--p~~~tv~~~~~~lRk~l~-l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys 111 (119)
-|-| +.+.||+++...|....+ ..+.+..=|.-.|++ ...+.+|++..+.-+ ..--++|.|+
T Consensus 15 ~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKi-LkD~~tL~~~~~~~~-~~~tiHLV~~ 79 (79)
T cd01790 15 DQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKL-LPDHLKLRDVLRKQD-EYHMVHLVCA 79 (79)
T ss_pred EEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCee-ccchhhHHHHhhccc-CCceEEEEeC
Confidence 3666 789999999999988764 333345556667788 578899999987753 3446777664
No 19
>PF03671 Ufm1: Ubiquitin fold modifier 1 protein; InterPro: IPR005375 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin-like molecules (UBLs) can be divided into two subclasses: type-1 UBLs, which ligate to target proteins in a manner similar, but not identical, to the ubiquitylation pathway, such as SUMO, NEDD8, and UCRP/ISG15, and type-2 UBLs (also called UDPs, ubiquitin-domain proteins), which contain ubiquitin-like structure embedded in a variety of different classes of large proteins with apparently distinct functions, such as Rad23, Elongin B, Scythe, Parkin, and HOIL-1. This entry represents Ufm1 (ubiquitin-fold modifier), which is a ubiquitin-like protein with structural similarities to ubiquitin [, ]. Ufm1 is one of a number of ubiquitin-like modifiers that conjugate to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting it has a potential role in multicellular organisms []. Human Ufm1 is synthesized as a precursor consisting of 85 amino-acid residues. Prior to activation by Uba5, the extra amino acids at the C-terminal region of Ufm1 are removed to expose Gly, which is necessary for conjugation to target molecule(s). C-terminal processing of Ufm1 requires two specific cysteine peptidases (IPR012462 from INTERPRO): UfSP1 and UfSP2; both peptidases are also able to release Ufm1 from Ufm1-conjugated cellular proteins. UfSP2 is present in most, if not all, of multi-cellular organisms including plant, nematode, fly, and mammal, whereas UfSP1 is not present in plants and nematodes []. For further information on ubiquitin, please see Protein of the Month [].; PDB: 1J0G_A 1WXS_A 1L7Y_A.
Probab=80.53 E-value=9.9 Score=24.86 Aligned_cols=60 Identities=8% Similarity=0.110 Sum_probs=44.8
Q ss_pred CCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcC
Q psy12247 41 LPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFAD 101 (119)
Q Consensus 41 ~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd 101 (119)
=|.+.-+.+-||++..+..++.+--...++++..|.-+--++.= -.+.++-|+++-+|+.
T Consensus 12 Dp~~p~kv~sVPE~apftaVlkfaAeeF~vp~~tsaiItndG~G-InP~QTag~vflKhGs 71 (76)
T PF03671_consen 12 DPKLPYKVISVPEEAPFTAVLKFAAEEFKVPPATSAIITNDGVG-INPQQTAGNVFLKHGS 71 (76)
T ss_dssp SSTS-EEEEEEETTSBHHHHHHHHHHHTTS-SSSEEEEESSS-E-E-TTSBHHHHHHHT-S
T ss_pred CCCCcceEEecCCCCchHHHHHHHHHHcCCCCceEEEEecCCcc-cccchhhhhhHhhcCc
Confidence 35677788899999999999999999999999988554444433 5567999999999974
No 20
>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi. They contain a characteristic GFDRL sequence motif.
Probab=79.37 E-value=10 Score=25.66 Aligned_cols=71 Identities=14% Similarity=0.170 Sum_probs=46.7
Q ss_pred CCCCCCcceEEecCCcchHhHHHHHHHhh-cCCCCCeEEEEEcCeecCCcCchHHHHHhHh---------cCCCC----e
Q psy12247 40 LLPQMPRSNYVVAYEMTVGHFFYLLRKKM-ALRPEEACFFFIESMIVPADSTRMETLSQRF---------ADKDG----L 105 (119)
Q Consensus 40 ~~p~L~k~Kflvp~~~tv~~~~~~lRk~l-~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~---------kd~DG----f 105 (119)
.+|+|.=. +--|.+.|+.++...||.++ .-.....|=|.-++.+++. ++.++..-... +..++ -
T Consensus 10 sipDl~L~-I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d-~t~l~~~l~~~~~~~~~~~gk~~~~~~~~~ 87 (97)
T PF10302_consen 10 SIPDLPLD-IPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLND-HTDLSSELKLPTARSSKGKGKAPERQEAPR 87 (97)
T ss_pred CCCCceee-cCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCc-cchhhhhhccccccCccccCcCccCCCCCe
Confidence 67775310 00448899999999999998 4456678888888998554 44444443333 22333 7
Q ss_pred EEEEecc
Q psy12247 106 IYMVYSD 112 (119)
Q Consensus 106 Lyl~Ys~ 112 (119)
.||++|.
T Consensus 88 ~yIhCsI 94 (97)
T PF10302_consen 88 IYIHCSI 94 (97)
T ss_pred EEEEEec
Confidence 8888874
No 21
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=79.31 E-value=10 Score=24.63 Aligned_cols=62 Identities=8% Similarity=0.107 Sum_probs=44.3
Q ss_pred CCcceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHH
Q psy12247 26 PNCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETL 95 (119)
Q Consensus 26 p~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~l 95 (119)
+.+|.|-|.- . .-+...|.|..+.+++.++..+..+.++++++--|+| ++.- ...+.|++++
T Consensus 9 ~~~i~I~v~~-~-----~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f-~G~~-L~~~~T~~~l 70 (87)
T cd01763 9 SEHINLKVKG-Q-----DGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLF-DGQR-IRDNQTPDDL 70 (87)
T ss_pred CCeEEEEEEC-C-----CCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEE-CCeE-CCCCCCHHHc
Confidence 4556666622 1 2355678999999999999999999999987655665 5555 3446677776
No 22
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=78.06 E-value=5.3 Score=24.89 Aligned_cols=44 Identities=16% Similarity=0.204 Sum_probs=34.8
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHH
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~ 94 (119)
+-|+.+.||+++...|..+.+++++ ..-|+.+++. ...+.++++
T Consensus 15 l~v~~~~tV~~lK~~i~~~~gi~~~-~q~L~~~G~~-L~d~~~L~~ 58 (74)
T cd01807 15 LQVSEKESVSTLKKLVSEHLNVPEE-QQRLLFKGKA-LADDKRLSD 58 (74)
T ss_pred EEECCCCcHHHHHHHHHHHHCCCHH-HeEEEECCEE-CCCCCCHHH
Confidence 4588999999999999999999875 4566688888 455667654
No 23
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=77.45 E-value=3.9 Score=25.96 Aligned_cols=45 Identities=16% Similarity=0.187 Sum_probs=36.7
Q ss_pred EecCCcchHhHHHHHHHhhcCCCCCeEEEE--EcCeecCCcCchHHHH
Q psy12247 50 VVAYEMTVGHFFYLLRKKMALRPEEACFFF--IESMIVPADSTRMETL 95 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~l~~~~slfl~--Vn~~~~p~~~~~m~~l 95 (119)
=|+.+.|+++|...|-...+++++.-=.+| +.++. +..+.+++++
T Consensus 15 ~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~-l~D~~~L~~~ 61 (74)
T cd01813 15 TTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKP-AEDDVKISAL 61 (74)
T ss_pred EECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCc-CCCCcCHHHc
Confidence 488999999999999999999987555666 45676 7778888876
No 24
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=77.16 E-value=6.2 Score=24.27 Aligned_cols=56 Identities=9% Similarity=0.128 Sum_probs=41.2
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEE
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMV 109 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~ 109 (119)
+-|+++.|++++...|-.+.+++++ ..-|+.+++. ...+.++++ |.-- ++-.|+|.
T Consensus 13 ~~v~~~~tV~~lK~~i~~~~gi~~~-~q~Li~~G~~-L~d~~~l~~-~~i~--~~stl~l~ 68 (70)
T cd01798 13 VEVDPDTDIKQLKEVVAKRQGVPPD-QLRVIFAGKE-LRNTTTIQE-CDLG--QQSILHAV 68 (70)
T ss_pred EEECCCChHHHHHHHHHHHHCCCHH-HeEEEECCeE-CCCCCcHHH-cCCC--CCCEEEEE
Confidence 4588999999999999999998765 5677788888 566788877 4322 23355553
No 25
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=77.06 E-value=7.6 Score=22.93 Aligned_cols=57 Identities=16% Similarity=0.213 Sum_probs=39.8
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcC-CCCeEEEEe
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFAD-KDGLIYMVY 110 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd-~DGfLyl~Y 110 (119)
.+-++.+.|++++...|.++.+++++. +=|..+++.+ ..+.++++ +.- ++..+|+..
T Consensus 11 ~~~~~~~~ti~~lK~~i~~~~~~~~~~-~~l~~~g~~l-~d~~~l~~----~~v~~~~~i~v~~ 68 (69)
T cd01769 11 ELEVSPDDTVAELKAKIAAKEGVPPEQ-QRLIYAGKIL-KDDKTLSD----YGIQDGSTLHLVL 68 (69)
T ss_pred EEEECCCChHHHHHHHHHHHHCcChHH-EEEEECCcCC-CCcCCHHH----CCCCCCCEEEEEE
Confidence 467889999999999999999987764 4446688774 55666654 222 344566653
No 26
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=76.72 E-value=8.3 Score=27.14 Aligned_cols=51 Identities=12% Similarity=0.117 Sum_probs=33.9
Q ss_pred cceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecC----------CcCchHHHHHhHh
Q psy12247 46 RSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVP----------ADSTRMETLSQRF 99 (119)
Q Consensus 46 k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p----------~~~~~m~~lY~~~ 99 (119)
..+|-|+.++|+++|+..++++.++... =|.++++++- ..+++|.+|++.-
T Consensus 34 WDr~~v~~~~Tl~~li~~~~~~~~lev~---ml~~g~~~LY~~f~~~~~~~rl~~~i~elv~~v 94 (125)
T PF09358_consen 34 WDRIEVNGDMTLQELIDYFKEKYGLEVT---MLSQGVSLLYSSFPPPKHKERLKMPISELVEEV 94 (125)
T ss_dssp T-EEEEES--BHHHHHHHHHHTTS-EEE---EEEETTEEEEETT-HHHHHHHTTSBHHHHHHHH
T ss_pred eeEEEEcCCCCHHHHHHHHHHHhCceEE---EEEeCCEEEEecCChhhhHHHhCCcHHHHHHHh
Confidence 4578899999999999999999988743 2333333321 1578899999964
No 27
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=76.30 E-value=10 Score=23.21 Aligned_cols=58 Identities=10% Similarity=0.119 Sum_probs=41.4
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCC-eEEEEec
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDG-LIYMVYS 111 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DG-fLyl~Ys 111 (119)
.+-|+.+.|++++...|..+.+++++.-- |+.++.. ...+.++++. .-.|| .|++...
T Consensus 14 ~~~v~~~~tv~~lK~~i~~~~g~~~~~qr-L~~~g~~-L~d~~tl~~~----~i~~g~~i~l~~~ 72 (76)
T cd01806 14 EIDIEPTDKVERIKERVEEKEGIPPQQQR-LIYSGKQ-MNDDKTAADY----KLEGGSVLHLVLA 72 (76)
T ss_pred EEEECCCCCHHHHHHHHhHhhCCChhhEE-EEECCeE-ccCCCCHHHc----CCCCCCEEEEEEE
Confidence 35699999999999999999999887533 3367777 4566777663 33344 6777654
No 28
>PF08154 NLE: NLE (NUC135) domain; InterPro: IPR012972 This domain is located N-terminal to WD40 repeats(IPR001680 from INTERPRO). It is found in the microtubule-associated protein Q12024 from SWISSPROT [].
Probab=74.65 E-value=18 Score=22.46 Aligned_cols=42 Identities=14% Similarity=0.142 Sum_probs=36.2
Q ss_pred CCCcceEEecCCcchHhHHHHHHHhh-cCCCCCeEEEEEcCee
Q psy12247 43 QMPRSNYVVAYEMTVGHFFYLLRKKM-ALRPEEACFFFIESMI 84 (119)
Q Consensus 43 ~L~k~Kflvp~~~tv~~~~~~lRk~l-~l~~~~slfl~Vn~~~ 84 (119)
.+...-+.||.+.|..++-..+.+-| ........=++||+.+
T Consensus 14 ~~~~~~~~VP~~~t~~~Ls~LvN~LL~~~~~~vpfdF~i~~~~ 56 (65)
T PF08154_consen 14 EVPGTPISVPSNITRKELSELVNQLLDDEEEPVPFDFLINGEE 56 (65)
T ss_pred cCCCCCEEEeCCCCHHHHHHHHHHHhccCCCCCcEEEEECCEE
Confidence 55668899999999999999999998 6667777778999877
No 29
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=74.50 E-value=9 Score=23.70 Aligned_cols=56 Identities=16% Similarity=0.188 Sum_probs=39.3
Q ss_pred eEEecCCcchHhHHHHHHHhhcC--CCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCC-eEEEE
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMAL--RPEEACFFFIESMIVPADSTRMETLSQRFADKDG-LIYMV 109 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l--~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DG-fLyl~ 109 (119)
.+=|+.+.||+++...|..+.++ +++ ..-|..++.. ...+.++++ |+-.|| .|++.
T Consensus 14 ~l~v~~~~TV~~lK~~i~~~~~i~~~~~-~q~L~~~G~~-L~d~~~L~~----~~i~~~~~i~~~ 72 (77)
T cd01805 14 PIEVDPDDTVAELKEKIEEEKGCDYPPE-QQKLIYSGKI-LKDDTTLEE----YKIDEKDFVVVM 72 (77)
T ss_pred EEEECCCCcHHHHHHHHHHhhCCCCChh-HeEEEECCEE-ccCCCCHHH----cCCCCCCEEEEE
Confidence 35588999999999999999888 554 4556678887 456667766 233343 56654
No 30
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=72.70 E-value=14 Score=22.58 Aligned_cols=58 Identities=10% Similarity=0.116 Sum_probs=40.8
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCC-CCeEEEEec
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADK-DGLIYMVYS 111 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~-DGfLyl~Ys 111 (119)
.+-|+.+.||+++...|.++.+++++. .=|+.++.. ...+.++++ | +-. +.-+++...
T Consensus 14 ~~~v~~~~tV~~lK~~i~~~~g~~~~~-q~L~~~g~~-L~d~~~L~~-~---~i~~~~~i~l~~~ 72 (76)
T cd01803 14 TLEVEPSDTIENVKAKIQDKEGIPPDQ-QRLIFAGKQ-LEDGRTLSD-Y---NIQKESTLHLVLR 72 (76)
T ss_pred EEEECCcCcHHHHHHHHHHHhCCCHHH-eEEEECCEE-CCCCCcHHH-c---CCCCCCEEEEEEE
Confidence 467999999999999999999987653 444567877 556667766 2 333 346666654
No 31
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=71.86 E-value=4.9 Score=30.30 Aligned_cols=47 Identities=19% Similarity=0.343 Sum_probs=37.4
Q ss_pred CcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCC-eEEEEeccccccc
Q psy12247 54 EMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDG-LIYMVYSDVNIFV 117 (119)
Q Consensus 54 ~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DG-fLyl~Ys~~~~fG 117 (119)
.+++..++.-|++.+++...+ + ...++++|... ..|| |++| +.+.||
T Consensus 30 ~~~F~dii~EI~~~~~~s~~e---------i----~~~i~~FYTdl-n~DgrFi~L---Gdn~Wg 77 (175)
T COG3343 30 PFNFSDIINEIQKLLGVSKEE---------I----RSRIGQFYTDL-NIDGRFISL---GDNKWG 77 (175)
T ss_pred CccHHHHHHHHHHHhCcCHHH---------H----HHHHHHHHHHh-ccCCceeec---cccccc
Confidence 689999999999999887554 2 36789999999 4676 7665 678887
No 32
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=71.33 E-value=22 Score=22.04 Aligned_cols=65 Identities=9% Similarity=0.109 Sum_probs=47.9
Q ss_pred CcceEEec-CCcchHhHHHHHHHhhcCCCCCeEEEEEc--Ceec-CCcCchHHHHHhHhcC-CCCeEEEE
Q psy12247 45 PRSNYVVA-YEMTVGHFFYLLRKKMALRPEEACFFFIE--SMIV-PADSTRMETLSQRFAD-KDGLIYMV 109 (119)
Q Consensus 45 ~k~Kflvp-~~~tv~~~~~~lRk~l~l~~~~slfl~Vn--~~~~-p~~~~~m~~lY~~~kd-~DGfLyl~ 109 (119)
+...|.++ .+.++.+|...|++++++....-.+-|.+ |-.. .+.++.+...++.+.. .++.|.|.
T Consensus 10 ~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~~~~~~~l~l~ 79 (81)
T cd05992 10 EIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSDEDLEEAIEEARRSGSKKLRLF 79 (81)
T ss_pred CCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCHHHHHHHHHHHhhcCCccEEEE
Confidence 34567888 99999999999999999876545555665 3333 4667888888888864 46666654
No 33
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=70.74 E-value=23 Score=22.08 Aligned_cols=64 Identities=6% Similarity=0.163 Sum_probs=47.0
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcC---eecCCcCchHHHHHhHhcCC-CCeEEE
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIES---MIVPADSTRMETLSQRFADK-DGLIYM 108 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~---~~~p~~~~~m~~lY~~~kd~-DGfLyl 108 (119)
+...|.+|.+.|+.+|...|.+++++..+.-..-|.++ -+..+.++.|....+.++.. .+.|-|
T Consensus 11 ~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~~~~~~~l~l 78 (81)
T smart00666 11 ETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDEDLEEAIEEYDSLGSKKLRL 78 (81)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHHHHHHHHHHHHHcCCceEEE
Confidence 34567899999999999999999998765555567772 34357788888888887643 344443
No 34
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=70.24 E-value=22 Score=21.78 Aligned_cols=57 Identities=16% Similarity=0.151 Sum_probs=40.2
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcC-CCCeEEEEe
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFAD-KDGLIYMVY 110 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd-~DGfLyl~Y 110 (119)
.+-|..+.||+++...|..+.+++++ .+-|..+++. ...+.++++. .- ++..|+|.-
T Consensus 13 ~l~v~~~~TV~~lK~~I~~~~~i~~~-~~~Li~~Gk~-L~d~~tL~~~----~i~~~stl~l~~ 70 (71)
T cd01808 13 EIEIAEDASVKDFKEAVSKKFKANQE-QLVLIFAGKI-LKDTDTLTQH----NIKDGLTVHLVI 70 (71)
T ss_pred EEEECCCChHHHHHHHHHHHhCCCHH-HEEEEECCeE-cCCCCcHHHc----CCCCCCEEEEEE
Confidence 46688999999999999988887544 4556557887 4456676553 23 455787753
No 35
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=68.71 E-value=10 Score=22.97 Aligned_cols=44 Identities=11% Similarity=0.208 Sum_probs=31.8
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHH
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~ 94 (119)
+-|+.+.|++++...|...-+++++ ..=|+.++.. ...+.++++
T Consensus 14 i~v~~~~tv~~lK~~i~~~~gi~~~-~q~L~~~g~~-l~d~~~L~~ 57 (71)
T cd01812 14 LSISSQATFGDLKKMLAPVTGVEPR-DQKLIFKGKE-RDDAETLDM 57 (71)
T ss_pred EEECCCCcHHHHHHHHHHhhCCChH-HeEEeeCCcc-cCccCcHHH
Confidence 4588999999999999999898775 3445566665 334555544
No 36
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=67.19 E-value=27 Score=21.61 Aligned_cols=58 Identities=12% Similarity=0.149 Sum_probs=42.1
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEec
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYS 111 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys 111 (119)
+-|..+.||+++...|..+-+++++ ..-|+.+++. ...+.++++ |.- + ++-.|+|.-.
T Consensus 13 l~v~~~~tV~~lK~~I~~~~gi~~~-~q~L~~~G~~-L~D~~tL~~-~~i-~-~~~tl~l~~~ 70 (74)
T cd01810 13 YEVQLTQTVATLKQQVSQRERVQAD-QFWLSFEGRP-MEDEHPLGE-YGL-K-PGCTVFMNLR 70 (74)
T ss_pred EEECCcChHHHHHHHHHHHhCCCHH-HeEEEECCEE-CCCCCCHHH-cCC-C-CCCEEEEEEE
Confidence 5688999999999999988888665 4556678888 556788877 422 2 3447777643
No 37
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=65.89 E-value=24 Score=21.20 Aligned_cols=46 Identities=13% Similarity=0.175 Sum_probs=34.5
Q ss_pred ceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHH
Q psy12247 47 SNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 47 ~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~ 94 (119)
..+-|+.+.|++++...|.++.+++++. .=|..++.. ...+.++++
T Consensus 13 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~-q~L~~~g~~-L~d~~~L~~ 58 (72)
T cd01809 13 HTFTVEEEITVLDLKEKIAEEVGIPVEQ-QRLIYSGRV-LKDDETLSE 58 (72)
T ss_pred EEEEECCCCcHHHHHHHHHHHHCcCHHH-eEEEECCEE-CCCcCcHHH
Confidence 3467889999999999999999987653 344458887 455667665
No 38
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=64.60 E-value=27 Score=21.66 Aligned_cols=60 Identities=8% Similarity=-0.004 Sum_probs=42.6
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEE
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMV 109 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~ 109 (119)
+...+-|.++.||+++...|..+-++++++ .-|+.+++. ...+.++++ |.-- ++--|++.
T Consensus 9 ~~~~l~v~~~~tV~~lK~~i~~~~gip~~~-q~Li~~Gk~-L~D~~tL~~-~~i~--~~~tl~l~ 68 (74)
T cd01793 9 NTHTLEVTGQETVSDIKAHVAGLEGIDVED-QVLLLAGVP-LEDDATLGQ-CGVE--ELCTLEVA 68 (74)
T ss_pred CEEEEEECCcCcHHHHHHHHHhhhCCCHHH-EEEEECCeE-CCCCCCHHH-cCCC--CCCEEEEE
Confidence 344567899999999999999998887654 556678887 567788877 4322 23355554
No 39
>cd01776 Rin1_RA Ubiquitin domain of RIN1 RAS effector. Rin1_RA RIN1 is a RAS effector that binds with specificity and high affinity to activated RAS via its carboxy-terminal RA (RAS-associated) domain. RIN1 competes directly with RAF1 for RAS binding and is thought to divert signaling away from RAF and the MAPK pathway while also shunting RAS signals through alternate pathways. In addition, Rin1 and Rin2 are Rab5-binding proteins, binding preferentially to the GTP-bound form, that enhance the GDP-GTP exchange reaction on Rab5 that regulate the docking and fusion processes of endocytic vesicles. In addition to the RA domain, RIN1 and RIN2 have an SH2 (Src homology 2) domain, a proline-rich SH3 domain, and a Vps9 domain.
Probab=64.59 E-value=13 Score=24.96 Aligned_cols=34 Identities=24% Similarity=0.325 Sum_probs=29.8
Q ss_pred EEecCCcchHhHHHHHHHhhcCC--CCCeEEEEEcC
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALR--PEEACFFFIES 82 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~--~~~slfl~Vn~ 82 (119)
-.|+++.|..++-...-.++.+. .+-+||+||++
T Consensus 18 L~V~P~~tt~~vc~lcA~Kf~V~qPe~y~LFl~vdg 53 (87)
T cd01776 18 LLVRPYITTEDVCQLCAEKFKVTQPEEYSLFLFVEE 53 (87)
T ss_pred eecCCCCcHHHHHHHHHHHhccCChhheeEEEEECC
Confidence 47999999999999999999875 45799999996
No 40
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=62.84 E-value=30 Score=21.55 Aligned_cols=53 Identities=8% Similarity=0.196 Sum_probs=43.6
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEc--C-eecCCcCchHHHHHhHhcC
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIE--S-MIVPADSTRMETLSQRFAD 101 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn--~-~~~p~~~~~m~~lY~~~kd 101 (119)
+-++.+.++.+|...|++++++.+..-..-|.+ | .+..+.+..+....+.++.
T Consensus 16 ~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~~ 71 (84)
T PF00564_consen 16 ISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDEDLQEAIEQAKE 71 (84)
T ss_dssp EEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHHHHHHHHHHHH
T ss_pred EEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHHHHHHHHHHHh
Confidence 678999999999999999999987777777887 3 3435778888888888864
No 41
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=61.96 E-value=11 Score=29.27 Aligned_cols=46 Identities=20% Similarity=0.314 Sum_probs=31.2
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEc---Ceec-CCcCchHHH
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIE---SMIV-PADSTRMET 94 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn---~~~~-p~~~~~m~~ 94 (119)
+.|+.+.+++++.-.|+++++++++..|-||-. +.+- ..++.++.+
T Consensus 89 ~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~~~ie~i~~~~t~~~ 138 (249)
T PF12436_consen 89 VYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKPNMIEPIDPNQTFEK 138 (249)
T ss_dssp EEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEETTEEEE--SSSBHHH
T ss_pred EEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEeccceeeEcCCCCchhh
Confidence 679999999999999999999999999988865 3322 245566665
No 42
>PTZ00044 ubiquitin; Provisional
Probab=61.05 E-value=22 Score=21.90 Aligned_cols=46 Identities=11% Similarity=0.137 Sum_probs=34.0
Q ss_pred ceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHH
Q psy12247 47 SNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 47 ~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~ 94 (119)
..+-|+.+.|++++...|..+.++++++ .=|+.++.. ...+.++++
T Consensus 13 ~~l~v~~~~tv~~lK~~i~~~~gi~~~~-q~L~~~g~~-L~d~~~l~~ 58 (76)
T PTZ00044 13 QSFNFEPDNTVQQVKMALQEKEGIDVKQ-IRLIYSGKQ-MSDDLKLSD 58 (76)
T ss_pred EEEEECCCCcHHHHHHHHHHHHCCCHHH-eEEEECCEE-ccCCCcHHH
Confidence 3467899999999999999999998753 333357777 446666653
No 43
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=60.66 E-value=22 Score=22.31 Aligned_cols=58 Identities=10% Similarity=0.143 Sum_probs=39.8
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEec
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYS 111 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys 111 (119)
+-|+.+.||++|...|....+++++ ..=|..++.. ...+.++++. . -+ ++..|+|.-.
T Consensus 12 l~v~~~~TV~~lK~~i~~~~gip~~-~q~L~~~G~~-L~d~~tL~~~-~-i~-~g~~l~v~~~ 69 (76)
T cd01800 12 FTLQLSDPVSVLKVKIHEETGMPAG-KQKLQYEGIF-IKDSNSLAYY-N-LA-NGTIIHLQLK 69 (76)
T ss_pred EEECCCCcHHHHHHHHHHHHCCCHH-HEEEEECCEE-cCCCCcHHHc-C-CC-CCCEEEEEEe
Confidence 4588999999999999999998765 3455567776 5566677543 2 21 3446666544
No 44
>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo
Probab=59.91 E-value=47 Score=21.83 Aligned_cols=58 Identities=14% Similarity=0.122 Sum_probs=42.2
Q ss_pred EecCCcchHhHHHHHHHhhcCCCCCeEEEEEc---C-eecCCc-CchHHHHHhHhcCCCCeEE
Q psy12247 50 VVAYEMTVGHFFYLLRKKMALRPEEACFFFIE---S-MIVPAD-STRMETLSQRFADKDGLIY 107 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn---~-~~~p~~-~~~m~~lY~~~kd~DGfLy 107 (119)
.||...+++++...|+++|.++++..-.=|=. + ...|-. ++.|.+.+.+=+|-=.-|.
T Consensus 12 ~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~~~~~~v~l~~e~~me~aW~~v~~~~ltLw 74 (78)
T cd06411 12 RAPRGADVSSLRALLSQALPQQAQRGQLSYRAPGEDGHWVPISGEESLQRAWQDVADGPRGLQ 74 (78)
T ss_pred EccCCCCHHHHHHHHHHHhcCChhhcEEEecCCCCCccEeecCcchHHHHHHHhccCCceEEE
Confidence 47888999999999999999998764444443 2 444655 8899999988774333333
No 45
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=58.95 E-value=4.3 Score=26.42 Aligned_cols=57 Identities=12% Similarity=0.227 Sum_probs=29.8
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCe---ecC-CcCchHHHHHhHhcCCCCeEEE
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESM---IVP-ADSTRMETLSQRFADKDGLIYM 108 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~---~~p-~~~~~m~~lY~~~kd~DGfLyl 108 (119)
..-++.+.|++++...|...++++.. +..||.+.. -+. +.+.+++++==+|+| .||+
T Consensus 17 Rie~~~~~t~~~L~~kI~~~l~~~~~-~~~L~~~~~~~~~l~s~~~~tl~~lglkHGd---mlyL 77 (80)
T PF11543_consen 17 RIEVSPSSTLSDLKEKISEQLSIPDS-SQSLSKDRNNKEELKSSDSKTLSSLGLKHGD---MLYL 77 (80)
T ss_dssp EEEE-TTSBHHHHHHHHHHHS---TT-T---BSSGGGGGCSSS-TT-CCCCT---TT----EEE-
T ss_pred EEEcCCcccHHHHHHHHHHHcCCCCc-ceEEEecCCCCcccccCCcCCHHHcCCCCcc---EEEE
Confidence 44688999999999999999998865 556666632 222 345666666555553 5554
No 46
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=58.27 E-value=10 Score=23.21 Aligned_cols=19 Identities=26% Similarity=0.080 Sum_probs=16.2
Q ss_pred cccCCHHHHHHHHHHHHhc
Q psy12247 6 TEKYSLEERIKIGENLARN 24 (119)
Q Consensus 6 k~~~~~e~R~~e~~~ir~k 24 (119)
....|||+|..+++..|++
T Consensus 35 ~~~kSlEERE~eY~~AR~R 53 (59)
T PF12752_consen 35 RPSKSLEEREAEYAEARAR 53 (59)
T ss_pred cccCCHHHHHHHHHHHHHH
Confidence 4567999999999999874
No 47
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=57.46 E-value=23 Score=23.09 Aligned_cols=55 Identities=7% Similarity=0.135 Sum_probs=38.1
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEE-EEcC---eecCCcCchHHHHHhHh
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFF-FIES---MIVPADSTRMETLSQRF 99 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl-~Vn~---~~~p~~~~~m~~lY~~~ 99 (119)
+...|-+|.+.++.++...|++++++.+...+-| |.++ -.+.+.++-+.+..+-+
T Consensus 10 d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~ 68 (82)
T cd06407 10 EKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVY 68 (82)
T ss_pred eEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHH
Confidence 4566889999999999999999999976445555 5652 22245666665544333
No 48
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=55.55 E-value=27 Score=21.63 Aligned_cols=55 Identities=9% Similarity=0.125 Sum_probs=36.3
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcC-chHHHHHhHhcCCCCeEEE
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADS-TRMETLSQRFADKDGLIYM 108 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~-~~m~~lY~~~kd~DGfLyl 108 (119)
.-|++++||+++...|-.+-++++++ .-|+.+++.+ ..+ .++++ |. -+ ++.+|++
T Consensus 14 l~v~~~~TV~~lK~~I~~~~gip~~~-q~Li~~Gk~L-~D~~~~L~~-~g-i~-~~~~l~l 69 (71)
T cd01796 14 LDVDPDLELENFKALCEAESGIPASQ-QQLIYNGREL-VDNKRLLAL-YG-VK-DGDLVVL 69 (71)
T ss_pred EEECCcCCHHHHHHHHHHHhCCCHHH-eEEEECCeEc-cCCcccHHH-cC-CC-CCCEEEE
Confidence 46889999999999999999997754 4555677763 333 33433 22 21 3456665
No 49
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=54.71 E-value=43 Score=20.80 Aligned_cols=46 Identities=22% Similarity=0.272 Sum_probs=35.1
Q ss_pred ceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHH
Q psy12247 47 SNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 47 ~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~ 94 (119)
..+-|+.+.||+++...|..+-++++++ .=|+.++.. ...+.++++
T Consensus 11 ~~l~v~~~~TV~~lK~~I~~~~gi~~~~-q~Li~~G~~-L~D~~~l~~ 56 (70)
T cd01794 11 VKLSVSSKDTVGQLKKQLQAAEGVDPCC-QRWFFSGKL-LTDKTRLQE 56 (70)
T ss_pred EEEEECCcChHHHHHHHHHHHhCCCHHH-eEEEECCeE-CCCCCCHHH
Confidence 3456889999999999999988887753 334456777 667788877
No 50
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=54.40 E-value=28 Score=22.03 Aligned_cols=56 Identities=16% Similarity=0.144 Sum_probs=36.9
Q ss_pred EecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEe
Q psy12247 50 VVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVY 110 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Y 110 (119)
-|+++.||+++...|-.+-+++++.--..| +++. ...+.++++ |. -+ ++--++|-|
T Consensus 17 ~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~-~Gk~-L~D~~tL~~-yg-i~-~~stv~l~~ 72 (73)
T cd01791 17 KCNPDDTIGDLKKLIAAQTGTRPEKIVLKK-WYTI-FKDHISLGD-YE-IH-DGMNLELYY 72 (73)
T ss_pred EeCCCCcHHHHHHHHHHHhCCChHHEEEEe-CCcC-CCCCCCHHH-cC-CC-CCCEEEEEe
Confidence 488999999999999888888877544444 4666 445667766 22 21 233555544
No 51
>PF00837 T4_deiodinase: Iodothyronine deiodinase; InterPro: IPR000643 Iodothyronine deiodinase (1.97.1.10 from EC) (DI) [] is the vertebrate enzyme responsible for the deiodination of the prohormone thyroxine (T4 or 3,5,3',5'-tetraiodothyronine) into the biologically active hormone T3 (3,5,3'-triiodothyronine) and of T3 into the inactive metabolite T2 (3,3'-diiodothyronine). All known DI are proteins of about 250 residues that contain a selenocysteine at their active site. Three types of DI are known, type II is essential for providing the brain with the appropriate levels of T3 during the critical period of development, and type III is essential for the regulation of thyroid hormone inactivation during embryological development.; GO: 0004800 thyroxine 5'-deiodinase activity, 0055114 oxidation-reduction process
Probab=54.24 E-value=17 Score=28.70 Aligned_cols=33 Identities=18% Similarity=0.436 Sum_probs=28.4
Q ss_pred CcccccCCHHHHHHHHHHHHhcCCCcceEEEEcC
Q psy12247 3 FQYTEKYSLEERIKIGENLARNHPNCAFVILERS 36 (119)
Q Consensus 3 ~~fk~~~~~e~R~~e~~~ir~kyp~~ipVIvE~~ 36 (119)
..+++..|+|+|..-++.+++++| ..||+|-.-
T Consensus 158 ~~i~qh~sledR~~aA~~l~~~~~-~~pi~vD~m 190 (237)
T PF00837_consen 158 YEIPQHRSLEDRLRAAKLLKEEFP-QCPIVVDTM 190 (237)
T ss_pred eeecCCCCHHHHHHHHHHHHhhCC-CCCEEEEcc
Confidence 467888999999999999999997 579999764
No 52
>PRK06437 hypothetical protein; Provisional
Probab=53.56 E-value=24 Score=21.92 Aligned_cols=33 Identities=18% Similarity=0.242 Sum_probs=25.4
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecC
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVP 86 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p 86 (119)
+-++...|+++++. .|++++ +.+-+.+|+.++|
T Consensus 15 ~~i~~~~tv~dLL~----~Lgi~~-~~vaV~vNg~iv~ 47 (67)
T PRK06437 15 IEIDHELTVNDIIK----DLGLDE-EEYVVIVNGSPVL 47 (67)
T ss_pred EEcCCCCcHHHHHH----HcCCCC-ccEEEEECCEECC
Confidence 45788899999864 457865 4678889999976
No 53
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=52.89 E-value=31 Score=20.88 Aligned_cols=38 Identities=18% Similarity=0.257 Sum_probs=27.9
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCC
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPA 87 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~ 87 (119)
..+.+-+++.+|+.++.. .+++++ +.+-+-||+.++|+
T Consensus 4 Ng~~~~~~~~~tv~~ll~----~l~~~~-~~v~v~vN~~iv~~ 41 (64)
T TIGR01683 4 NGEPVEVEDGLTLAALLE----SLGLDP-RRVAVAVNGEIVPR 41 (64)
T ss_pred CCeEEEcCCCCcHHHHHH----HcCCCC-CeEEEEECCEEcCH
Confidence 345567788899888765 456665 57788999999764
No 54
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=51.22 E-value=59 Score=20.31 Aligned_cols=64 Identities=9% Similarity=0.087 Sum_probs=43.3
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEE-E--EEc--C--eecCCcCchHHHHHhHhcCC--CCeEEEE
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACF-F--FIE--S--MIVPADSTRMETLSQRFADK--DGLIYMV 109 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slf-l--~Vn--~--~~~p~~~~~m~~lY~~~kd~--DGfLyl~ 109 (119)
.-+-+.|+.+.|+.+++..+-+++++..+..-| | +.. + .. ...++..-.+....... ++.+++.
T Consensus 17 ~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~~~~~~er~-L~~~E~pl~i~~~~~~~~~~~~f~lr 89 (93)
T PF00788_consen 17 TYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVEESGGEERP-LDDDECPLQIQLQWPKDSQNSRFVLR 89 (93)
T ss_dssp SEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEECTTTEEEE-ETTTSBHHHHHHTTSSGTTTEEEEEE
T ss_pred cEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEEcCCCEEEE-cCCCCchHHHHHhCccccCceEEEEE
Confidence 467789999999999999999999994333333 4 222 1 33 45566666777766543 6666654
No 55
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=51.18 E-value=12 Score=28.35 Aligned_cols=51 Identities=18% Similarity=0.191 Sum_probs=29.4
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCC--CeEEE--EEcCeec--CCcCchHHHH
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPE--EACFF--FIESMIV--PADSTRMETL 95 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~--~slfl--~Vn~~~~--p~~~~~m~~l 95 (119)
+.-.++||++-||++++..++++++++++ ..|-+ ..|+++. .+.+..+++|
T Consensus 34 ~~~~~~vpk~~tV~Dll~~l~~k~~~~~~~~~~lrl~ev~~~ki~~~~~~d~~i~~l 90 (213)
T PF14533_consen 34 QEYELLVPKTGTVSDLLEELQKKVGFSEEGTGKLRLWEVSNHKIYKILSEDEPISSL 90 (213)
T ss_dssp -EEEE--BTT-BHHHHHHHHHTT----TT----EEEEEEETTEEEEEE-TTSBGGGS
T ss_pred eEEEEEECCCCCHHHHHHHHHHHcCCCcCCcCcEEEEEeECCEEEeecCCCCchhhc
Confidence 55678999999999999999999998754 23333 2344442 5678888887
No 56
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=51.05 E-value=69 Score=21.10 Aligned_cols=63 Identities=10% Similarity=0.153 Sum_probs=46.4
Q ss_pred CcceEEecC--CcchHhHHHHHHHhhcCCCCCeEEE-EEcC---eecCCcCchHHHHHhHhcCCCCeEEEEe
Q psy12247 45 PRSNYVVAY--EMTVGHFFYLLRKKMALRPEEACFF-FIES---MIVPADSTRMETLSQRFADKDGLIYMVY 110 (119)
Q Consensus 45 ~k~Kflvp~--~~tv~~~~~~lRk~l~l~~~~slfl-~Vn~---~~~p~~~~~m~~lY~~~kd~DGfLyl~Y 110 (119)
+...|.++. +.++.++...|+++.+++ ++-+ |+++ -.+.+.++.+.+.++.+....+.|-|+-
T Consensus 10 d~~rf~~~~~~~~~~~~L~~ev~~rf~l~---~f~lKYlDde~e~v~lssd~eLeE~~rl~~~~~~~l~~~v 78 (81)
T cd06396 10 ESQSFLVSDSENTTWASVEAMVKVSFGLN---DIQIKYVDEENEEVSVNSQGEYEEALKSAVRQGNLLQMNV 78 (81)
T ss_pred eEEEEEecCCCCCCHHHHHHHHHHHhCCC---cceeEEEcCCCCEEEEEchhhHHHHHHHHHhCCCEEEEEE
Confidence 556789998 779999999999999998 3333 5652 2335667888888887765666666654
No 57
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=49.62 E-value=63 Score=20.59 Aligned_cols=55 Identities=25% Similarity=0.170 Sum_probs=39.2
Q ss_pred CCCCCcceEEecCCcchHhHHHHHHHhhcCCCCC-eEEEEEcCe-ecCCcCchHHHH
Q psy12247 41 LPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEE-ACFFFIESM-IVPADSTRMETL 95 (119)
Q Consensus 41 ~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~-slfl~Vn~~-~~p~~~~~m~~l 95 (119)
+|+-..+.-.|.+.+|+.++..-+-++-+++++. .+|+.-++. -.+..++.++.|
T Consensus 6 LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~~~~~~~~~~~~d~~~L 62 (72)
T cd01760 6 LPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLGLDEKKPLDLDTDSSSL 62 (72)
T ss_pred CcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEecCCCcCCcCchhhhhhh
Confidence 6777788889999999999999999999999763 333333341 225666665554
No 58
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=48.48 E-value=58 Score=20.61 Aligned_cols=45 Identities=13% Similarity=0.067 Sum_probs=32.0
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHH
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~ 94 (119)
-+-|+.+.||+++...|-.+-+++++. .-|| ++.-+-..+.++++
T Consensus 16 ~l~v~~~~TV~~lK~kI~~~~gip~~~-QrL~-~G~~L~dD~~tL~~ 60 (75)
T cd01799 16 WLTVRPDMTVAQLKDKVFLDYGFPPAV-QRWV-IGQRLARDQETLYS 60 (75)
T ss_pred EEEECCCCcHHHHHHHHHHHHCcCHHH-EEEE-cCCeeCCCcCCHHH
Confidence 356899999999999999999998752 3334 44442445567755
No 59
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=47.06 E-value=27 Score=22.06 Aligned_cols=58 Identities=10% Similarity=0.088 Sum_probs=38.3
Q ss_pred EecCCcchHhHHHHHHHhhcCCCC-CeEEEEEcCeecCCcCchHHHHHhHhcC-CCCeEEEEecc
Q psy12247 50 VVAYEMTVGHFFYLLRKKMALRPE-EACFFFIESMIVPADSTRMETLSQRFAD-KDGLIYMVYSD 112 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~l~~~-~slfl~Vn~~~~p~~~~~m~~lY~~~kd-~DGfLyl~Ys~ 112 (119)
-|+.+.||+++...|-++.+++++ +.|.+..++.. ...+.++++ |+- ++..|++.-+.
T Consensus 18 ~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~-L~D~~tL~~----~gi~~gs~l~l~~~~ 77 (80)
T cd01792 18 SLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREV-LQDGVPLVS----QGLGPGSTVLLVVQN 77 (80)
T ss_pred EcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCC-CCCCCCHHH----cCCCCCCEEEEEEEc
Confidence 468899999999999988888654 33332235666 445566654 233 45688877553
No 60
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=47.05 E-value=30 Score=21.70 Aligned_cols=54 Identities=9% Similarity=0.111 Sum_probs=34.9
Q ss_pred CCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEc--CeecCCcC-chHHHH
Q psy12247 42 PQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIE--SMIVPADS-TRMETL 95 (119)
Q Consensus 42 p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn--~~~~p~~~-~~m~~l 95 (119)
|+=.+-.-..+.+.|++++..+|...+........-|+.+ ...+...+ .+|+++
T Consensus 14 pdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~ 70 (82)
T PF00789_consen 14 PDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEA 70 (82)
T ss_dssp TTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCC
T ss_pred CCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHh
Confidence 3334445567799999999999999988776543555443 23334344 566554
No 61
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=46.97 E-value=71 Score=20.07 Aligned_cols=58 Identities=9% Similarity=0.059 Sum_probs=40.1
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEecc
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSD 112 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~ 112 (119)
.-|+.+.||+++...|..+.+++++ ..-|..+++.+. .+ ++++ .-=.++..|||.-+-
T Consensus 16 l~v~~~~TV~~LK~~I~~~~~~~~~-~qrL~~~Gk~L~-d~-~L~~---~gi~~~~~i~l~~~~ 73 (78)
T cd01804 16 LSVPPDETVEGLKKRISQRLKVPKE-RLALLHRETRLS-SG-KLQD---LGLGDGSKLTLVPTV 73 (78)
T ss_pred EEECCcCHHHHHHHHHHHHhCCChH-HEEEEECCcCCC-CC-cHHH---cCCCCCCEEEEEeec
Confidence 5689999999999999988888765 445556666633 33 5554 222256688887665
No 62
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=44.80 E-value=30 Score=21.76 Aligned_cols=39 Identities=21% Similarity=0.174 Sum_probs=28.6
Q ss_pred eEEecCC-cchHhHHHHHHHhhc-C-CCCCeEEEEEcCeecC
Q psy12247 48 NYVVAYE-MTVGHFFYLLRKKMA-L-RPEEACFFFIESMIVP 86 (119)
Q Consensus 48 Kflvp~~-~tv~~~~~~lRk~l~-l-~~~~slfl~Vn~~~~p 86 (119)
.+-++.+ .|+.++...|..+.. + .....+.+.||+..+.
T Consensus 19 ~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~ 60 (80)
T TIGR01682 19 TLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVT 60 (80)
T ss_pred EEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcC
Confidence 3456766 899999999988764 2 2235678999998854
No 63
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=44.58 E-value=24 Score=21.79 Aligned_cols=39 Identities=13% Similarity=0.059 Sum_probs=28.3
Q ss_pred eEEecCCcchHhHHHHHHHhhcC---CCCCeEEEEEcCeecC
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMAL---RPEEACFFFIESMIVP 86 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l---~~~~slfl~Vn~~~~p 86 (119)
.+-+|...|+++++..|..+..- .....+-++||+..++
T Consensus 19 ~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~ 60 (80)
T cd00754 19 ELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVR 60 (80)
T ss_pred EEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcC
Confidence 44567789999999988876431 1235678999998855
No 64
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=44.42 E-value=44 Score=20.30 Aligned_cols=42 Identities=19% Similarity=0.214 Sum_probs=32.4
Q ss_pred cceEEecCCcchHhHHHHHHHhhc-CCCCCeEEEEEcCeecCC
Q psy12247 46 RSNYVVAYEMTVGHFFYLLRKKMA-LRPEEACFFFIESMIVPA 87 (119)
Q Consensus 46 k~Kflvp~~~tv~~~~~~lRk~l~-l~~~~slfl~Vn~~~~p~ 87 (119)
.....++...|+++++..|..+.. +...+.+-++||+.+++.
T Consensus 13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~~v~~ 55 (77)
T PF02597_consen 13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGEIVPD 55 (77)
T ss_dssp EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEEEGG
T ss_pred CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEEcCC
Confidence 345678999999999999987752 223468899999999655
No 65
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=43.54 E-value=49 Score=22.02 Aligned_cols=54 Identities=7% Similarity=0.214 Sum_probs=36.2
Q ss_pred CcceEEecC-----CcchHhHHHHHHHhhcCCCCCeEEE-EEc--C-eecCCcCchHHHHHhH
Q psy12247 45 PRSNYVVAY-----EMTVGHFFYLLRKKMALRPEEACFF-FIE--S-MIVPADSTRMETLSQR 98 (119)
Q Consensus 45 ~k~Kflvp~-----~~tv~~~~~~lRk~l~l~~~~slfl-~Vn--~-~~~p~~~~~m~~lY~~ 98 (119)
+...|-+|. +.++.++...|++++++++...+-| |-+ + .+....|..+.+.-+.
T Consensus 10 ~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~ 72 (91)
T cd06398 10 TLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72 (91)
T ss_pred EEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHH
Confidence 345677785 7999999999999999987444433 444 2 3324555555555554
No 66
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
Probab=43.50 E-value=52 Score=21.30 Aligned_cols=55 Identities=13% Similarity=0.082 Sum_probs=34.7
Q ss_pred EecCCcchHhHHHHHHHhhc--CCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEE
Q psy12247 50 VVAYEMTVGHFFYLLRKKMA--LRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYM 108 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~--l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl 108 (119)
.-|.+.||+++...|..+.+ ..+.+..=|.-+++. ...+.+|++.= - .++.+|+|
T Consensus 16 ~~~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKi-L~D~~TL~dyg--I-~~gstlhL 72 (75)
T cd01815 16 VSPGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRK-LKDDQTLDFYG--I-QSGSTIHI 72 (75)
T ss_pred cCCccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcC-CCCCCcHHHcC--C-CCCCEEEE
Confidence 45889999999999999964 442333344455666 56667776521 1 13456665
No 67
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=42.30 E-value=63 Score=21.78 Aligned_cols=59 Identities=10% Similarity=0.025 Sum_probs=40.2
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEec
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYS 111 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys 111 (119)
.+-|..+.||+++...|..+-++++++ .=|+.+++. ...+.++++ |. - .++.-|+|.-.
T Consensus 41 ~leV~~~~TV~~lK~kI~~~~gip~~~-QrLi~~Gk~-L~D~~tL~d-y~-I-~~~stL~l~~~ 99 (103)
T cd01802 41 ELRVSPFETVISVKAKIQRLEGIPVAQ-QHLIWNNME-LEDEYCLND-YN-I-SEGCTLKLVLA 99 (103)
T ss_pred EEEeCCCCcHHHHHHHHHHHhCCChHH-EEEEECCEE-CCCCCcHHH-cC-C-CCCCEEEEEEe
Confidence 346899999999999999998887763 334567777 555667755 22 1 13456776543
No 68
>PRK13964 coaD phosphopantetheine adenylyltransferase; Provisional
Probab=41.72 E-value=82 Score=22.55 Aligned_cols=85 Identities=18% Similarity=0.192 Sum_probs=52.5
Q ss_pred cCCHHHHHHHHHHHHhcCCCcceEEEEcCCCCCCCCC---CcceEEecCCcchHhHHHHHH-----HhhcCCC-CCeEEE
Q psy12247 8 KYSLEERIKIGENLARNHPNCAFVILERSPSALLPQM---PRSNYVVAYEMTVGHFFYLLR-----KKMALRP-EEACFF 78 (119)
Q Consensus 8 ~~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~~~p~L---~k~Kflvp~~~tv~~~~~~lR-----k~l~l~~-~~slfl 78 (119)
..|+++|.+..+...+.+|+ |-|+. ...+-+-++ -...++|..=-.+++|-+.+. ++ |++ =+++||
T Consensus 44 ~~s~e~R~~~l~~~~~~~~~-v~v~~--~~~~l~v~~~~~~~a~~ivrGlR~~~DfeyE~~~a~~n~~--l~~~ietvfl 118 (140)
T PRK13964 44 ASDLDSRFKNVKNKLKDFKN-VEVLI--NENKLTAEIAKKLGANFLIRSARNNIDFQYEIVLAAGNKS--LNNDLETILI 118 (140)
T ss_pred CCCHHHHHHHHHHHHcCCCC-cEEec--CcCCcHHHHHHHCCCeEEEEecCCCccHHHHHHHHHHHHh--hcCCCeEEEe
Confidence 36899999999999998886 44432 111111111 134677777666776655444 33 433 479999
Q ss_pred EEcCeecCCcCchHHHHHh
Q psy12247 79 FIESMIVPADSTRMETLSQ 97 (119)
Q Consensus 79 ~Vn~~~~p~~~~~m~~lY~ 97 (119)
.-......=.|+.+.+|-.
T Consensus 119 ~~~~~~~~iSSs~vre~~~ 137 (140)
T PRK13964 119 IPDYDKIEYSSTLLRHKKF 137 (140)
T ss_pred ecCCCCCEEeHHHHHHHHH
Confidence 8886665545666676653
No 69
>PRK13669 hypothetical protein; Provisional
Probab=41.67 E-value=24 Score=23.25 Aligned_cols=27 Identities=15% Similarity=0.304 Sum_probs=22.3
Q ss_pred CeEEEEEcCeec--CCcCchHHHHHhHhc
Q psy12247 74 EACFFFIESMIV--PADSTRMETLSQRFA 100 (119)
Q Consensus 74 ~slfl~Vn~~~~--p~~~~~m~~lY~~~k 100 (119)
...|.+||+..+ +.+++.+..||+.-+
T Consensus 45 ~~~FAlVng~~V~a~t~eeL~~kI~~~i~ 73 (78)
T PRK13669 45 EGLFALVNGEVVEGETPEELVENIYAHLE 73 (78)
T ss_pred cCceEEECCeEeecCCHHHHHHHHHHHHh
Confidence 578999998664 778889999998765
No 70
>cd01795 USP48_C USP ubiquitin-specific protease. The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,
Probab=41.12 E-value=63 Score=22.49 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=28.5
Q ss_pred EecCCcchHhHHHHHHHhhcCCCC-CeEEEEEcCeecCCcCchHHH
Q psy12247 50 VVAYEMTVGHFFYLLRKKMALRPE-EACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~l~~~-~slfl~Vn~~~~p~~~~~m~~ 94 (119)
.|+++.||+++...|-.++++.|. +-|.+. +..+--.+.++++
T Consensus 20 ~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~d--G~~L~DDsrTLss 63 (107)
T cd01795 20 LVSANQTLKELKIQIMHAFSVAPFDQNLSID--GKILSDDCATLGT 63 (107)
T ss_pred EeCccccHHHHHHHHHHHhcCCcccceeeec--CceeccCCccHHh
Confidence 588999999999999999998875 333332 3332334444443
No 71
>PRK10953 cysJ sulfite reductase subunit alpha; Provisional
Probab=41.01 E-value=2.6e+02 Score=24.74 Aligned_cols=87 Identities=16% Similarity=0.203 Sum_probs=60.1
Q ss_pred CCcceEEEEcCCCCCCCCC-CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCC
Q psy12247 26 PNCAFVILERSPSALLPQM-PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDG 104 (119)
Q Consensus 26 p~~ipVIvE~~~~~~~p~L-~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DG 104 (119)
.+.|+|-+.+.+.=.+|.- ++.-.+|-.-.=++-|..+|+.+........+.||.+... ...|-.-.+=.+.+. .+|
T Consensus 433 Gd~v~v~~~~~~~F~lp~~~~~piImIg~GTGIAPfrsflq~r~~~~~~~~~~LffG~R~-~~~D~lY~~El~~~~-~~g 510 (600)
T PRK10953 433 EGEVRVFIEHNDNFRLPANPETPVIMIGPGTGIAPFRAFMQQRAADGAPGKNWLFFGNPH-FTEDFLYQVEWQRYV-KEG 510 (600)
T ss_pred CCEEEEEeccCCcccCCCCCCCCEEEEecCcCcHHHHHHHHHHHHcCCCCCeEEEeeccC-CccchhHHHHHHHHH-HcC
Confidence 4677877765433356643 4556688888899999999998887655556788888766 565656666666665 456
Q ss_pred e---EEEEecccc
Q psy12247 105 L---IYMVYSDVN 114 (119)
Q Consensus 105 f---Lyl~Ys~~~ 114 (119)
. |.+.||.++
T Consensus 511 ~l~~l~~afSRd~ 523 (600)
T PRK10953 511 LLTRIDLAWSRDQ 523 (600)
T ss_pred CcceEEEEECCCC
Confidence 4 668888554
No 72
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.71 E-value=1.7e+02 Score=24.51 Aligned_cols=64 Identities=8% Similarity=0.120 Sum_probs=44.8
Q ss_pred CCcceE--EecCCcchHhHHHHHHHhhc---CCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEecc
Q psy12247 44 MPRSNY--VVAYEMTVGHFFYLLRKKMA---LRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSD 112 (119)
Q Consensus 44 L~k~Kf--lvp~~~tv~~~~~~lRk~l~---l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~ 112 (119)
++.++| -|..+.||+++...|...-+ +..+ ..=|..++++ ...+.+|++ |. -+ ++.+|++.-+.
T Consensus 8 l~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~-~QkLIy~Gki-L~Dd~tL~d-y~-I~-e~~~Ivvmv~k 76 (378)
T TIGR00601 8 LQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVA-QQKLIYSGKI-LSDDKTVRE-YK-IK-EKDFVVVMVSK 76 (378)
T ss_pred CCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChh-HeEEEECCEE-CCCCCcHHH-cC-CC-CCCEEEEEecc
Confidence 344445 47789999999999988876 6544 4566678888 567778876 32 22 56788877654
No 73
>PF05717 TnpB_IS66: IS66 Orf2 like protein; InterPro: IPR008878 Thess proteins are found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=40.33 E-value=44 Score=22.89 Aligned_cols=27 Identities=22% Similarity=0.458 Sum_probs=22.5
Q ss_pred chHhHHHHHHHhhcCCC-CCeEEEEEcC
Q psy12247 56 TVGHFFYLLRKKMALRP-EEACFFFIES 82 (119)
Q Consensus 56 tv~~~~~~lRk~l~l~~-~~slfl~Vn~ 82 (119)
.+.-+..+++..++++| +.++|+|+|.
T Consensus 16 g~dgL~~lV~~~~~~dp~~g~~fvF~nr 43 (107)
T PF05717_consen 16 GIDGLAALVREELGLDPFSGDLFVFCNR 43 (107)
T ss_pred ChhHHHHHHHHhhcCCCCcceEEEEEec
Confidence 45678889999999875 5799999995
No 74
>COG0669 CoaD Phosphopantetheine adenylyltransferase [Coenzyme metabolism]
Probab=39.80 E-value=68 Score=23.86 Aligned_cols=98 Identities=19% Similarity=0.215 Sum_probs=65.4
Q ss_pred cccCCHHHHHHHHHHHHhcCCCcceEEEEcCCCC--CCCCCCcceEEecCCcchHhHHHHHHH-hh--cCCC-CCeEEEE
Q psy12247 6 TEKYSLEERIKIGENLARNHPNCAFVILERSPSA--LLPQMPRSNYVVAYEMTVGHFFYLLRK-KM--ALRP-EEACFFF 79 (119)
Q Consensus 6 k~~~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~--~~p~L~k~Kflvp~~~tv~~~~~~lRk-~l--~l~~-~~slfl~ 79 (119)
+--+|+|+|+.-.++.-...|+- -|.....= +.-.-...+++|..=-++++|-+.+.- .+ +|.+ =+++||.
T Consensus 43 ~plFsleER~~l~~~~~~~l~nV---~V~~f~~Llvd~ak~~~a~~ivRGLR~~sDfeYE~qma~~N~~L~~eveTvFl~ 119 (159)
T COG0669 43 KPLFSLEERVELIREATKHLPNV---EVVGFSGLLVDYAKKLGATVLVRGLRAVSDFEYELQMAHMNRKLAPEVETVFLM 119 (159)
T ss_pred CCCcCHHHHHHHHHHHhcCCCce---EEEecccHHHHHHHHcCCCEEEEeccccchHHHHHHHHHHHHhhcccccEEEec
Confidence 34578999999999998777764 33333210 111124567899988889988766652 11 2443 5799998
Q ss_pred EcCeecCCcCchHHHHHhHhcCCCCeE
Q psy12247 80 IESMIVPADSTRMETLSQRFADKDGLI 106 (119)
Q Consensus 80 Vn~~~~p~~~~~m~~lY~~~kd~DGfL 106 (119)
-......-.++.+.+|..--+|.++|+
T Consensus 120 ~s~~~~~iSSs~Vreia~~ggdvs~~V 146 (159)
T COG0669 120 PSPEYSFISSSLVREIAAFGGDVSEFV 146 (159)
T ss_pred CCcceehhhHHHHHHHHHhCCCchhhC
Confidence 887776666778888887777766653
No 75
>KOG1209|consensus
Probab=38.99 E-value=61 Score=25.95 Aligned_cols=53 Identities=15% Similarity=0.129 Sum_probs=42.3
Q ss_pred CCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcC----eecCCcCchHHHHHhHhc
Q psy12247 44 MPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIES----MIVPADSTRMETLSQRFA 100 (119)
Q Consensus 44 L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~----~~~p~~~~~m~~lY~~~k 100 (119)
|+-.|.=|.++..|..|...+|+. +..+|=+.+|| +..|..|.+++++=+||+
T Consensus 54 l~~~kLDV~~~~~V~~v~~evr~~----~~Gkld~L~NNAG~~C~~Pa~d~~i~ave~~f~ 110 (289)
T KOG1209|consen 54 LKPYKLDVSKPEEVVTVSGEVRAN----PDGKLDLLYNNAGQSCTFPALDATIAAVEQCFK 110 (289)
T ss_pred CeeEEeccCChHHHHHHHHHHhhC----CCCceEEEEcCCCCCcccccccCCHHHHHhhhc
Confidence 344555688999999999999875 45578888886 455999999999999996
No 76
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=37.35 E-value=91 Score=19.51 Aligned_cols=41 Identities=17% Similarity=0.100 Sum_probs=27.9
Q ss_pred CCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCee
Q psy12247 43 QMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMI 84 (119)
Q Consensus 43 ~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~ 84 (119)
...+.++.|.++.++.++...--++.+++++ .--|.-|++.
T Consensus 5 ~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~-~~~L~h~~k~ 45 (65)
T PF11470_consen 5 NFRRFKVKVTPNTTLNQVLEEACKKFGLDPS-SYDLKHNNKP 45 (65)
T ss_dssp TS-EEEE---TTSBHHHHHHHHHHHTT--GG-G-EEEETTEE
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHcCCCcc-ceEEEECCEE
Confidence 3577889999999999999999999999988 4556556655
No 77
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=37.20 E-value=77 Score=20.07 Aligned_cols=56 Identities=11% Similarity=0.116 Sum_probs=39.1
Q ss_pred ecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEec
Q psy12247 51 VAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYS 111 (119)
Q Consensus 51 vp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys 111 (119)
+..+.||+++...|-.+.++++++ .=|+.+++. ...+.++++ |. -+ ++.++++.-.
T Consensus 19 v~~~~TV~~lK~~i~~~~gi~~~~-QrLi~~Gk~-L~D~~tL~~-y~-i~-~~~~i~l~~~ 74 (78)
T cd01797 19 LSRLTKVEELREKIQELFNVEPEC-QRLFYRGKQ-MEDGHTLFD-YN-VG-LNDIIQLLVR 74 (78)
T ss_pred cCCcCcHHHHHHHHHHHhCCCHHH-eEEEeCCEE-CCCCCCHHH-cC-CC-CCCEEEEEEe
Confidence 678899999999999888887652 234457888 566778866 32 22 4567777544
No 78
>cd01768 RA RA (Ras-associating) ubiquitin domain. The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.
Probab=37.07 E-value=93 Score=19.53 Aligned_cols=55 Identities=13% Similarity=0.002 Sum_probs=35.6
Q ss_pred CCcceEEecCCcchHhHHHHHHHhhcCCC---CCeEEEEEcC----eecCCcCchHHHHHhHh
Q psy12247 44 MPRSNYVVAYEMTVGHFFYLLRKKMALRP---EEACFFFIES----MIVPADSTRMETLSQRF 99 (119)
Q Consensus 44 L~k~Kflvp~~~tv~~~~~~lRk~l~l~~---~~slfl~Vn~----~~~p~~~~~m~~lY~~~ 99 (119)
-.-+-..|+++.|.++++..+-++.+++. +=+||-.+++ .. ..+++..-.+....
T Consensus 12 ~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~ev~~~~~~er~-L~~~e~pl~~~~~~ 73 (87)
T cd01768 12 GTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALVEVLGDGGLERL-LLPDECPLQIQLNA 73 (87)
T ss_pred ccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEEEEECCceEEEE-eCCCCChHHHHHhc
Confidence 34455789999999999999999999983 3344444444 23 23344444444433
No 79
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=36.59 E-value=65 Score=19.78 Aligned_cols=35 Identities=14% Similarity=0.103 Sum_probs=29.6
Q ss_pred cceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEE
Q psy12247 46 RSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFI 80 (119)
Q Consensus 46 k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~V 80 (119)
..-|-|+.+.|+.+++..|-++|+|...+-+=|.+
T Consensus 8 ~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~ 42 (80)
T PF09379_consen 8 TKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQY 42 (80)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE
T ss_pred cEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEE
Confidence 45688999999999999999999998776555666
No 80
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=36.52 E-value=18 Score=23.33 Aligned_cols=17 Identities=24% Similarity=0.712 Sum_probs=14.2
Q ss_pred hcCCCCeEEEEeccccc
Q psy12247 99 FADKDGLIYMVYSDVNI 115 (119)
Q Consensus 99 ~kd~DGfLyl~Ys~~~~ 115 (119)
+-|+||-+|+.|+.++.
T Consensus 42 wiDe~G~vYi~~s~eel 58 (76)
T PF06970_consen 42 WIDENGNVYIIFSIEEL 58 (76)
T ss_pred cCCCCCCEEEEeeHHHH
Confidence 35899999999998763
No 81
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=36.28 E-value=50 Score=21.11 Aligned_cols=33 Identities=15% Similarity=0.058 Sum_probs=26.5
Q ss_pred ceEEecCCcchHhHHHHHHHhhcCCCC-CeEEEE
Q psy12247 47 SNYVVAYEMTVGHFFYLLRKKMALRPE-EACFFF 79 (119)
Q Consensus 47 ~Kflvp~~~tv~~~~~~lRk~l~l~~~-~slfl~ 79 (119)
..-.+|.++||+++...|-+..+++++ ..|+++
T Consensus 16 ~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~ 49 (87)
T PF14560_consen 16 VEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK 49 (87)
T ss_dssp EEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred EEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence 334799999999999999999999865 566665
No 82
>cd01775 CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase. CYR1 is a fungal adenylate cyclase with at least four domains, an N-terminal RA (Ras association) domain, a middle leucine-rich repeat domain, a catalytic domain. The N-terminal RA domain of CYR1 post-translationally modifies a small GTPase called Ras. The Ras-CYR1 pathway has been implicated in the transduction of a glucose-triggered signal to an intracellular environment where a protein phosphorylation cascade is initiated by cyclic AMP.
Probab=35.26 E-value=87 Score=21.44 Aligned_cols=35 Identities=17% Similarity=0.072 Sum_probs=28.7
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCC--CeEEEEEcC
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPE--EACFFFIES 82 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~--~slfl~Vn~ 82 (119)
-+.+|-+.||+|++..|.++..++++ -.|++.+++
T Consensus 16 Tls~~l~tTv~eli~~L~rK~~l~~~~ny~l~l~~~~ 52 (97)
T cd01775 16 TLSCPLNTTVSELIPQLAKKFYLPSGGNYQLSLKKHD 52 (97)
T ss_pred EEEcCCcCcHHHHHHHHHHhhcCCCCCCeEEEEEECC
Confidence 35788899999999999999988764 457777775
No 83
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=35.20 E-value=64 Score=20.40 Aligned_cols=20 Identities=10% Similarity=0.175 Sum_probs=17.2
Q ss_pred HHHHhhcCCCCCeEEEEEcC
Q psy12247 63 LLRKKMALRPEEACFFFIES 82 (119)
Q Consensus 63 ~lRk~l~l~~~~slfl~Vn~ 82 (119)
-++..|+|.+++.+++.+.+
T Consensus 17 ~i~~~lgl~~Gd~v~v~~~~ 36 (74)
T TIGR02609 17 EVLESLGLKEGDTLYVDEEE 36 (74)
T ss_pred HHHHHcCcCCCCEEEEEEEC
Confidence 46899999999999998774
No 84
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=34.93 E-value=62 Score=21.56 Aligned_cols=28 Identities=11% Similarity=0.187 Sum_probs=24.0
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEE
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFF 78 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl 78 (119)
..||++.++.+|..-||.+++++ +.+-+
T Consensus 16 i~v~~~i~f~dL~~kIrdkf~~~--~~~~i 43 (86)
T cd06408 16 IMIGPDTGFADFEDKIRDKFGFK--RRLKI 43 (86)
T ss_pred EEcCCCCCHHHHHHHHHHHhCCC--CceEE
Confidence 47999999999999999999996 45555
No 85
>PF00255 GSHPx: Glutathione peroxidase; InterPro: IPR000889 Glutathione peroxidase (GSHPx) (1.11.1.9 from EC) is an enzyme that catalyses the reduction of hydroxyperoxides by glutathione [, ]. Its main function is to protect against the damaging effect of endogenously formed hydroxyperoxides. In higher vertebrates, several forms of GSHPx are known, including a ubiquitous cytosolic form (GSHPx-1), a gastrointestinal cytosolic form (GSHPx-GI), a plasma secreted form (GSHPx-P), and an epididymal secretory form (GSHPx-EP). In addition to these characterised forms, the sequence of a protein of unknown function [] has been shown to be evolutionary related to those of GSHPx's. In filarial nematode parasites, the major soluble cuticular protein (gp29) is a secreted GSHPx, which may provide a mechanism of resistance to the immune reaction of the mammalian host by neutralising the products of the oxidative burst of leukocytes []. The Escherichia coli protein btuE, a periplasmic protein involved in vitamin B12 transport, is evolutionarily related to GSHPxs, although the significance of this relationship is unclear. The structure of bovine seleno-glutathione peroxidase has been determined []. The protein belongs to the alpha-beta class, with a 3 layer(aba) sandwich architecture. The catalyic site of GSHPx contains a conserved residue which is either a cysteine or, in many eukaryotic GSHPx, a selenocysteine []. ; GO: 0004602 glutathione peroxidase activity, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 3E0U_A 2VUP_A 2RM5_A 2RM6_A 3DWV_B 2P31_B 2R37_B 1GP1_B 2F8A_B 3KIJ_C ....
Probab=34.91 E-value=48 Score=22.75 Aligned_cols=40 Identities=10% Similarity=0.297 Sum_probs=27.3
Q ss_pred eEEEEEcCee----cCCcCchHHHHHhHhcCCCCeEEEEeccccccc
Q psy12247 75 ACFFFIESMI----VPADSTRMETLSQRFADKDGLIYMVYSDVNIFV 117 (119)
Q Consensus 75 slfl~Vn~~~----~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~~fG 117 (119)
.+-|.||=+. ++ .=..|.+||++|+ ++|+..|.+-..+ ||
T Consensus 22 kv~LIVNvAs~Cg~t~-qy~~L~~L~~ky~-~~gl~ILaFPcnq-Fg 65 (108)
T PF00255_consen 22 KVLLIVNVASKCGYTK-QYKQLNELYEKYK-DKGLEILAFPCNQ-FG 65 (108)
T ss_dssp SEEEEEEEESSSTTHH-HHHHHHHHHHHHG-GGTEEEEEEEBST-TT
T ss_pred CEEEEEecccccCCcc-ccHHHHHHHHHHh-cCCeEEEeeehHH-hc
Confidence 3456677222 12 3357899999998 5899999998654 54
No 86
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=34.48 E-value=80 Score=19.02 Aligned_cols=39 Identities=21% Similarity=0.222 Sum_probs=27.4
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCc
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPAD 88 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~ 88 (119)
....+-+++.+|+.+++..+ ++++ +.+-+.||+.++|..
T Consensus 5 Ng~~~~~~~~~tv~~ll~~l----~~~~-~~i~V~vNg~~v~~~ 43 (65)
T cd00565 5 NGEPREVEEGATLAELLEEL----GLDP-RGVAVALNGEIVPRS 43 (65)
T ss_pred CCeEEEcCCCCCHHHHHHHc----CCCC-CcEEEEECCEEcCHH
Confidence 34556688889999886544 4554 456788999996653
No 87
>COG1019 Predicted nucleotidyltransferase [General function prediction only]
Probab=33.28 E-value=2e+02 Score=21.35 Aligned_cols=66 Identities=18% Similarity=0.080 Sum_probs=45.4
Q ss_pred CCHHHHHHHHHHHHhcCCCcceEEEEc-CCCCCCCCCCcceEEe--cCCcchHhHHHHHHHhhcCCCCC
Q psy12247 9 YSLEERIKIGENLARNHPNCAFVILER-SPSALLPQMPRSNYVV--AYEMTVGHFFYLLRKKMALRPEE 74 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ipVIvE~-~~~~~~p~L~k~Kflv--p~~~tv~~~~~~lRk~l~l~~~~ 74 (119)
.+|+.|.+...+....--....+|+.- .+.+.++.-..--.+| |.+.+.+.-++-+|.+-+++|=+
T Consensus 54 ~p~~~R~~~l~~fl~~~~~~~~~iv~i~Dp~G~t~~~~~~e~iVVS~ET~~~Al~IN~~R~~~Gl~pL~ 122 (158)
T COG1019 54 EPYEVRLRNLRNFLESIKADYEEIVPIDDPYGPTVEDPDFEAIVVSPETYPGALKINEIREKRGLPPLE 122 (158)
T ss_pred CcHHHHHHHHHHHHHHhcCCcceEEEecCCCCCCCCcCceeEEEEccccchhHHHHHHHHHHCCCCCeE
Confidence 478999999888777665555566655 4445554443333443 55668888899999999999753
No 88
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=32.91 E-value=56 Score=20.23 Aligned_cols=34 Identities=9% Similarity=0.107 Sum_probs=25.4
Q ss_pred eEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecC
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVP 86 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p 86 (119)
.+-+++..|++++.. .|++++ +.+.+.+|+.+++
T Consensus 17 ~~~~~~~~tv~~ll~----~l~~~~-~~v~v~vNg~iv~ 50 (70)
T PRK08364 17 EIEWRKGMKVADILR----AVGFNT-ESAIAKVNGKVAL 50 (70)
T ss_pred EEEcCCCCcHHHHHH----HcCCCC-ccEEEEECCEECC
Confidence 344688889998864 456765 5689999999964
No 89
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 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 belong to MEROPS peptidase family C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=32.81 E-value=2.6e+02 Score=23.05 Aligned_cols=72 Identities=14% Similarity=0.282 Sum_probs=46.1
Q ss_pred CCcceEEEEcC----CCCCCCCCCcceEEecCCcchHhHHHHHHHhhc-CC------CCCeEEEEEc--CeecCCcCchH
Q psy12247 26 PNCAFVILERS----PSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMA-LR------PEEACFFFIE--SMIVPADSTRM 92 (119)
Q Consensus 26 p~~ipVIvE~~----~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~-l~------~~~slfl~Vn--~~~~p~~~~~m 92 (119)
...+-+|+.+. |-..+|.|.... |..--+++.+...+..+-. .. ..+.+|..+| +-+ +.+..++
T Consensus 203 ~~~~iLVlD~~l~~~PwEsl~~l~~~~--VsR~pSl~~l~~~~~~~~~~~~~~~~~~~~~~~~yvlNP~gDL-~~T~~~~ 279 (383)
T PF03568_consen 203 REHTILVLDKELQSFPWESLPCLRGQS--VSRMPSLHFLRDLLKRHSNSRSPGYESKDPKRGFYVLNPSGDL-KRTEKRF 279 (383)
T ss_pred CCCEEEEECcccccCchhhCccccCCe--eEecChHHHHHHHHHHhhhhcccccccccccceEEEECCCCCH-HHHHHHH
Confidence 35555666553 455788887766 5555567766666655322 11 2234888888 444 7888888
Q ss_pred HHHHhHhc
Q psy12247 93 ETLSQRFA 100 (119)
Q Consensus 93 ~~lY~~~k 100 (119)
..+++..+
T Consensus 280 ~~~~~~~~ 287 (383)
T PF03568_consen 280 EPFFKSWK 287 (383)
T ss_pred HHHHhccc
Confidence 88888776
No 90
>PF01704 UDPGP: UTP--glucose-1-phosphate uridylyltransferase; InterPro: IPR002618 This family consists of UTP--glucose-1-phosphate uridylyltransferases (2.7.7.9 from EC). Also known as UDP-glucose pyrophosphorylase (UDPGP) and Glucose-1-phosphate uridylyltransferase. UTP--glucose-1-phosphate uridylyltransferase catalyses the interconversion of MgUTP + glucose-1-phosphate and UDP-glucose + MgPPi []. UDP-glucose is an important intermediate in mammalian carbohydrate interconversion involved in various metabolic roles depending on tissue type []. In Dictyostelium discoideum (Slime mold), mutants in this enzyme abort the development cycle []. Also within this family is UDP-N-acetylglucosamine pyrophosphorylase (Q16222 from SWISSPROT) [] and two hypothetical proteins from Borrelia burgdorferi, the Lyme disease spirochaete (O51893 from SWISSPROT and O51036 from SWISSPROT).; GO: 0016779 nucleotidyltransferase activity, 0008152 metabolic process; PDB: 2OEG_A 2OEF_A 2YQS_A 2YQJ_A 2YQH_B 2YQC_A 3OH4_A 3OGZ_A 3OH3_A 3OH1_A ....
Probab=32.40 E-value=1.3e+02 Score=25.53 Aligned_cols=57 Identities=23% Similarity=0.208 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHhcCCCcceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCC
Q psy12247 11 LEERIKIGENLARNHPNCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPA 87 (119)
Q Consensus 11 ~e~R~~e~~~ir~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~ 87 (119)
|+-.....+.++++|--.||+++ ..+..|-++...++++.-+++.+ +++|.-+++ |.
T Consensus 88 ldl~~~qi~~l~~~~~~~iPl~i-----------------MtS~~T~~~T~~~l~kyfg~~~~--v~~F~Q~~~-P~ 144 (420)
T PF01704_consen 88 LDLIVEQIEALNKKYGVDIPLYI-----------------MTSFNTHEDTRKFLEKYFGLDVD--VFFFKQSKL-PA 144 (420)
T ss_dssp HHHHHHHHHHHHHHHTTT-EEEE-----------------EEETTTHHHHHHHHHHGCGSSCC--EEEEEE-EE-EE
T ss_pred HHHHHHHHHHHhccccccceEEE-----------------ecCcccHHHHHHHHHHhcCCCcc--eEEEeecCc-ce
Confidence 35556667777888877788665 45566778889999997777765 777766665 54
No 91
>smart00314 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)
Probab=32.08 E-value=1.3e+02 Score=18.93 Aligned_cols=39 Identities=15% Similarity=0.088 Sum_probs=30.8
Q ss_pred CCCCcceEEecCCcchHhHHHHHHHhhcCCCC---CeEEEEE
Q psy12247 42 PQMPRSNYVVAYEMTVGHFFYLLRKKMALRPE---EACFFFI 80 (119)
Q Consensus 42 p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~---~slfl~V 80 (119)
|.-.-+-..|+.+.|.++++..+-++++++.. =+||..+
T Consensus 13 ~~~~~kti~v~~~tTa~~Vi~~~l~k~~l~~~~~~y~L~e~~ 54 (90)
T smart00314 13 PGGTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLVEVL 54 (90)
T ss_pred CCCcEEEEEECCCCCHHHHHHHHHHHhCCCCCcccEEEEEEe
Confidence 44455667899999999999999999999763 4566555
No 92
>KOG4147|consensus
Probab=31.74 E-value=55 Score=23.17 Aligned_cols=57 Identities=16% Similarity=0.233 Sum_probs=37.2
Q ss_pred CCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEecccccc
Q psy12247 53 YEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSDVNIF 116 (119)
Q Consensus 53 ~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~~f 116 (119)
++.||-+|+.+|..+++++++=. .|=|-++ .++.=.-+.|+..-.-|.|+.-...-|
T Consensus 32 ad~Tvk~f~~~~~~~Iq~~~sl~--pfRn~kf-----DtLKIy~~Ah~sKT~nLvinldhDd~w 88 (127)
T KOG4147|consen 32 ADQTVKEFIVFLKQDIQLRTSLP--PFRNYKF-----DTLKIYHQAHKSKTNNLVINLDHDDRW 88 (127)
T ss_pred hHhhHHHHHHHHHHhcccCCCCC--ccccccc-----cceeeehhhhhcccceEEEeccCCcce
Confidence 47799999999999999886643 3334344 344445555665566666666555433
No 93
>cd01766 Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-fold modifier 1) is a post-translational UBL (ubiquitin-like) modifier with a tertiary structure similar to that of ubiquitin. Ufm1 is initially expressed as a precursor which undergoes C-terminal cleavage to expose a conserved glycine residue that is required for the conjugation reactions involving Ufm1.
Probab=31.49 E-value=71 Score=21.04 Aligned_cols=59 Identities=5% Similarity=0.081 Sum_probs=44.7
Q ss_pred CCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcC
Q psy12247 42 PQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFAD 101 (119)
Q Consensus 42 p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd 101 (119)
|.|.-+..-||++..+..++.+--...++++..|--+--++.= -.++++-|+++=+|+.
T Consensus 13 p~lpfkvlsVpE~aPftAvlkfaAEeFkv~~~TsAiiTndGvG-INP~qtAGnvflkhgs 71 (82)
T cd01766 13 PKLPFKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIG-INPAQTAGNVFLKHGS 71 (82)
T ss_pred CCCcceEEeccccCchHHHHHHHHHhcCCCccceeEEecCccc-cChhhcccceeeecCC
Confidence 4555666789999999999999999999998887444333333 5667888999988864
No 94
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=31.49 E-value=79 Score=22.23 Aligned_cols=16 Identities=25% Similarity=0.634 Sum_probs=14.7
Q ss_pred CCCCeEEEEecccccc
Q psy12247 101 DKDGLIYMVYSDVNIF 116 (119)
Q Consensus 101 d~DGfLyl~Ys~~~~f 116 (119)
|-+|..|+.|....+|
T Consensus 110 Dl~Gi~~~~~~~~~~w 125 (125)
T PF10137_consen 110 DLSGITYIRFDDNRSW 125 (125)
T ss_pred ccCCeEEEEcCCCCCC
Confidence 7899999999999887
No 95
>smart00148 PLCXc Phospholipase C, catalytic domain (part); domain X. Phosphoinositide-specific phospholipases C. These enzymes contain 2 regions (X and Y) which together form a TIM barrel-like structure containing the active site residues. Phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The bacterial enzyme [6] appears to be a homologue of the mammalian PLCs.
Probab=31.42 E-value=57 Score=22.89 Aligned_cols=43 Identities=7% Similarity=0.176 Sum_probs=32.9
Q ss_pred cCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHH
Q psy12247 52 AYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMET 94 (119)
Q Consensus 52 p~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~ 94 (119)
....++.+++..|++-+.-.+++.+.|-+++..-+.....|.+
T Consensus 66 ~~~~~~~dvL~~i~~fl~~~p~e~VIl~l~~~~~~~~~~~l~~ 108 (135)
T smart00148 66 TLPIKLSEVLEAIKDFAFVTSPYPVILSLENHCSPDQQAKMAQ 108 (135)
T ss_pred cccEEHHHHHHHHHHHHHhCCCCcEEEeehhhCCHHHHHHHHH
Confidence 3457899999999999999999999999987653333334543
No 96
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=30.83 E-value=1.2e+02 Score=23.44 Aligned_cols=53 Identities=17% Similarity=0.208 Sum_probs=33.9
Q ss_pred CcceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcC
Q psy12247 27 NCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIES 82 (119)
Q Consensus 27 ~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~ 82 (119)
+||-|.+.+....+-| .-..-++..+|..++...|-++|+++|..=-|.-+++
T Consensus 175 nrv~V~f~~~~~~~~~---~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~~~~~ 227 (249)
T PF12436_consen 175 NRVEVEFKPKDNPNDP---EFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFFTVNP 227 (249)
T ss_dssp HEEEEEEEETTSTT------EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE---T
T ss_pred CeEEEEEEECCCCCCC---CEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEEecc
Confidence 4677777664433322 4556799999999999999999999998766666653
No 97
>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27). SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.
Probab=30.80 E-value=1.2e+02 Score=20.30 Aligned_cols=43 Identities=19% Similarity=0.156 Sum_probs=33.1
Q ss_pred CCCCcceEEecCCcchHhHHHHHHHhhcCCCC----CeEEEEEcCee
Q psy12247 42 PQMPRSNYVVAYEMTVGHFFYLLRKKMALRPE----EACFFFIESMI 84 (119)
Q Consensus 42 p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~----~slfl~Vn~~~ 84 (119)
|+-.+-.--|..+.+..++...+-++|+|+.+ -+||+..+..|
T Consensus 9 pdg~~i~V~v~~s~~a~~Vleav~~kl~L~~e~~~YFaLFev~~~~f 55 (87)
T cd01777 9 PDKATVTVRVRKNATTDQVYQALVAKAGMDSYTQNYFALFEVINHSF 55 (87)
T ss_pred cCCCEEEEEEEEcccHHHHHHHHHHHhCCCHHHHhheeeeEEecceE
Confidence 34344444577788999999999999999876 67888888666
No 98
>PRK04115 hypothetical protein; Provisional
Probab=30.74 E-value=2.1e+02 Score=20.75 Aligned_cols=54 Identities=20% Similarity=0.170 Sum_probs=32.0
Q ss_pred HHHHHHhcCCC-----cceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCC----CCCeEEEE
Q psy12247 17 IGENLARNHPN-----CAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALR----PEEACFFF 79 (119)
Q Consensus 17 e~~~ir~kyp~-----~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~----~~~slfl~ 79 (119)
|.+.+.+--|. ++|+|+|..+. ...--|.|....-+ .+|.+-|+.. .++.+++|
T Consensus 51 ELe~L~~~l~~~~~~lrLPIile~~~~-----~~~g~~~VrG~~ev----k~IskiLg~~~~~~e~~~l~ly 113 (137)
T PRK04115 51 ELEFLKELLDEDACRLRLPIILEIDSS-----LGEGAIVVRGKEEV----KVISKILGKEDIFSEEDILYLY 113 (137)
T ss_pred HHHHHHHhccchhhheeeeEEEEEecC-----CCceEEEEcCHHHH----HHHHHHhCccccccCCCEEEEe
Confidence 55555555553 58999999752 23345677776633 3455555543 45666664
No 99
>COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=30.73 E-value=76 Score=23.68 Aligned_cols=38 Identities=11% Similarity=0.328 Sum_probs=28.6
Q ss_pred eEEEEEcC----eecCCcCchHHHHHhHhcCCCCeEEEEecccc
Q psy12247 75 ACFFFIES----MIVPADSTRMETLSQRFADKDGLIYMVYSDVN 114 (119)
Q Consensus 75 slfl~Vn~----~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~ 114 (119)
.+-|.||= -+.| .=+.+..||++|+ +.||-.+.+-..+
T Consensus 26 kVlLIVNtASkCGfTp-QYegLe~Ly~ky~-~~Gf~VLgFPcNQ 67 (162)
T COG0386 26 KVLLIVNTASKCGFTP-QYEGLEALYKKYK-DKGFEVLGFPCNQ 67 (162)
T ss_pred cEEEEEEcccccCCcH-hHHHHHHHHHHHh-hCCcEEEeccccc
Confidence 46788883 2324 4568999999998 5899999887665
No 100
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=30.42 E-value=55 Score=23.31 Aligned_cols=50 Identities=18% Similarity=0.210 Sum_probs=37.1
Q ss_pred cCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEeccccccc
Q psy12247 52 AYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSDVNIFV 117 (119)
Q Consensus 52 p~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~~fG 117 (119)
...+++.+++..|.+.++++.++ + ...++++|..- ..||- ..+.+++.||
T Consensus 17 ~~~m~f~dL~~ev~~~~~~s~e~---------~----~~~iaq~YtdL-n~DGR--Fi~lG~n~Wg 66 (129)
T PRK02363 17 KEPMSFYDLVNEIQKYLGKSDEE---------I----RERIAQFYTDL-NLDGR--FISLGDNKWG 66 (129)
T ss_pred CCcccHHHHHHHHHHHhCCCHHH---------H----HHHHHHHHHHH-hccCC--eeEcCCCcee
Confidence 35678889999888888865432 1 37889999998 57883 4466888888
No 101
>PF01886 DUF61: Protein of unknown function DUF61; InterPro: IPR002746 The proteins in this entry are functionally uncharacterised.
Probab=30.39 E-value=1.2e+02 Score=21.53 Aligned_cols=56 Identities=23% Similarity=0.290 Sum_probs=35.3
Q ss_pred HHHHHHHHhcCCCc------ceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHHHHhhcCCC----CCeEEEE
Q psy12247 15 IKIGENLARNHPNC------AFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRP----EEACFFF 79 (119)
Q Consensus 15 ~~e~~~ir~kyp~~------ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~----~~slfl~ 79 (119)
+.|.+.+.+.-|.. +|+|+|..+ .+....|.|....-+ .+|++=|++.. ++.+++|
T Consensus 46 k~ELe~L~~~lp~~~~~~lrLPIile~~~-----~~~~g~~~V~g~~e~----k~i~~ilg~~~~~~~~~~l~i~ 111 (132)
T PF01886_consen 46 KEELERLAEILPEYEWSKLRLPIILEIDP-----TLGEGSYRVRGKEEV----KAISKILGKEREFEEEDELYIY 111 (132)
T ss_pred HHHHHHHHHhCCHHHHhceeccEEEEEec-----cCCCceEEEeCHHHH----HHHHHHhCCCcccccCCeEEEc
Confidence 45777777777754 899999854 245566778777633 33455555443 4566664
No 102
>KOG0010|consensus
Probab=30.22 E-value=1.3e+02 Score=26.22 Aligned_cols=54 Identities=17% Similarity=0.304 Sum_probs=40.7
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCC
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDG 104 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DG 104 (119)
+|.-|-|+.+.||.+|...|-++.+.+++. +-|...+++ .+.+.++. .|+-.||
T Consensus 25 dk~~~~V~~~ssV~qlKE~I~~~f~a~~dq-lvLIfaGrI-LKD~dTL~----~~gI~Dg 78 (493)
T KOG0010|consen 25 DKYEVNVASDSSVLQLKELIAQRFGAPPDQ-LVLIYAGRI-LKDDDTLK----QYGIQDG 78 (493)
T ss_pred cceeEecccchHHHHHHHHHHHhcCCChhH-eeeeecCcc-ccChhhHH----HcCCCCC
Confidence 367789999999999999999999888775 555555666 56676764 3555677
No 103
>PF08825 E2_bind: E2 binding domain; InterPro: IPR014929 E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains []. ; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0045116 protein neddylation; PDB: 3GZN_D 3DBL_F 1R4N_H 1R4M_D 2NVU_B 1TT5_D 3DBR_D 3DBH_H 1YOV_B 3FN1_A ....
Probab=29.69 E-value=57 Score=21.42 Aligned_cols=46 Identities=20% Similarity=0.252 Sum_probs=29.9
Q ss_pred EecCCcchHhHHHHHHHh--hcCC------CCCeEEEE-E---cCeecCCcCchHHHH
Q psy12247 50 VVAYEMTVGHFFYLLRKK--MALR------PEEACFFF-I---ESMIVPADSTRMETL 95 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~--l~l~------~~~slfl~-V---n~~~~p~~~~~m~~l 95 (119)
-|+++.|+++|+..|..+ +++. .+++||+= + ....-|..+.+|.+|
T Consensus 2 ~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL 59 (84)
T PF08825_consen 2 EVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL 59 (84)
T ss_dssp EESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT
T ss_pred CcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH
Confidence 378999999999999988 5554 24555551 1 112236677788888
No 104
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=29.09 E-value=65 Score=21.01 Aligned_cols=21 Identities=5% Similarity=0.264 Sum_probs=18.8
Q ss_pred HHHHHhhcCCCCCeEEEEEcC
Q psy12247 62 YLLRKKMALRPEEACFFFIES 82 (119)
Q Consensus 62 ~~lRk~l~l~~~~slfl~Vn~ 82 (119)
.-+|++|++.+.+.+-+++.+
T Consensus 20 keiR~~lgi~~Gd~lei~~~~ 40 (89)
T COG2002 20 KEIREALGIKEGDVLEIIVDG 40 (89)
T ss_pred HHHHHHhCCCCCCEEEEEEeC
Confidence 357999999999999999995
No 105
>smart00295 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
Probab=28.92 E-value=1.5e+02 Score=21.00 Aligned_cols=52 Identities=10% Similarity=0.019 Sum_probs=35.3
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCC--CeEEEEEcCe---ecCCcCchHHHHH
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPE--EACFFFIESM---IVPADSTRMETLS 96 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~--~slfl~Vn~~---~~p~~~~~m~~lY 96 (119)
....+.+.+..|+.+++..+.+++++... =+||....+. .-+.++.+|.+.-
T Consensus 14 ~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~ 70 (207)
T smart00295 14 TTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQD 70 (207)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHhc
Confidence 45578899999999999999999999643 3444444331 2244555655543
No 106
>PRK13125 trpA tryptophan synthase subunit alpha; Provisional
Probab=28.27 E-value=62 Score=24.78 Aligned_cols=17 Identities=12% Similarity=-0.222 Sum_probs=13.0
Q ss_pred cCCCCeEEEEecccccccC
Q psy12247 100 ADKDGLIYMVYSDVNIFVD 118 (119)
Q Consensus 100 kd~DGfLyl~Ys~~~~fG~ 118 (119)
+..|||||| +..+.+|.
T Consensus 150 ~~~~~~l~m--sv~~~~g~ 166 (244)
T PRK13125 150 KLSPLFIYY--GLRPATGV 166 (244)
T ss_pred HhCCCEEEE--EeCCCCCC
Confidence 347999999 67777774
No 107
>cd01617 DCX Ubiquitin-like domain of DCX. DCX The ubiquitin-like DCX domain is present in tandem within the N-terminal half of the doublecortin protein. Doublecortin is expressed in migrating neurons. Mutations in the gene encoding doublecortin cause lissencephaly in males and 'double-cortex syndrome' in females.
Probab=28.07 E-value=1.6e+02 Score=18.64 Aligned_cols=61 Identities=15% Similarity=0.244 Sum_probs=39.8
Q ss_pred CCcceEEecCC--cchHhHHHHHHHhhcCCCCCeEEEE-EcC-eecCCcCchHHHHHhHhcCCCCeEEEEecccc
Q psy12247 44 MPRSNYVVAYE--MTVGHFFYLLRKKMALRPEEACFFF-IES-MIVPADSTRMETLSQRFADKDGLIYMVYSDVN 114 (119)
Q Consensus 44 L~k~Kflvp~~--~tv~~~~~~lRk~l~l~~~~slfl~-Vn~-~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~ 114 (119)
-...+++|+.. -|+.++...|.+.+++.+...=-|| .++ .. -...+.. +||--||..+.|.
T Consensus 13 ~~g~~~~i~~~~~~sfd~lL~~lt~~l~l~~~~Vr~lyt~~g~~~--------v~~~~~l--~~g~~yVa~g~e~ 77 (80)
T cd01617 13 FKGVRLLVNRRRFKSFDALLDDLTEKVQLDPGAVRKLYTLDGGHR--------VSLLDEL--EDGGVYVASGREP 77 (80)
T ss_pred CCCEEEEEChhhhCCHHHHHHHHHHHhCCCCCcEEEEEcCCCCeE--------eccHHHh--cCCCEEEEECCCC
Confidence 36678899987 4899999999999998644322222 122 33 1222233 5889999987664
No 108
>PF07929 PRiA4_ORF3: Plasmid pRiA4b ORF-3-like protein; InterPro: IPR012912 Members of this family are similar to the protein product of ORF-3 (Q44206 from SWISSPROT) found on plasmid pRiA4 in the bacterium Agrobacterium rhizogenes. This plasmid is responsible for tumourigenesis at wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process []. Other proteins found in this family are annotated as being putative TnpR resolvases (Q9LCU7 from SWISSPROT, Q50439 from SWISSPROT), but no further evidence was found to back this. Moreover, another member of this family is described as a probable lexA repressor (Q7UEI4 from SWISSPROT) and in fact carries a LexA DNA binding domain (IPR006199 from INTERPRO), but no references were found to expand on this. ; PDB: 2I1S_A.
Probab=27.67 E-value=1.3e+02 Score=21.77 Aligned_cols=29 Identities=7% Similarity=0.184 Sum_probs=21.4
Q ss_pred cceEEecCCcchHhHHHHHHHhhcCCCCC
Q psy12247 46 RSNYVVAYEMTVGHFFYLLRKKMALRPEE 74 (119)
Q Consensus 46 k~Kflvp~~~tv~~~~~~lRk~l~l~~~~ 74 (119)
-..+.||.++|+++|-.+|..-++.....
T Consensus 19 wRri~Vp~~~tl~~Lh~~Iq~afgw~~~H 47 (179)
T PF07929_consen 19 WRRIEVPADITLADLHEVIQAAFGWDDDH 47 (179)
T ss_dssp EEEEEEETT-BHHHHHHHHHHHTT----S
T ss_pred EEEEEECCCCCHHHHHHHHHHHhCcCCCE
Confidence 45679999999999999999999987653
No 109
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=27.44 E-value=1.6e+02 Score=18.43 Aligned_cols=56 Identities=20% Similarity=0.282 Sum_probs=38.5
Q ss_pred eEEecCCcchHhHHHHHHHhhc---CCCCCeEEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEecc
Q psy12247 48 NYVVAYEMTVGHFFYLLRKKMA---LRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSD 112 (119)
Q Consensus 48 Kflvp~~~tv~~~~~~lRk~l~---l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~ 112 (119)
+|.-....++.++...||+.-= +......|+.-||.- +-=.||..+||-+..+|..
T Consensus 5 ~~vp~~~~~v~d~K~~Lr~y~~~~I~~d~tGfYIvF~~~~---------Ea~rC~~~~~~~~~f~y~m 63 (66)
T PF11767_consen 5 KFVPVHGVTVEDFKKRLRKYRWDRIRDDRTGFYIVFNDSK---------EAERCFRAEDGTLFFTYRM 63 (66)
T ss_pred ccCCCCCccHHHHHHHHhcCCcceEEecCCEEEEEECChH---------HHHHHHHhcCCCEEEEEEE
Confidence 3444556788888777765431 345567777766543 7778888899999988863
No 110
>PF12251 zf-SNAP50_C: snRNA-activating protein of 50kDa MW C terminal; InterPro: IPR022042 This domain family is found in eukaryotes, and is typically between 196 and 207 amino acids in length. There is a conserved CEH sequence motif. SNAP50 is part of the snRNA-activating protein complex which activates RNA polymerases II and III. There is a cysteine-histidine cluster which contains two possible zinc finger motifs.
Probab=27.34 E-value=70 Score=24.15 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=26.4
Q ss_pred ceEEecCCcchHhHHHHHHHhhcCC-------CCCeEEEEEcCeec
Q psy12247 47 SNYVVAYEMTVGHFFYLLRKKMALR-------PEEACFFFIESMIV 85 (119)
Q Consensus 47 ~Kflvp~~~tv~~~~~~lRk~l~l~-------~~~slfl~Vn~~~~ 85 (119)
..|+|-.+.|++++...|.-.-... ...+-|+|++|+|=
T Consensus 2 qe~~vLgsQtLteLrD~i~C~~D~~~~~~~~~~~~s~fffIe~tFY 47 (196)
T PF12251_consen 2 QEFLVLGSQTLTELRDKISCPSDQQPFGLAKDKYPSSFFFIEGTFY 47 (196)
T ss_pred CEEEEecCCCHHHHhhCcCCCCCCccccccccCCCCeEEEECCEee
Confidence 3578888888888755554333222 24677999999883
No 111
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=26.94 E-value=90 Score=17.68 Aligned_cols=20 Identities=25% Similarity=0.483 Sum_probs=17.6
Q ss_pred HHHHhhcCCCCCeEEEEEcC
Q psy12247 63 LLRKKMALRPEEACFFFIES 82 (119)
Q Consensus 63 ~lRk~l~l~~~~slfl~Vn~ 82 (119)
.+|+.+++.+++.+.+.+.+
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEET
T ss_pred HHHHHcCCCCCCEEEEEEeC
Confidence 47899999999999998875
No 112
>cd00137 PI-PLCc Catalytic domain of prokaryotic and eukaryotic phosphoinositide-specific phospholipase C. This subfamily corresponds to the catalytic domain present in prokaryotic and eukaryotic phosphoinositide-specific phospholipase C (PI-PLC), which is a ubiquitous enzyme catalyzing the cleavage of the sn3-phosphodiester bond in the membrane phosphoinositides (phosphatidylinositol, PI; Phosphatidylinositol-4-phosphate, PIP; phosphatidylinositol 4,5-bisphosphate, PIP2) to yield inositol phosphates (inositol monosphosphate, InsP; inositol diphosphate, InsP2; inositol trisphosphate, InsP3) and diacylglycerol (DAG). The higher eukaryotic PI-PLCs (EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. They play a critical role in most signal transduction pathways, controlling numerous cellular events, such as cell growth, proliferation, excitation and secretion. These PI-PLCs strictly require Ca2+ for their catalytic a
Probab=26.72 E-value=80 Score=24.84 Aligned_cols=53 Identities=6% Similarity=0.162 Sum_probs=40.8
Q ss_pred CcchHhHHHHHHHhhcCCCCCeEEEEEcCeecC--CcCchHHHHHhHhcCCCCeEEE
Q psy12247 54 EMTVGHFFYLLRKKMALRPEEACFFFIESMIVP--ADSTRMETLSQRFADKDGLIYM 108 (119)
Q Consensus 54 ~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p--~~~~~m~~lY~~~kd~DGfLyl 108 (119)
..++.+++..|++-+.-.+++.|.|-+++.-.+ .....|.+.+.... +.+||.
T Consensus 73 ~~~f~dvl~~i~~fl~~~p~e~vIlsl~~~~~~~~~~q~~~~~~~~~~~--g~~l~~ 127 (274)
T cd00137 73 DIFLKEVIEAIAQFLKKNPPETIIMSLKNEVDSMDSFQAKMAEYCRTIF--GDMLLT 127 (274)
T ss_pred CcCHHHHHHHHHHHHHHCCCCeEEEEEEecCCCcHHHHHHHHHHHHHhh--hhhhcc
Confidence 678999999999999999999999999976533 45667777776654 335543
No 113
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=26.61 E-value=71 Score=25.45 Aligned_cols=29 Identities=10% Similarity=0.101 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHHhcCCCcceEEEEcCC
Q psy12247 9 YSLEERIKIGENLARNHPNCAFVILERSP 37 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ipVIvE~~~ 37 (119)
-|.|||..-.+...+.-.+++|||+--..
T Consensus 58 Lt~eEr~~v~~~~~~~~~grvpvi~Gv~~ 86 (309)
T cd00952 58 LTWEEKQAFVATVVETVAGRVPVFVGATT 86 (309)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCEEEEecc
Confidence 46799999999999988999999997754
No 114
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=26.28 E-value=65 Score=21.05 Aligned_cols=28 Identities=14% Similarity=0.351 Sum_probs=22.2
Q ss_pred CeEEEEEcCeec--CCcCchHHHHHhHhcC
Q psy12247 74 EACFFFIESMIV--PADSTRMETLSQRFAD 101 (119)
Q Consensus 74 ~slfl~Vn~~~~--p~~~~~m~~lY~~~kd 101 (119)
...|.+||+..+ ++.++.+..|++.=+.
T Consensus 45 ~~pFAlVnG~~V~A~t~eeL~~kI~~~i~e 74 (78)
T PF07293_consen 45 KKPFALVNGEIVAAETAEELLEKIKEKIEE 74 (78)
T ss_pred CCccEEECCEEEecCCHHHHHHHHHHHHhc
Confidence 678999998764 7788888888887653
No 115
>cd01782 AF6_RA_repeat1 Ubiquitin domain of AT-6, first repeat. The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
Probab=26.08 E-value=1.4e+02 Score=20.99 Aligned_cols=34 Identities=18% Similarity=0.126 Sum_probs=26.9
Q ss_pred EEecCCcchHhHHHHHHHhhcCC------CCCeEEEEEcC
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALR------PEEACFFFIES 82 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~------~~~slfl~Vn~ 82 (119)
--|++++|..+++..|-++...+ ++-|||....+
T Consensus 40 VrVsS~~tt~eVI~~LLeKFk~d~~~~s~p~FALYevh~n 79 (112)
T cd01782 40 IRVSSTATTRDVIDTLSEKFRPDMRMLSNPTYSLYEVHEN 79 (112)
T ss_pred EEEecCCCHHHHHHHHHHHhcccccccCCcceEEEEEecC
Confidence 45999999999999999888733 56778876553
No 116
>PF10336 DUF2420: Protein of unknown function (DUF2420); InterPro: IPR018822 This entry represents a family of proteins conserved in fungi. Their function is not known.
Probab=25.83 E-value=2.3e+02 Score=19.48 Aligned_cols=62 Identities=13% Similarity=0.233 Sum_probs=40.8
Q ss_pred CcchHhHHHHHHHhhc------CCCCCeEEEEEcC--------eecCCcCchHHHH---HhHhcCC---------CCeEE
Q psy12247 54 EMTVGHFFYLLRKKMA------LRPEEACFFFIES--------MIVPADSTRMETL---SQRFADK---------DGLIY 107 (119)
Q Consensus 54 ~~tv~~~~~~lRk~l~------l~~~~slfl~Vn~--------~~~p~~~~~m~~l---Y~~~kd~---------DGfLy 107 (119)
+.++++|+..+|+.+. +..++-|.|-|.. .+ ...+-++.+| |+..+.. =+-||
T Consensus 10 ~~~l~~lf~~lR~~le~~~g~~~~~~~ELvl~i~~L~L~i~EDn~-y~~~iTl~di~~lf~~L~~n~~~~~~~~~p~~L~ 88 (113)
T PF10336_consen 10 NEPLEELFAALRQFLENEEGELFSAEDELVLDIPELGLEISEDNV-YCSDITLSDIVDLFDILCENDGKNEEPDLPEPLY 88 (113)
T ss_pred hCCHHHHHHHHHHHHHhccccccCCCCEEEEEeccCCcEEecccc-ccccCcHHHHHHHHHHHHhccCccccCCCCCcEE
Confidence 4578899999999984 4556666665442 22 4456666655 4444222 23899
Q ss_pred EEecccccc
Q psy12247 108 MVYSDVNIF 116 (119)
Q Consensus 108 l~Ys~~~~f 116 (119)
+.-+..+.|
T Consensus 89 i~LstrPRF 97 (113)
T PF10336_consen 89 ITLSTRPRF 97 (113)
T ss_pred EEEecCccH
Confidence 999988877
No 117
>KOG3483|consensus
Probab=25.69 E-value=1.1e+02 Score=20.37 Aligned_cols=61 Identities=7% Similarity=0.074 Sum_probs=45.4
Q ss_pred CCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCCcCchHHHHHhHhcCC
Q psy12247 41 LPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADK 102 (119)
Q Consensus 41 ~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~~~~~m~~lY~~~kd~ 102 (119)
-|.|.-+.+-||+...+..+..+--...+.++..|--+ -|+-+-..+.++-|++|=+|.+|
T Consensus 23 dpklpfkv~svpestpftavlkfaaeefkvpaatsaii-tndgiginpaq~agnvflkhgse 83 (94)
T KOG3483|consen 23 DPKLPFKVLSVPESTPFTAVLKFAAEEFKVPAATSAII-TNDGIGINPAQTAGNVFLKHGSE 83 (94)
T ss_pred CCCCccceecCCCCCchHHHHHHHHHHccCCccceeEE-ecCccccCccccccceeeccCCE
Confidence 46777888889999999999888888988888766544 34333245567788888887643
No 118
>KOG3218|consensus
Probab=25.53 E-value=1.1e+02 Score=23.64 Aligned_cols=29 Identities=17% Similarity=0.112 Sum_probs=16.3
Q ss_pred CcchHhHHHHHHHhhcCCCCCeEEEEEcCee
Q psy12247 54 EMTVGHFFYLLRKKMALRPEEACFFFIESMI 84 (119)
Q Consensus 54 ~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~ 84 (119)
++|..+|...--.++ +.-+.|.+.++...
T Consensus 36 ~ltLe~F~~~yg~~~--p~r~~L~~~~~~~~ 64 (208)
T KOG3218|consen 36 DLTLEEFKARYGDKM--PDREDLRILAAHRD 64 (208)
T ss_pred hhhHHHHHHHhccCC--cchhhEEEEeccCC
Confidence 457777755443332 44566777666444
No 119
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=25.24 E-value=1.7e+02 Score=18.01 Aligned_cols=52 Identities=6% Similarity=0.022 Sum_probs=30.1
Q ss_pred CCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEc--CeecCC--cCchHHHH
Q psy12247 42 PQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIE--SMIVPA--DSTRMETL 95 (119)
Q Consensus 42 p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn--~~~~p~--~~~~m~~l 95 (119)
|+=.+..--.+.+.|++++..+|...... ..+.-|..+ .+.+.. .+.+|.++
T Consensus 10 pdG~~~~~~F~~~~tl~~l~~fv~~~~~~--~~~f~L~t~~Pr~~~~~~~~~~TL~e~ 65 (77)
T cd01767 10 PDGKRLEQRFNSTHKLSDVRDFVESNGPP--AEPFTLMTSFPRRVLTDLDYELTLQEA 65 (77)
T ss_pred CCCCEEEEEeCCCCCHHHHHHHHHHcCCC--CCCEEEEeCCCCccCCCCCccCcHHHc
Confidence 33344444578999999999999877543 334444433 122122 45566553
No 120
>PF14060 DUF4252: Domain of unknown function (DUF4252)
Probab=25.20 E-value=93 Score=21.72 Aligned_cols=25 Identities=8% Similarity=0.321 Sum_probs=21.1
Q ss_pred cCchHHHHHhHhcCCCCeEEEEecc
Q psy12247 88 DSTRMETLSQRFADKDGLIYMVYSD 112 (119)
Q Consensus 88 ~~~~m~~lY~~~kd~DGfLyl~Ys~ 112 (119)
..+.+..+|++|++.+|+.+++-+.
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~v~i~~ 44 (155)
T PF14060_consen 20 QGQSLQKYFDKYSENKGVTSVNISK 44 (155)
T ss_pred cchhHHHHHHHhCCCCCeEEEEECH
Confidence 4578899999999999999988653
No 121
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=25.12 E-value=1.1e+02 Score=19.17 Aligned_cols=38 Identities=32% Similarity=0.283 Sum_probs=27.8
Q ss_pred CCCCCcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEE
Q psy12247 41 LPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFF 79 (119)
Q Consensus 41 ~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~ 79 (119)
+|+-+...--|.+.+|+.+++.-+-++-+|+++. .++|
T Consensus 7 LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~-~~V~ 44 (71)
T PF02196_consen 7 LPNGQRTVVQVRPGMTIRDALSKACKKRGLNPEC-CDVR 44 (71)
T ss_dssp ETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCC-EEEE
T ss_pred CCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHH-EEEE
Confidence 4566666778899999999999999999999874 4555
No 122
>PRK08577 hypothetical protein; Provisional
Probab=24.89 E-value=77 Score=22.02 Aligned_cols=21 Identities=10% Similarity=0.259 Sum_probs=18.4
Q ss_pred HHHHhhcCCCCCeEEEEEcCe
Q psy12247 63 LLRKKMALRPEEACFFFIESM 83 (119)
Q Consensus 63 ~lRk~l~l~~~~slfl~Vn~~ 83 (119)
-+|+.|++.+++.+-+++++.
T Consensus 20 ~~r~~l~~~~g~~~~~~~~~~ 40 (136)
T PRK08577 20 EIREALGIREGMYVLLIADTD 40 (136)
T ss_pred HHHHHcCcCCCCEEEEEEECC
Confidence 479999999999999998853
No 123
>TIGR01408 Ube1 ubiquitin-activating enzyme E1. This model represents the full length, over a thousand amino acids, of a multicopy family of eukaryotic proteins, many of which are designated ubiquitin-activating enzyme E1. Members have two copies of the ThiF family domain (pfam00899), a repeat found in ubiquitin-activating proteins (pfam02134), and other regions.
Probab=24.56 E-value=1.6e+02 Score=27.82 Aligned_cols=58 Identities=14% Similarity=0.210 Sum_probs=37.3
Q ss_pred EEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeec-----C----CcCchHHHHHhHhcC---CCCeEEEE
Q psy12247 49 YVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIV-----P----ADSTRMETLSQRFAD---KDGLIYMV 109 (119)
Q Consensus 49 flvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~-----p----~~~~~m~~lY~~~kd---~DGfLyl~ 109 (119)
|.|+.++|+.+|+..+.++.++... + +.++++++ + ..+.+|.+|++.=.. .++..|+.
T Consensus 916 ~~i~~~~Tl~~~i~~~~~~~~~~v~-~--is~g~~~lY~~~~~~~~erl~~~l~el~~~~~k~~~~~~~~~l~ 985 (1008)
T TIGR01408 916 WTLHGDFTLLEFINAVKEKYGLEPT-M--VSQGVKLLYVPVMPGHAERLKLKMHKLVKPTTKKKLPPYRVHLT 985 (1008)
T ss_pred EEecCCCcHHHHHHHHHHHhCCeeE-E--EEcCceEEEeccchhhHHhcCCCHHHHHHHhccCCCCCCceEEE
Confidence 5688899999999999999887632 1 11222221 2 234578999988732 45555553
No 124
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=24.56 E-value=85 Score=24.79 Aligned_cols=102 Identities=11% Similarity=0.014 Sum_probs=53.6
Q ss_pred CCHHHHHHHHHHHHhcCCCcceEEEEcCCCC--CC-------CCCC-cceEEecCCc---chHhHHHHHHHhhcCCCCCe
Q psy12247 9 YSLEERIKIGENLARNHPNCAFVILERSPSA--LL-------PQMP-RSNYVVAYEM---TVGHFFYLLRKKMALRPEEA 75 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~--~~-------p~L~-k~Kflvp~~~---tv~~~~~~lRk~l~l~~~~s 75 (119)
-|.+||+.-.+...+...+++|||+--...+ ++ -.+. .--.++|+-. +-.+++...+.=..-.++-.
T Consensus 50 Ls~~Er~~l~~~~~~~~~g~~pvi~gv~~~~t~~ai~~a~~A~~~Gad~v~v~pP~y~~~~~~~l~~~f~~ia~a~~~lp 129 (294)
T TIGR02313 50 LTLEERKQAIENAIDQIAGRIPFAPGTGALNHDETLELTKFAEEAGADAAMVIVPYYNKPNQEALYDHFAEVADAVPDFP 129 (294)
T ss_pred CCHHHHHHHHHHHHHHhCCCCcEEEECCcchHHHHHHHHHHHHHcCCCEEEEcCccCCCCCHHHHHHHHHHHHHhccCCC
Confidence 4679999999999998899999998654322 10 0000 0011222211 11334443333222222457
Q ss_pred EEEEEcCeec--CCcCchHHHHHhHhcCCCCeEEEEeccc
Q psy12247 76 CFFFIESMIV--PADSTRMETLSQRFADKDGLIYMVYSDV 113 (119)
Q Consensus 76 lfl~Vn~~~~--p~~~~~m~~lY~~~kd~DGfLyl~Ys~~ 113 (119)
+++|=+-... .-+...+.+|-+++ .++..+..|+.
T Consensus 130 v~iYn~P~~tg~~l~~~~l~~L~~~~---pnv~giK~ss~ 166 (294)
T TIGR02313 130 IIIYNIPGRAAQEIAPKTMARLRKDC---PNIVGAKESNK 166 (294)
T ss_pred EEEEeCchhcCcCCCHHHHHHHHhhC---CCEEEEEeCCC
Confidence 8888332110 11234666666554 45777777654
No 125
>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor. Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.
Probab=24.55 E-value=1.3e+02 Score=19.83 Aligned_cols=34 Identities=26% Similarity=0.259 Sum_probs=26.9
Q ss_pred CCCCCcceEEecCCcchHhHHHHHHHhhcCCCCC
Q psy12247 41 LPQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEE 74 (119)
Q Consensus 41 ~p~L~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~ 74 (119)
+|.=...--.|.+++|+.++....-++-+++|.+
T Consensus 6 lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~e 39 (77)
T cd01818 6 LPDNQPVLTYLRPGMSVEDFLESACKRKQLDPME 39 (77)
T ss_pred CCCCceEEEEECCCCCHHHHHHHHHHhcCCChhH
Confidence 3444455568999999999999999998988763
No 126
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=24.24 E-value=1.8e+02 Score=18.61 Aligned_cols=33 Identities=9% Similarity=-0.011 Sum_probs=26.7
Q ss_pred EecCCcchHhHHHHHHHhhcCCCC-CeEEEEEcC
Q psy12247 50 VVAYEMTVGHFFYLLRKKMALRPE-EACFFFIES 82 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~l~~~-~slfl~Vn~ 82 (119)
-+|.++|++++...|-+..+++++ ..|.+|-+.
T Consensus 18 r~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~ 51 (84)
T cd01789 18 KYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD 51 (84)
T ss_pred ecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence 589999999999999999899765 566566654
No 127
>PF00388 PI-PLC-X: Phosphatidylinositol-specific phospholipase C, X domain This entry is for the whole phospholipase C protein; InterPro: IPR000909 Phosphatidylinositol-specific phospholipase C (3.1.4.11 from EC), a eukaryotic intracellular enzyme, plays an important role in signal transduction processes []. It catalyzes the hydrolysis of 1-phosphatidyl-D-myo-inositol-3,4,5-triphosphate into the second messenger molecules diacylglycerol and inositol-1,4,5-triphosphate. This catalytic process is tightly regulated by reversible phosphorylation and binding of regulatory proteins [, , ]. In mammals, there are at least 6 different isoforms of PI-PLC, they differ in their domain structure, their regulation, and their tissue distribution. Lower eukaryotes also possess multiple isoforms of PI-PLC. All eukaryotic PI-PLCs contain two regions of homology, sometimes referred to as the 'X-box' and 'Y-box'. The order of these two regions is always the same (NH2-X-Y-COOH), but the spacing is variable. In most isoforms, the distance between these two regions is only 50-100 residues but in the gamma isoforms one PH domain, two SH2 domains, and one SH3 domain are inserted between the two PLC-specific domains. The two conserved regions have been shown to be important for the catalytic activity. By profile analysis, we could show that sequences with significant similarity to the X-box domain occur also in prokaryotic and trypanosome PI-specific phospholipases C. Apart from this region, the prokaryotic enzymes show no similarity to their eukaryotic counterparts.; GO: 0004629 phospholipase C activity, 0006629 lipid metabolic process, 0035556 intracellular signal transduction; PDB: 2FJU_B 2ZKM_X 3V18_A 3V1H_A 3V16_A 3QR1_D 3EA3_A 3EA1_A 2OR2_A 1T6M_B ....
Probab=24.23 E-value=56 Score=22.78 Aligned_cols=32 Identities=13% Similarity=0.155 Sum_probs=27.1
Q ss_pred CCcchHhHHHHHHHhhcCCCCCeEEEEEcCee
Q psy12247 53 YEMTVGHFFYLLRKKMALRPEEACFFFIESMI 84 (119)
Q Consensus 53 ~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~ 84 (119)
...++.+++..+++-|.-.|++.+.|-+++..
T Consensus 65 ~~~~~~dvL~~i~~fl~~~p~E~VIl~~~~~~ 96 (146)
T PF00388_consen 65 SGITFEDVLNDIRDFLFEHPSEPVILSLKHEY 96 (146)
T ss_dssp -EEEHHHHHHHHHHHTTHSTTS-EEEEEEEES
T ss_pred eeEeHHHHHHHHHHHHhcCCCeEEEEEeeccc
Confidence 46799999999999999999999999998655
No 128
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=24.07 E-value=91 Score=23.98 Aligned_cols=100 Identities=11% Similarity=0.042 Sum_probs=53.8
Q ss_pred CCHHHHHHHHHHHHhcCCCcceEEEEcCCCCCCCCCC----------cceEEecCCc---chHhHHHHHHHhhcCCCCCe
Q psy12247 9 YSLEERIKIGENLARNHPNCAFVILERSPSALLPQMP----------RSNYVVAYEM---TVGHFFYLLRKKMALRPEEA 75 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~~~p~L~----------k~Kflvp~~~---tv~~~~~~lRk~l~l~~~~s 75 (119)
-|.+||+.-.+..++.-.+++|||+--...+..-.++ .--.++|+.. +-.+++...+.=..- ..-.
T Consensus 47 ls~~Er~~l~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~Gad~v~v~pP~y~~~~~~~~~~~~~~ia~~-~~~p 125 (281)
T cd00408 47 LTDEERKEVIEAVVEAVAGRVPVIAGVGANSTREAIELARHAEEAGADGVLVVPPYYNKPSQEGIVAHFKAVADA-SDLP 125 (281)
T ss_pred CCHHHHHHHHHHHHHHhCCCCeEEEecCCccHHHHHHHHHHHHHcCCCEEEECCCcCCCCCHHHHHHHHHHHHhc-CCCC
Confidence 4679999999999998889999999765432100000 0011222211 223444444333222 3457
Q ss_pred EEEEEcCee--cCCcCchHHHHHhHhcCCCCeEEEEeccc
Q psy12247 76 CFFFIESMI--VPADSTRMETLSQRFADKDGLIYMVYSDV 113 (119)
Q Consensus 76 lfl~Vn~~~--~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~ 113 (119)
+++|=+-.. .+-+.+.+.+|-+ .+++..+.+|+.
T Consensus 126 i~iYn~P~~tg~~l~~~~~~~L~~----~~~v~giK~s~~ 161 (281)
T cd00408 126 VILYNIPGRTGVDLSPETIARLAE----HPNIVGIKDSSG 161 (281)
T ss_pred EEEEECccccCCCCCHHHHHHHhc----CCCEEEEEeCCC
Confidence 888844221 0212345566653 467888887763
No 129
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=23.99 E-value=1.1e+02 Score=19.33 Aligned_cols=35 Identities=17% Similarity=0.058 Sum_probs=24.0
Q ss_pred CcchHhHHHHHHHhhc-----CCCCCeEEEEEcCeecCCcCc
Q psy12247 54 EMTVGHFFYLLRKKMA-----LRPEEACFFFIESMIVPADST 90 (119)
Q Consensus 54 ~~tv~~~~~~lRk~l~-----l~~~~slfl~Vn~~~~p~~~~ 90 (119)
..|++++...|.++.. +. ...+-++||+.+. +.++
T Consensus 25 ~~tv~~l~~~L~~~~~~~~~~~~-~~~~~~aVN~~~~-~~~~ 64 (81)
T PRK11130 25 FPTVEALRQHLAQKGDRWALALE-DGKLLAAVNQTLV-SFDH 64 (81)
T ss_pred CCCHHHHHHHHHHhCccHHhhhc-CCCEEEEECCEEc-CCCC
Confidence 5799999999987742 22 3446689998873 3343
No 130
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=23.75 E-value=84 Score=24.65 Aligned_cols=99 Identities=5% Similarity=0.008 Sum_probs=53.0
Q ss_pred CCHHHHHHHHHHHHhcCCCcceEEEEcCCCC--CC-------CCCCcce-EEecCCc---chHhHHHHHHHhhcCCCCCe
Q psy12247 9 YSLEERIKIGENLARNHPNCAFVILERSPSA--LL-------PQMPRSN-YVVAYEM---TVGHFFYLLRKKMALRPEEA 75 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~--~~-------p~L~k~K-flvp~~~---tv~~~~~~lRk~l~l~~~~s 75 (119)
-|.|||..-.+...+.-.+++|||+--.. + ++ -.+.=.- .++|+-. +-.+++...+.=..- .+-.
T Consensus 50 Ls~eEr~~l~~~~~~~~~~~~pvi~gv~~-~t~~~i~~a~~a~~~Gad~v~~~pP~y~~~~~~~i~~~f~~v~~~-~~~p 127 (289)
T cd00951 50 LTPDEYAQVVRAAVEETAGRVPVLAGAGY-GTATAIAYAQAAEKAGADGILLLPPYLTEAPQEGLYAHVEAVCKS-TDLG 127 (289)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCEEEecCC-CHHHHHHHHHHHHHhCCCEEEECCCCCCCCCHHHHHHHHHHHHhc-CCCC
Confidence 47799999999888888899999996542 2 10 0000001 1222221 223444444433322 2356
Q ss_pred EEEEEcCeecCCcCchHHHHHhHhcCCCCeEEEEeccc
Q psy12247 76 CFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSDV 113 (119)
Q Consensus 76 lfl~Vn~~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~ 113 (119)
+++|=+... .-+.+.+.+|-+.+ +.+..|.+|+.
T Consensus 128 i~lYn~~g~-~l~~~~l~~L~~~~---pnivgiKds~~ 161 (289)
T cd00951 128 VIVYNRANA-VLTADSLARLAERC---PNLVGFKDGVG 161 (289)
T ss_pred EEEEeCCCC-CCCHHHHHHHHhcC---CCEEEEEeCCC
Confidence 888843222 11234666665333 46777887754
No 131
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=23.61 E-value=89 Score=21.57 Aligned_cols=27 Identities=19% Similarity=0.331 Sum_probs=18.2
Q ss_pred CCeEEEEEcCeec--CCcCchHHHHHhHh
Q psy12247 73 EEACFFFIESMIV--PADSTRMETLSQRF 99 (119)
Q Consensus 73 ~~slfl~Vn~~~~--p~~~~~m~~lY~~~ 99 (119)
.+..|+|||+... +.....+.+.|..+
T Consensus 47 ~~~q~~fVNgR~V~~~~l~~aI~~~Y~~~ 75 (127)
T cd03483 47 KIIFILFINNRLVECSALRRAIENVYANY 75 (127)
T ss_pred CceEEEEEcCCEecCHHHHHHHHHHHHHh
Confidence 4678999999773 33444556666665
No 132
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=23.34 E-value=99 Score=16.37 Aligned_cols=17 Identities=35% Similarity=0.430 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHhcCCC
Q psy12247 11 LEERIKIGENLARNHPN 27 (119)
Q Consensus 11 ~e~R~~e~~~ir~kyp~ 27 (119)
|-+|.++....-++||+
T Consensus 12 FY~rlk~Ike~Hrr~Pn 28 (28)
T PF12108_consen 12 FYERLKEIKEYHRRYPN 28 (28)
T ss_dssp HHHHHHHHHHHHHS--S
T ss_pred HHHHHHHHHHHHHhCCC
Confidence 56899999999999986
No 133
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=23.34 E-value=1.8e+02 Score=17.62 Aligned_cols=37 Identities=16% Similarity=0.164 Sum_probs=26.6
Q ss_pred cceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCC
Q psy12247 46 RSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPA 87 (119)
Q Consensus 46 k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~ 87 (119)
.+.+-++..+|+++++. .++++. ..+-+-||+.++|.
T Consensus 7 g~~~~~~~~~tl~~ll~----~l~~~~-~~vaVavN~~iv~r 43 (66)
T PRK08053 7 DQPMQCAAGQTVHELLE----QLNQLQ-PGAALAINQQIIPR 43 (66)
T ss_pred CeEEEcCCCCCHHHHHH----HcCCCC-CcEEEEECCEEeCh
Confidence 34566788889988865 355553 46888999999774
No 134
>PF04663 Phenol_monoox: Phenol hydroxylase conserved region; InterPro: IPR006756 Under aerobic conditions, phenol is usually hydroxylated to catechol and degraded via the meta or ortho pathways. Two types of phenol hydroxylase are known: one is a multi-component enzyme the other is a single-component monooxygenase. This signature is found in both types of enzymes [, ].; PDB: 3U52_F 2INN_F 2INP_E.
Probab=22.83 E-value=79 Score=20.22 Aligned_cols=41 Identities=10% Similarity=0.105 Sum_probs=21.8
Q ss_pred HhcCCCcceEEEEcCCCCCCCCCCcceEEecCCcchHhHHHHH
Q psy12247 22 ARNHPNCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLL 64 (119)
Q Consensus 22 r~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~l 64 (119)
+++|++...|-|-=. ..+=.-.=.-|.||.+|++++++.-+
T Consensus 5 ~enF~g~qLlYigWd--~HllFcap~~~plpP~mpFg~l~~~v 45 (67)
T PF04663_consen 5 VENFHGNQLLYIGWD--DHLLFCAPFAFPLPPDMPFGALVEQV 45 (67)
T ss_dssp GGGGTT-EEEEEE-T--T-TTS-S-EEEEE-TTSBHHHHHHHT
T ss_pred hhhCCCceEEEEEec--CCeeeecceeecCCCCCcHHHHHHHh
Confidence 456666555555321 11212234568899999999997643
No 135
>cd00329 TopoII_MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch
Probab=22.73 E-value=94 Score=19.56 Aligned_cols=27 Identities=19% Similarity=0.243 Sum_probs=17.2
Q ss_pred CCeEEEEEcCeecCCcCch---HHHHHhHh
Q psy12247 73 EEACFFFIESMIVPADSTR---METLSQRF 99 (119)
Q Consensus 73 ~~slfl~Vn~~~~p~~~~~---m~~lY~~~ 99 (119)
.+..|+|||+..+...... +.+.|...
T Consensus 43 ~~~~~~fvN~r~v~~~~~~~~~i~~~~~~~ 72 (107)
T cd00329 43 KDRQFSFVNGRPVREGGTHVKAVREAYTRA 72 (107)
T ss_pred CCcEEEEEcCeEEcCCHHHHHHHHHHHHHH
Confidence 4678999999885434444 44555554
No 136
>PRK07440 hypothetical protein; Provisional
Probab=22.73 E-value=1.8e+02 Score=18.02 Aligned_cols=36 Identities=6% Similarity=0.109 Sum_probs=26.9
Q ss_pred ceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCC
Q psy12247 47 SNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPA 87 (119)
Q Consensus 47 ~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~ 87 (119)
+..-++..+|+.+++. .+++++ +.+-+-+|+.++|.
T Consensus 12 ~~~~~~~~~tl~~lL~----~l~~~~-~~vav~~N~~iv~r 47 (70)
T PRK07440 12 ETRTCSSGTSLPDLLQ----QLGFNP-RLVAVEYNGEILHR 47 (70)
T ss_pred EEEEcCCCCCHHHHHH----HcCCCC-CeEEEEECCEEeCH
Confidence 3456788899998864 556654 58889999999774
No 137
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 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 belong to the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=22.69 E-value=1e+02 Score=24.14 Aligned_cols=31 Identities=16% Similarity=0.381 Sum_probs=25.4
Q ss_pred cCCcchHhHHHHHH--------HhhcCCCCCeEEEEEcC
Q psy12247 52 AYEMTVGHFFYLLR--------KKMALRPEEACFFFIES 82 (119)
Q Consensus 52 p~~~tv~~~~~~lR--------k~l~l~~~~slfl~Vn~ 82 (119)
..+.|..+|+.+|+ +.|...+++.||+|..+
T Consensus 77 g~~v~~~~fl~vL~G~~~~~~~kvl~s~~~D~vfiy~~~ 115 (256)
T PF01650_consen 77 GEDVTPENFLNVLTGDKSVPSGKVLNSTENDNVFIYFTG 115 (256)
T ss_pred ccccCHHHHHHHhcCCCCCCccccccCCCCCeEEEEEec
Confidence 45789999999999 44567889999999874
No 138
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=22.05 E-value=55 Score=20.55 Aligned_cols=39 Identities=13% Similarity=0.169 Sum_probs=26.1
Q ss_pred ceEEecCCcchHhHHHHHHHhh-cCCC-CCeEEEEEcCeec
Q psy12247 47 SNYVVAYEMTVGHFFYLLRKKM-ALRP-EEACFFFIESMIV 85 (119)
Q Consensus 47 ~Kflvp~~~tv~~~~~~lRk~l-~l~~-~~slfl~Vn~~~~ 85 (119)
..+-++...|++++...|..+. .+.. ...+.+.||+..+
T Consensus 21 ~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~~v 61 (82)
T PLN02799 21 MTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYT 61 (82)
T ss_pred EEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEc
Confidence 4455788899999988886543 1111 1245688999884
No 139
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=21.87 E-value=98 Score=24.38 Aligned_cols=101 Identities=8% Similarity=-0.015 Sum_probs=54.1
Q ss_pred CCHHHHHHHHHHHHhcCCCcceEEEEcCCCC--CCCCC-------C-cceEEecCC---cchHhHHHHHHHhhcCCCCCe
Q psy12247 9 YSLEERIKIGENLARNHPNCAFVILERSPSA--LLPQM-------P-RSNYVVAYE---MTVGHFFYLLRKKMALRPEEA 75 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~--~~p~L-------~-k~Kflvp~~---~tv~~~~~~lRk~l~l~~~~s 75 (119)
-|.|||+.-.+...+.-.+++|||+--...+ ++-.+ . .--.++|+. .+-.+++...+.=..-.++-.
T Consensus 51 Lt~eEr~~~~~~~~~~~~~~~pvi~gv~~~~t~~~i~la~~a~~~Gad~v~v~~P~y~~~~~~~i~~yf~~v~~~~~~lp 130 (290)
T TIGR00683 51 LSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSFPEIKHYYDTIIAETGGLN 130 (290)
T ss_pred CCHHHHHHHHHHHHHHhCCCCcEEEecCCCCHHHHHHHHHHHHHhCCCEEEEeCCcCCCCCHHHHHHHHHHHHhhCCCCC
Confidence 4789999998889988889999999764322 10000 0 001122221 123455555544332233467
Q ss_pred EEEEEcCeec--CCcCchHHHHHhHhcCCCCeEEEEeccc
Q psy12247 76 CFFFIESMIV--PADSTRMETLSQRFADKDGLIYMVYSDV 113 (119)
Q Consensus 76 lfl~Vn~~~~--p~~~~~m~~lY~~~kd~DGfLyl~Ys~~ 113 (119)
+++|=+-... +-+.+++.+|- +.+.+..|.+|+.
T Consensus 131 v~lYn~P~~tg~~l~~~~i~~L~----~~pnv~giK~s~~ 166 (290)
T TIGR00683 131 MIVYSIPFLTGVNMGIEQFGELY----KNPKVLGVKFTAG 166 (290)
T ss_pred EEEEeCccccccCcCHHHHHHHh----cCCCEEEEEeCCC
Confidence 8888442221 11223455554 2356777777653
No 140
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=21.68 E-value=1.6e+02 Score=19.72 Aligned_cols=45 Identities=13% Similarity=0.099 Sum_probs=30.1
Q ss_pred EecCCcchHhHHHHHHHhhcCCCCCeEEEEEc-Cee--cCCcCchHHH
Q psy12247 50 VVAYEMTVGHFFYLLRKKMALRPEEACFFFIE-SMI--VPADSTRMET 94 (119)
Q Consensus 50 lvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn-~~~--~p~~~~~m~~ 94 (119)
..++..||+.+...+|+.+.++.+-.|+-+-+ |.+ +..++.|+.+
T Consensus 19 ~FSk~DTI~~v~~~~rklf~i~~E~RLW~~~~~~~~e~L~~~~~Tv~d 66 (88)
T PF14836_consen 19 QFSKTDTIGFVEKEMRKLFNIQEETRLWNKYSENSYELLNNPEITVED 66 (88)
T ss_dssp EE-TTSBHHHHHHHHHHHCT-TS-EEEEEECTTTCEEEE--TTSBTTT
T ss_pred hccccChHHHHHHHHHHHhCCCccceehhccCCcchhhhCCCCccHHH
Confidence 57889999999999999999977778877555 433 2345556644
No 141
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=21.41 E-value=94 Score=20.97 Aligned_cols=28 Identities=18% Similarity=0.214 Sum_probs=17.9
Q ss_pred CCCCCeEEEEEcCeec--CCcCchHHHHHh
Q psy12247 70 LRPEEACFFFIESMIV--PADSTRMETLSQ 97 (119)
Q Consensus 70 l~~~~slfl~Vn~~~~--p~~~~~m~~lY~ 97 (119)
....+..|+|||+..+ +.....+.++|.
T Consensus 36 ~~~~~~q~ifVN~R~V~~~~l~~~I~~~y~ 65 (119)
T PF01119_consen 36 RSSRDRQFIFVNGRPVENKALSKAINEAYR 65 (119)
T ss_dssp BSSCTCEEEEETTEEE--HHHHHHHHHHHH
T ss_pred cCCCCcEEEEeCCCeEeChHHHHHHHHHHh
Confidence 3445789999999884 233344455555
No 142
>cd09001 GH43_XYL_2 Glycosyl hydrolase family 43, beta-D-xylosidase. This glycosyl hydrolase family 43 (GH43) includes mostly enzymes that have been characterized to have beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity. They are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extend
Probab=21.40 E-value=44 Score=25.73 Aligned_cols=15 Identities=40% Similarity=0.736 Sum_probs=12.4
Q ss_pred hcCCCCeEEEEeccc
Q psy12247 99 FADKDGLIYMVYSDV 113 (119)
Q Consensus 99 ~kd~DGfLyl~Ys~~ 113 (119)
|.|+||-.||.|+..
T Consensus 126 f~D~dG~~Yl~~~~~ 140 (269)
T cd09001 126 LFDDDGTAYLVYGGG 140 (269)
T ss_pred EEcCCCCEEEEeCCC
Confidence 467899999999864
No 143
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=20.98 E-value=3.1e+02 Score=19.25 Aligned_cols=62 Identities=6% Similarity=-0.043 Sum_probs=37.1
Q ss_pred cCCHHHHHHHHHHHHhcCCCcceEEEEcCCC---CCC----CCCCcceE--EecCCcchHhHHHHHHHhhc
Q psy12247 8 KYSLEERIKIGENLARNHPNCAFVILERSPS---ALL----PQMPRSNY--VVAYEMTVGHFFYLLRKKMA 69 (119)
Q Consensus 8 ~~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~---~~~----p~L~k~Kf--lvp~~~tv~~~~~~lRk~l~ 69 (119)
.++...=..-.+.++++.+..++|++-=... ++. +.+.+.=| ..+++....+++..||+.++
T Consensus 65 ~~~~~~~~~~~~~L~~~~~~~~~i~vGG~~~~~~~~~~~~~~~l~~~G~~~vf~~~~~~~~i~~~l~~~~~ 135 (137)
T PRK02261 65 GHGEIDCRGLREKCIEAGLGDILLYVGGNLVVGKHDFEEVEKKFKEMGFDRVFPPGTDPEEAIDDLKKDLN 135 (137)
T ss_pred ccCHHHHHHHHHHHHhcCCCCCeEEEECCCCCCccChHHHHHHHHHcCCCEEECcCCCHHHHHHHHHHHhc
Confidence 3444444555677777767778988844321 001 12333222 46777788999999988764
No 144
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=20.89 E-value=1.1e+02 Score=23.94 Aligned_cols=101 Identities=9% Similarity=0.010 Sum_probs=53.9
Q ss_pred cCCHHHHHHHHHHHHhcCCCcceEEEEcCCCC--CC-------CCCC-cceEEecCCc---chHhHHHHHHHhhcCCCCC
Q psy12247 8 KYSLEERIKIGENLARNHPNCAFVILERSPSA--LL-------PQMP-RSNYVVAYEM---TVGHFFYLLRKKMALRPEE 74 (119)
Q Consensus 8 ~~~~e~R~~e~~~ir~kyp~~ipVIvE~~~~~--~~-------p~L~-k~Kflvp~~~---tv~~~~~~lRk~l~l~~~~ 74 (119)
.-|.+||++-.+..++.-++++|||+--...+ ++ -.+. .--.++|+.. +-.+++.+.+.=..-. .-
T Consensus 50 ~ls~~Er~~~~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~G~d~v~~~pP~~~~~~~~~i~~~~~~ia~~~-~~ 128 (292)
T PRK03170 50 TLTHEEHEELIRAVVEAVNGRVPVIAGTGSNSTAEAIELTKFAEKAGADGALVVTPYYNKPTQEGLYQHFKAIAEAT-DL 128 (292)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCcEEeecCCchHHHHHHHHHHHHHcCCCEEEECCCcCCCCCHHHHHHHHHHHHhcC-CC
Confidence 45789999999999998899999998664322 10 0010 0112223322 2234444444332221 35
Q ss_pred eEEEEEcCee--cCCcCchHHHHHhHhcCCCCeEEEEeccc
Q psy12247 75 ACFFFIESMI--VPADSTRMETLSQRFADKDGLIYMVYSDV 113 (119)
Q Consensus 75 slfl~Vn~~~--~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~ 113 (119)
.+++|=+-.. ..-+...+.+| .++ .++..+.+|+.
T Consensus 129 pv~lYn~P~~~g~~l~~~~~~~L-~~~---p~v~giK~s~~ 165 (292)
T PRK03170 129 PIILYNVPGRTGVDILPETVARL-AEH---PNIVGIKEATG 165 (292)
T ss_pred CEEEEECccccCCCCCHHHHHHH-HcC---CCEEEEEECCC
Confidence 7888843111 01123466666 333 56777877654
No 145
>KOG1651|consensus
Probab=20.83 E-value=2.1e+02 Score=21.50 Aligned_cols=41 Identities=12% Similarity=0.313 Sum_probs=29.9
Q ss_pred eEEEEEcC----eecCCcCchHHHHHhHhcCCCCeEEEEeccccccc
Q psy12247 75 ACFFFIES----MIVPADSTRMETLSQRFADKDGLIYMVYSDVNIFV 117 (119)
Q Consensus 75 slfl~Vn~----~~~p~~~~~m~~lY~~~kd~DGfLyl~Ys~~~~fG 117 (119)
.+-|.||= .+.++.=..|.+||++|+ +.||..+.+--.+ ||
T Consensus 35 kV~LiVNVAS~Cg~T~~~Y~~l~~L~~ky~-~~Gl~ILaFPCNQ-Fg 79 (171)
T KOG1651|consen 35 KVVLIVNVASQCGLTESQYTELNELYEKYK-DQGLEILAFPCNQ-FG 79 (171)
T ss_pred eEEEEEEcccccccchhcchhHHHHHHHHh-hCCeEEEEecccc-cc
Confidence 46677772 223555668999999998 6999999986655 44
No 146
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=20.82 E-value=1.7e+02 Score=19.07 Aligned_cols=38 Identities=18% Similarity=0.360 Sum_probs=28.3
Q ss_pred CcceEEecCCcchHhHHHHHHHhhcCCCCCeEEEEEcCeecCC
Q psy12247 45 PRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPA 87 (119)
Q Consensus 45 ~k~Kflvp~~~tv~~~~~~lRk~l~l~~~~slfl~Vn~~~~p~ 87 (119)
.-+.+-++..+|+++++.. +++++ +.+-+-+|+.++|.
T Consensus 24 NG~~~~~~~~~tl~~LL~~----l~~~~-~~vAVevNg~iVpr 61 (84)
T PRK06083 24 NDQSIQVDISSSLAQIIAQ----LSLPE-LGCVFAINNQVVPR 61 (84)
T ss_pred CCeEEEcCCCCcHHHHHHH----cCCCC-ceEEEEECCEEeCH
Confidence 3445677888999988775 46654 57788999999775
No 147
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=20.74 E-value=1.1e+02 Score=24.24 Aligned_cols=28 Identities=11% Similarity=0.036 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHHHhcCCCcceEEEEcC
Q psy12247 9 YSLEERIKIGENLARNHPNCAFVILERS 36 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ipVIvE~~ 36 (119)
-|.|||+.-.+...+.-.+++|||+--.
T Consensus 57 Lt~eEr~~~~~~~~~~~~~~~pvi~gv~ 84 (303)
T PRK03620 57 LTPDEYSQVVRAAVETTAGRVPVIAGAG 84 (303)
T ss_pred CCHHHHHHHHHHHHHHhCCCCcEEEecC
Confidence 4679999999989888899999998554
No 148
>PF08216 CTNNBL: Catenin-beta-like, Arm-motif containing nuclear; InterPro: IPR013180 This domain is found in eukaryotic proteins. A human nuclear protein with this domain (Q8WYA6 from SWISSPROT) is thought to have a role in apoptosis [].
Probab=20.47 E-value=92 Score=21.66 Aligned_cols=20 Identities=25% Similarity=0.408 Sum_probs=17.4
Q ss_pred CCHHHHHHHHHHHHhcCCCc
Q psy12247 9 YSLEERIKIGENLARNHPNC 28 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ 28 (119)
..||.|...-+..|-|||+.
T Consensus 33 l~fek~i~kN~e~R~K~~dd 52 (108)
T PF08216_consen 33 LSFEKRINKNQEMRIKYPDD 52 (108)
T ss_pred HHHHHHHHHhHHHHHhCCCC
Confidence 35899999999999999874
No 149
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=20.12 E-value=1.1e+02 Score=24.02 Aligned_cols=29 Identities=21% Similarity=0.155 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHHHhcCCCcceEEEEcCC
Q psy12247 9 YSLEERIKIGENLARNHPNCAFVILERSP 37 (119)
Q Consensus 9 ~~~e~R~~e~~~ir~kyp~~ipVIvE~~~ 37 (119)
-|.+||..-.+..++.-.+++|||+--..
T Consensus 54 Ls~eEr~~~~~~~~~~~~~~~~viagvg~ 82 (293)
T PRK04147 54 LSTEEKKQVLEIVAEEAKGKVKLIAQVGS 82 (293)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCEEecCCC
Confidence 46799999999999988999999996643
Done!