Query 015999
Match_columns 397
No_of_seqs 320 out of 1497
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 02:52:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015999.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015999hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0011 Nucleotide excision re 100.0 2.2E-88 4.8E-93 651.9 30.6 339 1-395 1-340 (340)
2 TIGR00601 rad23 UV excision re 100.0 1.4E-87 3.1E-92 674.6 33.7 362 1-394 1-378 (378)
3 KOG0010 Ubiquitin-like protein 99.8 3E-18 6.4E-23 174.1 27.9 78 1-82 16-93 (493)
4 cd01807 GDX_N ubiquitin-like d 99.8 2.2E-18 4.7E-23 135.6 9.2 72 1-75 1-72 (74)
5 cd01805 RAD23_N Ubiquitin-like 99.7 1.1E-17 2.5E-22 131.9 10.0 75 1-78 1-77 (77)
6 PF09280 XPC-binding: XPC-bind 99.7 4.4E-18 9.5E-23 128.1 6.6 57 272-328 1-57 (59)
7 cd01797 NIRF_N amino-terminal 99.7 1.1E-17 2.4E-22 133.3 9.1 74 1-77 1-76 (78)
8 cd01793 Fubi Fubi ubiquitin-li 99.7 2.1E-17 4.6E-22 130.0 9.1 73 1-78 1-73 (74)
9 cd01791 Ubl5 UBL5 ubiquitin-li 99.7 1.9E-17 4.1E-22 130.4 8.6 71 1-74 2-72 (73)
10 PTZ00044 ubiquitin; Provisiona 99.7 4.1E-17 8.9E-22 128.5 9.5 74 1-77 1-74 (76)
11 cd01802 AN1_N ubiquitin-like d 99.7 5.5E-17 1.2E-21 136.0 9.4 75 1-78 28-102 (103)
12 cd01804 midnolin_N Ubiquitin-l 99.7 7.6E-17 1.6E-21 128.4 8.9 73 1-77 2-74 (78)
13 cd01806 Nedd8 Nebb8-like ubiq 99.7 2.1E-16 4.5E-21 124.0 10.1 74 1-77 1-74 (76)
14 cd01792 ISG15_repeat1 ISG15 ub 99.7 9.6E-17 2.1E-21 128.3 8.3 74 1-77 3-78 (80)
15 cd01810 ISG15_repeat2 ISG15 ub 99.7 1.3E-16 2.7E-21 125.6 8.6 72 3-77 1-72 (74)
16 cd01803 Ubiquitin Ubiquitin. U 99.7 2.1E-16 4.6E-21 123.9 9.4 74 1-77 1-74 (76)
17 cd01794 DC_UbP_C dendritic cel 99.7 1.2E-16 2.7E-21 124.7 7.8 69 3-74 1-69 (70)
18 cd01798 parkin_N amino-termina 99.7 1.7E-16 3.8E-21 123.4 8.0 70 3-75 1-70 (70)
19 cd01809 Scythe_N Ubiquitin-lik 99.7 3.8E-16 8.2E-21 121.2 9.3 72 1-75 1-72 (72)
20 cd01790 Herp_N Homocysteine-re 99.7 3.2E-16 6.9E-21 124.9 8.1 73 1-74 2-78 (79)
21 cd01808 hPLIC_N Ubiquitin-like 99.7 4.9E-16 1.1E-20 121.2 8.7 71 1-75 1-71 (71)
22 PF00240 ubiquitin: Ubiquitin 99.6 7.8E-16 1.7E-20 118.8 7.9 69 6-77 1-69 (69)
23 cd01813 UBP_N UBP ubiquitin pr 99.6 1.6E-15 3.5E-20 119.7 8.2 70 1-74 1-73 (74)
24 cd01796 DDI1_N DNA damage indu 99.6 3E-15 6.5E-20 117.1 7.6 67 3-72 1-69 (71)
25 KOG0005 Ubiquitin-like protein 99.6 2.6E-15 5.6E-20 111.3 4.9 70 1-73 1-70 (70)
26 cd01812 BAG1_N Ubiquitin-like 99.6 1.1E-14 2.3E-19 112.9 8.3 70 1-74 1-70 (71)
27 cd01800 SF3a120_C Ubiquitin-li 99.5 2.2E-14 4.7E-19 113.6 8.4 68 8-78 5-72 (76)
28 KOG0003 Ubiquitin/60s ribosoma 99.5 4.6E-15 1E-19 122.3 -0.3 76 1-79 1-76 (128)
29 smart00213 UBQ Ubiquitin homol 99.4 3.3E-13 7.2E-18 101.6 7.8 64 1-68 1-64 (64)
30 KOG0004 Ubiquitin/40S ribosoma 99.4 7.2E-14 1.6E-18 122.9 4.7 78 1-81 1-78 (156)
31 cd01763 Sumo Small ubiquitin-r 99.4 6.4E-13 1.4E-17 108.0 9.9 75 1-78 12-86 (87)
32 cd01815 BMSC_UbP_N Ubiquitin-l 99.4 3.4E-13 7.4E-18 106.3 5.4 55 19-74 19-74 (75)
33 cd01814 NTGP5 Ubiquitin-like N 99.3 2.6E-12 5.7E-17 108.0 6.8 78 2-79 6-94 (113)
34 cd01769 UBL Ubiquitin-like dom 99.3 1.2E-11 2.6E-16 94.3 8.0 68 4-74 1-68 (69)
35 cd01799 Hoil1_N Ubiquitin-like 99.3 1.1E-11 2.4E-16 98.1 7.5 65 6-74 8-74 (75)
36 PF11976 Rad60-SLD: Ubiquitin- 99.2 7.6E-11 1.7E-15 91.7 8.1 71 1-74 1-72 (72)
37 cd01795 USP48_C USP ubiquitin- 99.0 6.3E-10 1.4E-14 91.4 7.0 61 12-75 16-77 (107)
38 PF00627 UBA: UBA/TS-N domain; 98.9 2.1E-09 4.6E-14 73.5 5.1 36 167-205 2-37 (37)
39 PF13881 Rad60-SLD_2: Ubiquiti 98.9 8.6E-09 1.9E-13 87.6 9.8 75 2-76 4-89 (111)
40 KOG0001 Ubiquitin and ubiquiti 98.9 1.4E-08 3E-13 77.0 9.5 72 3-77 2-73 (75)
41 KOG4248 Ubiquitin-like protein 98.9 2.8E-09 6E-14 116.5 6.8 70 2-75 4-73 (1143)
42 cd01789 Alp11_N Ubiquitin-like 98.9 1.1E-08 2.4E-13 82.6 8.6 70 2-74 3-80 (84)
43 cd00194 UBA Ubiquitin Associat 98.8 8.2E-09 1.8E-13 70.7 5.3 36 355-390 3-38 (38)
44 PF00627 UBA: UBA/TS-N domain; 98.8 8.2E-09 1.8E-13 70.6 5.0 35 354-388 3-37 (37)
45 PLN02560 enoyl-CoA reductase 98.8 1.3E-08 2.8E-13 100.9 8.6 70 1-72 1-80 (308)
46 smart00165 UBA Ubiquitin assoc 98.7 1.6E-08 3.4E-13 68.9 4.7 36 354-389 2-37 (37)
47 cd00194 UBA Ubiquitin Associat 98.7 3.6E-08 7.9E-13 67.4 5.0 37 168-207 2-38 (38)
48 PF14560 Ubiquitin_2: Ubiquiti 98.7 7.5E-08 1.6E-12 78.0 7.5 71 2-75 3-83 (87)
49 cd01801 Tsc13_N Ubiquitin-like 98.7 7.3E-08 1.6E-12 76.4 7.0 69 2-72 2-74 (77)
50 cd01788 ElonginB Ubiquitin-lik 98.6 1.3E-07 2.8E-12 79.7 7.6 73 1-76 1-81 (119)
51 smart00165 UBA Ubiquitin assoc 98.6 6.3E-08 1.4E-12 65.9 4.7 36 168-206 2-37 (37)
52 cd00196 UBQ Ubiquitin-like pro 98.4 1.6E-06 3.6E-11 62.0 7.8 67 5-74 2-68 (69)
53 PF11543 UN_NPL4: Nuclear pore 98.4 5.9E-07 1.3E-11 72.0 5.5 68 1-72 5-77 (80)
54 cd01811 OASL_repeat1 2'-5' oli 98.3 5E-06 1.1E-10 65.0 8.2 71 1-75 1-76 (80)
55 KOG1872 Ubiquitin-specific pro 98.2 4.6E-06 1E-10 85.4 7.6 71 3-77 6-77 (473)
56 KOG0006 E3 ubiquitin-protein l 98.0 8.6E-06 1.9E-10 79.6 5.9 72 1-75 1-75 (446)
57 KOG3493 Ubiquitin-like protein 97.8 1.1E-05 2.3E-10 61.4 1.7 69 2-73 3-71 (73)
58 TIGR00601 rad23 UV excision re 97.7 5.6E-05 1.2E-09 77.1 5.4 40 354-393 157-196 (378)
59 KOG2561 Adaptor protein NUB1, 97.6 0.00058 1.2E-08 69.9 11.6 58 15-75 54-111 (568)
60 KOG1769 Ubiquitin-like protein 97.4 0.0012 2.6E-08 54.6 9.3 72 2-76 22-93 (99)
61 KOG0944 Ubiquitin-specific pro 97.4 0.00085 1.8E-08 71.7 9.7 38 357-394 639-676 (763)
62 KOG4495 RNA polymerase II tran 97.4 0.00027 5.9E-09 57.9 4.7 62 1-65 1-65 (110)
63 PF10302 DUF2407: DUF2407 ubiq 97.3 0.00056 1.2E-08 56.8 6.4 59 3-62 3-64 (97)
64 KOG4583 Membrane-associated ER 97.3 3.5E-05 7.5E-10 76.0 -1.5 78 2-80 11-92 (391)
65 PF08817 YukD: WXG100 protein 97.1 0.001 2.2E-08 52.9 5.3 71 2-72 4-78 (79)
66 PF00789 UBX: UBX domain; Int 97.0 0.0042 9E-08 49.3 8.3 68 2-72 8-80 (82)
67 smart00166 UBX Domain present 97.0 0.0051 1.1E-07 48.9 8.5 68 2-72 6-78 (80)
68 COG5417 Uncharacterized small 96.8 0.0045 9.8E-08 48.6 6.7 68 5-72 11-80 (81)
69 PF02845 CUE: CUE domain; Int 96.8 0.0022 4.7E-08 44.9 4.3 38 168-208 2-41 (42)
70 PF11470 TUG-UBL1: GLUT4 regul 96.8 0.0052 1.1E-07 47.4 6.7 63 7-72 3-65 (65)
71 KOG1639 Steroid reductase requ 96.8 0.0031 6.8E-08 60.2 6.4 70 1-72 1-76 (297)
72 cd01767 UBX UBX (ubiquitin reg 96.7 0.012 2.7E-07 46.3 8.7 67 2-73 4-75 (77)
73 COG5207 UBP14 Isopeptidase T [ 96.7 0.0019 4E-08 67.3 5.0 43 354-396 559-602 (749)
74 cd01770 p47_UBX p47-like ubiqu 96.6 0.014 3E-07 46.6 8.4 65 2-68 6-73 (79)
75 cd01772 SAKS1_UBX SAKS1-like U 96.6 0.016 3.5E-07 46.1 8.6 67 2-72 6-77 (79)
76 KOG0013 Uncharacterized conser 96.6 0.0041 8.9E-08 58.0 5.6 61 9-72 155-215 (231)
77 KOG0011 Nucleotide excision re 96.4 0.0042 9.1E-08 61.6 5.1 40 355-394 137-176 (340)
78 KOG0944 Ubiquitin-specific pro 96.4 0.0023 5.1E-08 68.4 3.0 43 165-210 633-675 (763)
79 smart00727 STI1 Heat shock cha 96.3 0.0046 1E-07 42.8 3.4 35 275-313 7-41 (41)
80 PF02845 CUE: CUE domain; Int 96.2 0.01 2.2E-07 41.5 4.8 37 355-391 3-41 (42)
81 cd01773 Faf1_like1_UBX Faf1 ik 96.1 0.049 1.1E-06 43.9 8.8 69 2-74 7-80 (82)
82 PF13019 Telomere_Sde2: Telome 96.0 0.049 1.1E-06 49.3 9.1 77 1-80 1-89 (162)
83 KOG0418 Ubiquitin-protein liga 95.9 0.0091 2E-07 54.8 4.3 45 347-391 156-200 (200)
84 PF14555 UBA_4: UBA-like domai 95.9 0.02 4.2E-07 40.3 5.1 40 355-394 2-42 (43)
85 cd01774 Faf1_like2_UBX Faf1 ik 95.9 0.062 1.3E-06 43.5 8.5 68 2-73 6-83 (85)
86 KOG0418 Ubiquitin-protein liga 95.6 0.015 3.4E-07 53.3 4.5 45 161-208 156-200 (200)
87 cd01771 Faf1_UBX Faf1 UBX doma 95.4 0.12 2.6E-06 41.3 8.5 68 2-73 6-78 (80)
88 smart00546 CUE Domain that may 95.3 0.047 1E-06 38.2 5.2 39 167-208 2-42 (43)
89 COG5227 SMT3 Ubiquitin-like pr 95.0 0.097 2.1E-06 42.7 6.6 68 3-73 27-94 (103)
90 KOG3206 Alpha-tubulin folding 94.9 0.064 1.4E-06 50.2 6.3 70 2-74 3-80 (234)
91 smart00546 CUE Domain that may 94.9 0.067 1.5E-06 37.4 4.9 37 355-391 4-42 (43)
92 PF15044 CLU_N: Mitochondrial 94.4 0.067 1.4E-06 42.4 4.4 56 17-74 1-57 (76)
93 PF09288 UBA_3: Fungal ubiquit 93.8 0.05 1.1E-06 40.4 2.4 37 354-390 10-51 (55)
94 PF09288 UBA_3: Fungal ubiquit 93.2 0.097 2.1E-06 38.9 3.1 23 168-193 10-32 (55)
95 PF14453 ThiS-like: ThiS-like 93.2 0.31 6.7E-06 36.6 5.8 56 1-75 1-56 (57)
96 PF11626 Rap1_C: TRF2-interact 93.1 0.12 2.6E-06 41.9 3.8 35 357-391 1-35 (87)
97 KOG0012 DNA damage inducible p 92.6 0.17 3.7E-06 51.0 4.9 69 1-72 1-73 (380)
98 PF11626 Rap1_C: TRF2-interact 92.4 0.23 4.9E-06 40.3 4.5 35 171-208 1-35 (87)
99 PRK06437 hypothetical protein; 92.4 0.95 2.1E-05 34.8 7.8 54 9-74 9-62 (67)
100 PLN02799 Molybdopterin synthas 90.9 0.92 2E-05 35.9 6.6 66 1-73 2-76 (82)
101 cd06409 PB1_MUG70 The MUG70 pr 90.8 2 4.3E-05 35.0 8.4 70 2-74 2-83 (86)
102 KOG0010 Ubiquitin-like protein 90.2 0.44 9.5E-06 50.0 5.1 40 166-208 453-493 (493)
103 PF07499 RuvA_C: RuvA, C-termi 89.7 0.49 1.1E-05 33.8 3.6 37 167-206 3-39 (47)
104 PRK08364 sulfur carrier protei 89.6 2.3 4.9E-05 32.9 7.6 53 9-73 10-64 (70)
105 PF09379 FERM_N: FERM N-termin 89.0 2.4 5.1E-05 33.0 7.5 67 5-74 1-74 (80)
106 PRK06488 sulfur carrier protei 89.0 1.7 3.6E-05 32.9 6.4 60 1-74 1-60 (65)
107 cd06406 PB1_P67 A PB1 domain i 88.7 1.4 3E-05 35.4 5.9 37 12-51 12-48 (80)
108 cd00754 MoaD Ubiquitin domain 88.7 2 4.4E-05 33.3 6.8 57 12-73 17-74 (80)
109 PF14836 Ubiquitin_3: Ubiquiti 88.6 2.5 5.5E-05 34.5 7.4 62 11-76 14-81 (88)
110 PF06972 DUF1296: Protein of u 88.5 1.3 2.8E-05 33.4 5.2 40 167-207 5-44 (60)
111 PF10209 DUF2340: Uncharacteri 87.1 2.3 5.1E-05 36.7 6.6 60 16-75 21-108 (122)
112 PF10790 DUF2604: Protein of U 87.0 2.9 6.3E-05 32.2 6.3 67 9-75 4-71 (76)
113 PF11547 E3_UbLigase_EDD: E3 u 86.6 1.4 3.1E-05 31.8 4.3 28 364-391 22-49 (53)
114 PF12754 Blt1: Cell-cycle cont 86.6 0.21 4.5E-06 49.6 0.0 59 2-63 80-158 (309)
115 KOG2561 Adaptor protein NUB1, 86.5 0.85 1.8E-05 47.4 4.3 41 168-211 430-470 (568)
116 cd07922 CarBa CarBa is the A s 84.5 7.2 0.00016 31.4 7.9 59 296-378 7-70 (81)
117 smart00295 B41 Band 4.1 homolo 83.4 11 0.00023 34.2 9.8 69 2-73 5-81 (207)
118 TIGR01682 moaD molybdopterin c 83.1 6.6 0.00014 30.8 7.3 58 10-73 14-74 (80)
119 PF14555 UBA_4: UBA-like domai 82.9 3.6 7.8E-05 28.7 5.0 36 168-206 1-37 (43)
120 PRK05863 sulfur carrier protei 81.7 5.3 0.00011 30.3 5.9 60 1-74 1-60 (65)
121 smart00666 PB1 PB1 domain. Pho 81.5 7 0.00015 30.4 6.8 45 2-50 3-47 (81)
122 PF11620 GABP-alpha: GA-bindin 81.3 4.2 9.2E-05 33.0 5.4 63 12-77 4-66 (88)
123 KOG2086 Protein tyrosine phosp 80.9 2.8 6E-05 42.9 5.3 67 2-70 307-376 (380)
124 PF02597 ThiS: ThiS family; I 80.6 5 0.00011 30.7 5.6 60 12-74 13-72 (77)
125 PF08938 HBS1_N: HBS1 N-termin 80.6 1.2 2.7E-05 35.3 2.2 45 347-391 18-70 (79)
126 cd06407 PB1_NLP A PB1 domain i 80.4 7.1 0.00015 31.3 6.5 70 1-74 1-80 (82)
127 PF08938 HBS1_N: HBS1 N-termin 80.1 1.1 2.3E-05 35.7 1.7 27 182-208 43-70 (79)
128 PRK05659 sulfur carrier protei 79.0 9.4 0.0002 28.7 6.6 61 1-74 1-61 (66)
129 TIGR01687 moaD_arch MoaD famil 78.9 9.8 0.00021 30.2 7.0 58 12-73 17-82 (88)
130 COG5207 UBP14 Isopeptidase T [ 78.8 2.8 6E-05 44.5 4.6 39 168-209 559-598 (749)
131 cd01760 RBD Ubiquitin-like dom 78.5 6.2 0.00013 31.0 5.5 64 3-72 2-69 (72)
132 PF11069 DUF2870: Protein of u 78.0 3.4 7.3E-05 34.4 4.0 33 45-78 3-35 (98)
133 cd06408 PB1_NoxR The PB1 domai 77.4 9.8 0.00021 31.0 6.5 46 2-51 2-48 (86)
134 smart00455 RBD Raf-like Ras-bi 77.2 8.5 0.00019 29.9 5.9 51 3-56 2-54 (70)
135 TIGR00264 alpha-NAC-related pr 76.7 5.6 0.00012 34.2 5.1 39 348-389 76-115 (116)
136 PRK08053 sulfur carrier protei 76.2 15 0.00033 27.8 7.0 61 1-74 1-61 (66)
137 PRK06944 sulfur carrier protei 74.6 19 0.00041 26.8 7.2 60 1-74 1-60 (65)
138 COG5100 NPL4 Nuclear pore prot 73.0 13 0.00027 38.5 7.3 73 1-75 1-79 (571)
139 PRK06369 nac nascent polypepti 73.0 7.8 0.00017 33.3 5.1 40 348-390 74-114 (115)
140 PF12616 DUF3775: Protein of u 72.0 5.1 0.00011 31.8 3.5 40 170-210 20-60 (75)
141 PRK06083 sulfur carrier protei 70.7 15 0.00032 29.7 6.0 57 8-74 23-79 (84)
142 cd00565 ThiS ThiaminS ubiquiti 70.6 16 0.00035 27.5 5.9 57 8-74 4-60 (65)
143 PF14732 UAE_UbL: Ubiquitin/SU 70.3 8.5 0.00018 31.2 4.6 52 19-73 7-67 (87)
144 KOG2982 Uncharacterized conser 69.6 5 0.00011 40.3 3.6 54 17-73 354-415 (418)
145 PF06972 DUF1296: Protein of u 69.5 17 0.00037 27.5 5.6 38 354-391 6-45 (60)
146 PF08337 Plexin_cytopl: Plexin 69.2 14 0.00031 39.7 7.2 65 11-76 202-290 (539)
147 PRK07696 sulfur carrier protei 68.8 22 0.00048 27.1 6.4 61 1-74 1-62 (67)
148 smart00727 STI1 Heat shock cha 67.9 9.3 0.0002 26.0 3.7 32 284-318 4-36 (41)
149 COG2104 ThiS Sulfur transfer p 67.9 28 0.0006 27.0 6.7 63 1-74 1-63 (68)
150 PF02954 HTH_8: Bacterial regu 67.7 4.7 0.0001 27.9 2.2 24 365-388 5-28 (42)
151 cd05992 PB1 The PB1 domain is 67.0 22 0.00047 27.4 6.2 45 2-50 2-47 (81)
152 PF10407 Cytokin_check_N: Cdc1 66.5 18 0.00038 28.6 5.4 62 11-75 3-70 (73)
153 TIGR02958 sec_mycoba_snm4 secr 66.4 33 0.00072 36.2 9.2 72 2-74 4-79 (452)
154 PF08587 UBA_2: Ubiquitin asso 66.3 1.2 2.6E-05 32.0 -1.0 21 170-193 5-26 (46)
155 PRK07440 hypothetical protein; 66.3 27 0.00058 27.0 6.5 57 8-74 9-65 (70)
156 PF00564 PB1: PB1 domain; Int 65.7 21 0.00045 27.7 5.9 44 3-50 4-48 (84)
157 PF02196 RBD: Raf-like Ras-bin 63.6 39 0.00084 26.2 6.9 56 3-61 3-60 (71)
158 PF14533 USP7_C2: Ubiquitin-sp 63.0 30 0.00065 32.6 7.4 48 12-62 35-90 (213)
159 PF07746 LigA: Aromatic-ring-o 62.0 26 0.00057 28.6 5.9 45 295-364 1-50 (88)
160 PF07499 RuvA_C: RuvA, C-termi 61.7 6.6 0.00014 27.9 2.1 24 355-378 5-28 (47)
161 PF14451 Ub-Mut7C: Mut7-C ubiq 61.5 32 0.0007 27.5 6.2 52 10-73 22-74 (81)
162 cd01611 GABARAP Ubiquitin doma 61.4 47 0.001 28.2 7.6 59 15-76 45-107 (112)
163 PF07223 DUF1421: Protein of u 61.0 9.1 0.0002 39.1 3.7 30 160-192 314-343 (358)
164 KOG4250 TANK binding protein k 60.8 26 0.00055 38.8 7.2 42 9-53 323-364 (732)
165 cd01787 GRB7_RA RA (RAS-associ 60.3 55 0.0012 26.6 7.4 66 3-70 5-80 (85)
166 TIGR01683 thiS thiamine biosyn 60.0 35 0.00075 25.6 5.9 57 8-74 3-59 (64)
167 PRK11840 bifunctional sulfur c 60.0 25 0.00055 35.5 6.6 64 1-77 1-64 (326)
168 PRK06369 nac nascent polypepti 59.6 21 0.00045 30.7 5.1 38 168-208 77-115 (115)
169 PF13556 HTH_30: PucR C-termin 59.3 10 0.00022 28.1 2.9 23 369-391 3-25 (59)
170 PRK12332 tsf elongation factor 59.2 16 0.00034 34.3 4.7 36 169-207 6-42 (198)
171 cd01768 RA RA (Ras-associating 59.1 85 0.0018 24.6 8.7 66 10-76 12-86 (87)
172 smart00144 PI3K_rbd PI3-kinase 59.1 60 0.0013 27.2 7.8 74 3-76 20-105 (108)
173 TIGR00116 tsf translation elon 57.2 16 0.00035 36.2 4.7 36 169-207 6-42 (290)
174 cd06411 PB1_p51 The PB1 domain 57.1 40 0.00088 27.0 6.0 35 12-49 8-42 (78)
175 PF02954 HTH_8: Bacterial regu 57.0 10 0.00022 26.2 2.3 27 182-210 5-31 (42)
176 COG1308 EGD2 Transcription fac 56.8 24 0.00052 30.6 5.0 39 348-389 82-121 (122)
177 PF09280 XPC-binding: XPC-bind 56.0 9.1 0.0002 28.9 2.1 23 274-296 16-40 (59)
178 PTZ00380 microtubule-associate 55.7 31 0.00067 29.9 5.5 57 16-75 46-105 (121)
179 KOG2507 Ubiquitin regulatory p 55.4 21 0.00045 37.3 5.1 74 2-78 316-394 (506)
180 PF00788 RA: Ras association ( 53.8 1E+02 0.0023 23.9 8.2 52 3-57 5-68 (93)
181 KOG1364 Predicted ubiquitin re 53.2 15 0.00032 37.3 3.7 66 2-69 279-349 (356)
182 cd06398 PB1_Joka2 The PB1 doma 52.8 73 0.0016 26.1 7.1 70 3-76 3-88 (91)
183 cd01612 APG12_C Ubiquitin-like 52.1 1.2E+02 0.0026 24.6 8.2 60 14-76 19-82 (87)
184 PF00794 PI3K_rbd: PI3-kinase 51.5 61 0.0013 26.7 6.7 75 2-76 18-103 (106)
185 KOG3391 Transcriptional co-rep 51.4 16 0.00034 32.3 3.1 30 51-80 112-141 (151)
186 PF08825 E2_bind: E2 binding d 50.9 23 0.0005 28.6 3.8 58 15-73 1-69 (84)
187 PRK09377 tsf elongation factor 50.9 24 0.00052 35.1 4.7 36 169-207 7-43 (290)
188 CHL00098 tsf elongation factor 50.6 26 0.00056 33.0 4.7 36 169-207 3-39 (200)
189 KOG2689 Predicted ubiquitin re 50.5 48 0.001 32.7 6.5 68 2-72 212-284 (290)
190 PF02991 Atg8: Autophagy prote 48.6 70 0.0015 26.9 6.5 56 17-75 39-98 (104)
191 cd06396 PB1_NBR1 The PB1 domai 48.5 74 0.0016 25.6 6.3 39 2-46 2-42 (81)
192 cd06410 PB1_UP2 Uncharacterize 47.8 66 0.0014 26.7 6.2 40 5-48 17-56 (97)
193 PF15652 Tox-SHH: HNH/Endo VII 47.6 24 0.00052 29.5 3.5 31 163-196 67-97 (100)
194 PRK13901 ruvA Holliday junctio 47.5 25 0.00055 32.9 4.1 31 165-198 142-172 (196)
195 cd07921 PCA_45_Doxase_A_like S 47.3 58 0.0013 27.6 5.8 45 295-364 16-65 (106)
196 PRK11130 moaD molybdopterin sy 47.1 1.2E+02 0.0025 23.8 7.4 54 15-73 19-75 (81)
197 cd07321 Extradiol_Dioxygenase_ 46.9 45 0.00098 26.4 4.9 41 304-367 13-58 (77)
198 TIGR00264 alpha-NAC-related pr 46.9 41 0.00088 29.0 4.8 36 168-206 79-115 (116)
199 cd01764 Urm1 Urm1-like ubuitin 46.6 66 0.0014 26.3 6.0 54 15-73 23-88 (94)
200 PLN03196 MOC1-like protein; Pr 46.0 1.8E+02 0.0039 31.0 10.7 49 344-392 330-386 (487)
201 TIGR00084 ruvA Holliday juncti 44.1 26 0.00057 32.5 3.6 30 165-197 145-174 (191)
202 PF12053 DUF3534: Domain of un 43.9 1.1E+02 0.0024 27.3 7.3 74 1-76 1-81 (145)
203 PF02017 CIDE-N: CIDE-N domain 41.3 66 0.0014 25.7 4.9 62 4-73 6-70 (78)
204 PF06234 TmoB: Toluene-4-monoo 41.2 91 0.002 25.4 5.8 63 13-75 17-84 (85)
205 PF12436 USP7_ICP0_bdg: ICP0-b 40.9 41 0.00089 32.4 4.5 70 3-75 71-152 (249)
206 KOG2689 Predicted ubiquitin re 40.6 43 0.00094 33.0 4.6 35 172-209 5-41 (290)
207 cd01817 RGS12_RBD Ubiquitin do 40.2 1.1E+02 0.0024 24.2 5.9 49 5-56 4-54 (73)
208 PF08783 DWNN: DWNN domain; I 40.0 63 0.0014 25.5 4.6 32 4-35 2-35 (74)
209 KOG3439 Protein conjugation fa 38.8 84 0.0018 26.9 5.4 61 11-74 45-109 (116)
210 PRK14602 ruvA Holliday junctio 37.8 39 0.00084 31.7 3.7 28 165-195 153-180 (203)
211 PRK08769 DNA polymerase III su 36.5 66 0.0014 32.3 5.4 42 164-208 171-212 (319)
212 KOG1071 Mitochondrial translat 36.5 55 0.0012 33.0 4.6 39 352-390 45-84 (340)
213 PLN03196 MOC1-like protein; Pr 36.4 83 0.0018 33.5 6.3 36 283-318 140-186 (487)
214 PF14551 MCM_N: MCM N-terminal 35.6 11 0.00024 31.3 -0.3 54 273-326 7-64 (121)
215 PF07862 Nif11: Nitrogen fixat 35.0 62 0.0013 22.9 3.6 30 296-326 7-38 (49)
216 COG0632 RuvA Holliday junction 34.7 44 0.00095 31.5 3.5 36 165-203 154-190 (201)
217 TIGR03260 met_CoM_red_D methyl 34.5 66 0.0014 28.9 4.4 43 13-62 76-118 (150)
218 PRK01777 hypothetical protein; 33.3 1.9E+02 0.0041 23.9 6.7 62 1-74 4-75 (95)
219 cd07923 Gallate_dioxygenase_C 33.2 1.5E+02 0.0031 24.7 5.9 45 295-364 8-57 (94)
220 KOG4248 Ubiquitin-like protein 32.7 29 0.00063 39.9 2.3 66 6-74 330-395 (1143)
221 PRK14606 ruvA Holliday junctio 32.3 56 0.0012 30.3 3.8 28 166-196 142-169 (188)
222 PF00276 Ribosomal_L23: Riboso 31.5 86 0.0019 25.5 4.3 41 11-54 21-62 (91)
223 PRK14604 ruvA Holliday junctio 31.4 55 0.0012 30.6 3.6 28 167-197 149-176 (195)
224 smart00266 CAD Domains present 30.8 1.5E+02 0.0033 23.5 5.4 48 21-73 19-68 (74)
225 PRK14600 ruvA Holliday junctio 30.4 59 0.0013 30.1 3.6 27 166-195 144-170 (186)
226 PRK07993 DNA polymerase III su 30.4 95 0.0021 31.3 5.4 39 167-208 169-208 (334)
227 COG5272 UBI4 Ubiquitin [Posttr 30.3 15 0.00032 27.2 -0.4 46 348-394 7-52 (57)
228 PRK05738 rplW 50S ribosomal pr 30.2 1.2E+02 0.0026 24.8 5.0 41 10-53 20-61 (92)
229 cd06539 CIDE_N_A CIDE_N domain 29.9 1.4E+02 0.0031 23.9 5.1 48 21-73 21-70 (78)
230 PF13936 HTH_38: Helix-turn-he 29.7 35 0.00076 23.8 1.5 22 348-369 4-25 (44)
231 cd01775 CYR1_RA Ubiquitin doma 29.2 2E+02 0.0042 24.1 6.0 67 4-73 6-85 (97)
232 PRK14601 ruvA Holliday junctio 29.1 64 0.0014 29.9 3.6 26 166-194 141-166 (183)
233 PF11212 DUF2999: Protein of u 29.0 57 0.0012 25.8 2.7 24 280-303 45-68 (82)
234 PF02824 TGS: TGS domain; Int 28.9 1.4E+02 0.0031 22.1 4.8 59 3-73 1-59 (60)
235 PF03474 DMA: DMRTA motif; In 28.7 1.1E+02 0.0023 21.4 3.7 24 366-389 16-39 (39)
236 PF14847 Ras_bdg_2: Ras-bindin 28.7 1.5E+02 0.0032 25.0 5.4 57 3-62 3-70 (105)
237 PF09722 DUF2384: Protein of u 28.2 1.3E+02 0.0028 21.5 4.5 20 189-208 2-21 (54)
238 PRK14603 ruvA Holliday junctio 27.9 76 0.0017 29.6 3.9 27 166-195 151-177 (197)
239 cd01615 CIDE_N CIDE_N domain, 27.8 1.7E+02 0.0037 23.4 5.3 48 21-73 21-70 (78)
240 PF11816 DUF3337: Domain of un 27.1 2E+02 0.0042 29.0 7.0 64 14-77 251-329 (331)
241 COG3760 Uncharacterized conser 27.0 94 0.002 28.0 4.0 58 2-72 47-104 (164)
242 PF02505 MCR_D: Methyl-coenzym 26.4 1.2E+02 0.0026 27.4 4.6 43 13-62 77-120 (153)
243 KOG0943 Predicted ubiquitin-pr 25.9 1.7E+02 0.0036 35.1 6.5 44 351-395 189-233 (3015)
244 KOG0514 Ankyrin repeat protein 25.8 64 0.0014 33.3 3.1 34 350-383 316-368 (452)
245 PHA01748 hypothetical protein 25.6 1.2E+02 0.0026 22.7 3.9 31 346-376 6-37 (60)
246 PF14848 HU-DNA_bdg: DNA-bindi 25.5 1.5E+02 0.0032 25.4 5.0 40 167-212 31-72 (124)
247 PF14689 SPOB_a: Sensor_kinase 25.2 75 0.0016 23.8 2.8 20 169-206 28-47 (62)
248 PRK09814 beta-1,6-galactofuran 23.9 85 0.0018 31.0 3.7 38 173-212 208-264 (333)
249 KOG2019 Metalloendoprotease HM 23.7 2E+02 0.0043 32.4 6.4 40 268-307 445-485 (998)
250 PF14483 Cut8_M: Cut8 dimerisa 23.6 66 0.0014 22.1 2.0 23 292-314 12-34 (38)
251 PF14533 USP7_C2: Ubiquitin-sp 23.6 67 0.0015 30.2 2.7 50 10-62 132-193 (213)
252 PF09469 Cobl: Cordon-bleu ubi 23.4 70 0.0015 25.6 2.3 42 29-76 2-46 (79)
253 PF03671 Ufm1: Ubiquitin fold 23.4 3.7E+02 0.008 21.3 6.2 57 14-73 19-76 (76)
254 PF09030 Creb_binding: Creb bi 23.3 61 0.0013 27.3 2.1 22 280-301 71-92 (104)
255 COG0264 Tsf Translation elonga 23.1 1.3E+02 0.0028 30.0 4.7 36 169-206 7-42 (296)
256 PF11834 DUF3354: Domain of un 22.6 1E+02 0.0023 24.0 3.1 43 21-73 26-69 (69)
257 PF06755 DUF1219: Protein of u 22.5 87 0.0019 26.7 2.8 28 364-391 42-69 (114)
258 PF04126 Cyclophil_like: Cyclo 22.4 51 0.0011 28.2 1.5 29 1-30 1-29 (120)
259 COG0089 RplW Ribosomal protein 22.1 1.8E+02 0.0038 24.2 4.6 60 10-72 21-90 (94)
260 PF11333 DUF3135: Protein of u 21.7 65 0.0014 26.0 1.9 26 277-302 2-27 (83)
261 PF03931 Skp1_POZ: Skp1 family 21.6 68 0.0015 23.9 1.9 32 1-32 1-32 (62)
262 TIGR01446 DnaD_dom DnaD and ph 21.4 92 0.002 23.6 2.7 32 348-379 12-44 (73)
263 KOG4147 Uncharacterized conser 20.8 2E+02 0.0042 24.7 4.6 59 16-74 28-112 (127)
264 KOG4598 Putative ubiquitin-spe 20.7 1.6E+02 0.0035 33.0 5.1 59 12-75 878-942 (1203)
265 PF04110 APG12: Ubiquitin-like 20.6 2.9E+02 0.0063 22.5 5.4 70 3-75 4-81 (87)
266 PF14807 AP4E_app_platf: Adapt 20.4 2.4E+02 0.0052 23.7 5.1 63 13-76 23-86 (104)
267 PF12436 USP7_ICP0_bdg: ICP0-b 20.2 1.7E+02 0.0038 28.1 4.9 43 2-47 178-223 (249)
268 cd06397 PB1_UP1 Uncharacterize 20.2 3.5E+02 0.0076 21.9 5.7 57 2-62 2-63 (82)
No 1
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=100.00 E-value=2.2e-88 Score=651.88 Aligned_cols=339 Identities=55% Similarity=0.810 Sum_probs=271.0
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecCCC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVIRF 80 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~~~ 80 (397)
|+|+||++++.+|+++|.+++||.++|++|+...|.+ +|+++|||||+||+|+|+++|++|+|+++++|+||++|+|..
T Consensus 1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~d-yP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~k~~ 79 (340)
T KOG0011|consen 1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPD-YPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKDKSA 79 (340)
T ss_pred CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCC-CchhhheeeecceeccCCcchhhhccccCceEEEEEecCccc
Confidence 8999999999999999999999999999999999988 999999999999999999999999999999999999998831
Q ss_pred CCCCCCcccccCCCCCccccccCCCCCchhhHHHHhhhhhhccccchhhHHHHHHHHHHHHHHhhccCCCCccccccccc
Q 015999 81 HQVGPQLFQLHQQIRPKLQVLRLLPRHNQRLHLRLLHQLWHRHNLSLNLLLLLLLLLLLLLLLLLQLHSVSDVYGQAASN 160 (397)
Q Consensus 81 ~~~~~~~~~~~~~~~p~~~~~a~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~s~ 160 (397)
.+..++.+. +..+-| ..+.+|+.+.. . .. .++ ++ ..++..+.++.++|+
T Consensus 80 ~t~~ap~s~-~~~~~p---~~~~ap~~s~a------------~-~~-s~~-~~------------~~~~~~~~~~~aas~ 128 (340)
T KOG0011|consen 80 STQVAPQSS-AATHLP---KAAEAPPSSAA------------E-DA-SPA-TP------------AQTSQEDTYEIAAST 128 (340)
T ss_pred ccCCCCCCc-cccCCC---ccCCCCCcccc------------c-cC-CCC-cc------------ccccccchhhhhhhh
Confidence 111110000 000000 11111111110 0 00 000 00 011234456778899
Q ss_pred ccCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHcCCCCCCCCCccccccCCCCCCCCCCccccCCCC
Q 015999 161 LVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQPA 240 (397)
Q Consensus 161 l~~g~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~GIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (397)
|++|+++|.+|.+||+|| |+||+|+|||||||||||||||||++|||++...+.+...++..
T Consensus 129 Lv~G~~~e~~V~~Im~MG---y~re~V~~AlRAafNNPeRAVEYLl~GIP~~~~~~~~~~~~~~~--------------- 190 (340)
T KOG0011|consen 129 LVVGSEYEQTVQQIMEMG---YDREEVERALRAAFNNPERAVEYLLNGIPEDAEVPEPEKSTAAA--------------- 190 (340)
T ss_pred hhccchhHHHHHHHHHhC---ccHHHHHHHHHHhhCChhhhHHHHhcCCcccccCCcccCCcccC---------------
Confidence 999999999999999999 99999999999999999999999999999987666643211100
Q ss_pred CCCCCCCCCCCCCCCcCCCCCCCCCCCCCCchHHhhccHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHhHHHH
Q 015999 241 APAPTSGPNANPLDLFPQGLPNMGSNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDF 320 (397)
Q Consensus 241 ~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~l~~L~~~P~f~~lrq~vq~NP~ll~~~Lqqi~~~nP~l~~~I~~n~~~F 320 (397)
...++ +.+|.++|++++.... |+++|+|||++|+|++||++|++||++|+++||+|+++||+|+++|++||++|
T Consensus 191 ~~~p~---~~~p~~~~~~~~~~~~---~~~~l~fLr~~~qf~~lR~~iqqNP~ll~~~Lqqlg~~nP~L~q~Iq~nqe~F 264 (340)
T KOG0011|consen 191 AELPA---NAQPLDLFPQGAVEAS---GGDPLEFLRNQPQFQQLRQMIQQNPELLHPLLQQLGKQNPQLLQLIQENQEAF 264 (340)
T ss_pred CCCCC---CCChhhcCCccchhhh---cCCchhhhhccHHHHHHHHHHhhCHHHHHHHHHHHhhhCHHHHHHHHHHHHHH
Confidence 00011 3356788988665543 34899999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCCCCcccccccccCC-CcccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015999 321 LRLINEPVEGGEGNVLGQLASAMP-QAVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEF 395 (397)
Q Consensus 321 l~~l~~~~~~~~g~~~~~~~~~~~-~~~~lt~Ee~~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~~~~d~ 395 (397)
|+||+++.+++++++.++.+..++ ..|++||||+++|+||++|||+|..|||||||||||||+||||||+++|||
T Consensus 265 l~mlnep~~~~~~~~~~~~~~~~~~~~I~vtpee~eAIeRL~alGF~ralViqayfACdKNEelAAN~Ll~~~f~d 340 (340)
T KOG0011|consen 265 LQLLNEPVEGGDGGGTGAPAAEGPGHQIQVTPEEKEAIERLEALGFPRALVIQAYFACDKNEELAANYLLSHSFED 340 (340)
T ss_pred HHHhhcccccccccccccccccCCcceEecCHHHHHHHHHHHHhCCcHHHHHHHHHhcCccHHHHHHHHHhhccCC
Confidence 999999988766666676666665 689999999999999999999999999999999999999999999998543
No 2
>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=100.00 E-value=1.4e-87 Score=674.58 Aligned_cols=362 Identities=41% Similarity=0.623 Sum_probs=255.4
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecCCC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVIRF 80 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~~~ 80 (397)
|+|+||+++|++|.|+|++++||.+||++|+.+.|++.+++++|||||+||+|+|+++|++|+|+++++|+||++|+|..
T Consensus 1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k~k~~ 80 (378)
T TIGR00601 1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSKPKTG 80 (378)
T ss_pred CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEeccCCCC
Confidence 89999999999999999999999999999999987555899999999999999999999999999999999999988764
Q ss_pred CCCCCCcc-cccCCCCCccccccCCCCCchhhHHHHhhhhhhccccchhhHHHHHHHHHHH-HHHhhccCCCCccccccc
Q 015999 81 HQVGPQLF-QLHQQIRPKLQVLRLLPRHNQRLHLRLLHQLWHRHNLSLNLLLLLLLLLLLL-LLLLLQLHSVSDVYGQAA 158 (397)
Q Consensus 81 ~~~~~~~~-~~~~~~~p~~~~~a~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~-~~~~~~~~~~~~~~~~~~ 158 (397)
.+.+++++ .+.+++.++.+.++ +|...+. .+.++..+..++. ...++ +....++.........+.
T Consensus 81 ~~~~~~~~~~~~~~p~~~~~~~~-~~~~~~~-----------~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 147 (378)
T TIGR00601 81 TGKSAPPAATPTSAPTPTPSPPA-SPASGMS-----------AAPASAVEEKSPS-EESATATAPESPSTSVPSSGSDAA 147 (378)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCC-CCCCCCC-----------CCCCCCCcccccc-CCCCCCCCCCCCCccccccCCCcc
Confidence 32221111 11011111100000 0100000 0000000000000 00000 000000000000011457
Q ss_pred ccccCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHcCCCCCCCCCccccccCCCCCCCCCCccccCC
Q 015999 159 SNLVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQTAVPPVARASAGGQAGNPPAQTQAQQ 238 (397)
Q Consensus 159 s~l~~g~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~GIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (397)
|+||+|+++|++|++||+|| |+|++|+|||||||||||||||||++|||++++...+. .. +... .
T Consensus 148 s~l~~g~~~e~~I~~i~eMG---f~R~qV~~ALRAafNNPdRAVEYL~tGIP~~~~~~~~~----~~----~~~~-~--- 212 (378)
T TIGR00601 148 STLVVGSERETTIEEIMEMG---YEREEVERALRAAFNNPDRAVEYLLTGIPEDPEQPEPV----QQ----TAAS-T--- 212 (378)
T ss_pred cccccchHHHHHHHHHHHhC---CCHHHHHHHHHHHhCCHHHHHHHHHhCCCccccccccC----CC----cccc-c---
Confidence 89999999999999999999 99999999999999999999999999999886521111 00 1000 0
Q ss_pred CCCCCCCCCCCCCCCCCcCCCCCCCC------CCCCCCchHHhhccHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHH
Q 015999 239 PAAPAPTSGPNANPLDLFPQGLPNMG------SNAGAGTLDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRL 312 (397)
Q Consensus 239 ~~~~~~~~~~~~~~~~lf~~~~~~~~------~~~~~~~l~~L~~~P~f~~lrq~vq~NP~ll~~~Lqqi~~~nP~l~~~ 312 (397)
. ....+....+ |||++++.++. .+.|+++|+|||++|+|++||++||+||++|+++||+|+++||+|+++
T Consensus 213 --~-~~~~~~~~~~-~lf~~a~~~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLqql~~~nP~l~q~ 288 (378)
T TIGR00601 213 --A-AATTETPQHG-SVFEQAAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQQIGQENPQLLQQ 288 (378)
T ss_pred --c-cccCCCCCCc-chhhhhhcccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHHHHHhhCHHHHHH
Confidence 0 0111122223 89998764331 112456899999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHhcCCCCC--CCCccc---ccccc-cCCC--cccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHH
Q 015999 313 IQEHQTDFLRLINEPVEG--GEGNVL---GQLAS-AMPQ--AVTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELA 384 (397)
Q Consensus 313 I~~n~~~Fl~~l~~~~~~--~~g~~~---~~~~~-~~~~--~~~lt~Ee~~ai~rL~~lGF~r~~~iqAy~ac~kne~~A 384 (397)
|++||++||+||+++... ++++.. +.... ..+. .|+||+||+++|+|||+|||+|++|||||||||||||+|
T Consensus 289 I~~n~e~Fl~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~lT~eE~~AIeRL~~LGF~r~~viqaY~ACdKNEelA 368 (378)
T TIGR00601 289 ISQHPEQFLQMLNEPVGELAGESDMEGGVGAIAEAGLPQMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFACDKNEELA 368 (378)
T ss_pred HHHCHHHHHHHhcCcccccccccccccccccccccCcccccccccCHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHH
Confidence 999999999999998522 111111 11111 1112 589999999999999999999999999999999999999
Q ss_pred HHHHhccCCC
Q 015999 385 ANYLLDHMHE 394 (397)
Q Consensus 385 an~L~~~~~d 394 (397)
|||||++.+|
T Consensus 369 An~Lf~~~~~ 378 (378)
T TIGR00601 369 ANYLLSQNFD 378 (378)
T ss_pred HHHHHhhcCC
Confidence 9999999776
No 3
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=99.83 E-value=3e-18 Score=174.14 Aligned_cols=78 Identities=29% Similarity=0.418 Sum_probs=72.2
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecCCC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVIRF 80 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~~~ 80 (397)
++|+||+.++ ++.|.|..+.||.+||++|...++ +++++++|||.||+|+|++||..|||++|.|||||++....+
T Consensus 16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~---a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~~~~ 91 (493)
T KOG0010|consen 16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFG---APPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQPRP 91 (493)
T ss_pred eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcC---CChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccCCCC
Confidence 5799999988 899999999999999999999999 999999999999999999999999999999999999876554
Q ss_pred CC
Q 015999 81 HQ 82 (397)
Q Consensus 81 ~~ 82 (397)
..
T Consensus 92 ~~ 93 (493)
T KOG0010|consen 92 TG 93 (493)
T ss_pred CC
Confidence 44
No 4
>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=99.76 E-value=2.2e-18 Score=135.61 Aligned_cols=72 Identities=28% Similarity=0.411 Sum_probs=70.6
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
|+|+||+++|+++.++|++++||.+||++|+++.| +|+++|||+|+||.|+|+.+|++|||+++++|||+++
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~g---i~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~ 72 (74)
T cd01807 1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLN---VPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVR 72 (74)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEc
Confidence 89999999999999999999999999999999999 9999999999999999999999999999999999986
No 5
>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=99.74 E-value=1.1e-17 Score=131.95 Aligned_cols=75 Identities=53% Similarity=0.757 Sum_probs=72.3
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCC--CCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVY--PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVI 78 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~i--p~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~ 78 (397)
|+|+||+++|+++.++|++++||.+||++|++..| + ++++|||+|+|++|+|+.+|++|||++|++|++++++++
T Consensus 1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~---i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~~~ 77 (77)
T cd01805 1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKG---CDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSKPK 77 (77)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhC---CCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEecCC
Confidence 89999999999999999999999999999999999 7 999999999999999999999999999999999998764
No 6
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=99.74 E-value=4.4e-18 Score=128.13 Aligned_cols=57 Identities=60% Similarity=1.068 Sum_probs=54.3
Q ss_pred hHHhhccHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHhHHHHHHHhcCCC
Q 015999 272 LDFLRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPV 328 (397)
Q Consensus 272 l~~L~~~P~f~~lrq~vq~NP~ll~~~Lqqi~~~nP~l~~~I~~n~~~Fl~~l~~~~ 328 (397)
|++||++|+|++||++|++||++|+++|++|+++||+|+++|++||++|+++|+++.
T Consensus 1 L~~Lr~~Pqf~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~n~e~Fl~ll~~~~ 57 (59)
T PF09280_consen 1 LEFLRNNPQFQQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQNPEEFLRLLNEPA 57 (59)
T ss_dssp CGGGTTSHHHHHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHHTHHHHHHHHHSTS
T ss_pred ChHHHcChHHHHHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHHCHHHHHHHHcCCC
Confidence 579999999999999999999999999999999999999999999999999999975
No 7
>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=99.73 E-value=1.1e-17 Score=133.31 Aligned_cols=74 Identities=22% Similarity=0.339 Sum_probs=70.3
Q ss_pred CEEEEEeCCCcE-EEEE-eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 1 MKVFVKTLKGTH-FEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 1 MkI~Vktl~gk~-~~ve-V~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+|+||+++|++ +.++ +++++||.+||.+|++..| +|+++|||+|+||+|+|+.+|++|||+++++|+|+++..
T Consensus 1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~g---i~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~~ 76 (78)
T cd01797 1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFN---VEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQD 76 (78)
T ss_pred CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhC---CCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence 899999999997 7895 8999999999999999999 999999999999999999999999999999999998753
No 8
>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=99.72 E-value=2.1e-17 Score=130.05 Aligned_cols=73 Identities=27% Similarity=0.374 Sum_probs=69.3
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVI 78 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~ 78 (397)
|+|+||+ ++++.++|++++||.+||.+|+++.| +|+++|||+|+||+|+|+++|++|+|+++++||++++.++
T Consensus 1 mqi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~g---ip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~G 73 (74)
T cd01793 1 MQLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEG---IDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLG 73 (74)
T ss_pred CEEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhC---CCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence 8999998 47899999999999999999999999 9999999999999999999999999999999999998654
No 9
>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=99.72 E-value=1.9e-17 Score=130.39 Aligned_cols=71 Identities=18% Similarity=0.328 Sum_probs=68.5
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+||++.|+.+.++|++++||.+||++|++..| +++++|||||+||+|+|+++|++|||++|++|||..
T Consensus 2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~---~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~ 72 (73)
T cd01791 2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTG---TRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY 72 (73)
T ss_pred EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhC---CChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence 78999999999999999999999999999999999 999999999999999999999999999999999863
No 10
>PTZ00044 ubiquitin; Provisional
Probab=99.71 E-value=4.1e-17 Score=128.54 Aligned_cols=74 Identities=28% Similarity=0.438 Sum_probs=71.9
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+|+||+++|+++.++|++++||.+||.+|++..| +|+++|||+|+|+.|+|+.+|++|+|+++++|||+++.+
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~ 74 (76)
T PTZ00044 1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEG---IDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLR 74 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---CCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEcc
Confidence 89999999999999999999999999999999999 999999999999999999999999999999999998864
No 11
>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=99.70 E-value=5.5e-17 Score=135.98 Aligned_cols=75 Identities=33% Similarity=0.523 Sum_probs=72.3
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVI 78 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~ 78 (397)
|+|+||+++|+++.++|++++||.+||++|+++.| +|+++|||+|+||+|+|+++|++|+|+++++|+|+++.+.
T Consensus 28 M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~g---ip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l~G 102 (103)
T cd01802 28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEG---IPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAMRG 102 (103)
T ss_pred EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhC---CChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEecCC
Confidence 89999999999999999999999999999999999 9999999999999999999999999999999999998653
No 12
>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=99.69 E-value=7.6e-17 Score=128.40 Aligned_cols=73 Identities=23% Similarity=0.397 Sum_probs=69.9
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+|+||+..|+.+.++|+++.||.+||++|+++.+ +++++|||+|+||+|+|+ +|++|||++|++|+|+....
T Consensus 2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~---~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~ 74 (78)
T cd01804 2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLK---VPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVE 74 (78)
T ss_pred eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhC---CChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecc
Confidence 89999999999999999999999999999999999 999999999999999999 99999999999999998753
No 13
>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=99.68 E-value=2.1e-16 Score=123.96 Aligned_cols=74 Identities=36% Similarity=0.549 Sum_probs=71.6
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+|+||+.+|+++.++|+++.||.+||++|++..| +|+++|||+|+|+.|+|+++|++|+|++|++|||+++.+
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g---~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~ 74 (76)
T cd01806 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALR 74 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhC---CChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEcc
Confidence 89999999999999999999999999999999999 999999999999999999999999999999999998754
No 14
>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=99.68 E-value=9.6e-17 Score=128.28 Aligned_cols=74 Identities=28% Similarity=0.400 Sum_probs=71.0
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrL--iy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+|+||+++|+++.++|+++.||.+||++|++..| +++++||| +|+|++|+|+++|++|||++|++|+|++++-
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~---i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~~ 78 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIG---VPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQNC 78 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhC---CCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEcc
Confidence 78999999999999999999999999999999999 99999999 9999999999999999999999999999853
No 15
>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=99.68 E-value=1.3e-16 Score=125.64 Aligned_cols=72 Identities=22% Similarity=0.263 Sum_probs=69.4
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+||++.|+++.++|++++||.+||++|++..| +|+++|+|+|+||+|+|+++|++|||+++++|+++++..
T Consensus 1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g---i~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~ 72 (74)
T cd01810 1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRER---VQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLR 72 (74)
T ss_pred CEEECCCCCEEEEEECCcChHHHHHHHHHHHhC---CCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEcc
Confidence 689999999999999999999999999999999 999999999999999999999999999999999998764
No 16
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=99.68 E-value=2.1e-16 Score=123.91 Aligned_cols=74 Identities=38% Similarity=0.610 Sum_probs=71.7
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+|+||+.+|+++.++|++++||.+||++|++.+| +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~ 74 (76)
T cd01803 1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74 (76)
T ss_pred CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhC---CCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcc
Confidence 89999999999999999999999999999999999 999999999999999999999999999999999999864
No 17
>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=99.68 E-value=1.2e-16 Score=124.73 Aligned_cols=69 Identities=28% Similarity=0.462 Sum_probs=66.7
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
++||.++|+++.++|++++||.+||.+|++..| +|+++|||+|+||+|+|+++|++|+|+++++|||++
T Consensus 1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~g---i~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~ 69 (70)
T cd01794 1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEG---VDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV 69 (70)
T ss_pred CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhC---CCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence 468999999999999999999999999999999 999999999999999999999999999999999987
No 18
>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=99.67 E-value=1.7e-16 Score=123.38 Aligned_cols=70 Identities=30% Similarity=0.546 Sum_probs=67.6
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
|+||++.|+++.++|++++||.+||++|+++.| +|+++|+|+|+||.|+|+.+|++|||+++++|||+.|
T Consensus 1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g---i~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~ 70 (70)
T cd01798 1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQG---VPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR 70 (70)
T ss_pred CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHC---CCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence 689999999999999999999999999999999 9999999999999999999999999999999999864
No 19
>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=99.66 E-value=3.8e-16 Score=121.23 Aligned_cols=72 Identities=36% Similarity=0.459 Sum_probs=69.7
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
|+|+||+++|+++.+++++++||.+||++|++.+| +|++.|+|+|+|+.|+|+.+|++|||++|++|||+.+
T Consensus 1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~ 72 (72)
T cd01809 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVG---IPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR 72 (72)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHC---cCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence 89999999999999999999999999999999999 9999999999999999999999999999999999864
No 20
>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=99.65 E-value=3.2e-16 Score=124.87 Aligned_cols=73 Identities=21% Similarity=0.207 Sum_probs=64.7
Q ss_pred CEEEEEeCCCcE--EEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcc--cCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTH--FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENK--VAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~--~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~g--I~~gstI~v~v 74 (397)
|.|+||+.++++ |++++++++||.+||++|++..+.. +++++|||||+||+|+|+.+|++|+ |+++.+|||+.
T Consensus 2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~-~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~ 78 (79)
T cd01790 2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSK-PLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC 78 (79)
T ss_pred eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCC-CChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence 579999999998 5556689999999999999887421 5689999999999999999999996 99999999986
No 21
>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=99.65 E-value=4.9e-16 Score=121.20 Aligned_cols=71 Identities=32% Similarity=0.428 Sum_probs=67.5
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
|+|+||+..|+ +.++|++++||.+||++|++..| ++.++|||+|+||+|+|+++|++|||+++++|||+++
T Consensus 1 ~~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~---i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~ 71 (71)
T cd01808 1 IKVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFK---ANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK 71 (71)
T ss_pred CEEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhC---CCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence 68999999997 58999999999999999999999 9999999999999999999999999999999999874
No 22
>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=99.63 E-value=7.8e-16 Score=118.81 Aligned_cols=69 Identities=38% Similarity=0.595 Sum_probs=66.1
Q ss_pred EeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 6 ktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+++|+.|.++|++++||.+||++|+...+ +|++.|+|+|+|++|+|+.+|++|||++|++|+|+++++
T Consensus 1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~---~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~~ 69 (69)
T PF00240_consen 1 KTLSGKTFTLEVDPDDTVADLKQKIAEETG---IPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKPR 69 (69)
T ss_dssp EETTSEEEEEEEETTSBHHHHHHHHHHHHT---STGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESSE
T ss_pred CCCCCcEEEEEECCCCCHHHhhhhcccccc---cccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEecC
Confidence 688999999999999999999999999999 999999999999999999999999999999999998753
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=99.61 E-value=1.6e-15 Score=119.68 Aligned_cols=70 Identities=29% Similarity=0.414 Sum_probs=67.1
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe---CCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy---~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+|| ++|++|.|+|++++||.+||++|++.+| +|+++|||+| +||+|+|+.+|++|+|++|++|+||.
T Consensus 1 ~~i~vk-~~g~~~~v~v~~~~Tv~~lK~~i~~~tg---vp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lmG 73 (74)
T cd01813 1 VPVIVK-WGGQEYSVTTLSEDTVLDLKQFIKTLTG---VLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMMG 73 (74)
T ss_pred CEEEEE-ECCEEEEEEECCCCCHHHHHHHHHHHHC---CCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEEe
Confidence 689999 7899999999999999999999999999 9999999997 99999999999999999999999985
No 24
>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=99.59 E-value=3e-15 Score=117.06 Aligned_cols=67 Identities=34% Similarity=0.450 Sum_probs=64.1
Q ss_pred EEEEeC-CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC-CchhhcccCCCCEEEE
Q 015999 3 VFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV-TTLEENKVAENSFVVV 72 (397)
Q Consensus 3 I~Vktl-~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~-~tL~d~gI~~gstI~v 72 (397)
|+||+. +|+++.++|++++||.+||.+|+++.| +|+++|||+|+||.|+|+ .+|++|||++|++|||
T Consensus 1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~g---ip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l 69 (71)
T cd01796 1 ITVYTARSETTFSLDVDPDLELENFKALCEAESG---IPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVL 69 (71)
T ss_pred CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhC---CCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEE
Confidence 689999 999999999999999999999999999 999999999999999987 6899999999999987
No 25
>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.57 E-value=2.6e-15 Score=111.28 Aligned_cols=70 Identities=36% Similarity=0.548 Sum_probs=68.3
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
|.|.||+++|+.+.+++++.++|..+|++|+++.| ||+.+|||||.||.+.|++|-++|++.-|++||++
T Consensus 1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeG---IPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv 70 (70)
T KOG0005|consen 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEG---IPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV 70 (70)
T ss_pred CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcC---CCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence 88999999999999999999999999999999999 99999999999999999999999999999999974
No 26
>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=99.56 E-value=1.1e-14 Score=112.92 Aligned_cols=70 Identities=29% Similarity=0.421 Sum_probs=67.0
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+||+. |+.+.++|++++||.+||.+|++.+| +|+++|||+|+|+.|+|+++|++|||++|++|+|+.
T Consensus 1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~ 70 (71)
T cd01812 1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTG---VEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE 70 (71)
T ss_pred CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhC---CChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence 68999986 99999999999999999999999999 999999999999999999999999999999999874
No 27
>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=99.54 E-value=2.2e-14 Score=113.58 Aligned_cols=68 Identities=26% Similarity=0.370 Sum_probs=65.0
Q ss_pred CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecC
Q 015999 8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVI 78 (397)
Q Consensus 8 l~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~ 78 (397)
++|+++.|+|++++||.+||.+|+..+| +|+++|+|+|+|+.|+|+++|++|+|+++++|+|+++.+.
T Consensus 5 l~g~~~~l~v~~~~TV~~lK~~i~~~~g---ip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~g 72 (76)
T cd01800 5 LNGQMLNFTLQLSDPVSVLKVKIHEETG---MPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERG 72 (76)
T ss_pred cCCeEEEEEECCCCcHHHHHHHHHHHHC---CCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCC
Confidence 5799999999999999999999999999 9999999999999999999999999999999999998654
No 28
>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]
Probab=99.48 E-value=4.6e-15 Score=122.33 Aligned_cols=76 Identities=37% Similarity=0.570 Sum_probs=73.4
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecCC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVIR 79 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~~ 79 (397)
|+++|+++.|++++++|++++||..||.+|....| +|++.|+|+|+||+|+|..||++|||...++||++.+.+..
T Consensus 1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~G---i~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~GG 76 (128)
T KOG0003|consen 1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (128)
T ss_pred CcEEEEEeeCceEEEEecccchHHHHHHHhccccC---CCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHhcC
Confidence 78999999999999999999999999999999999 99999999999999999999999999999999999988764
No 29
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=99.44 E-value=3.3e-13 Score=101.61 Aligned_cols=64 Identities=42% Similarity=0.649 Sum_probs=61.3
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENS 68 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gs 68 (397)
|+|+||+.+ +.+.++|+++.||.+||.+|+..+| +++++|+|+|+|+.|.|+++|++|||++|+
T Consensus 1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~---~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~ 64 (64)
T smart00213 1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTG---IPVEQQRLIYKGKVLEDDRTLADYNIQDGS 64 (64)
T ss_pred CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHC---CCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence 899999998 7899999999999999999999999 999999999999999999999999999875
No 30
>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]
Probab=99.44 E-value=7.2e-14 Score=122.92 Aligned_cols=78 Identities=35% Similarity=0.521 Sum_probs=74.6
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecCCC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVIRF 80 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~~~ 80 (397)
|+|+|+++.++++.++|+.++||..+|.+|++..| ||+++|||||.|+.|+|.++|+||+|+..++|+|+++.+...
T Consensus 1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~eg---Ip~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg~ 77 (156)
T KOG0004|consen 1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGA 77 (156)
T ss_pred CccchhhccccceeeeecccccHHHHHHhhhcccC---CCchhhhhhhhhcccccCCccccccccccceEEEEEEecCCc
Confidence 89999999999999999999999999999999999 999999999999999999999999999999999999977655
Q ss_pred C
Q 015999 81 H 81 (397)
Q Consensus 81 ~ 81 (397)
.
T Consensus 78 k 78 (156)
T KOG0004|consen 78 K 78 (156)
T ss_pred c
Confidence 4
No 31
>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=99.44 E-value=6.4e-13 Score=107.97 Aligned_cols=75 Identities=16% Similarity=0.243 Sum_probs=71.7
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeecC
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVI 78 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~ 78 (397)
|+|+|++.+|+.+.+.|.+++||..||.+++++.| +++++|||+|+|+.|+|+.|+.+|+|+++++|+|+++.++
T Consensus 12 i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~g---i~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~G 86 (87)
T cd01763 12 INLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQG---LSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTG 86 (87)
T ss_pred EEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhC---CCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEeccc
Confidence 67999999999999999999999999999999999 9999999999999999999999999999999999988654
No 32
>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=99.40 E-value=3.4e-13 Score=106.25 Aligned_cols=55 Identities=25% Similarity=0.237 Sum_probs=49.2
Q ss_pred CCCCHHHHHHHHHHHhCCCCC-CCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 19 PEDKVSDVKKNIETVQGSDVY-PASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 19 ~~~TV~dLK~~I~~~~g~~~i-p~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
.++||.+||++|+++.+.. + ++++|||||+||+|+|+++|++|||++|++|||+.
T Consensus 19 ~~~TV~~LK~kI~~~~~eg-i~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~ 74 (75)
T cd01815 19 GGYQVSTLKQLIAAQLPDS-LPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR 74 (75)
T ss_pred ccCcHHHHHHHHHHhhccC-CCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence 3689999999999996322 5 59999999999999999999999999999999985
No 33
>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.
Probab=99.33 E-value=2.6e-12 Score=108.02 Aligned_cols=78 Identities=17% Similarity=0.242 Sum_probs=64.1
Q ss_pred EEEEEeCCCcEE-EEEeCCCCCHHHHHHHHHHHhCC--CCCC--CCCeEEEeCCeecCCCCchhhcc------cCCCCEE
Q 015999 2 KVFVKTLKGTHF-EIEVKPEDKVSDVKKNIETVQGS--DVYP--ASQQMLIHQGKVLKDVTTLEENK------VAENSFV 70 (397)
Q Consensus 2 kI~Vktl~gk~~-~veV~~~~TV~dLK~~I~~~~g~--~~ip--~~~qrLiy~GKiL~D~~tL~d~g------I~~gstI 70 (397)
.|.||..+|..+ ...+.+++||.+||++|++..+. ..+| +++|||||+||+|+|++||++|+ +....|+
T Consensus 6 e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~Tm 85 (113)
T cd01814 6 EIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVITM 85 (113)
T ss_pred EEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceEE
Confidence 578887788654 46778999999999999966642 1255 99999999999999999999999 7778999
Q ss_pred EEEEeecCC
Q 015999 71 VVMLTKVIR 79 (397)
Q Consensus 71 ~v~v~k~~~ 79 (397)
||+++.+..
T Consensus 86 Hvvlr~~~~ 94 (113)
T cd01814 86 HVVVQPPLA 94 (113)
T ss_pred EEEecCCCC
Confidence 999875443
No 34
>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=99.29 E-value=1.2e-11 Score=94.35 Aligned_cols=68 Identities=43% Similarity=0.663 Sum_probs=64.4
Q ss_pred EEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 4 FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 4 ~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
+||..+|+.+.+++.++.||.+||++|+..+| +++++|+|+|+||.|+|+.+|.+|+|+++++|+|+.
T Consensus 1 ~v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~---~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~ 68 (69)
T cd01769 1 TVKTLTGKTFELEVSPDDTVAELKAKIAAKEG---VPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL 68 (69)
T ss_pred CeEccCCCEEEEEECCCChHHHHHHHHHHHHC---cChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence 37888899999999999999999999999999 999999999999999999999999999999999875
No 35
>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=99.28 E-value=1.1e-11 Score=98.10 Aligned_cols=65 Identities=18% Similarity=0.274 Sum_probs=58.9
Q ss_pred EeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecC-CCCchhhcccC-CCCEEEEEE
Q 015999 6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLK-DVTTLEENKVA-ENSFVVVML 74 (397)
Q Consensus 6 ktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~-D~~tL~d~gI~-~gstI~v~v 74 (397)
|...|+++.++|++++||.+||.+|+.++| +|+++||| |.|+.|. |+++|++|||+ +|++++|.+
T Consensus 8 ~~~~~~t~~l~v~~~~TV~~lK~kI~~~~g---ip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~ 74 (75)
T cd01799 8 AQSHTVTIWLTVRPDMTVAQLKDKVFLDYG---FPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI 74 (75)
T ss_pred cccCCCeEEEEECCCCcHHHHHHHHHHHHC---cCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence 344688999999999999999999999999 99999999 9999985 67999999999 889999865
No 36
>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=99.19 E-value=7.6e-11 Score=91.74 Aligned_cols=71 Identities=24% Similarity=0.391 Sum_probs=65.9
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-CCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~-~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+|++.+|+.+.+.|.++.+|..|+.+++++.+ ++. +.++|+|.|+.|++++|+++|||++|++|+|++
T Consensus 1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~---i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I 72 (72)
T PF11976_consen 1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKG---IPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII 72 (72)
T ss_dssp EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHT---TTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhC---CCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence 78999999999999999999999999999999999 999 999999999999999999999999999999874
No 37
>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=99.03 E-value=6.3e-10 Score=91.38 Aligned_cols=61 Identities=21% Similarity=0.236 Sum_probs=56.5
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCC-CCchhhcccCCCCEEEEEEe
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKD-VTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D-~~tL~d~gI~~gstI~v~v~ 75 (397)
...++|++++||.+||.+|.+.++ +++.+|||+|.|+.|.| .+||++|||..+++|+|.+.
T Consensus 16 ~~~L~V~~~~TVg~LK~lImQ~f~---V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llid 77 (107)
T cd01795 16 EKALLVSANQTLKELKIQIMHAFS---VAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKAD 77 (107)
T ss_pred CceEEeCccccHHHHHHHHHHHhc---CCcccceeeecCceeccCCccHHhcCCCCCCEEEEEec
Confidence 457889999999999999999999 99999999999999965 68999999999999999875
No 38
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=98.91 E-value=2.1e-09 Score=73.51 Aligned_cols=36 Identities=50% Similarity=0.723 Sum_probs=33.6
Q ss_pred hHHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHH
Q 015999 167 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYL 205 (397)
Q Consensus 167 ~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL 205 (397)
.++.|++|++|| |++++|++||+++.||.++||+||
T Consensus 2 ~~~~v~~L~~mG---f~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 2 DEEKVQQLMEMG---FSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHHT---S-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHcC---CCHHHHHHHHHHcCCCHHHHHHhC
Confidence 478999999999 999999999999999999999998
No 39
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=98.91 E-value=8.6e-09 Score=87.58 Aligned_cols=75 Identities=20% Similarity=0.284 Sum_probs=56.0
Q ss_pred EEEEEeCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCC----CCCCCCeEEEeCCeecCCCCchhhcccCCCC------EE
Q 015999 2 KVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSD----VYPASQQMLIHQGKVLKDVTTLEENKVAENS------FV 70 (397)
Q Consensus 2 kI~Vktl~gk-~~~veV~~~~TV~dLK~~I~~~~g~~----~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gs------tI 70 (397)
.|+++..+|+ +-.+.+++++||.+||++|......+ ...+..+||||.||+|+|+++|++|++..++ ++
T Consensus 4 ~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~vm 83 (111)
T PF13881_consen 4 ELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTVM 83 (111)
T ss_dssp EEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EEE
T ss_pred EEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEEE
Confidence 5777878998 77889999999999999999776433 1345678999999999999999999998777 46
Q ss_pred EEEEee
Q 015999 71 VVMLTK 76 (397)
Q Consensus 71 ~v~v~k 76 (397)
||+++.
T Consensus 84 Hlvvrp 89 (111)
T PF13881_consen 84 HLVVRP 89 (111)
T ss_dssp EEEE-S
T ss_pred EEEecC
Confidence 666653
No 40
>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=98.89 E-value=1.4e-08 Score=76.96 Aligned_cols=72 Identities=39% Similarity=0.577 Sum_probs=68.2
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
+++++..|+.+.+++.+..+|..+|.+|....+ ++...|+|+|.|+.|.|+.+|.+|+|..+++++++.+.+
T Consensus 2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~---~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~ 73 (75)
T KOG0001|consen 2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEG---IPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLR 73 (75)
T ss_pred EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcC---CCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecC
Confidence 678889999999999999999999999999999 999999999999999999999999999999999988754
No 41
>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]
Probab=98.87 E-value=2.8e-09 Score=116.51 Aligned_cols=70 Identities=26% Similarity=0.400 Sum_probs=67.6
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
.|+|||++.++.+|.|...+||++||.+|..+.. |+.+.|||||.|++|.|+|++.+|+| +|.+|||+-|
T Consensus 4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~n---i~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlver 73 (1143)
T KOG4248|consen 4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVN---IPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVER 73 (1143)
T ss_pred ceeeeecccceeEEEechHHHHHHHHHHHHHhcc---cccccceeeecceeeccchhhhhccC-CCeEEEeecc
Confidence 4899999999999999999999999999999999 99999999999999999999999999 9999999987
No 42
>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=98.86 E-value=1.1e-08 Score=82.63 Aligned_cols=70 Identities=26% Similarity=0.321 Sum_probs=58.8
Q ss_pred EEEEEeCC-CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE-EeCCe-----ec-CCCCchhhcccCCCCEEEEE
Q 015999 2 KVFVKTLK-GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQGK-----VL-KDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 2 kI~Vktl~-gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrL-iy~GK-----iL-~D~~tL~d~gI~~gstI~v~ 73 (397)
+|.|+... ....+..+.+++||.+||.+|+..+| +++..||| +|.|+ .| +|+++|++|++++|..|||+
T Consensus 3 ~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G---~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVv 79 (84)
T cd01789 3 TVNITSSADSFSFEKKYSRGLTIAELKKKLELVVG---TPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVI 79 (84)
T ss_pred EEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHC---CCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEE
Confidence 56666543 33455669999999999999999999 99999999 58888 46 67889999999999999997
Q ss_pred E
Q 015999 74 L 74 (397)
Q Consensus 74 v 74 (397)
-
T Consensus 80 D 80 (84)
T cd01789 80 D 80 (84)
T ss_pred e
Confidence 5
No 43
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=98.81 E-value=8.2e-09 Score=70.67 Aligned_cols=36 Identities=39% Similarity=0.543 Sum_probs=34.5
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhc
Q 015999 355 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLD 390 (397)
Q Consensus 355 ~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~ 390 (397)
+.|++|++|||+++.+++||..|++|++.|++|||+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 579999999999999999999999999999999985
No 44
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=98.80 E-value=8.2e-09 Score=70.56 Aligned_cols=35 Identities=40% Similarity=0.634 Sum_probs=32.5
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHH
Q 015999 354 REAIERLEAMGFDRALVLEVFFACNKNEELAANYL 388 (397)
Q Consensus 354 ~~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L 388 (397)
.+.|++|++|||+++.+++||.+|++|++.|++||
T Consensus 3 ~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 46799999999999999999999999999999998
No 45
>PLN02560 enoyl-CoA reductase
Probab=98.80 E-value=1.3e-08 Score=100.89 Aligned_cols=70 Identities=33% Similarity=0.440 Sum_probs=62.0
Q ss_pred CEEEEEeCCCcEE---EEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---C----eecCCCCchhhcccCCCCEE
Q 015999 1 MKVFVKTLKGTHF---EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G----KVLKDVTTLEENKVAENSFV 70 (397)
Q Consensus 1 MkI~Vktl~gk~~---~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~---G----KiL~D~~tL~d~gI~~gstI 70 (397)
|+|+|+..+|+.+ +|+|+++.||++||++|+++.+. +++++|||++. | +.|+|+++|++|||+++++|
T Consensus 1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~--~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstL 78 (308)
T PLN02560 1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKK--YYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTV 78 (308)
T ss_pred CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCC--CChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceE
Confidence 8999998889887 79999999999999999999771 38999999982 3 48899999999999999988
Q ss_pred EE
Q 015999 71 VV 72 (397)
Q Consensus 71 ~v 72 (397)
++
T Consensus 79 y~ 80 (308)
T PLN02560 79 VF 80 (308)
T ss_pred EE
Confidence 65
No 46
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=98.73 E-value=1.6e-08 Score=68.87 Aligned_cols=36 Identities=47% Similarity=0.629 Sum_probs=34.2
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHh
Q 015999 354 REAIERLEAMGFDRALVLEVFFACNKNEELAANYLL 389 (397)
Q Consensus 354 ~~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~ 389 (397)
.+.|++|++|||+++.+++||..|++|++.|++|||
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 357999999999999999999999999999999997
No 47
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=98.67 E-value=3.6e-08 Score=67.43 Aligned_cols=37 Identities=51% Similarity=0.788 Sum_probs=35.1
Q ss_pred HHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHc
Q 015999 168 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 207 (397)
Q Consensus 168 e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~ 207 (397)
++.|++|++|| |+|++|++||+++.+|.++|++||++
T Consensus 2 ~~~v~~L~~mG---f~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 2 EEKLEQLLEMG---FSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 57899999999 99999999999999999999999974
No 48
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=98.66 E-value=7.5e-08 Score=78.01 Aligned_cols=71 Identities=24% Similarity=0.316 Sum_probs=57.4
Q ss_pred EEEEEeCCC--cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC----Ce---ec-CCCCchhhcccCCCCEEE
Q 015999 2 KVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ----GK---VL-KDVTTLEENKVAENSFVV 71 (397)
Q Consensus 2 kI~Vktl~g--k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~----GK---iL-~D~~tL~d~gI~~gstI~ 71 (397)
+|+|..... +..+..+..++||.+||.+|+..+| ++++.|+|.+. +. .| +|+++|++||+++|.+||
T Consensus 3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~G---i~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~ 79 (87)
T PF14560_consen 3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTG---IPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIH 79 (87)
T ss_dssp EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHT---S-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEE
T ss_pred EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhC---CCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEE
Confidence 577776654 4788999999999999999999999 99999999775 21 24 567899999999999999
Q ss_pred EEEe
Q 015999 72 VMLT 75 (397)
Q Consensus 72 v~v~ 75 (397)
|.=.
T Consensus 80 V~D~ 83 (87)
T PF14560_consen 80 VVDT 83 (87)
T ss_dssp EEE-
T ss_pred EEeC
Confidence 9754
No 49
>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.
Probab=98.65 E-value=7.3e-08 Score=76.40 Aligned_cols=69 Identities=23% Similarity=0.253 Sum_probs=54.7
Q ss_pred EEEEEeCC-CcEEEEEeC-CCCCHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecCCCCchhhcccCCCCEEEE
Q 015999 2 KVFVKTLK-GTHFEIEVK-PEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 2 kI~Vktl~-gk~~~veV~-~~~TV~dLK~~I~~~~g~~~ip~~~qrL--iy~GKiL~D~~tL~d~gI~~gstI~v 72 (397)
.|.++..+ .....++++ ++.||.+||+.|++..+. +++++||| ++.|++|.|+++|.+|||++|++|+|
T Consensus 2 ~i~~~~~~~k~~~~~~~~~~~aTV~dlk~~i~~~~~~--~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv 74 (77)
T cd01801 2 EILDAKRSDKPIGKLKVSSGDATIADLKKLIAKSSPQ--LTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV 74 (77)
T ss_pred eeeccccCcCceeecccCCCCccHHHHHHHHHHHcCC--CCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence 56666555 333234444 789999999999988652 57899888 58999999999999999999999876
No 50
>cd01788 ElonginB Ubiquitin-like domain of Elongin B. Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.
Probab=98.61 E-value=1.3e-07 Score=79.70 Aligned_cols=73 Identities=22% Similarity=0.287 Sum_probs=62.1
Q ss_pred CEEEEEeCCC-cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhccc-------CCCCEEEE
Q 015999 1 MKVFVKTLKG-THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKV-------AENSFVVV 72 (397)
Q Consensus 1 MkI~Vktl~g-k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI-------~~gstI~v 72 (397)
|-++++.+.. .++.+++.++.||.+||++|+.... .|++.|||+..+.+|+|++||++||+ +...+|-+
T Consensus 1 MdvFlmIrR~KTTiF~dakes~tVlelK~~iegI~k---~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgL 77 (119)
T cd01788 1 MDVFLMIRRHKTTIFTDAKESTTVYELKRIVEGILK---RPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGL 77 (119)
T ss_pred CceEEEEEecceEEEeecCCcccHHHHHHHHHHHhc---CChhHheeecCceeecccccHHHcCccccccccCCCCeEEE
Confidence 5566665544 4577899999999999999999999 99999999977788999999999999 66788888
Q ss_pred EEee
Q 015999 73 MLTK 76 (397)
Q Consensus 73 ~v~k 76 (397)
.+++
T Consensus 78 a~r~ 81 (119)
T cd01788 78 AFRS 81 (119)
T ss_pred EEec
Confidence 7774
No 51
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=98.61 E-value=6.3e-08 Score=65.90 Aligned_cols=36 Identities=53% Similarity=0.850 Sum_probs=34.5
Q ss_pred HHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 015999 168 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY 206 (397)
Q Consensus 168 e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~ 206 (397)
++.|++|++|| |++++|++||+...||.++|++||+
T Consensus 2 ~~~v~~L~~mG---f~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 2 EEKIDQLLEMG---FSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHHHcC---CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 67899999999 9999999999999999999999995
No 52
>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=98.39 E-value=1.6e-06 Score=62.01 Aligned_cols=67 Identities=31% Similarity=0.457 Sum_probs=60.6
Q ss_pred EEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 5 Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+..++....+.+.+..||.+||.+|..+.| ++++.++|+++|+.+.+...+.++++.+++.|++..
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 68 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLG---LPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP 68 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHC---cChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence 4444688888999999999999999999999 899999999999999999988999999999998864
No 53
>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=98.38 E-value=5.9e-07 Score=72.03 Aligned_cols=68 Identities=28% Similarity=0.371 Sum_probs=43.5
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---Ceec--CCCCchhhcccCCCCEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---GKVL--KDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~---GKiL--~D~~tL~d~gI~~gstI~v 72 (397)
|-|.||+.+| .+.|++++++||.+||++|.+..+ ++...+.|..+ .+.| .++++|+++||+.||.|+|
T Consensus 5 milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~---~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL 77 (80)
T PF11543_consen 5 MILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLS---IPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYL 77 (80)
T ss_dssp -EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS------TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE-
T ss_pred EEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcC---CCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEE
Confidence 6688888776 678999999999999999999999 88888888532 2345 4678999999999999976
No 54
>cd01811 OASL_repeat1 2'-5' oligoadenylate synthetase-like protein, repeat 1 of 2. OASL_repeat1 (2'-5' oligoadenylate synthetase-like protein) belongs to a family of interferon-induced 2'-5' oligoadenylate synthetases which are important for the antiviral activity of interferons. While each member of this famliy has a conserved N-terminal OAS catalytic domain, only OASL has two tandem ubiquitin-like repeats located at the C-terminus and this CD represents one of those repeats.
Probab=98.27 E-value=5e-06 Score=64.98 Aligned_cols=71 Identities=18% Similarity=0.309 Sum_probs=62.4
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC---C--eecCCCCchhhcccCCCCEEEEEEe
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ---G--KVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~---G--KiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
++|+|+-+.+..+++.|+|..+|..||++|....+ ++ ..|||.|. | ..|.+.++|++|||-.+..|.|+-.
T Consensus 1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~---~~-g~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lleT 76 (80)
T cd01811 1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRN---CS-GLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLET 76 (80)
T ss_pred CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhC---cc-cceEEEeecCCcccccccccccHhhhcceeccEEEEEec
Confidence 58999999999999999999999999999999998 54 59999983 3 3478999999999999888887754
No 55
>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.16 E-value=4.6e-06 Score=85.44 Aligned_cols=71 Identities=23% Similarity=0.362 Sum_probs=65.9
Q ss_pred EEEEeCCCcEEEEE-eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 3 VFVKTLKGTHFEIE-VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 3 I~Vktl~gk~~~ve-V~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|.|| |.|+.|.++ ++.++|+..||.++...+| ++|++||++++|+.|.|+-.+..++||+|.+|+||.+.-
T Consensus 6 v~VK-W~gk~y~v~~l~~d~t~~vlKaqlf~LTg---V~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e 77 (473)
T KOG1872|consen 6 VIVK-WGGKKYPVETLSTDETPSVLKAQLFALTG---VPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAE 77 (473)
T ss_pred Eeee-ecCccccceeccCCCchHHHHHHHHHhcC---CCccceeEEEecccccccccccccccCCCCEEEeecccc
Confidence 5666 899999988 9999999999999999999 999999999999999999899999999999999997643
No 56
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=98.01 E-value=8.6e-06 Score=79.61 Aligned_cols=72 Identities=28% Similarity=0.391 Sum_probs=63.3
Q ss_pred CEEEEEeC---CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 1 MKVFVKTL---KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 1 MkI~Vktl---~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
|.+.|+.. ....+.|+|+.+.+|.+||+.++.+.| +|+++.|+||.||.|.|+.++..+.+.-.+.+|+|.-
T Consensus 1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~g---vp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~l 75 (446)
T KOG0006|consen 1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQG---VPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIMLL 75 (446)
T ss_pred CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhC---CChhheEEEEeccccccCceeecccccccchhhhhcc
Confidence 66777754 234588999999999999999999999 9999999999999999999999999988899988843
No 57
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=1.1e-05 Score=61.35 Aligned_cols=69 Identities=19% Similarity=0.308 Sum_probs=60.4
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
++.+...-|++..|...+++||+|+|+.|+.++| -.++.++|---+.+++|.-+|++|.|++|-.+.+.
T Consensus 3 ev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtG---T~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely 71 (73)
T KOG3493|consen 3 EVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTG---TRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY 71 (73)
T ss_pred eehhhhhcCceEEEEeCCcccccCHHHHHHHhhC---CChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence 4666777799999999999999999999999999 77888888766778899999999999999887664
No 58
>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=97.66 E-value=5.6e-05 Score=77.13 Aligned_cols=40 Identities=30% Similarity=0.449 Sum_probs=36.9
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCC
Q 015999 354 REAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMH 393 (397)
Q Consensus 354 ~~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~~~~ 393 (397)
...|++|++|||+|++|..|++|+..|-+.|++||+..--
T Consensus 157 e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~tGIP 196 (378)
T TIGR00601 157 ETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTGIP 196 (378)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHHhCCC
Confidence 3669999999999999999999999999999999998643
No 59
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.60 E-value=0.00058 Score=69.93 Aligned_cols=58 Identities=21% Similarity=0.166 Sum_probs=49.1
Q ss_pred EEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 15 IEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 15 veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
++.....|=.+|...|.++.| |+..-.|.|-+||+|.-.+||.+-|++.+-.+.|++.
T Consensus 54 ~k~sL~i~Gselqa~iakklg---i~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~~ 111 (568)
T KOG2561|consen 54 KKCSLHITGSELQALIAKKLG---IKENHVKCIINGKILSCRKTLAEQGLKINQELMVAVG 111 (568)
T ss_pred hhcccccccHHHHHHHHHHcC---CchhhhheeeccceeecccchhhhhhhhhhHHHHHhc
Confidence 334445667789999999999 9888899999999999999999999998887766655
No 60
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=97.43 E-value=0.0012 Score=54.60 Aligned_cols=72 Identities=14% Similarity=0.234 Sum_probs=63.9
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEee
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTK 76 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k 76 (397)
+|.|+.-++....+.|..+.+...|++..+++.| +....+|++|.|+.+.+.+|=.+++.+++|.|.++...
T Consensus 22 ~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~G---l~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q 93 (99)
T KOG1769|consen 22 NLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQG---LSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQ 93 (99)
T ss_pred EEEEecCCCCEEEEEeecCChHHHHHHHHHHHcC---CccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeec
Confidence 4556655566778899999999999999999999 99999999999999999999999999999999988654
No 61
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=0.00085 Score=71.65 Aligned_cols=38 Identities=29% Similarity=0.535 Sum_probs=35.4
Q ss_pred HHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015999 357 IERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE 394 (397)
Q Consensus 357 i~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~~~~d 394 (397)
+.-+++|||++.+++.|+.+.++|+|.|++|+|.|+.+
T Consensus 639 v~si~smGf~~~qa~~aL~~~n~nveravDWif~h~d~ 676 (763)
T KOG0944|consen 639 VASIVSMGFSRNQAIKALKATNNNVERAVDWIFSHMDI 676 (763)
T ss_pred heeeeeecCcHHHHHHHHHhcCccHHHHHHHHHhcccc
Confidence 67788999999999999999999999999999998763
No 62
>KOG4495 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription]
Probab=97.37 E-value=0.00027 Score=57.92 Aligned_cols=62 Identities=24% Similarity=0.368 Sum_probs=50.0
Q ss_pred CEEEEEeC-CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe-CC-eecCCCCchhhcccC
Q 015999 1 MKVFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-QG-KVLKDVTTLEENKVA 65 (397)
Q Consensus 1 MkI~Vktl-~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy-~G-KiL~D~~tL~d~gI~ 65 (397)
|.++++.. ...++.++.+++.||-+||.+++.... -|++.|||.. .. .+|+|.++|++||..
T Consensus 1 ~~~f~~VrR~kttif~da~es~tV~elK~~l~gi~~---~Pvn~qrL~kmd~eqlL~D~ktL~d~gft 65 (110)
T KOG4495|consen 1 MDVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILK---RPVNEQRLYKMDTEQLLDDGKTLGDCGFT 65 (110)
T ss_pred CceeeeeeecceeEEeecCccccHHHHHHHHHHHHh---CCCcchheeecCHHHHhhccchhhhcccc
Confidence 34455443 345678899999999999999999988 7999999976 33 678999999999864
No 63
>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=97.34 E-value=0.00056 Score=56.85 Aligned_cols=59 Identities=17% Similarity=0.216 Sum_probs=45.6
Q ss_pred EEEEeCC-CcEEEEEeC--CCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhc
Q 015999 3 VFVKTLK-GTHFEIEVK--PEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN 62 (397)
Q Consensus 3 I~Vktl~-gk~~~veV~--~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~ 62 (397)
|+||..+ -..+.+++. .+.||..||..|.+..+.. ..-.++||||+||+|.|...|+..
T Consensus 3 l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~-~s~~rLRlI~~Gr~L~d~t~l~~~ 64 (97)
T PF10302_consen 3 LTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPE-PSRRRLRLIYAGRLLNDHTDLSSE 64 (97)
T ss_pred EEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCC-CccccEEeeecCcccCccchhhhh
Confidence 5666555 234667777 7899999999999998422 556788999999999998877654
No 64
>KOG4583 consensus Membrane-associated ER protein involved in stress response (contains ubiquitin-like domain) [Posttranslational modification, protein turnover, chaperones]
Probab=97.29 E-value=3.5e-05 Score=75.97 Aligned_cols=78 Identities=19% Similarity=0.175 Sum_probs=58.6
Q ss_pred EEEEEeCCC--cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCC--CCEEEEEEeec
Q 015999 2 KVFVKTLKG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAE--NSFVVVMLTKV 77 (397)
Q Consensus 2 kI~Vktl~g--k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~--gstI~v~v~k~ 77 (397)
.++||..+. +...|+.+..+||++||..++..+..+ --...|||||.||.|.|...|.|.=+|. ..++||++..+
T Consensus 11 ~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPsk-pl~~dqrliYsgkllld~qcl~d~lrkq~k~Hv~hlvcnsk 89 (391)
T KOG4583|consen 11 TLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSK-PLELDQRLIYSGKLLLDHQCLTDWLRKQVKEHVKHLVCNSK 89 (391)
T ss_pred EEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCC-CchhhHHHHhhccccccchhHHHHHHHHHHHHHHHHhcCCC
Confidence 466776654 446677888999999999999887654 3356899999999999999999885543 44677776654
Q ss_pred CCC
Q 015999 78 IRF 80 (397)
Q Consensus 78 ~~~ 80 (397)
...
T Consensus 90 ~v~ 92 (391)
T KOG4583|consen 90 EVV 92 (391)
T ss_pred CCC
Confidence 433
No 65
>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []. Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.
Probab=97.09 E-value=0.001 Score=52.90 Aligned_cols=71 Identities=18% Similarity=0.271 Sum_probs=49.7
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC---CeEEE-eCCeecCCCCchhhcccCCCCEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS---QQMLI-HQGKVLKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~---~qrLi-y~GKiL~D~~tL~d~gI~~gstI~v 72 (397)
+|+|...+|+.+.+.+..+.+|.+|...|.+..+....... ..+|. -+|..|+++++|+++||.+|+.|++
T Consensus 4 rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L 78 (79)
T PF08817_consen 4 RVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGDVLVL 78 (79)
T ss_dssp EEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred EEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence 56777655688999999999999999999988773212222 35666 6899999999999999999999986
No 66
>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=97.03 E-value=0.0042 Score=49.32 Aligned_cols=68 Identities=22% Similarity=0.299 Sum_probs=57.2
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCC-eEEE--eCCeecCCC--CchhhcccCCCCEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQ-QMLI--HQGKVLKDV--TTLEENKVAENSFVVV 72 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~-qrLi--y~GKiL~D~--~tL~d~gI~~gstI~v 72 (397)
+|.||..+|+.+.-.+..++||.+|..-|..... .+... .+|+ |-.+.|.++ ++|+++|+..+.+|+|
T Consensus 8 ~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~---~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v 80 (82)
T PF00789_consen 8 RIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLF---SPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV 80 (82)
T ss_dssp EEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHH---CTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred EEEEECCCCCEEEEEECCcchHHHHHHHHHHhcC---CCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence 6889999999999999999999999999988776 44443 7886 677888553 6999999999999876
No 67
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=96.99 E-value=0.0051 Score=48.89 Aligned_cols=68 Identities=13% Similarity=0.135 Sum_probs=56.4
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCchhhcccCCCCEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVV 72 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y~GKiL~D---~~tL~d~gI~~gstI~v 72 (397)
+|.||..+|+.+...+..++||.+|.+-|....+ ......+|+ |-.|.|.+ ++||.++|+..+.+|+|
T Consensus 6 ~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~---~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v 78 (80)
T smart00166 6 RLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALT---DGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL 78 (80)
T ss_pred EEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHccc---CCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence 6889999999999999999999999999966555 445667775 66788854 47999999998888865
No 68
>COG5417 Uncharacterized small protein [Function unknown]
Probab=96.85 E-value=0.0045 Score=48.58 Aligned_cols=68 Identities=7% Similarity=0.218 Sum_probs=55.9
Q ss_pred EEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC--CCCeEEEeCCeecCCCCchhhcccCCCCEEEE
Q 015999 5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP--ASQQMLIHQGKVLKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 5 Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip--~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v 72 (397)
++..+|++|.+.+....+|+.|-..+.+...-+-.+ -..+|+.-++++|.+++.|.+|+|.+|+.+.+
T Consensus 11 ~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei 80 (81)
T COG5417 11 FTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI 80 (81)
T ss_pred eEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence 466789999999999999999998887766532112 24578899999999999999999999999865
No 69
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=96.80 E-value=0.0022 Score=44.90 Aligned_cols=38 Identities=34% Similarity=0.431 Sum_probs=34.4
Q ss_pred HHHHHHHHHc--CCCCCCHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 168 EATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 168 e~~I~~i~~M--G~~~f~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
++.|+.|.+| . |+++.|+++|++.-+|.|+||++|+.|
T Consensus 2 ~~~v~~L~~mFP~---~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 2 EEMVQQLQEMFPD---LDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHHSSS---S-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 6789999999 6 999999999999999999999999865
No 70
>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=96.79 E-value=0.0052 Score=47.37 Aligned_cols=63 Identities=17% Similarity=0.210 Sum_probs=46.8
Q ss_pred eCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEE
Q 015999 7 TLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 7 tl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v 72 (397)
..+++.+.|.|.++.++.++-+..+.+++ +.+++-.|.|++|.|+-+.++.-.|+.+|.++.+
T Consensus 3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~---l~~~~~~L~h~~k~ldlslp~R~snL~n~akLeL 65 (65)
T PF11470_consen 3 CYNFRRFKVKVTPNTTLNQVLEEACKKFG---LDPSSYDLKHNNKPLDLSLPFRLSNLPNNAKLEL 65 (65)
T ss_dssp -TTS-EEEE---TTSBHHHHHHHHHHHTT-----GGG-EEEETTEEESSS-BHHHH---SS-EEEE
T ss_pred ccCCcEEEEEECCCCCHHHHHHHHHHHcC---CCccceEEEECCEEeccccceeecCCCCCCEEeC
Confidence 46788999999999999999999999999 8899999999999999999999999999998864
No 71
>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]
Probab=96.76 E-value=0.0031 Score=60.23 Aligned_cols=70 Identities=17% Similarity=0.212 Sum_probs=53.7
Q ss_pred CEEEEEeCCCc-EEE-EEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE----EeCCeecCCCCchhhcccCCCCEEEE
Q 015999 1 MKVFVKTLKGT-HFE-IEVKPEDKVSDVKKNIETVQGSDVYPASQQML----IHQGKVLKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 1 MkI~Vktl~gk-~~~-veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrL----iy~GKiL~D~~tL~d~gI~~gstI~v 72 (397)
|+|++++.++. ..+ .+...+.||.|++++|..+..+ +.+.++|+ --+||.|.|+.+|++|+..++.+|.|
T Consensus 1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k--~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~v 76 (297)
T KOG1639|consen 1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLK--ITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIYV 76 (297)
T ss_pred CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhc--cCccchhheeeccCCCccccchhHHHHhccCCCCEEEE
Confidence 88999987663 333 5677889999999888766543 55544444 34899999999999999999987765
No 72
>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=96.73 E-value=0.012 Score=46.27 Aligned_cols=67 Identities=28% Similarity=0.392 Sum_probs=53.2
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCchhhcccCCCCEEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVVM 73 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y~GKiL~D---~~tL~d~gI~~gstI~v~ 73 (397)
+|.||..+|+.+...+..++||.+|..-|..... .....+|+ |-.|.|.| +.||.++|+. .+.+.+.
T Consensus 4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~----~~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~-~s~~~~~ 75 (77)
T cd01767 4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGP----PAEPFTLMTSFPRRVLTDLDYELTLQEAGLV-NEVVFQR 75 (77)
T ss_pred EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCC----CCCCEEEEeCCCCccCCCCCccCcHHHcCCc-cceEEEE
Confidence 6889999999999999999999999999976544 24567776 56788854 7899999999 4555443
No 73
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=96.73 E-value=0.0019 Score=67.25 Aligned_cols=43 Identities=26% Similarity=0.392 Sum_probs=39.1
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhCC-CHHHHHHHHhccCCCCC
Q 015999 354 REAIERLEAMGFDRALVLEVFFACNK-NEELAANYLLDHMHEFE 396 (397)
Q Consensus 354 ~~ai~rL~~lGF~r~~~iqAy~ac~k-ne~~Aan~L~~~~~d~~ 396 (397)
+.+|++|++|||+...+.+||+++.. |-|-|-||||+||.|-|
T Consensus 559 qs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqHMdDPd 602 (749)
T COG5207 559 QSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQHMDDPD 602 (749)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhhccCcc
Confidence 36799999999999999999999976 89999999999998764
No 74
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=96.63 E-value=0.014 Score=46.59 Aligned_cols=65 Identities=22% Similarity=0.305 Sum_probs=52.6
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC-CCchhhcccCCCC
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENS 68 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y~GKiL~D-~~tL~d~gI~~gs 68 (397)
+|.||..+|+.+...+..++||.+|..-|....+. .......|+ |-.|.|.| +.||++.|+.+..
T Consensus 6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~--~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s~ 73 (79)
T cd01770 6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPE--FAARPFTLMTAFPVKELSDESLTLKEANLLNAV 73 (79)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCC--CCCCCEEEecCCCCcccCCCCCcHHHCCCcCcE
Confidence 68899999999999999999999999999876541 223567776 67888855 7899999999643
No 75
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=96.60 E-value=0.016 Score=46.09 Aligned_cols=67 Identities=19% Similarity=0.358 Sum_probs=55.6
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC---CCchhhcccCCCCEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD---VTTLEENKVAENSFVVV 72 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y~GKiL~D---~~tL~d~gI~~gstI~v 72 (397)
+|.||..+|+.+...+..++||.+|..-|....+ . ....+|+ |-.|.+.+ ++||.++|+.+..+|+|
T Consensus 6 ~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~---~-~~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v 77 (79)
T cd01772 6 RIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTG---N-GGPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV 77 (79)
T ss_pred EEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCC---C-CCCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence 6889999999999999999999999999976544 2 3567776 67888854 48999999999988876
No 76
>KOG0013 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.56 E-value=0.0041 Score=58.01 Aligned_cols=61 Identities=26% Similarity=0.380 Sum_probs=54.0
Q ss_pred CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEE
Q 015999 9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 9 ~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v 72 (397)
.++.|.+.+...+||.++|.++....+ +++-.|+++|+|++|.|...|..|+|..|...+|
T Consensus 155 T~~d~~lta~~~Dtv~eik~~L~Aaeg---~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvl 215 (231)
T KOG0013|consen 155 TREDFWLTAPHYDTVGEIKRALRAAEG---VDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVL 215 (231)
T ss_pred hhhheeecccCcCcHHHHHHHHHHhhc---cchhhheeeccCCceeccccceeeeecCCCEEEE
Confidence 466788888899999999999999999 7788999999999999999999999999954333
No 77
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=96.43 E-value=0.0042 Score=61.58 Aligned_cols=40 Identities=33% Similarity=0.519 Sum_probs=36.7
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015999 355 EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE 394 (397)
Q Consensus 355 ~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~~~~d 394 (397)
..|.+|++|||+|++|+.|+.|..+|-|.|++||+..--+
T Consensus 137 ~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~GIP~ 176 (340)
T KOG0011|consen 137 QTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLNGIPE 176 (340)
T ss_pred HHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhcCCcc
Confidence 5599999999999999999999999999999999986544
No 78
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=96.35 E-value=0.0023 Score=68.40 Aligned_cols=43 Identities=40% Similarity=0.652 Sum_probs=40.2
Q ss_pred cchHHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHcCCC
Q 015999 165 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIP 210 (397)
Q Consensus 165 ~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~GIP 210 (397)
+..|..|.-|++|| |.|.|++.||++..||.+|||||+++-+-
T Consensus 633 ~~~e~~v~si~smG---f~~~qa~~aL~~~n~nveravDWif~h~d 675 (763)
T KOG0944|consen 633 EVDEESVASIVSMG---FSRNQAIKALKATNNNVERAVDWIFSHMD 675 (763)
T ss_pred CCChhHheeeeeec---CcHHHHHHHHHhcCccHHHHHHHHHhccc
Confidence 56789999999999 99999999999999999999999999855
No 79
>smart00727 STI1 Heat shock chaperonin-binding motif.
Probab=96.32 E-value=0.0046 Score=42.82 Aligned_cols=35 Identities=46% Similarity=0.652 Sum_probs=29.3
Q ss_pred hhccHHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHH
Q 015999 275 LRNSQQFQALRTMVQANPQILQPMLQELGKQNPHLMRLI 313 (397)
Q Consensus 275 L~~~P~f~~lrq~vq~NP~ll~~~Lqqi~~~nP~l~~~I 313 (397)
+..+|+|+++++.+++||+++..+++. ||++++.|
T Consensus 7 ~l~~P~~~~~l~~~~~nP~~~~~~~~~----nP~~~~~i 41 (41)
T smart00727 7 RLQNPQVQSLLQDMQQNPDMLAQMLQE----NPQLLQLI 41 (41)
T ss_pred HHcCHHHHHHHHHHHHCHHHHHHHHHh----CHHhHhhC
Confidence 345999999999999999988877765 99998754
No 80
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=96.24 E-value=0.01 Score=41.46 Aligned_cols=37 Identities=32% Similarity=0.475 Sum_probs=32.9
Q ss_pred HHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015999 355 EAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 355 ~ai~rL~~l--GF~r~~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
+.|++|.+| .++++.+..+|.+|++|++.|++.||+.
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 468999998 6899999999999999999999999974
No 81
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=96.10 E-value=0.049 Score=43.92 Aligned_cols=69 Identities=19% Similarity=0.338 Sum_probs=59.1
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC---CCCchhhcccCCCCEEEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK---DVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y~GKiL~---D~~tL~d~gI~~gstI~v~v 74 (397)
+|.||..+|+.++-.+..++++.+|-.-|.. .| .+.+..+|+ |--|++. .+.||.++|+.+..+|+|--
T Consensus 7 ~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g---~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq~ 80 (82)
T cd01773 7 RLMLRYPDGKREQIALPEQAKLLALVRHVQS-KG---YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE 80 (82)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cC---CCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEec
Confidence 6899999999999999999999999998877 56 778899997 6678773 35899999999999998743
No 82
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=95.98 E-value=0.049 Score=49.30 Aligned_cols=77 Identities=18% Similarity=0.210 Sum_probs=55.5
Q ss_pred CEEEEEeCCC----cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCe-EEEe-CCeec--CCCCchhhcccCCCC----
Q 015999 1 MKVFVKTLKG----THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQ-MLIH-QGKVL--KDVTTLEENKVAENS---- 68 (397)
Q Consensus 1 MkI~Vktl~g----k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~q-rLiy-~GKiL--~D~~tL~d~gI~~gs---- 68 (397)
|+|+|++++| .++.+.+..+.||.+|+.+|....+ ++...+ .|.+ .++.| .++..++++.-...+
T Consensus 1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~---~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~~~~ 77 (162)
T PF13019_consen 1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLP---IPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDSDFI 77 (162)
T ss_pred CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcC---CCccceeEEEEeCCCeeCCCccccHHhhccCcCCCCce
Confidence 7899999999 5888999999999999999999998 777763 3444 34444 456667777544433
Q ss_pred EEEEEEeecCCC
Q 015999 69 FVVVMLTKVIRF 80 (397)
Q Consensus 69 tI~v~v~k~~~~ 80 (397)
+|+|.++..+..
T Consensus 78 ~l~l~~rl~GGK 89 (162)
T PF13019_consen 78 TLRLSLRLRGGK 89 (162)
T ss_pred EEEEEEeccCCC
Confidence 456666655433
No 83
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.95 E-value=0.0091 Score=54.77 Aligned_cols=45 Identities=22% Similarity=0.287 Sum_probs=40.9
Q ss_pred ccCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015999 347 VTVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 347 ~~lt~Ee~~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
....+.+...|++|++|||+|..++.+|...++|.+.|.+.||+.
T Consensus 156 ~~~~~~~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~~~~s~ 200 (200)
T KOG0418|consen 156 LPDDPWDKKKVDSLIEMGFSELEAILVLSGSDWNLADATEQLLSG 200 (200)
T ss_pred CCCCchhHHHHHHHHHhcccHHHHHHHhhccccchhhhhHhhccC
Confidence 455677788999999999999999999999999999999999873
No 84
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=95.93 E-value=0.02 Score=40.28 Aligned_cols=40 Identities=25% Similarity=0.298 Sum_probs=32.6
Q ss_pred HHHHHHHHc-CCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015999 355 EAIERLEAM-GFDRALVLEVFFACNKNEELAANYLLDHMHE 394 (397)
Q Consensus 355 ~ai~rL~~l-GF~r~~~iqAy~ac~kne~~Aan~L~~~~~d 394 (397)
+.|.+++++ |.+++.+++.|.+|++|.+.|++..|++..+
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~~~ 42 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDGEA 42 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS-S
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence 457888876 8999999999999999999999999987543
No 85
>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=95.88 E-value=0.062 Score=43.52 Aligned_cols=68 Identities=16% Similarity=0.170 Sum_probs=55.9
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC--CeecC--------CCCchhhcccCCCCEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--GKVLK--------DVTTLEENKVAENSFVV 71 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~--GKiL~--------D~~tL~d~gI~~gstI~ 71 (397)
+|.||..+|+.+.-.+..++||.+|..-|.. .+ ..++..+|+++ -|++. .+.||++.||.+..+|.
T Consensus 6 ~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~---~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L~ 81 (85)
T cd01774 6 KIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LK---ETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLF 81 (85)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CC---CCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEE
Confidence 6889999999999999999999999999953 44 45688899864 37885 36799999999888877
Q ss_pred EE
Q 015999 72 VM 73 (397)
Q Consensus 72 v~ 73 (397)
|-
T Consensus 82 V~ 83 (85)
T cd01774 82 VQ 83 (85)
T ss_pred Ee
Confidence 63
No 86
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.64 E-value=0.015 Score=53.29 Aligned_cols=45 Identities=27% Similarity=0.300 Sum_probs=43.0
Q ss_pred ccCCcchHHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 161 LVAGSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 161 l~~g~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
...+..+.+.|.+|.+|| |+|+.++.+|+-..-|-.+|.|+|++|
T Consensus 156 ~~~~~~~~~~v~~l~~mG---f~~~~~i~~L~~~~w~~~~a~~~~~s~ 200 (200)
T KOG0418|consen 156 LPDDPWDKKKVDSLIEMG---FSELEAILVLSGSDWNLADATEQLLSG 200 (200)
T ss_pred CCCCchhHHHHHHHHHhc---ccHHHHHHHhhccccchhhhhHhhccC
Confidence 678889999999999999 999999999999999999999999886
No 87
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=95.42 E-value=0.12 Score=41.32 Aligned_cols=68 Identities=22% Similarity=0.274 Sum_probs=57.5
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecC--C-CCchhhcccCCCCEEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLK--D-VTTLEENKVAENSFVVVM 73 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y~GKiL~--D-~~tL~d~gI~~gstI~v~ 73 (397)
+|.||..+|+.+.-.+..++++.+|..-|... | ++....+|+ |--|.+. | +.||.+.|+....+|+|-
T Consensus 6 ~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~---~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~Ve 78 (80)
T cd01771 6 KLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-G---YPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLILE 78 (80)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-C---CCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEEE
Confidence 68899999999988999999999999999754 6 667788886 6778884 2 579999999999988773
No 88
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=95.31 E-value=0.047 Score=38.20 Aligned_cols=39 Identities=26% Similarity=0.406 Sum_probs=35.3
Q ss_pred hHHHHHHHHHc--CCCCCCHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 167 LEATVQQILDM--GGGSWDRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 167 ~e~~I~~i~~M--G~~~f~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
.++.|..|.+| . ++++.|++.|++.-+|.|+|++.|+.|
T Consensus 2 ~~~~v~~L~~mFP~---l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 2 NDEALHDLKDMFPN---LDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred hHHHHHHHHHHCCC---CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 35788999999 5 799999999999999999999999876
No 89
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=94.95 E-value=0.097 Score=42.73 Aligned_cols=68 Identities=16% Similarity=0.181 Sum_probs=58.2
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
|.|..-+|..+.+.|..+.+...|.+..+.+.| -..+..|++|.|+-++-++|-.+++..+++.|.++
T Consensus 27 Lkvv~qd~telfFkiKktT~f~klm~af~~rqG---K~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav 94 (103)
T COG5227 27 LKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQG---KNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAV 94 (103)
T ss_pred eEEecCCCCEEEEEEeccchHHHHHHHHHHHhC---cCcceeEEEEcceecCCCCChhhcCCccchHHHHH
Confidence 444445677788899999999999999999999 45789999999999999999999999999987554
No 90
>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]
Probab=94.93 E-value=0.064 Score=50.16 Aligned_cols=70 Identities=19% Similarity=0.221 Sum_probs=54.3
Q ss_pred EEEEEeCCCc-EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE-EeCC-----eecC-CCCchhhcccCCCCEEEEE
Q 015999 2 KVFVKTLKGT-HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQG-----KVLK-DVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 2 kI~Vktl~gk-~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrL-iy~G-----KiL~-D~~tL~d~gI~~gstI~v~ 73 (397)
+|.|.+...+ .++.....+.||.+||.+++..+| .+++.++| +|.| -.|. ++..|..|+..+|-.|||+
T Consensus 3 ~v~Iss~~~~~~~Ekr~~~~ltl~q~K~KLe~~~G---~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihvi 79 (234)
T KOG3206|consen 3 RVVISSSLNDFRTEKRLSNSLTLAQFKDKLELLTG---TEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVI 79 (234)
T ss_pred EEEEecccccchhhhhcCCcCcHHHHHhhhhhhhC---CCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEE
Confidence 4555543222 245567889999999999999999 89999998 5766 2464 5689999999999999987
Q ss_pred E
Q 015999 74 L 74 (397)
Q Consensus 74 v 74 (397)
=
T Consensus 80 D 80 (234)
T KOG3206|consen 80 D 80 (234)
T ss_pred e
Confidence 4
No 91
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=94.86 E-value=0.067 Score=37.39 Aligned_cols=37 Identities=35% Similarity=0.442 Sum_probs=32.5
Q ss_pred HHHHHHHHc--CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015999 355 EAIERLEAM--GFDRALVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 355 ~ai~rL~~l--GF~r~~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
+.|++|.+| .+++..+...|.+|++|.+.|+|.||+.
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 468999999 3369999999999999999999999974
No 92
>PF15044 CLU_N: Mitochondrial function, CLU-N-term
Probab=94.38 E-value=0.067 Score=42.43 Aligned_cols=56 Identities=23% Similarity=0.351 Sum_probs=46.1
Q ss_pred eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhc-ccCCCCEEEEEE
Q 015999 17 VKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN-KVAENSFVVVML 74 (397)
Q Consensus 17 V~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~-gI~~gstI~v~v 74 (397)
|.++++|.+||+-|...... ..-....|.++|+.|+|...|+++ |++++.+|.|+.
T Consensus 1 v~~~d~v~dvrq~L~~~~~t--~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lve 57 (76)
T PF15044_consen 1 VSPTDTVQDVRQVLAESPET--CYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELVE 57 (76)
T ss_pred CChhhHHHHHHHHHHhCccc--cceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEEe
Confidence 56789999999999766442 445677999999999998899888 699999998874
No 93
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=93.76 E-value=0.05 Score=40.43 Aligned_cols=37 Identities=27% Similarity=0.526 Sum_probs=25.0
Q ss_pred HHHHHHHHHcCCChHHHHHHHHHhC-----CCHHHHHHHHhc
Q 015999 354 REAIERLEAMGFDRALVLEVFFACN-----KNEELAANYLLD 390 (397)
Q Consensus 354 ~~ai~rL~~lGF~r~~~iqAy~ac~-----kne~~Aan~L~~ 390 (397)
.+.|+|++.|||+++.||+||.--+ ++-+...|+.++
T Consensus 10 ~~lVd~F~~mGF~~dkVvevlrrlgik~~n~~dn~t~~~ilE 51 (55)
T PF09288_consen 10 KDLVDQFENMGFERDKVVEVLRRLGIKSMNGVDNETENKILE 51 (55)
T ss_dssp HHHHHHHHHHT--HHHHHHHHHHS--SS--SS--HHHHHHHH
T ss_pred HHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCccchhHHHHHH
Confidence 4669999999999999999998643 345566666554
No 94
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=93.20 E-value=0.097 Score=38.94 Aligned_cols=23 Identities=35% Similarity=0.679 Sum_probs=19.3
Q ss_pred HHHHHHHHHcCCCCCCHHHHHHHHHH
Q 015999 168 EATVQQILDMGGGSWDRETVIRALRA 193 (397)
Q Consensus 168 e~~I~~i~~MG~~~f~r~~v~~ALrA 193 (397)
...|+++++|| |+|+.|+.|||.
T Consensus 10 ~~lVd~F~~mG---F~~dkVvevlrr 32 (55)
T PF09288_consen 10 KDLVDQFENMG---FERDKVVEVLRR 32 (55)
T ss_dssp HHHHHHHHHHT-----HHHHHHHHHH
T ss_pred HHHHHHHHHcC---CcHHHHHHHHHH
Confidence 57899999999 999999999985
No 95
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=93.18 E-value=0.31 Score=36.61 Aligned_cols=56 Identities=20% Similarity=0.293 Sum_probs=40.4
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
|+|+|. |+. +++....|+.+||.++.. +.=.+||+|-..+++.. +++||.|+++-|
T Consensus 1 M~I~vN---~k~--~~~~~~~tl~~lr~~~k~---------~~DI~I~NGF~~~~d~~-----L~e~D~v~~Ikk 56 (57)
T PF14453_consen 1 MKIKVN---EKE--IETEENTTLFELRKESKP---------DADIVILNGFPTKEDIE-----LKEGDEVFLIKK 56 (57)
T ss_pred CEEEEC---CEE--EEcCCCcCHHHHHHhhCC---------CCCEEEEcCcccCCccc-----cCCCCEEEEEeC
Confidence 666664 554 566778899999987632 23378999999987654 677999987643
No 96
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=93.05 E-value=0.12 Score=41.89 Aligned_cols=35 Identities=29% Similarity=0.637 Sum_probs=30.9
Q ss_pred HHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015999 357 IERLEAMGFDRALVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 357 i~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
|+++.++||++..|++|+.+|-+|..+|..|+++.
T Consensus 1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~ 35 (87)
T PF11626_consen 1 IKHYEELGYSREFVTHALYATSGDPELARRFVLNF 35 (87)
T ss_dssp -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 57789999999999999999999999999988875
No 97
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=92.58 E-value=0.17 Score=50.95 Aligned_cols=69 Identities=14% Similarity=0.135 Sum_probs=60.3
Q ss_pred CEEEEEeC--CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCC--CchhhcccCCCCEEEE
Q 015999 1 MKVFVKTL--KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDV--TTLEENKVAENSFVVV 72 (397)
Q Consensus 1 MkI~Vktl--~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~--~tL~d~gI~~gstI~v 72 (397)
|.++|.+. ..++|.++|..+.....|+..++...| +..+..-|||+++.|.++ ..|..||++.+++|.+
T Consensus 1 M~~tvs~~l~~~~~~~i~v~~dg~L~nl~aL~~~d~g---~~~~~~~li~n~~~l~s~~s~~l~Q~g~~~~dsl~l 73 (380)
T KOG0012|consen 1 MSLTVSVALNFEKKFPIPVTTDGELNNLAALCWKDTG---IVYDPSDLIYNPRPLVSNESQGLTQIGLKDGDSLAL 73 (380)
T ss_pred CeEEEEEEecceeeeccccccccchhhHHHHHHHHhC---cccchhhcccCCCccccchhhhhhhcccccceeEec
Confidence 67777665 667889999999999999999999999 999999999999999764 6799999999998854
No 98
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=92.36 E-value=0.23 Score=40.30 Aligned_cols=35 Identities=29% Similarity=0.469 Sum_probs=31.0
Q ss_pred HHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 171 VQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 171 I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
|+.+.+.| |.++.|.+||++.-.+|..|..|++++
T Consensus 1 i~~~~~~g---~~~~~v~~aL~~tSgd~~~a~~~vl~~ 35 (87)
T PF11626_consen 1 IKHYEELG---YSREFVTHALYATSGDPELARRFVLNF 35 (87)
T ss_dssp -HHHHHHT---B-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred CchHHHhC---CCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 56678899 999999999999999999999999888
No 99
>PRK06437 hypothetical protein; Provisional
Probab=92.36 E-value=0.95 Score=34.84 Aligned_cols=54 Identities=22% Similarity=0.327 Sum_probs=43.0
Q ss_pred CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 9 ~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
.++...++++...||.+|-+. .+ ++++...+..+|+++. .++-|++||.|.++-
T Consensus 9 g~~~~~~~i~~~~tv~dLL~~----Lg---i~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 9 GHINKTIEIDHELTVNDIIKD----LG---LDEEEYVVIVNGSPVL-----EDHNVKKEDDVLILE 62 (67)
T ss_pred CCcceEEEcCCCCcHHHHHHH----cC---CCCccEEEEECCEECC-----CceEcCCCCEEEEEe
Confidence 456677888888899987654 47 8888899999999997 556788999998763
No 100
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=90.94 E-value=0.92 Score=35.87 Aligned_cols=66 Identities=11% Similarity=0.160 Sum_probs=45.2
Q ss_pred CEEEEEeCC------C-cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC--CCeEEEeCCeecCCCCchhhcccCCCCEEE
Q 015999 1 MKVFVKTLK------G-THFEIEVKPEDKVSDVKKNIETVQGSDVYPA--SQQMLIHQGKVLKDVTTLEENKVAENSFVV 71 (397)
Q Consensus 1 MkI~Vktl~------g-k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~--~~qrLiy~GKiL~D~~tL~d~gI~~gstI~ 71 (397)
|+|+|+... | ....+++....||.+|++.|...... +.. ....+..+|+...++ +-|++||.|.
T Consensus 2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~--l~~~~~~~~vavN~~~v~~~-----~~l~dgDeVa 74 (82)
T PLN02799 2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPS--LEEVRSCCVLALNEEYTTES-----AALKDGDELA 74 (82)
T ss_pred eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChh--HHHHhhCcEEEECCEEcCCC-----cCcCCCCEEE
Confidence 678888653 3 45677888889999999999766421 111 123466788886533 4578899998
Q ss_pred EE
Q 015999 72 VM 73 (397)
Q Consensus 72 v~ 73 (397)
++
T Consensus 75 i~ 76 (82)
T PLN02799 75 II 76 (82)
T ss_pred Ee
Confidence 76
No 101
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. 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 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid 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
Probab=90.82 E-value=2 Score=34.99 Aligned_cols=70 Identities=17% Similarity=0.160 Sum_probs=49.9
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCeEEEe----CCeec-CCCCchhhc----ccCCCCE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA---SQQMLIH----QGKVL-KDVTTLEEN----KVAENSF 69 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~---~~qrLiy----~GKiL-~D~~tL~d~----gI~~gst 69 (397)
..++|+.+|+.+.+.+.+++.+.+|+..|.++.| +.. ....|.| +-++| .-+.-|.+| ......+
T Consensus 2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~---~d~~~~~~~~L~YlDDEgD~VllT~D~DL~e~v~iar~~g~~~ 78 (86)
T cd06409 2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLG---DDDFETHLYALSYVDDEGDIVLITSDSDLVAAVLVARSAGLKK 78 (86)
T ss_pred cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhC---CccccCCcccEEEEcCCCCEEEEeccchHHHHHHHHHHcCCCE
Confidence 4678899999999999999999999999999999 554 5778877 33444 333334333 2344455
Q ss_pred EEEEE
Q 015999 70 VVVML 74 (397)
Q Consensus 70 I~v~v 74 (397)
|.+.+
T Consensus 79 v~L~v 83 (86)
T cd06409 79 LDLHL 83 (86)
T ss_pred EEEEE
Confidence 65555
No 102
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=90.20 E-value=0.44 Score=49.95 Aligned_cols=40 Identities=38% Similarity=0.553 Sum_probs=36.2
Q ss_pred chHHHHHHHHHcCCCCC-CHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 166 NLEATVQQILDMGGGSW-DRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 166 ~~e~~I~~i~~MG~~~f-~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
.|..-.+++-+|| | +|+.-.+||+|.+.+.++|||-|+.+
T Consensus 453 r~q~QLeQL~~MG---F~nre~nlqAL~atgGdi~aAverll~s 493 (493)
T KOG0010|consen 453 RYQTQLEQLNDMG---FLDREANLQALRATGGDINAAVERLLGS 493 (493)
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHHHHhcCcHHHHHHHHhcC
Confidence 4666789999999 9 99999999999999999999999753
No 103
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=89.71 E-value=0.49 Score=33.83 Aligned_cols=37 Identities=22% Similarity=0.463 Sum_probs=29.5
Q ss_pred hHHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 015999 167 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY 206 (397)
Q Consensus 167 ~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~ 206 (397)
.++.+..|+..| |.+.++.+|++....+++.-+|.++
T Consensus 3 ~~d~~~AL~~LG---y~~~e~~~av~~~~~~~~~~~e~~i 39 (47)
T PF07499_consen 3 LEDALEALISLG---YSKAEAQKAVSKLLEKPGMDVEELI 39 (47)
T ss_dssp HHHHHHHHHHTT---S-HHHHHHHHHHHHHSTTS-HHHHH
T ss_pred HHHHHHHHHHcC---CCHHHHHHHHHHhhcCCCCCHHHHH
Confidence 468899999999 9999999999988766666676665
No 104
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=89.57 E-value=2.3 Score=32.88 Aligned_cols=53 Identities=26% Similarity=0.458 Sum_probs=40.4
Q ss_pred CCc--EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 9 KGT--HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 9 ~gk--~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
+|+ ...++++...||.+|.+.+ + ++.....+..+|+++.. +.-+++||.|.++
T Consensus 10 ng~~~~~~~~~~~~~tv~~ll~~l----~---~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii 64 (70)
T PRK08364 10 IGRGIEKEIEWRKGMKVADILRAV----G---FNTESAIAKVNGKVALE-----DDPVKDGDYVEVI 64 (70)
T ss_pred eccccceEEEcCCCCcHHHHHHHc----C---CCCccEEEEECCEECCC-----CcCcCCCCEEEEE
Confidence 454 5677888888999988665 5 66777788899999854 4557889998876
No 105
>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=89.03 E-value=2.4 Score=32.97 Aligned_cols=67 Identities=21% Similarity=0.207 Sum_probs=49.6
Q ss_pred EEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCC-CCCeEEEe----CC--eecCCCCchhhcccCCCCEEEEEE
Q 015999 5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYP-ASQQMLIH----QG--KVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 5 Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip-~~~qrLiy----~G--KiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+.++|...+++|+.+.|+.+|=..|+...+ +. .+-.-|.| +| .-|+.+++|.+...+......+..
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~---l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~~~~~~~l~f 74 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLG---LKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKKNNPPFTLYF 74 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHHT---TSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBTSSSSEEEEE
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcC---CCCccEEEEEEeecCCCcceeccCcccHHHHcCCCCCCEEEEE
Confidence 6778999999999999999999999999998 53 33456777 23 236888899998777334333333
No 106
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=89.02 E-value=1.7 Score=32.93 Aligned_cols=60 Identities=13% Similarity=0.258 Sum_probs=42.0
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+| +|+.+.+ + ..||.+|...+ + +..+...+-++++++. .....+.-+++||.|-++-
T Consensus 1 m~i~~---Ng~~~~~--~-~~tl~~Ll~~l----~---~~~~~vavavN~~iv~-~~~~~~~~L~dgD~Ieiv~ 60 (65)
T PRK06488 1 MKLFV---NGETLQT--E-ATTLALLLAEL----D---YEGNWLATAVNGELVH-KEARAQFVLHEGDRIEILS 60 (65)
T ss_pred CEEEE---CCeEEEc--C-cCcHHHHHHHc----C---CCCCeEEEEECCEEcC-HHHcCccccCCCCEEEEEE
Confidence 55555 4777776 3 35899888654 5 6566677889999986 2334556789999998763
No 107
>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=88.72 E-value=1.4 Score=35.39 Aligned_cols=37 Identities=16% Similarity=0.169 Sum_probs=34.3
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCe
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK 51 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GK 51 (397)
++.|.|.+..+..+|+++|.++.+ ++.+..+|.|+-.
T Consensus 12 tIaIrvp~~~~y~~L~~ki~~kLk---l~~e~i~LsYkde 48 (80)
T cd06406 12 TVAIQVARGLSYATLLQKISSKLE---LPAEHITLSYKSE 48 (80)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHhC---CCchhcEEEeccC
Confidence 889999999999999999999999 9999999999643
No 108
>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=88.65 E-value=2 Score=33.30 Aligned_cols=57 Identities=11% Similarity=0.142 Sum_probs=41.2
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCC-CCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGS-DVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~-~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
...++++...||.+|.+.+...++. .........+..+|+... .+.-|++||.|.++
T Consensus 17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~-----~~~~l~~gD~v~i~ 74 (80)
T cd00754 17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVR-----LDTPLKDGDEVAII 74 (80)
T ss_pred eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcC-----CCcccCCCCEEEEe
Confidence 4567777789999999999887541 001234556778999887 34568899999886
No 109
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=88.56 E-value=2.5 Score=34.54 Aligned_cols=62 Identities=13% Similarity=0.198 Sum_probs=42.4
Q ss_pred cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--e--CCe-ecCC-CCchhhcccCCCCEEEEEEee
Q 015999 11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--H--QGK-VLKD-VTTLEENKVAENSFVVVMLTK 76 (397)
Q Consensus 11 k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y--~GK-iL~D-~~tL~d~gI~~gstI~v~v~k 76 (397)
..++..+...+||..+++.+.+.+. | ....||- | ++. .|.+ +.||.+.||.+|-+|++-.+.
T Consensus 14 ~~~t~~FSk~DTI~~v~~~~rklf~---i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn 81 (88)
T PF14836_consen 14 SVLTKQFSKTDTIGFVEKEMRKLFN---I-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERN 81 (88)
T ss_dssp EEEEEEE-TTSBHHHHHHHHHHHCT-----TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--
T ss_pred cHhHhhccccChHHHHHHHHHHHhC---C-CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeec
Confidence 4577788999999999999999999 8 6778883 2 232 3644 579999999999988776554
No 110
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=88.53 E-value=1.3 Score=33.43 Aligned_cols=40 Identities=30% Similarity=0.388 Sum_probs=36.1
Q ss_pred hHHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHc
Q 015999 167 LEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYS 207 (397)
Q Consensus 167 ~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~ 207 (397)
.-++|+.|-|.-|+ +..+++-..|+-.+++||.||+-|++
T Consensus 5 ~rk~VQ~iKEiv~~-hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 5 SRKTVQSIKEIVGC-HSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHHHHHHhcC-CCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 46789999998655 89999999999999999999999986
No 111
>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown.
Probab=87.05 E-value=2.3 Score=36.75 Aligned_cols=60 Identities=17% Similarity=0.176 Sum_probs=43.6
Q ss_pred EeCC-CCCHHHHHHHHHHHhCCC-------CCCCCCeEEEeCC-----------------eec---CCCCchhhcccCCC
Q 015999 16 EVKP-EDKVSDVKKNIETVQGSD-------VYPASQQMLIHQG-----------------KVL---KDVTTLEENKVAEN 67 (397)
Q Consensus 16 eV~~-~~TV~dLK~~I~~~~g~~-------~ip~~~qrLiy~G-----------------KiL---~D~~tL~d~gI~~g 67 (397)
.|+. +.||++|++.+.+..... ++.-+.+||++.. .+| +++++|.+|||.+.
T Consensus 21 ~vdL~~~Tv~~l~~~v~~~I~t~~~~~Pfrn~~yDtlKIy~~AHg~Kt~nLvInle~De~~iL~~~~~~~tL~~~gv~nE 100 (122)
T PF10209_consen 21 NVDLKDTTVKDLKEQVKQDIKTRPGLPPFRNVKYDTLKIYTKAHGSKTNNLVINLEDDEDWILDVSDDDKTLKELGVENE 100 (122)
T ss_pred cCCcccCcHHHHHHHHHHHHhcCCCCCCceeeecceEEEEecCCCCCcCCceeeccCCcceeeecCCCCCcHHHcCCCcc
Confidence 4776 899999999987664321 2445667777532 367 67889999999999
Q ss_pred CEEEEEEe
Q 015999 68 SFVVVMLT 75 (397)
Q Consensus 68 stI~v~v~ 75 (397)
.-|-+..+
T Consensus 101 TEiSfF~~ 108 (122)
T PF10209_consen 101 TEISFFNM 108 (122)
T ss_pred ceeeeeCH
Confidence 98877654
No 112
>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function.
Probab=86.96 E-value=2.9 Score=32.19 Aligned_cols=67 Identities=16% Similarity=0.209 Sum_probs=53.1
Q ss_pred CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE-eCCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI-HQGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 9 ~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi-y~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
+|+...++........-+..+.-+..|...-|++...|- -+|.+|+-++.++|||+.++-++.+.++
T Consensus 4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLK 71 (76)
T PF10790_consen 4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLK 71 (76)
T ss_pred CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEee
Confidence 578888888888887777777666665433677777775 4789999999999999999999988765
No 113
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=86.64 E-value=1.4 Score=31.82 Aligned_cols=28 Identities=29% Similarity=0.401 Sum_probs=25.1
Q ss_pred CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015999 364 GFDRALVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 364 GF~r~~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
|=+|+..|+-+..++-|+++|+|-||+.
T Consensus 22 gksR~vIirELqrTnLdVN~AvNNlLsR 49 (53)
T PF11547_consen 22 GKSRNVIIRELQRTNLDVNLAVNNLLSR 49 (53)
T ss_dssp TS-HHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred CCcHHHHHHHHHHhcccHHHHHHHHhcc
Confidence 8899999999999999999999999987
No 114
>PF12754 Blt1: Cell-cycle control medial ring component; InterPro: IPR024737 During size-dependent cell cycle transitions controlled by the ubiquitous cyclin-dependent kinase Cdk1, Blt1 has been shown to co-localise with Cdr2 in the medial interphase nodes, as well as with Mid1 which was previously shown to localise to similar interphase structures. Physical interactions between Blt1-Mid1, Blt1-Cdr2 and Cdr2-Mid1 were detected, indicating that medial cortical nodes are formed by the ordered, Cdr2-dependent assembly of multiple interacting proteins during interphase[].; PDB: 2LO0_A.
Probab=86.57 E-value=0.21 Score=49.59 Aligned_cols=59 Identities=25% Similarity=0.396 Sum_probs=0.0
Q ss_pred EEEEEeCCCcEEEEEeC---C--CCCHHHHHHHHHH----------HhCCCCCCCCCeE-----EEeCCeecCCCCchhh
Q 015999 2 KVFVKTLKGTHFEIEVK---P--EDKVSDVKKNIET----------VQGSDVYPASQQM-----LIHQGKVLKDVTTLEE 61 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~---~--~~TV~dLK~~I~~----------~~g~~~ip~~~qr-----Liy~GKiL~D~~tL~d 61 (397)
.|++|.+.+-.+.|.+. + +.+|.+||..++. +.+ +|.+.+| |+|+-|.+.|.++|.+
T Consensus 80 tV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~---vp~dKik~~~~~lL~~kkPv~~~ktl~e 156 (309)
T PF12754_consen 80 TVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETR---VPLDKIKNFRCRLLYKKKPVGDSKTLAE 156 (309)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred EEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhccccccccccc---CCHHHhhhhhhhheecCccCCCcCcHHH
Confidence 35566665555444333 2 5789999999999 777 9999999 9999999999999888
Q ss_pred cc
Q 015999 62 NK 63 (397)
Q Consensus 62 ~g 63 (397)
..
T Consensus 157 ~l 158 (309)
T PF12754_consen 157 VL 158 (309)
T ss_dssp --
T ss_pred HH
Confidence 74
No 115
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=86.53 E-value=0.85 Score=47.42 Aligned_cols=41 Identities=22% Similarity=0.385 Sum_probs=38.1
Q ss_pred HHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHcCCCC
Q 015999 168 EATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPE 211 (397)
Q Consensus 168 e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~GIP~ 211 (397)
...|.+|+.|| |++-..+.||++.-||-|.|.++|+--++.
T Consensus 430 ~~~la~Lv~mG---F~e~~A~~ALe~~gnn~~~a~~~L~~s~~n 470 (568)
T KOG2561|consen 430 GISLAELVSMG---FEEGKARSALEAGGNNEDTAQRLLSASVAN 470 (568)
T ss_pred hhhHHHHHHhc---cccchHHHHHHhcCCcHHHHHHHHHHhCCC
Confidence 46799999999 999999999999999999999999988774
No 116
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=84.54 E-value=7.2 Score=31.40 Aligned_cols=59 Identities=25% Similarity=0.460 Sum_probs=44.1
Q ss_pred HHHHHHHhhhCHHHHHHHHHhHHHHHHHhcCCCCCCCCcccccccccCCCcccCCHHHHHHH-----HHHHHcCCChHHH
Q 015999 296 QPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAI-----ERLEAMGFDRALV 370 (397)
Q Consensus 296 ~~~Lqqi~~~nP~l~~~I~~n~~~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~Ee~~ai-----~rL~~lGF~r~~~ 370 (397)
+.++++| ..+|.+++...++|+.|+. .-.||+||+++| ..|..+|-+--..
T Consensus 7 nrli~~L-~~dp~~rerF~~DPea~~~-----------------------~~gLt~eE~~aL~~~D~~~L~~lGvhp~L~ 62 (81)
T cd07922 7 NRLIQEL-FKDPGLIERFQDDPSAVFE-----------------------EYGLTPAERAALREGTFGALTSIGVHPILQ 62 (81)
T ss_pred HHHHHHH-hcCHHHHHHHHHCHHHHHH-----------------------HcCCCHHHHHHHHccCHHHHHHcCCCHHHH
Confidence 5677775 4689999999999998876 225799999885 4588888777666
Q ss_pred HHHHHHhC
Q 015999 371 LEVFFACN 378 (397)
Q Consensus 371 iqAy~ac~ 378 (397)
..-++..|
T Consensus 63 mh~~~~~n 70 (81)
T cd07922 63 MHYLMYTN 70 (81)
T ss_pred HHHHHHcC
Confidence 66666554
No 117
>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=83.44 E-value=11 Score=34.24 Aligned_cols=69 Identities=19% Similarity=0.161 Sum_probs=48.9
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-CCeEEEeC---C---eecCCCCchhhcccCC-CCEEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQ---G---KVLKDVTTLEENKVAE-NSFVVVM 73 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~-~~qrLiy~---G---KiL~D~~tL~d~gI~~-gstI~v~ 73 (397)
.|.|..++|....+.++++.||.+|...|+.+.| +.. ...-|.+. + .-|+..++|.+...+. ...+++-
T Consensus 5 ~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~---l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~l~fr 81 (207)
T smart00295 5 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLG---IRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVKSEPLTLYFR 81 (207)
T ss_pred EEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhC---CCccceeEEEEEcCCCCcCeeCCCccCHHHhcCCCCCcEEEEE
Confidence 5788889999999999999999999999999999 643 22244331 1 3466677777776552 3344443
No 118
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=83.14 E-value=6.6 Score=30.79 Aligned_cols=58 Identities=19% Similarity=0.244 Sum_probs=41.2
Q ss_pred CcE-EEEEeCCC-CCHHHHHHHHHHHhCCCCCC-CCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 10 GTH-FEIEVKPE-DKVSDVKKNIETVQGSDVYP-ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 10 gk~-~~veV~~~-~TV~dLK~~I~~~~g~~~ip-~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
|+. ..+++... .||.+|+..+.++++.- .. .....+..+|+...+ +.-|++||.|.++
T Consensus 14 g~~~~~~~~~~~~~tv~~L~~~L~~~~p~l-~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~ 74 (80)
T TIGR01682 14 GTDEETLELPDESTTVGELKEHLAKEGPEL-AASRGQVMVAVNEEYVTD-----DALLNEGDEVAFI 74 (80)
T ss_pred CCCeEEEECCCCCcCHHHHHHHHHHhCchh-hhhccceEEEECCEEcCC-----CcCcCCCCEEEEe
Confidence 443 56788876 89999999998886410 11 134566778888875 4578899999886
No 119
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=82.87 E-value=3.6 Score=28.68 Aligned_cols=36 Identities=25% Similarity=0.403 Sum_probs=29.7
Q ss_pred HHHHHHHHHc-CCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 015999 168 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY 206 (397)
Q Consensus 168 e~~I~~i~~M-G~~~f~r~~v~~ALrAafnNpdrAveyL~ 206 (397)
++.|.+.|+. | -+++.++.-|+.+.+|.++||+.-+
T Consensus 1 ~e~i~~F~~iTg---~~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 1 DEKIAQFMSITG---ADEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHHHHHH----SSHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred CHHHHHHHHHHC---cCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4678888886 6 6999999999999999999998665
No 120
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=81.66 E-value=5.3 Score=30.34 Aligned_cols=60 Identities=17% Similarity=0.240 Sum_probs=42.7
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+| +|+.+.+ ....||.+|-.. .+ ++....-+.++|+++..+.- +.+ +++||.|-++-
T Consensus 1 m~i~v---NG~~~~~--~~~~tl~~ll~~----l~---~~~~~vav~~N~~iv~r~~~-~~~-L~~gD~ieIv~ 60 (65)
T PRK05863 1 MIVVV---NEEQVEV--DEQTTVAALLDS----LG---FPEKGIAVAVDWSVLPRSDW-ATK-LRDGARLEVVT 60 (65)
T ss_pred CEEEE---CCEEEEc--CCCCcHHHHHHH----cC---CCCCcEEEEECCcCcChhHh-hhh-cCCCCEEEEEe
Confidence 55555 4776655 467788877543 46 88889999999998864432 345 89999998764
No 121
>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=81.48 E-value=7 Score=30.43 Aligned_cols=45 Identities=16% Similarity=0.178 Sum_probs=37.2
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG 50 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~G 50 (397)
+|+|+. ++..+.+.+....|..+|+.+|..+++ +.....+|-|..
T Consensus 3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~---~~~~~~~l~Y~D 47 (81)
T smart00666 3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFG---LDNQSFTLKYQD 47 (81)
T ss_pred cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhC---CCCCCeEEEEEC
Confidence 455654 677888999999999999999999998 666788888864
No 122
>PF11620 GABP-alpha: GA-binding protein alpha chain; InterPro: IPR024668 GA-binding protein alpha is a transcription factor capable of interacting with purine rich repeats (GA repeats). This N-terminal domain found in the transcription factor GABP alpha consists of a five-stranded beta-sheet crossed by a distorted helix and has been termed OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300 [].; PDB: 2JUO_A.
Probab=81.35 E-value=4.2 Score=33.01 Aligned_cols=63 Identities=17% Similarity=0.125 Sum_probs=44.4
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
.+...++-..++..||..++.+.+ +.-+...+......|+.+++|-+-||+-...+.+.+--+
T Consensus 4 vI~q~mDI~epl~~Lk~lLe~Rl~---~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQi~ 66 (88)
T PF11620_consen 4 VIMQHMDIREPLSTLKKLLERRLG---ISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQIK 66 (88)
T ss_dssp EEEEEEESSSBGGGHHHHSHHHH----S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEEEE
T ss_pred eEEEEEecCCcHHHHHHHHHHhhC---CCcCCCeEEeccceecCCccHHHhhccccCEEEEEEEEE
Confidence 345567778899999999999999 777888888888889999999999999999998877643
No 123
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=80.87 E-value=2.8 Score=42.88 Aligned_cols=67 Identities=24% Similarity=0.370 Sum_probs=52.5
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCCeecCC-CCchhhcccCCCCEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQGKVLKD-VTTLEENKVAENSFV 70 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y~GKiL~D-~~tL~d~gI~~gstI 70 (397)
.|-||..+|+.+...++.+.||.||+..|...... .+...+.|+ |--|.|.| +.||++.|+.+.-.|
T Consensus 307 sIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~--~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsvlv 376 (380)
T KOG2086|consen 307 SIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPG--DSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSVLV 376 (380)
T ss_pred eEEEEecCCceeeeeccCcccHHHHHHHHHhcCCC--CcCCceeeeecCCCcccCCcchhHHhccchhhhhh
Confidence 47889889999999999999999999999887652 334456665 56788865 679999999865433
No 124
>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=80.59 E-value=5 Score=30.71 Aligned_cols=60 Identities=15% Similarity=0.150 Sum_probs=46.1
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
...+.+....||.+|.+.+..+++.- .......+..+|+...+ .-.+.-+++||.|.++-
T Consensus 13 ~~~~~~~~~~tv~~ll~~l~~~~p~~-~~~~~~~v~vN~~~v~~--~~~~~~l~~gD~V~i~p 72 (77)
T PF02597_consen 13 EEEIEVPEGSTVRDLLEALAERYPEL-ALRDRVAVAVNGEIVPD--DGLDTPLKDGDEVAILP 72 (77)
T ss_dssp EEEEEESSTSBHHHHHHHHCHHTGGG-HTTTTEEEEETTEEEGG--GTTTSBEETTEEEEEEE
T ss_pred CeEEecCCCCcHHHHHHHHHhhcccc-ccCccEEEEECCEEcCC--ccCCcCcCCCCEEEEEC
Confidence 56778889999999999998886411 12367888899999987 35566788999998863
No 125
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=80.59 E-value=1.2 Score=35.32 Aligned_cols=45 Identities=20% Similarity=0.397 Sum_probs=34.0
Q ss_pred ccCCHHHHHHHH----HHH-HcC--C-ChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015999 347 VTVTPEEREAIE----RLE-AMG--F-DRALVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 347 ~~lt~Ee~~ai~----rL~-~lG--F-~r~~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
..||+||++.+. +++ .|| . ++..+++|++-|..|++.|++||++.
T Consensus 18 ~~Ls~ed~~~L~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 18 DELSPEDQAQLYSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp HH-TCHHHHHHCHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred ccCCHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 468888886643 343 366 5 89999999999999999999999975
No 126
>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=80.37 E-value=7.1 Score=31.35 Aligned_cols=70 Identities=16% Similarity=0.158 Sum_probs=47.1
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-CCeEEEeCCe----e-cCCCCchhh----cccCCCCEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQGK----V-LKDVTTLEE----NKVAENSFV 70 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~-~~qrLiy~GK----i-L~D~~tL~d----~gI~~gstI 70 (397)
|+|++. .+|..+.+.+.++.+..+|+.+|.++++ +.. ....|-|..- + |..+.-|.+ |.....++|
T Consensus 1 ~~vK~~-~~~d~~r~~l~~~~~~~~L~~~i~~r~~---~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~~~~~~~~v 76 (82)
T cd06407 1 VRVKAT-YGEEKIRFRLPPSWGFTELKQEIAKRFK---LDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVYRSSGSHTI 76 (82)
T ss_pred CEEEEE-eCCeEEEEEcCCCCCHHHHHHHHHHHhC---CCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHHHHCCCCeE
Confidence 455555 3677889999999999999999999998 644 5677777432 2 333333444 344456666
Q ss_pred EEEE
Q 015999 71 VVML 74 (397)
Q Consensus 71 ~v~v 74 (397)
.+.+
T Consensus 77 ~l~v 80 (82)
T cd06407 77 RLLV 80 (82)
T ss_pred EEEe
Confidence 6655
No 127
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=80.12 E-value=1.1 Score=35.71 Aligned_cols=27 Identities=33% Similarity=0.434 Sum_probs=23.8
Q ss_pred C-CHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 182 W-DRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 182 f-~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
. ++.+++.||.-.|+++++||.||++-
T Consensus 43 ~~~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 43 VPPEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp C--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred CCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 5 89999999999999999999999987
No 128
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=79.02 E-value=9.4 Score=28.68 Aligned_cols=61 Identities=13% Similarity=0.251 Sum_probs=42.1
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+| +|+.+ ++....||.+|-.. .+ ++.....+.++|+++.-.. -.+.-+++||.|-++-
T Consensus 1 m~i~v---NG~~~--~~~~~~tl~~lL~~----l~---~~~~~vav~vNg~iv~r~~-~~~~~l~~gD~vei~~ 61 (66)
T PRK05659 1 MNIQL---NGEPR--ELPDGESVAALLAR----EG---LAGRRVAVEVNGEIVPRSQ-HASTALREGDVVEIVH 61 (66)
T ss_pred CEEEE---CCeEE--EcCCCCCHHHHHHh----cC---CCCCeEEEEECCeEeCHHH-cCcccCCCCCEEEEEE
Confidence 55554 47765 45667888887654 46 7788888899999886332 2334488999998764
No 129
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=78.92 E-value=9.8 Score=30.24 Aligned_cols=58 Identities=12% Similarity=0.268 Sum_probs=40.0
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCC---CCCC-----CCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGS---DVYP-----ASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~---~~ip-----~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
...+++. ..||.+|.+.+.++++. ..+. -....+..+|+...++.. .-|++||.|.++
T Consensus 17 ~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~ 82 (88)
T TIGR01687 17 SEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIF 82 (88)
T ss_pred eEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEe
Confidence 4677776 88999999999887541 0011 123566778888765432 568899999886
No 130
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=78.77 E-value=2.8 Score=44.45 Aligned_cols=39 Identities=31% Similarity=0.601 Sum_probs=35.1
Q ss_pred HHHHHHHHHcCCCCCCHHHHHHHHHHhcC-ChHHHHHHHHcCC
Q 015999 168 EATVQQILDMGGGSWDRETVIRALRAAYN-NPERAVEYLYSGI 209 (397)
Q Consensus 168 e~~I~~i~~MG~~~f~r~~v~~ALrAafn-NpdrAveyL~~GI 209 (397)
..+|.+|++|| |+.+.+.|||-+.-| +.+.|..||.--+
T Consensus 559 qs~I~qL~~mG---fp~~~~~rAL~~tgNqDaEsAMNWLFqHM 598 (749)
T COG5207 559 QSLIRQLVDMG---FPEEDAARALGITGNQDAESAMNWLFQHM 598 (749)
T ss_pred HHHHHHHHHcC---CCHHHHHHHHhhccCcchHHHHHHHHhhc
Confidence 57899999999 999999999998877 7899999998664
No 131
>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=78.54 E-value=6.2 Score=30.98 Aligned_cols=64 Identities=19% Similarity=0.064 Sum_probs=46.7
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC--C--eecCCCCchhhcccCCCCEEEE
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ--G--KVLKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~--G--KiL~D~~tL~d~gI~~gstI~v 72 (397)
+.|-..+|+.-.+.|.+..||.++-.++.++.| +.++...|.+. + +.++.+... .+-.+..|.|
T Consensus 2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~---l~~~~~~v~~~~~~~~~~~~~~~d~---~~L~~~El~V 69 (72)
T cd01760 2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRG---LNPECCDVFLLGLDEKKPLDLDTDS---SSLAGEELEV 69 (72)
T ss_pred EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcC---CCHHHEEEEEecCCCcCCcCchhhh---hhhcCCEEEE
Confidence 467777899999999999999999999999999 88887776654 4 555444333 2334445544
No 132
>PF11069 DUF2870: Protein of unknown function (DUF2870); InterPro: IPR021298 This is a eukaryotic family of proteins with unknown function.
Probab=78.01 E-value=3.4 Score=34.40 Aligned_cols=33 Identities=18% Similarity=0.217 Sum_probs=22.9
Q ss_pred EEEeCCeecCCCCchhhcccCCCCEEEEEEeecC
Q 015999 45 MLIHQGKVLKDVTTLEENKVAENSFVVVMLTKVI 78 (397)
Q Consensus 45 rLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~~ 78 (397)
.|-|.||.|..+++|++| |..+..--|+++..+
T Consensus 3 ~LW~aGK~l~~~k~l~dy-~GkNEKtKiivKl~~ 35 (98)
T PF11069_consen 3 QLWWAGKELQRGKKLSDY-IGKNEKTKIIVKLQK 35 (98)
T ss_pred eEEeccccccCCCcHHHh-cCCCcceeEEEEecc
Confidence 477999999999999999 444443444444433
No 133
>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=77.38 E-value=9.8 Score=31.00 Aligned_cols=46 Identities=17% Similarity=0.262 Sum_probs=35.9
Q ss_pred EEEEEeC-CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCe
Q 015999 2 KVFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK 51 (397)
Q Consensus 2 kI~Vktl-~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GK 51 (397)
+|+||.. .|..+.+.|.++.+..+|..+|.++++ +. ...+|-|...
T Consensus 2 ~ikVKv~~~~Dv~~i~v~~~i~f~dL~~kIrdkf~---~~-~~~~iKykDE 48 (86)
T cd06408 2 KIRVKVHAQDDTRYIMIGPDTGFADFEDKIRDKFG---FK-RRLKIKMKDD 48 (86)
T ss_pred cEEEEEEecCcEEEEEcCCCCCHHHHHHHHHHHhC---CC-CceEEEEEcC
Confidence 3555544 677899999999999999999999999 63 5666666544
No 134
>smart00455 RBD Raf-like Ras-binding domain.
Probab=77.22 E-value=8.5 Score=29.88 Aligned_cols=51 Identities=18% Similarity=0.154 Sum_probs=42.4
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC--eecCCC
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG--KVLKDV 56 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~G--KiL~D~ 56 (397)
+.|-..+|+...|.+.|..||.++-.+|.++.| +.++...|...| |.|+-+
T Consensus 2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~---l~~~~~~v~~~g~~k~ldl~ 54 (70)
T smart00455 2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRG---LNPECCVVRLRGEKKPLDLN 54 (70)
T ss_pred eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcC---CCHHHEEEEEcCCCcceecC
Confidence 356667899999999999999999999999999 888888888754 555433
No 135
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=76.70 E-value=5.6 Score=34.18 Aligned_cols=39 Identities=15% Similarity=0.152 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHHH-cCCChHHHHHHHHHhCCCHHHHHHHHh
Q 015999 348 TVTPEEREAIERLEA-MGFDRALVLEVFFACNKNEELAANYLL 389 (397)
Q Consensus 348 ~lt~Ee~~ai~rL~~-lGF~r~~~iqAy~ac~kne~~Aan~L~ 389 (397)
.+++|+ |+.+++ -|-+|+.+++||..|++|.--|+-+|-
T Consensus 76 ~i~~eD---I~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 76 EITEDD---IELVMKQCNVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred CCCHHH---HHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 356666 666665 488999999999999999999998874
No 136
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=76.17 E-value=15 Score=27.78 Aligned_cols=61 Identities=7% Similarity=0.166 Sum_probs=41.5
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+|. |+.+.+ ....||.+|.+. .+ +......+-.+++++..+ .-+++-+++||.|.++-
T Consensus 1 m~i~vN---g~~~~~--~~~~tl~~ll~~----l~---~~~~~vaVavN~~iv~r~-~w~~~~L~~gD~Ieii~ 61 (66)
T PRK08053 1 MQILFN---DQPMQC--AAGQTVHELLEQ----LN---QLQPGAALAINQQIIPRE-QWAQHIVQDGDQILLFQ 61 (66)
T ss_pred CEEEEC---CeEEEc--CCCCCHHHHHHH----cC---CCCCcEEEEECCEEeChH-HcCccccCCCCEEEEEE
Confidence 566654 776655 567789988765 34 555667888999998522 23344588999998763
No 137
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=74.61 E-value=19 Score=26.84 Aligned_cols=60 Identities=10% Similarity=0.130 Sum_probs=38.9
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+|. |+.+ ++....||.+|.+.+ + +. ....+.++|+++..+. -.+.-+++||.|.++-
T Consensus 1 m~i~vN---g~~~--~~~~~~tl~~ll~~l----~---~~-~~~~v~vN~~~v~~~~-~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 1 MDIQLN---QQTL--SLPDGATVADALAAY----G---AR-PPFAVAVNGDFVARTQ-HAARALAAGDRLDLVQ 60 (65)
T ss_pred CEEEEC---CEEE--ECCCCCcHHHHHHhh----C---CC-CCeEEEECCEEcCchh-cccccCCCCCEEEEEe
Confidence 555554 7665 446678999888654 4 43 3467788999875322 2233488899998863
No 138
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=73.00 E-value=13 Score=38.55 Aligned_cols=73 Identities=15% Similarity=0.233 Sum_probs=56.9
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe----CCee--cCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH----QGKV--LKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy----~GKi--L~D~~tL~d~gI~~gstI~v~v 74 (397)
|.+.||...| ...++++++++.+.|-.+|-.-...+ +.++++.++- .|.+ +..+.|+.++|++.|..|+|-.
T Consensus 1 Mi~rfRsk~G-~~Rve~qe~d~lg~l~~kll~~~~~n-~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~y 78 (571)
T COG5100 1 MIFRFRSKEG-QRRVEVQESDVLGMLSPKLLAFFEVN-YSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEY 78 (571)
T ss_pred CeEEEecCCC-ceeeeccccchhhhhhHHHHhhhccC-CCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEe
Confidence 7788997766 46789999999999998887665433 7788888864 3433 3457899999999999999876
Q ss_pred e
Q 015999 75 T 75 (397)
Q Consensus 75 ~ 75 (397)
+
T Consensus 79 s 79 (571)
T COG5100 79 S 79 (571)
T ss_pred c
Confidence 3
No 139
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=72.98 E-value=7.8 Score=33.27 Aligned_cols=40 Identities=18% Similarity=0.138 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHHH-cCCChHHHHHHHHHhCCCHHHHHHHHhc
Q 015999 348 TVTPEEREAIERLEA-MGFDRALVLEVFFACNKNEELAANYLLD 390 (397)
Q Consensus 348 ~lt~Ee~~ai~rL~~-lGF~r~~~iqAy~ac~kne~~Aan~L~~ 390 (397)
.+++|+ |+.+++ -|-+|+.+++||..|++|.--|+-+|-+
T Consensus 74 ~i~~ed---I~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 74 EIPEED---IELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred CCCHHH---HHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 467776 666665 4889999999999999999999988853
No 140
>PF12616 DUF3775: Protein of unknown function (DUF3775); InterPro: IPR022254 This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=72.00 E-value=5.1 Score=31.79 Aligned_cols=40 Identities=25% Similarity=0.494 Sum_probs=31.2
Q ss_pred HHHHHHHcCCCCCCHHHHHHHHHHhcCC-hHHHHHHHHcCCC
Q 015999 170 TVQQILDMGGGSWDRETVIRALRAAYNN-PERAVEYLYSGIP 210 (397)
Q Consensus 170 ~I~~i~~MG~~~f~r~~v~~ALrAafnN-pdrAveyL~~GIP 210 (397)
-+-.||=+|+|.|+-++-..|++.|-.+ -.++++||+ |.|
T Consensus 20 eLvALmwiGRGd~~~eew~~a~~~A~~~~~~~ta~YLl-~~p 60 (75)
T PF12616_consen 20 ELVALMWIGRGDFEAEEWEEAVAEARERASARTADYLL-GTP 60 (75)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHHHhccchHHHHHH-cCC
Confidence 3556788999999999999999877544 457889997 444
No 141
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=70.73 E-value=15 Score=29.68 Aligned_cols=57 Identities=4% Similarity=0.159 Sum_probs=40.6
Q ss_pred CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 8 l~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
++|+.+.+ +...||.+|-+. .+ ++....-+-++|.++. ....+++-+++||.|.++-
T Consensus 23 VNG~~~~~--~~~~tl~~LL~~----l~---~~~~~vAVevNg~iVp-r~~w~~t~L~egD~IEIv~ 79 (84)
T PRK06083 23 INDQSIQV--DISSSLAQIIAQ----LS---LPELGCVFAINNQVVP-RSEWQSTVLSSGDAISLFQ 79 (84)
T ss_pred ECCeEEEc--CCCCcHHHHHHH----cC---CCCceEEEEECCEEeC-HHHcCcccCCCCCEEEEEE
Confidence 45665544 567788877654 45 7777778889999994 3345566799999998764
No 142
>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=70.64 E-value=16 Score=27.46 Aligned_cols=57 Identities=9% Similarity=0.242 Sum_probs=40.6
Q ss_pred CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 8 l~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
++|+.+. ++...||.+|.+++ + ++.+...+.++|+++..+ .-.++-|++||.|.++-
T Consensus 4 iNg~~~~--~~~~~tv~~ll~~l----~---~~~~~i~V~vNg~~v~~~-~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 4 VNGEPRE--VEEGATLAELLEEL----G---LDPRGVAVALNGEIVPRS-EWASTPLQDGDRIEIVT 60 (65)
T ss_pred ECCeEEE--cCCCCCHHHHHHHc----C---CCCCcEEEEECCEEcCHH-HcCceecCCCCEEEEEE
Confidence 4566654 45678999988664 4 667888889999998543 22334588999998763
No 143
>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B.
Probab=70.33 E-value=8.5 Score=31.20 Aligned_cols=52 Identities=12% Similarity=0.100 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHHHH-HhCCCCCCCC----CeEEEeCCee----cCCCCchhhcccCCCCEEEEE
Q 015999 19 PEDKVSDVKKNIET-VQGSDVYPAS----QQMLIHQGKV----LKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 19 ~~~TV~dLK~~I~~-~~g~~~ip~~----~qrLiy~GKi----L~D~~tL~d~gI~~gstI~v~ 73 (397)
...|+++|-++|-+ +.| +-.- .-++||..-. -..+++|+++||++|++|.|.
T Consensus 7 ~~~TL~~lv~~Vlk~~Lg---~~~P~v~~~~~ilyd~de~~~~~~l~k~L~elgi~~gs~L~v~ 67 (87)
T PF14732_consen 7 KKMTLGDLVEKVLKKKLG---MNEPDVSVGGTILYDSDEEEYDDNLPKKLSELGIVNGSILTVD 67 (87)
T ss_dssp TT-BHHHHHHHCCCCCS-----SSEEEEES-EEEE-SSSSSSTTCTTSBGGGGT--TT-EEEEE
T ss_pred hhCcHHHHHHHHHHhccC---CCCCEEEeCCCEEEcCCcchhhhcccCChhHcCCCCCCEEEEE
Confidence 36799999988743 445 2111 2344443322 122579999999999998764
No 144
>KOG2982 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.55 E-value=5 Score=40.34 Aligned_cols=54 Identities=17% Similarity=0.142 Sum_probs=43.9
Q ss_pred eCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe---CCeec-----CCCCchhhcccCCCCEEEEE
Q 015999 17 VKPEDKVSDVKKNIETVQGSDVYPASQQMLIH---QGKVL-----KDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 17 V~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy---~GKiL-----~D~~tL~d~gI~~gstI~v~ 73 (397)
|.-.-||.|+|+++..+.| +...++||+| .||.- +-++.|-.|+|.+||.+.|-
T Consensus 354 I~~~~TV~D~~~~Ld~~VG---vk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~lvq 415 (418)
T KOG2982|consen 354 ICMTRTVLDFMKILDPKVG---VKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFLVQ 415 (418)
T ss_pred EEeehHHHHHHHHhccccc---cccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEeeee
Confidence 4446699999999999999 8999999987 45542 33578889999999998764
No 145
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=69.50 E-value=17 Score=27.53 Aligned_cols=38 Identities=18% Similarity=0.443 Sum_probs=32.6
Q ss_pred HHHHHHHHHc-C-CChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015999 354 REAIERLEAM-G-FDRALVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 354 ~~ai~rL~~l-G-F~r~~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
+.-|+-|++. | ++++++.-.|.-|+-|-+.|++.||..
T Consensus 6 rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 6 RKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 4557777775 4 599999999999999999999999974
No 146
>PF08337 Plexin_cytopl: Plexin cytoplasmic RasGAP domain; InterPro: IPR013548 This domain is found at C terminus of various plexins (e.g. P51805 from SWISSPROT). Plexins are receptors for semaphorins, and plexin signalling is important in pathfinding and patterning of both neurons and developing blood vessels [, ]. The cytoplasmic region, which has been called a SEX domain [], and is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins []. ; PDB: 3H6N_A 4E71_A 4E74_A 3IG3_A 2REX_C 2JPH_A 2R2O_A 3HM6_X 3SU8_X 3SUA_E ....
Probab=69.22 E-value=14 Score=39.69 Aligned_cols=65 Identities=25% Similarity=0.340 Sum_probs=42.0
Q ss_pred cEEEEEeCCCCCHHHHHHHHHHHhCCCCCC------CCCeEEEe--C--Ce-ecCCC-------------CchhhcccCC
Q 015999 11 THFEIEVKPEDKVSDVKKNIETVQGSDVYP------ASQQMLIH--Q--GK-VLKDV-------------TTLEENKVAE 66 (397)
Q Consensus 11 k~~~veV~~~~TV~dLK~~I~~~~g~~~ip------~~~qrLiy--~--GK-iL~D~-------------~tL~d~gI~~ 66 (397)
..+.|.|-..|||.++|+||-+..=++ .| ++..-|-| + |+ +|.|. .||.+|+|.+
T Consensus 202 ~~i~VkVLdCDTItQVKeKiLDavyk~-~p~S~rp~~~d~dLEwr~~~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~d 280 (539)
T PF08337_consen 202 EEIPVKVLDCDTITQVKEKILDAVYKN-TPYSQRPRADDVDLEWRQGRGGRLILQDEDSTSKVEGGWKRLNTLAHYKVPD 280 (539)
T ss_dssp TCEEEEEETTSBHHHHHHHHHHHHTTT-S-GGGS--GGGEEEEEEETTSEEEEESSSSTTSEEETTEEE--BHHHHT--T
T ss_pred ceEEEEEEecCcccHHHHHHHHHHHcC-CCCCCCCCccccceeeecCCCCcccccCCCCCcccCCCceEeccHhhcCCCC
Confidence 457888889999999999997654222 22 34444433 2 23 56553 3789999999
Q ss_pred CCEEEEEEee
Q 015999 67 NSFVVVMLTK 76 (397)
Q Consensus 67 gstI~v~v~k 76 (397)
|++|.++.+.
T Consensus 281 ga~vaLv~k~ 290 (539)
T PF08337_consen 281 GATVALVPKQ 290 (539)
T ss_dssp TEEEEEEES-
T ss_pred CceEEEeecc
Confidence 9999887654
No 147
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=68.82 E-value=22 Score=27.15 Aligned_cols=61 Identities=10% Similarity=0.205 Sum_probs=41.5
Q ss_pred CEEEEEeCCCcEEEEEeCCC-CCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPE-DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~-~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|+|+| +|+.+.+ ... .||.+|-+ ..+ +++...-+-++|+++.-+ ...++-+++||.|.++.
T Consensus 1 m~I~v---NG~~~~~--~~~~~tv~~lL~----~l~---~~~~~vav~vN~~iv~r~-~w~~~~L~~gD~iEIv~ 62 (67)
T PRK07696 1 MNLKI---NGNQIEV--PESVKTVAELLT----HLE---LDNKIVVVERNKDILQKD-DHTDTSVFDGDQIEIVT 62 (67)
T ss_pred CEEEE---CCEEEEc--CCCcccHHHHHH----HcC---CCCCeEEEEECCEEeCHH-HcCceecCCCCEEEEEE
Confidence 55555 4776654 444 57887764 356 777778888999998533 34455689999998764
No 148
>smart00727 STI1 Heat shock chaperonin-binding motif.
Probab=67.92 E-value=9.3 Score=26.05 Aligned_cols=32 Identities=31% Similarity=0.646 Sum_probs=18.2
Q ss_pred HHHHHHhCccchHHHHHHHhhhCHHHHHHHHH-hHH
Q 015999 284 LRTMVQANPQILQPMLQELGKQNPHLMRLIQE-HQT 318 (397)
Q Consensus 284 lrq~vq~NP~ll~~~Lqqi~~~nP~l~~~I~~-n~~ 318 (397)
++++++ ||.+ ..++++| .+||++++.+.+ ||.
T Consensus 4 ~~~~l~-~P~~-~~~l~~~-~~nP~~~~~~~~~nP~ 36 (41)
T smart00727 4 MALRLQ-NPQV-QSLLQDM-QQNPDMLAQMLQENPQ 36 (41)
T ss_pred HHHHHc-CHHH-HHHHHHH-HHCHHHHHHHHHhCHH
Confidence 344444 7763 3355544 568887766655 554
No 149
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=67.90 E-value=28 Score=27.03 Aligned_cols=63 Identities=16% Similarity=0.282 Sum_probs=43.1
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
|.++|. ++|+.. ++....||.+|-.. .+ ++.+..-+.++|.++..+. -.+.-++++|.|-++-
T Consensus 1 ~~m~i~-~ng~~~--e~~~~~tv~dLL~~----l~---~~~~~vav~vNg~iVpr~~-~~~~~l~~gD~ievv~ 63 (68)
T COG2104 1 MPMTIQ-LNGKEV--EIAEGTTVADLLAQ----LG---LNPEGVAVAVNGEIVPRSQ-WADTILKEGDRIEVVR 63 (68)
T ss_pred CcEEEE-ECCEEE--EcCCCCcHHHHHHH----hC---CCCceEEEEECCEEccchh-hhhccccCCCEEEEEE
Confidence 445555 346654 45555899988654 56 7788888899999986432 2345678889887763
No 150
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=67.70 E-value=4.7 Score=27.90 Aligned_cols=24 Identities=29% Similarity=0.505 Sum_probs=20.5
Q ss_pred CChHHHHHHHHHhCCCHHHHHHHH
Q 015999 365 FDRALVLEVFFACNKNEELAANYL 388 (397)
Q Consensus 365 F~r~~~iqAy~ac~kne~~Aan~L 388 (397)
|+++.+.+|+..|++|...||..|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH
Confidence 457889999999999999999987
No 151
>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=67.02 E-value=22 Score=27.43 Aligned_cols=45 Identities=22% Similarity=0.131 Sum_probs=34.4
Q ss_pred EEEEEeCCCcEEEEEeC-CCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 015999 2 KVFVKTLKGTHFEIEVK-PEDKVSDVKKNIETVQGSDVYPASQQMLIHQG 50 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~-~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~G 50 (397)
+|+++. +|..+.+.+. .+.|..+|+.+|.++++ +.....+|-|..
T Consensus 2 ~vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~---~~~~~~~l~y~D 47 (81)
T cd05992 2 RVKVKY-GGEIRRFVVVSRSISFEDLRSKIAEKFG---LDAVSFKLKYPD 47 (81)
T ss_pred cEEEEe-cCCCEEEEEecCCCCHHHHHHHHHHHhC---CCCCcEEEEeeC
Confidence 455553 4567788888 89999999999999998 555667777754
No 152
>PF10407 Cytokin_check_N: Cdc14 phosphatase binding protein N-terminus ; InterPro: IPR018844 Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus. This is the highly conserved N terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance [].
Probab=66.45 E-value=18 Score=28.62 Aligned_cols=62 Identities=24% Similarity=0.282 Sum_probs=40.1
Q ss_pred cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe------CCeecCCCCchhhcccCCCCEEEEEEe
Q 015999 11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH------QGKVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 11 k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy------~GKiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
++|-+=.+++.||.+|+..|.+++.+- +|-+ ..+.- .|--|+.+-++++. ...+++|.|+++
T Consensus 3 kKFLhlt~~~~tl~~L~~eI~~~f~kL-YP~~-~~~~I~~LQD~~~cDLD~d~~V~DV-f~~~~~vrvi~~ 70 (73)
T PF10407_consen 3 KKFLHLTDPNNTLSQLKEEIEERFKKL-YPNE-PELEILSLQDSDGCDLDPDFLVKDV-FNSNNVVRVILK 70 (73)
T ss_pred cEEEEEeCCCCcHHHHHHHHHHHHHHH-CCCC-CCceEEEeecCCCCCCCcccEeeee-eccCCEEEEEec
Confidence 456666889999999999999887642 4333 33321 23345445555554 346888888775
No 153
>TIGR02958 sec_mycoba_snm4 secretion protein snm4. Members of this family are the 12-transmembrane domain protein snm4, where snm stands for secretion in mycocbacteria. This system acts on Mycobacterium tuberculosis related pair of virulence factors ESAT-6 and CFP-10 and on other homologs. The system is conserved in many Actinobacteria, including the non-pathogenic Mycobacterium smegmatis.
Probab=66.41 E-value=33 Score=36.16 Aligned_cols=72 Identities=15% Similarity=0.206 Sum_probs=53.7
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCC---CCCCCeEEE-eCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDV---YPASQQMLI-HQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~---ip~~~qrLi-y~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
+|+|...+ +...+-+..+..|.+|-..|-+..+.+. .....-.|. -+|..|+.+.+|.+.+|.||+.+++.-
T Consensus 4 RVtV~~~~-~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L~p 79 (452)
T TIGR02958 4 RVTVLAGR-RAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVLVP 79 (452)
T ss_pred EEEEeeCC-eeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEEee
Confidence 56777543 4577778888899999999988877321 122334553 478899999999999999999998864
No 154
>PF08587 UBA_2: Ubiquitin associated domain (UBA) ; InterPro: IPR013896 This is a UBA (ubiquitin associated) protein []. Ubiquitin is involved in intracellular proteolysis. ; GO: 0004674 protein serine/threonine kinase activity; PDB: 3H4J_B.
Probab=66.32 E-value=1.2 Score=31.96 Aligned_cols=21 Identities=29% Similarity=0.667 Sum_probs=13.7
Q ss_pred HHHHHHH-cCCCCCCHHHHHHHHHH
Q 015999 170 TVQQILD-MGGGSWDRETVIRALRA 193 (397)
Q Consensus 170 ~I~~i~~-MG~~~f~r~~v~~ALrA 193 (397)
.|..|.. || |+|++|..||+.
T Consensus 5 vv~~Ls~tMG---Y~kdeI~eaL~~ 26 (46)
T PF08587_consen 5 VVSKLSKTMG---YDKDEIYEALES 26 (46)
T ss_dssp CHHHHHCTT------HHHHHHHCCS
T ss_pred HHHHHHHHhC---CCHHHHHHHHHc
Confidence 3445544 99 999999999986
No 155
>PRK07440 hypothetical protein; Provisional
Probab=66.30 E-value=27 Score=26.99 Aligned_cols=57 Identities=12% Similarity=0.217 Sum_probs=40.3
Q ss_pred CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 8 l~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
++|+.+ ++....||.+|-+ ..+ +++...-+-++|+++.-+ ...++-+++||.|.++.
T Consensus 9 vNG~~~--~~~~~~tl~~lL~----~l~---~~~~~vav~~N~~iv~r~-~w~~~~L~~gD~IEIv~ 65 (70)
T PRK07440 9 VNGETR--TCSSGTSLPDLLQ----QLG---FNPRLVAVEYNGEILHRQ-FWEQTQVQPGDRLEIVT 65 (70)
T ss_pred ECCEEE--EcCCCCCHHHHHH----HcC---CCCCeEEEEECCEEeCHH-HcCceecCCCCEEEEEE
Confidence 467764 4566788988764 345 777788888999998522 23455688999998764
No 156
>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=65.68 E-value=21 Score=27.74 Aligned_cols=44 Identities=18% Similarity=0.184 Sum_probs=34.5
Q ss_pred EEEEeCCCcEEE-EEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC
Q 015999 3 VFVKTLKGTHFE-IEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG 50 (397)
Q Consensus 3 I~Vktl~gk~~~-veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~G 50 (397)
|.++. ++..+. +.+....+..+|+.+|...++ .+....+|.|..
T Consensus 4 vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~---~~~~~~~l~Y~D 48 (84)
T PF00564_consen 4 VKVRY-GGDIRRIISLPSDVSFDDLRSKIREKFG---LLDEDFQLKYKD 48 (84)
T ss_dssp EEEEE-TTEEEEEEEECSTSHHHHHHHHHHHHHT---TSTSSEEEEEEE
T ss_pred EEEEE-CCeeEEEEEcCCCCCHHHHHHHHHHHhC---CCCccEEEEeeC
Confidence 44443 455555 899999999999999999999 667888998853
No 157
>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=63.64 E-value=39 Score=26.20 Aligned_cols=56 Identities=14% Similarity=0.068 Sum_probs=40.5
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecCCCCchhh
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEE 61 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy--~GKiL~D~~tL~d 61 (397)
+.|--.+|+.-.+.|.+..||.++-.++.++.+ +.++...+.. ..|.|..+.....
T Consensus 3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~---L~~~~~~V~~~~~~k~l~~~~d~~~ 60 (71)
T PF02196_consen 3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRG---LNPECCDVRLVGEKKPLDWDQDSSS 60 (71)
T ss_dssp EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT-----CCCEEEEEEEEEEEE-TTSBGGG
T ss_pred EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcC---CCHHHEEEEEcCCCccccCCCceee
Confidence 556777899999999999999999999999999 8777766543 4466766555443
No 158
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=62.98 E-value=30 Score=32.56 Aligned_cols=48 Identities=19% Similarity=0.362 Sum_probs=31.4
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC---CeEE--EeCCee---cCCCCchhhc
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPAS---QQML--IHQGKV---LKDVTTLEEN 62 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~---~qrL--iy~GKi---L~D~~tL~d~ 62 (397)
.+.+-|..+.||.||.+.+..+.+ ++.+ .+|| ++++|+ +..+..|.++
T Consensus 35 ~~~~~vpk~~tV~Dll~~l~~k~~---~~~~~~~~lrl~ev~~~ki~~~~~~d~~i~~l 90 (213)
T PF14533_consen 35 EYELLVPKTGTVSDLLEELQKKVG---FSEEGTGKLRLWEVSNHKIYKILSEDEPISSL 90 (213)
T ss_dssp EEEE--BTT-BHHHHHHHHHTT-------TT----EEEEEEETTEEEEEE-TTSBGGGS
T ss_pred EEEEEECCCCCHHHHHHHHHHHcC---CCcCCcCcEEEEEeECCEEEeecCCCCchhhc
Confidence 477889999999999999999988 5544 5566 578876 6778888876
No 159
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=61.97 E-value=26 Score=28.57 Aligned_cols=45 Identities=27% Similarity=0.324 Sum_probs=32.6
Q ss_pred hHHHHHHHhhhCHHHHHHHHHhHHHHHHHhcCCCCCCCCcccccccccCCCcccCCHHHHHH-----HHHHHHcC
Q 015999 295 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREA-----IERLEAMG 364 (397)
Q Consensus 295 l~~~Lqqi~~~nP~l~~~I~~n~~~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~Ee~~a-----i~rL~~lG 364 (397)
|+.++.+| .+|+.++...++++.++. .-.||+||+++ +.+|..+|
T Consensus 1 lNkf~~~L--~~~~~r~~F~~D~~a~~~-----------------------~~~Lt~eer~av~~rD~~~L~~~G 50 (88)
T PF07746_consen 1 LNKFCWSL--NDPENRERFLADPEAYLD-----------------------EYGLTEEERQAVLDRDWLALIALG 50 (88)
T ss_dssp HHHHHHGG--GSHHHHHHHHH-HHHHHH-----------------------CCT--HHHHHHHHCT-HHHHHHTT
T ss_pred ChHHHHHH--cCHHHHHHHHHCHHHHHH-----------------------HcCCCHHHHHHHHcCCHHHHHHCC
Confidence 34567777 789999999999998876 22579999988 56688888
No 160
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=61.74 E-value=6.6 Score=27.94 Aligned_cols=24 Identities=21% Similarity=0.318 Sum_probs=20.1
Q ss_pred HHHHHHHHcCCChHHHHHHHHHhC
Q 015999 355 EAIERLEAMGFDRALVLEVFFACN 378 (397)
Q Consensus 355 ~ai~rL~~lGF~r~~~iqAy~ac~ 378 (397)
++++-|..|||++.++-+|+....
T Consensus 5 d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 5 DALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhh
Confidence 678999999999999988887774
No 161
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=61.46 E-value=32 Score=27.55 Aligned_cols=52 Identities=23% Similarity=0.285 Sum_probs=40.8
Q ss_pred CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe-CCeecCCCCchhhcccCCCCEEEEE
Q 015999 10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-QGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 10 gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy-~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
++.+.+.++...||+++-+ ..| +|..+..+|+ +|+...-+ |-+++|+.|.|.
T Consensus 22 ~~~~~~~~~~~~tvkd~IE----sLG---VP~tEV~~i~vNG~~v~~~-----~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 22 GGPFTHPFDGGATVKDVIE----SLG---VPHTEVGLILVNGRPVDFD-----YRLKDGDRVAVY 74 (81)
T ss_pred CCceEEecCCCCcHHHHHH----HcC---CChHHeEEEEECCEECCCc-----ccCCCCCEEEEE
Confidence 3567788899999988754 578 9999998765 88877543 668899999876
No 162
>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=61.44 E-value=47 Score=28.24 Aligned_cols=59 Identities=10% Similarity=0.137 Sum_probs=41.7
Q ss_pred EEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe-CCeecCCCCchhhc--ccC-CCCEEEEEEee
Q 015999 15 IEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-QGKVLKDVTTLEEN--KVA-ENSFVVVMLTK 76 (397)
Q Consensus 15 veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy-~GKiL~D~~tL~d~--gI~-~gstI~v~v~k 76 (397)
+-|..+.||.++...|..... +.+++--.+| ++.....+.+++++ ..+ ++.+|+|..+.
T Consensus 45 flVp~~~tv~~f~~~irk~l~---l~~~~slfl~Vn~~~p~~~~~~~~lY~~~kd~DGfLyl~Ys~ 107 (112)
T cd01611 45 YLVPSDLTVGQFVYIIRKRIQ---LRPEKALFLFVNNSLPPTSATMSQLYEEHKDEDGFLYMTYSS 107 (112)
T ss_pred EEecCCCCHHHHHHHHHHHhC---CCccceEEEEECCccCCchhHHHHHHHHhCCCCCEEEEEEec
Confidence 348899999999999999988 6666644444 55545667777766 233 36788887653
No 163
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=60.97 E-value=9.1 Score=39.11 Aligned_cols=30 Identities=17% Similarity=0.360 Sum_probs=24.3
Q ss_pred cccCCcchHHHHHHHHHcCCCCCCHHHHHHHHH
Q 015999 160 NLVAGSNLEATVQQILDMGGGSWDRETVIRALR 192 (397)
Q Consensus 160 ~l~~g~~~e~~I~~i~~MG~~~f~r~~v~~ALr 192 (397)
.++..--+++.|+.++.|| |.||+|+.-.|
T Consensus 314 ~~~~~~p~ddvidKv~~MG---f~rDqV~a~v~ 343 (358)
T PF07223_consen 314 QSGNRHPYDDVIDKVASMG---FRRDQVRATVR 343 (358)
T ss_pred cccccCcHHHHHHHHHHcC---CcHHHHHHHHH
Confidence 3455566899999999999 99999976443
No 164
>KOG4250 consensus TANK binding protein kinase TBK1 [Signal transduction mechanisms]
Probab=60.79 E-value=26 Score=38.85 Aligned_cols=42 Identities=21% Similarity=0.394 Sum_probs=37.6
Q ss_pred CCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeec
Q 015999 9 KGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVL 53 (397)
Q Consensus 9 ~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL 53 (397)
+...+++-++++.|+..++.+|...+| ||.+.|-|+|.|...
T Consensus 323 ~~~~~~~~~~~~ntl~~~~~~I~~~Tg---ipe~~qeLL~e~~~~ 364 (732)
T KOG4250|consen 323 QATSHEYYVHADNTLHSLIERISKQTG---IPEGKQELLFEGGLS 364 (732)
T ss_pred cceEEEEecChhhhHHHHHHHHHHhhC---CCCccceeeeecCcc
Confidence 456678889999999999999999999 999999999997654
No 165
>cd01787 GRB7_RA RA (RAS-associated like) domain of Grb7. Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.
Probab=60.34 E-value=55 Score=26.63 Aligned_cols=66 Identities=21% Similarity=0.196 Sum_probs=45.4
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE------eCCeecCCCCchhhc----ccCCCCEE
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI------HQGKVLKDVTTLEEN----KVAENSFV 70 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi------y~GKiL~D~~tL~d~----gI~~gstI 70 (397)
|.|-..+|....|.|+...|+.++-+.+..+.++. +...--|+ +=.+.++|...|-++ ++..+..|
T Consensus 5 vkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~--~~~~W~LvE~~P~l~lER~~EDHE~vvdvl~~W~~~~~n~l 80 (85)
T cd01787 5 VKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQ--DDSSWTLVEHLPHLQLERLFEDHELVVEVLSTWHSAGNSVL 80 (85)
T ss_pred EEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCC--CCCCeEEEEecchhhhhhhccchHHHHHHHHhcccCCCcEE
Confidence 45556789999999999999999999999998852 23333443 124567887665554 45444444
No 166
>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=60.02 E-value=35 Score=25.56 Aligned_cols=57 Identities=9% Similarity=0.258 Sum_probs=40.2
Q ss_pred CCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 8 LKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 8 l~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
++|+.+.+ ....||.+|.+.+ + ++++...+.++|+++..+ .-.++-|++||.|-++-
T Consensus 3 iNg~~~~~--~~~~tv~~ll~~l----~---~~~~~v~v~vN~~iv~~~-~~~~~~L~~gD~veii~ 59 (64)
T TIGR01683 3 VNGEPVEV--EDGLTLAALLESL----G---LDPRRVAVAVNGEIVPRS-EWDDTILKEGDRIEIVT 59 (64)
T ss_pred ECCeEEEc--CCCCcHHHHHHHc----C---CCCCeEEEEECCEEcCHH-HcCceecCCCCEEEEEE
Confidence 46776554 5677899988753 5 667778888999998432 23345689999998763
No 167
>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional
Probab=60.02 E-value=25 Score=35.47 Aligned_cols=64 Identities=8% Similarity=0.105 Sum_probs=45.1
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEEeec
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVMLTKV 77 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v~k~ 77 (397)
|+|+| +|+.+. +....||.+|-+. .+ ++.+...+.++|+++.- ....++-|++||.|.++---.
T Consensus 1 M~I~V---NGk~~e--l~e~~TL~dLL~~----L~---i~~~~VAVeVNgeIVpr-~~w~~t~LkeGD~IEII~~Vg 64 (326)
T PRK11840 1 MRIRL---NGEPRQ--VPAGLTIAALLAE----LG---LAPKKVAVERNLEIVPR-SEYGQVALEEGDELEIVHFVG 64 (326)
T ss_pred CEEEE---CCEEEe--cCCCCcHHHHHHH----cC---CCCCeEEEEECCEECCH-HHcCccccCCCCEEEEEEEec
Confidence 55555 477654 4567788887654 46 88889999999999953 234556689999998875433
No 168
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=59.56 E-value=21 Score=30.71 Aligned_cols=38 Identities=24% Similarity=0.281 Sum_probs=33.2
Q ss_pred HHHHHHHHHc-CCCCCCHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 168 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 168 e~~I~~i~~M-G~~~f~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
++-|+-+++- | -.|+++++||+.+.++.-.|+-||..+
T Consensus 77 ~edI~lv~~q~g---vs~~~A~~AL~~~~gDl~~AI~~L~~~ 115 (115)
T PRK06369 77 EEDIELVAEQTG---VSEEEARKALEEANGDLAEAILKLSSE 115 (115)
T ss_pred HHHHHHHHHHHC---cCHHHHHHHHHHcCCcHHHHHHHHhcC
Confidence 5678888885 7 899999999999999999999999753
No 169
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=59.27 E-value=10 Score=28.11 Aligned_cols=23 Identities=26% Similarity=0.209 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCCHHHHHHHHhcc
Q 015999 369 LVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 369 ~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
..+.+|+.|++|...||..|+=|
T Consensus 3 ~TL~~yl~~~~n~~~tA~~L~iH 25 (59)
T PF13556_consen 3 ETLRAYLENNGNISKTARALHIH 25 (59)
T ss_dssp -HHHHHHHTTT-HHHHHHHHTS-
T ss_pred hHHHHHHHcCCCHHHHHHHHCCC
Confidence 46899999999999999999854
No 170
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=59.15 E-value=16 Score=34.33 Aligned_cols=36 Identities=25% Similarity=0.341 Sum_probs=31.8
Q ss_pred HHHHHHHHc-CCCCCCHHHHHHHHHHhcCChHHHHHHHHc
Q 015999 169 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS 207 (397)
Q Consensus 169 ~~I~~i~~M-G~~~f~r~~v~~ALrAafnNpdrAveyL~~ 207 (397)
..|.+|-++ | ..=-+|..||..+-+|-|.|++||--
T Consensus 6 ~~ik~LR~~tg---a~~~~ck~AL~~~~gd~~~A~~~lr~ 42 (198)
T PRK12332 6 KLVKELREKTG---AGMMDCKKALEEANGDMEKAIEWLRE 42 (198)
T ss_pred HHHHHHHHHHC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 467888886 7 88899999999999999999999973
No 171
>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=59.14 E-value=85 Score=24.56 Aligned_cols=66 Identities=20% Similarity=0.206 Sum_probs=41.3
Q ss_pred CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE--eCC----eecCC-CCchhh--cccCCCCEEEEEEee
Q 015999 10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI--HQG----KVLKD-VTTLEE--NKVAENSFVVVMLTK 76 (397)
Q Consensus 10 gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi--y~G----KiL~D-~~tL~d--~gI~~gstI~v~v~k 76 (397)
+...+|.|..++|..+|-..+.++++.+. .+....|+ +.+ +.|.| ++.|.- .....+....+++++
T Consensus 12 ~~~kti~V~~~~t~~~Vi~~~l~k~~l~~-~~~~y~L~ev~~~~~~er~L~~~e~pl~~~~~~~~~~~~~~F~lr~ 86 (87)
T cd01768 12 GTYKTLRVSKDTTAQDVIQQLLKKFGLDD-DPEDYALVEVLGDGGLERLLLPDECPLQIQLNAPRQREDLRFLLRK 86 (87)
T ss_pred ccEEEEEECCCCCHHHHHHHHHHHhCCcC-CcccEEEEEEECCceEEEEeCCCCChHHHHHhcCCCCCcEEEEEec
Confidence 55578999999999999999999999321 35566664 233 45655 445442 233334444444443
No 172
>smart00144 PI3K_rbd PI3-kinase family, Ras-binding domain. Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding RA domains (unpublished observation).
Probab=59.12 E-value=60 Score=27.20 Aligned_cols=74 Identities=20% Similarity=0.119 Sum_probs=46.9
Q ss_pred EEEEeCC-CcEEEEEeCCCCCHHHHHHHHHHHh--CCC-CCCCC-CeEEEeCCee--cCCCCchhhc-----ccCCCCEE
Q 015999 3 VFVKTLK-GTHFEIEVKPEDKVSDVKKNIETVQ--GSD-VYPAS-QQMLIHQGKV--LKDVTTLEEN-----KVAENSFV 70 (397)
Q Consensus 3 I~Vktl~-gk~~~veV~~~~TV~dLK~~I~~~~--g~~-~ip~~-~qrLiy~GKi--L~D~~tL~d~-----gI~~gstI 70 (397)
|.|...+ ...+++.+++++|+.+|.+.+-.+. ..+ .-+.+ ...|--.|+. |..+..|.+| .++.+..+
T Consensus 20 v~i~~~~~~~~~t~~v~~~~~p~~li~~~l~k~~~~~~~~~~~~~dyvLkV~G~~Eyl~~~~~L~~~~yIr~cl~~~~~~ 99 (108)
T smart00144 20 IVVHLEKDQQTKTLKVNPNCTPDSVLAQAFTKMLSLHDQVDPTSEDYILKVCGRDEYLLGDHPLGSFEYIRNCLKNGREP 99 (108)
T ss_pred EEEEEccCceeEEEEECCCCCHHHHHHHHHHHHHhccccccCCCCcEEEEecCcEEEEeCCeeeechHHHHHHHhcCCCc
Confidence 4444333 3568999999999999998886652 111 11222 4555455653 5566667666 37888888
Q ss_pred EEEEee
Q 015999 71 VVMLTK 76 (397)
Q Consensus 71 ~v~v~k 76 (397)
+|++..
T Consensus 100 ~L~L~~ 105 (108)
T smart00144 100 HLVLMT 105 (108)
T ss_pred eEEEEe
Confidence 887754
No 173
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=57.22 E-value=16 Score=36.25 Aligned_cols=36 Identities=22% Similarity=0.249 Sum_probs=31.9
Q ss_pred HHHHHHHHc-CCCCCCHHHHHHHHHHhcCChHHHHHHHHc
Q 015999 169 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS 207 (397)
Q Consensus 169 ~~I~~i~~M-G~~~f~r~~v~~ALrAafnNpdrAveyL~~ 207 (397)
..|++|-++ | +.=-+|..||..+-+|-|+|++||--
T Consensus 6 ~~IK~LRe~Tg---agm~dCKkAL~e~~gDiekAi~~LRk 42 (290)
T TIGR00116 6 QLVKELRERTG---AGMMDCKKALTEANGDFEKAIKNLRE 42 (290)
T ss_pred HHHHHHHHHHC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 468888886 7 88899999999999999999999963
No 174
>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=57.15 E-value=40 Score=26.97 Aligned_cols=35 Identities=11% Similarity=0.096 Sum_probs=31.8
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ 49 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~ 49 (397)
++.|.+.+..+..+|..+|+++.. .+++..+|.|.
T Consensus 8 TVai~v~~g~~y~~L~~~ls~kL~---l~~~~~~LSY~ 42 (78)
T cd06411 8 TVALRAPRGADVSSLRALLSQALP---QQAQRGQLSYR 42 (78)
T ss_pred EEEEEccCCCCHHHHHHHHHHHhc---CChhhcEEEec
Confidence 566788899999999999999999 99999999995
No 175
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=57.00 E-value=10 Score=26.18 Aligned_cols=27 Identities=26% Similarity=0.464 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHhcCChHHHHHHHHcCCC
Q 015999 182 WDRETVIRALRAAYNNPERAVEYLYSGIP 210 (397)
Q Consensus 182 f~r~~v~~ALrAafnNpdrAveyL~~GIP 210 (397)
|+|+-+..||+..-+|..+|.+.| ||+
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L--gis 31 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL--GIS 31 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH--TS-
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH--CCC
Confidence 789999999999999999999999 654
No 176
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=56.79 E-value=24 Score=30.58 Aligned_cols=39 Identities=15% Similarity=0.176 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHHHH-cCCChHHHHHHHHHhCCCHHHHHHHHh
Q 015999 348 TVTPEEREAIERLEA-MGFDRALVLEVFFACNKNEELAANYLL 389 (397)
Q Consensus 348 ~lt~Ee~~ai~rL~~-lGF~r~~~iqAy~ac~kne~~Aan~L~ 389 (397)
.+++|| |+...+ -|-+|+.++.||.+|++|.--|+-.|-
T Consensus 82 ~i~eeD---IkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 82 DISEED---IKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred CCCHHH---HHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 477777 444443 589999999999999999999987774
No 177
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=55.99 E-value=9.1 Score=28.88 Aligned_cols=23 Identities=35% Similarity=0.595 Sum_probs=11.2
Q ss_pred HhhccHHHH--HHHHHHHhCccchH
Q 015999 274 FLRNSQQFQ--ALRTMVQANPQILQ 296 (397)
Q Consensus 274 ~L~~~P~f~--~lrq~vq~NP~ll~ 296 (397)
.+++||.+. -|.++-++||++++
T Consensus 16 ~vq~NP~lL~~lLqql~~~nP~l~q 40 (59)
T PF09280_consen 16 LVQQNPQLLPPLLQQLGQSNPQLLQ 40 (59)
T ss_dssp HHHC-GGGHHHHHHHHHCCSHHHHH
T ss_pred HHHHCHHHHHHHHHHHhccCHHHHH
Confidence 344555533 44555556666444
No 178
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=55.70 E-value=31 Score=29.91 Aligned_cols=57 Identities=14% Similarity=0.239 Sum_probs=43.0
Q ss_pred EeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhc---ccCCCCEEEEEEe
Q 015999 16 EVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN---KVAENSFVVVMLT 75 (397)
Q Consensus 16 eV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~---gI~~gstI~v~v~ 75 (397)
=|..+.||.++...|..+.+ +.+++.-|..++.++.-+.+++++ .-.++.+|+|..+
T Consensus 46 lVP~d~tV~qF~~iIRkrl~---l~~~k~flfVnn~lp~~s~~mg~lYe~~KDeDGFLYi~Ys 105 (121)
T PTZ00380 46 ALPRDATVAELEAAVRQALG---TSAKKVTLAIEGSTPAVTATVGDIADACKRDDGFLYVSVR 105 (121)
T ss_pred EcCCCCcHHHHHHHHHHHcC---CChhHEEEEECCccCCccchHHHHHHHhcCCCCeEEEEEc
Confidence 58899999999999999998 888885444566566677788776 1234668888764
No 179
>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]
Probab=55.45 E-value=21 Score=37.26 Aligned_cols=74 Identities=16% Similarity=0.148 Sum_probs=59.2
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecCC---CCchhhcccCCCCEEEEEEee
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKD---VTTLEENKVAENSFVVVMLTK 76 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrL--iy~GKiL~D---~~tL~d~gI~~gstI~v~v~k 76 (397)
+|.||..+|..|+=++..++-+..+|..|....+ +.....-| .|--|+..| +++|.++.+.+...|+|+-++
T Consensus 316 rLqiRLPdGssfte~Fps~~vL~~vr~yvrq~~~---i~~g~f~LatpyPRReft~eDy~KtllEl~L~psaalvvlpk~ 392 (506)
T KOG2507|consen 316 RLQIRLPDGSSFTEKFPSTSVLRMVRDYVRQNQT---IGLGAFDLATPYPRREFTDEDYDKTLLELRLFPSAALVVLPKK 392 (506)
T ss_pred EEEEecCCccchhhcCCcchHHHHHHHHHHhccc---ccccceeeccccccccccchhhhhhHHHhccCCcceEEEEecC
Confidence 6889999999998888777778899999887777 66777766 588888844 479999999999988877654
Q ss_pred cC
Q 015999 77 VI 78 (397)
Q Consensus 77 ~~ 78 (397)
+.
T Consensus 393 r~ 394 (506)
T KOG2507|consen 393 RA 394 (506)
T ss_pred Cc
Confidence 43
No 180
>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=53.77 E-value=1e+02 Score=23.93 Aligned_cols=52 Identities=21% Similarity=0.177 Sum_probs=36.9
Q ss_pred EEEEeCCCc----EEEEEeCCCCCHHHHHHHHHHHhCCCCC--CCCCeEEE-e---CC--eecCCCC
Q 015999 3 VFVKTLKGT----HFEIEVKPEDKVSDVKKNIETVQGSDVY--PASQQMLI-H---QG--KVLKDVT 57 (397)
Q Consensus 3 I~Vktl~gk----~~~veV~~~~TV~dLK~~I~~~~g~~~i--p~~~qrLi-y---~G--KiL~D~~ 57 (397)
|.|-..++. ..+|.|..+.|+.+|-..+.++++ + .+....|+ + .| +.|.|+.
T Consensus 5 lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~---l~~~~~~y~L~~~~~~~~~er~L~~~E 68 (93)
T PF00788_consen 5 LRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFG---LAEDPSDYCLVEVEESGGEERPLDDDE 68 (93)
T ss_dssp EEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTT---TSSSGGGEEEEEEECTTTEEEEETTTS
T ss_pred EEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhC---CCCCCCCEEEEEEEcCCCEEEEcCCCC
Confidence 445555555 678999999999999999999999 5 34555663 2 23 4676554
No 181
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=53.20 E-value=15 Score=37.27 Aligned_cols=66 Identities=14% Similarity=0.062 Sum_probs=51.0
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC---eecC--CCCchhhcccCCCCE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---KVLK--DVTTLEENKVAENSF 69 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~G---KiL~--D~~tL~d~gI~~gst 69 (397)
.|.||..+|+.+...+-.+++|..|=.-+...... .+-+..+|++.= |.|. -+.||.++||.+..+
T Consensus 279 ~i~vR~pdG~R~qrkf~~sepv~ll~~~~~s~~dg--~~k~~FkLv~a~P~~k~l~~~~daT~~eaGL~nS~~ 349 (356)
T KOG1364|consen 279 SIQVRFPDGRRKQRKFLKSEPVQLLWSFCYSHMDG--SDKKRFKLVQAIPASKTLDYGADATFKEAGLANSET 349 (356)
T ss_pred EEEEecCCccHHHHhhccccHHHHHHHHHHHhhcc--cccccceeeecccchhhhhccccchHHHhccCcccc
Confidence 48899999988877778899998877665544332 667889999876 6664 367999999998875
No 182
>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=52.84 E-value=73 Score=26.08 Aligned_cols=70 Identities=16% Similarity=0.144 Sum_probs=45.5
Q ss_pred EEEEeCCCcEEEEEeC-----CCCCHHHHHHHHHHHhCCCCCCC-CCeEEEeCC---e--ecCCCCchhhc-----ccCC
Q 015999 3 VFVKTLKGTHFEIEVK-----PEDKVSDVKKNIETVQGSDVYPA-SQQMLIHQG---K--VLKDVTTLEEN-----KVAE 66 (397)
Q Consensus 3 I~Vktl~gk~~~veV~-----~~~TV~dLK~~I~~~~g~~~ip~-~~qrLiy~G---K--iL~D~~tL~d~-----gI~~ 66 (397)
|+|+ .+|....+.+. ++.+..+|+.+|.+.++ ++. ....|.|.. . .|.++.-|.++ +-..
T Consensus 3 vKv~-y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~---l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~~~~~~~ 78 (91)
T cd06398 3 VKVK-YGGTLRRFTFPVAENQLDLNMDGLREKVEELFS---LSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYFCSGSR 78 (91)
T ss_pred EEEE-eCCEEEEEEeccccccCCCCHHHHHHHHHHHhC---CCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHHhccCC
Confidence 3444 25555566665 47899999999999998 876 677887843 2 24444444433 2336
Q ss_pred CCEEEEEEee
Q 015999 67 NSFVVVMLTK 76 (397)
Q Consensus 67 gstI~v~v~k 76 (397)
..+|.+.++.
T Consensus 79 ~~~lrl~v~~ 88 (91)
T cd06398 79 LNPLRIDVTV 88 (91)
T ss_pred CceEEEEEEE
Confidence 7788777653
No 183
>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=52.07 E-value=1.2e+02 Score=24.57 Aligned_cols=60 Identities=10% Similarity=0.075 Sum_probs=41.6
Q ss_pred EEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCee-c-CCCCchhhc--ccCCCCEEEEEEee
Q 015999 14 EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKV-L-KDVTTLEEN--KVAENSFVVVMLTK 76 (397)
Q Consensus 14 ~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKi-L-~D~~tL~d~--gI~~gstI~v~v~k 76 (397)
.+-|..+.||.++...|.++.+ +.+++--.+|-+.. + ..+.+++++ ..+++.+|+|..+.
T Consensus 19 kflv~~~~tv~~~~~~lrk~L~---l~~~~slflyvnn~f~p~~d~~~g~LY~~~~~dGfLyi~Ys~ 82 (87)
T cd01612 19 VFKISATQSFQAVIDFLRKRLK---LKASDSLFLYINNSFAPSPDENVGNLYRCFGTNGELIVSYCK 82 (87)
T ss_pred EEEeCCCCCHHHHHHHHHHHhC---CCccCeEEEEECCccCCCchhHHHHHHHhcCCCCEEEEEEeC
Confidence 3458899999999999999988 66665444454443 4 345666665 23678889887653
No 184
>PF00794 PI3K_rbd: PI3-kinase family, ras-binding domain; InterPro: IPR000341 Phosphatidylinositol 3-kinase (PI3K) (2.7.1.137 from EC) is an enzyme that phosphorylates phosphoinositides on the 3-hydroxyl group of the inositol ring. A subset of PI3Ks has the capacity to bind and be activated by the GTP-bound small GTPase p21Ras (Ras). PI3Ks are recognised as one of the principal effectors of Ras signalling to the cell-cycle control machinery. In the structure of the Ras-PI3K gamma complex, contacts between the two molecules are made primarily via the so-called switch I region of Ras and the PI3K RBD. The RBD fold comprises a five-stranded mixed beta-sheet, flanked by two alpha-helices. Interaction between Ras and the PI3K RBD is primarily polar in character and, as characterised by kinetic measurements, is reversible and transient [].; GO: 0016303 1-phosphatidylinositol-3-kinase activity, 0005942 phosphatidylinositol 3-kinase complex; PDB: 2RD0_A 3HIZ_A 3HHM_A 1E8W_A 1E8X_A 1E7V_A 1E90_A 1E7U_A 2Y3A_A 3L54_A ....
Probab=51.47 E-value=61 Score=26.74 Aligned_cols=75 Identities=15% Similarity=0.107 Sum_probs=45.4
Q ss_pred EEEEEeC-CCcEEEEEeCCCCCHHHHHHHHHHHh--CCCCCCCC-CeEEEeCCe--ecCCCCchhhcc-----cCCCCEE
Q 015999 2 KVFVKTL-KGTHFEIEVKPEDKVSDVKKNIETVQ--GSDVYPAS-QQMLIHQGK--VLKDVTTLEENK-----VAENSFV 70 (397)
Q Consensus 2 kI~Vktl-~gk~~~veV~~~~TV~dLK~~I~~~~--g~~~ip~~-~qrLiy~GK--iL~D~~tL~d~g-----I~~gstI 70 (397)
.|.|... .+..+++.++.+.|+.+|...+..+. +....... ...|--.|+ -|..+..|.+|. ++.+..+
T Consensus 18 ~v~v~~~~~~~~~t~~~~~~~t~~~li~~~l~k~~~~~~~~~~~~dyvLKV~G~~EyL~g~~~L~~y~yIr~cl~~~~~~ 97 (106)
T PF00794_consen 18 KVSVHFENSQQSFTFQVDPNSTPEELIAQALKKKLKDLLPPDPEDDYVLKVCGREEYLLGDHPLSQYEYIRQCLKRGKDP 97 (106)
T ss_dssp EEEEEETTCSEEEEEEEETTS-HHHHHHHHHHHHHHHTT-CHHHHGEEEEETTSSEEE-SSS-GGGBHHHHHHHHCT--E
T ss_pred EEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHHHhhcCCcccccCEEEEecCceEEeeCCeeeeccHHHHHHHhcCCCc
Confidence 4666666 45678999999999999998886661 21001111 455545554 366778888883 6777778
Q ss_pred EEEEee
Q 015999 71 VVMLTK 76 (397)
Q Consensus 71 ~v~v~k 76 (397)
+|++..
T Consensus 98 ~L~Lv~ 103 (106)
T PF00794_consen 98 HLVLVH 103 (106)
T ss_dssp EEEEEE
T ss_pred EEEEEe
Confidence 877654
No 185
>KOG3391 consensus Transcriptional co-repressor component [Transcription]
Probab=51.44 E-value=16 Score=32.30 Aligned_cols=30 Identities=27% Similarity=0.290 Sum_probs=25.0
Q ss_pred eecCCCCchhhcccCCCCEEEEEEeecCCC
Q 015999 51 KVLKDVTTLEENKVAENSFVVVMLTKVIRF 80 (397)
Q Consensus 51 KiL~D~~tL~d~gI~~gstI~v~v~k~~~~ 80 (397)
|-.+|++||..++++-||+|.|.++.++..
T Consensus 112 Kg~ddnktL~~~kf~iGD~lDVaI~~p~~~ 141 (151)
T KOG3391|consen 112 KGIDDNKTLQQTKFEIGDYLDVAITPPNRR 141 (151)
T ss_pred ccCCccchhhhCCccccceEEEEecCcccC
Confidence 345789999999999999999999766544
No 186
>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=50.89 E-value=23 Score=28.59 Aligned_cols=58 Identities=19% Similarity=0.203 Sum_probs=38.3
Q ss_pred EEeCCCCCHHHHHHHHHHHhCC----CCCCCCCeEEEeCCe-ec------CCCCchhhcccCCCCEEEEE
Q 015999 15 IEVKPEDKVSDVKKNIETVQGS----DVYPASQQMLIHQGK-VL------KDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 15 veV~~~~TV~dLK~~I~~~~g~----~~ip~~~qrLiy~GK-iL------~D~~tL~d~gI~~gstI~v~ 73 (397)
|+|++++|+.+|-+.+++.... ..+..+.-.|++.+- .| +=+++|.++ +.+|+.|+|.
T Consensus 1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL-~~~g~ei~Vt 69 (84)
T PF08825_consen 1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL-LSDGEEITVT 69 (84)
T ss_dssp EEESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT-HHSSEEEEEE
T ss_pred CCcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH-hcCCCEEEEE
Confidence 6789999999999999887430 012223334444432 12 125889999 9999998874
No 187
>PRK09377 tsf elongation factor Ts; Provisional
Probab=50.86 E-value=24 Score=35.09 Aligned_cols=36 Identities=28% Similarity=0.343 Sum_probs=32.0
Q ss_pred HHHHHHHHc-CCCCCCHHHHHHHHHHhcCChHHHHHHHHc
Q 015999 169 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS 207 (397)
Q Consensus 169 ~~I~~i~~M-G~~~f~r~~v~~ALrAafnNpdrAveyL~~ 207 (397)
..|++|-++ | +.=-+|.+||..+-+|-|.|++||-.
T Consensus 7 ~~IK~LR~~Tg---agm~dCKkAL~e~~gD~ekAi~~Lrk 43 (290)
T PRK09377 7 ALVKELRERTG---AGMMDCKKALTEADGDIEKAIEWLRK 43 (290)
T ss_pred HHHHHHHHHHC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 468888886 7 88899999999999999999999973
No 188
>CHL00098 tsf elongation factor Ts
Probab=50.64 E-value=26 Score=32.95 Aligned_cols=36 Identities=28% Similarity=0.293 Sum_probs=31.5
Q ss_pred HHHHHHHHc-CCCCCCHHHHHHHHHHhcCChHHHHHHHHc
Q 015999 169 ATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYS 207 (397)
Q Consensus 169 ~~I~~i~~M-G~~~f~r~~v~~ALrAafnNpdrAveyL~~ 207 (397)
..|.+|-++ | ..=-+|.+||..+-+|-|.|++||--
T Consensus 3 ~~ik~LR~~Tg---ag~~dck~AL~e~~gd~~~A~~~Lr~ 39 (200)
T CHL00098 3 ELVKELRDKTG---AGMMDCKKALQEANGDFEKALESLRQ 39 (200)
T ss_pred HHHHHHHHHHC---CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 457777776 6 78889999999999999999999975
No 189
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=50.49 E-value=48 Score=32.69 Aligned_cols=68 Identities=9% Similarity=0.200 Sum_probs=51.8
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecC-C--CCchhhcccCCCCEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLK-D--VTTLEENKVAENSFVVV 72 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrL--iy~GKiL~-D--~~tL~d~gI~~gstI~v 72 (397)
.|.||..+|+++...+....|...|+.-|.-..+ ...+-..| -|--+.+. | .++|..+++.+.++|++
T Consensus 212 rlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~~---~~~~P~~f~t~fPR~tf~edD~~KpLq~L~L~Psa~lil 284 (290)
T KOG2689|consen 212 RLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRG---DGLDPYSFHTGFPRVTFTEDDELKPLQELDLVPSAVLIL 284 (290)
T ss_pred EEEEEcCCCCeeeeecCchhhHHHHHHHHHHhcc---CCCCCeeeecCCCceecccccccccHHHhccccchheec
Confidence 4789988999999999999999999999998887 33323333 24445553 2 47899999998888764
No 190
>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=48.60 E-value=70 Score=26.88 Aligned_cols=56 Identities=16% Similarity=0.147 Sum_probs=40.3
Q ss_pred eCCCCCHHHHHHHHHHHhCCCCCCCCC-eEEEeCCeecCCCCchhhc---ccCCCCEEEEEEe
Q 015999 17 VKPEDKVSDVKKNIETVQGSDVYPASQ-QMLIHQGKVLKDVTTLEEN---KVAENSFVVVMLT 75 (397)
Q Consensus 17 V~~~~TV~dLK~~I~~~~g~~~ip~~~-qrLiy~GKiL~D~~tL~d~---gI~~gstI~v~v~ 75 (397)
|..+.||.+|...|..+.. +.+++ +-|+.++..+..+.+++++ .-.++.+|+|...
T Consensus 39 vp~~~tv~qf~~~ir~rl~---l~~~~alfl~Vn~~lp~~s~tm~elY~~~kdeDGFLY~~Ys 98 (104)
T PF02991_consen 39 VPKDLTVGQFVYIIRKRLQ---LSPEQALFLFVNNTLPSTSSTMGELYEKYKDEDGFLYMTYS 98 (104)
T ss_dssp EETTSBHHHHHHHHHHHTT-----TTS-EEEEBTTBESSTTSBHHHHHHHHB-TTSSEEEEEE
T ss_pred EcCCCchhhHHHHhhhhhc---CCCCceEEEEEcCcccchhhHHHHHHHHhCCCCCeEEEEec
Confidence 5778999999999999988 65554 4555677666788898876 2245778888764
No 191
>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=48.53 E-value=74 Score=25.62 Aligned_cols=39 Identities=13% Similarity=0.153 Sum_probs=29.8
Q ss_pred EEEEEeCCCcEEEEEeCC--CCCHHHHHHHHHHHhCCCCCCCCCeEE
Q 015999 2 KVFVKTLKGTHFEIEVKP--EDKVSDVKKNIETVQGSDVYPASQQML 46 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~--~~TV~dLK~~I~~~~g~~~ip~~~qrL 46 (397)
+|++. .+|.+..+.+++ +.+..+|+..|...++ ++ .+.|
T Consensus 2 ~vKat-y~~d~~rf~~~~~~~~~~~~L~~ev~~rf~---l~--~f~l 42 (81)
T cd06396 2 NLKVT-YNGESQSFLVSDSENTTWASVEAMVKVSFG---LN--DIQI 42 (81)
T ss_pred EEEEE-ECCeEEEEEecCCCCCCHHHHHHHHHHHhC---CC--ccee
Confidence 34444 467788888888 7799999999999999 76 4444
No 192
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction 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 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.
Probab=47.80 E-value=66 Score=26.67 Aligned_cols=40 Identities=10% Similarity=0.101 Sum_probs=32.8
Q ss_pred EEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe
Q 015999 5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH 48 (397)
Q Consensus 5 Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy 48 (397)
++..+|.+..+.|+.+.|..+|+.++.+..+ +... +.|-|
T Consensus 17 l~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~---~~~~-~~lky 56 (97)
T cd06410 17 LRYVGGETRIVSVDRSISFKELVSKLSELFG---AGVV-VTLKY 56 (97)
T ss_pred EEEcCCceEEEEEcCCCCHHHHHHHHHHHhC---CCCc-eEEEE
Confidence 4566788889999999999999999999998 6554 55544
No 193
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=47.56 E-value=24 Score=29.50 Aligned_cols=31 Identities=23% Similarity=0.457 Sum_probs=27.3
Q ss_pred CCcchHHHHHHHHHcCCCCCCHHHHHHHHHHhcC
Q 015999 163 AGSNLEATVQQILDMGGGSWDRETVIRALRAAYN 196 (397)
Q Consensus 163 ~g~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafn 196 (397)
.-.++...+.+|.+-| |+++...++|+++|+
T Consensus 67 ~~~Ef~~~~~eM~dAG---V~~~~~~~~l~~~Yk 97 (100)
T PF15652_consen 67 LQEEFNNSYREMFDAG---VSKECRKKALKAQYK 97 (100)
T ss_pred HHHHHHHHHHHHHHcC---CCHHHHHHHHHHHHh
Confidence 3467888899999999 999999999999875
No 194
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.49 E-value=25 Score=32.92 Aligned_cols=31 Identities=26% Similarity=0.359 Sum_probs=26.6
Q ss_pred cchHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCh
Q 015999 165 SNLEATVQQILDMGGGSWDRETVIRALRAAYNNP 198 (397)
Q Consensus 165 ~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNp 198 (397)
...+++|..|+++| |.+.++.+|++...++-
T Consensus 142 ~~~~ea~~AL~~LG---y~~~ea~~al~~v~~~~ 172 (196)
T PRK13901 142 FKFKELEQSIVNMG---FDRKLVNSAIKEIMLLD 172 (196)
T ss_pred ccHHHHHHHHHHcC---CCHHHHHHHHHHHhcch
Confidence 34688999999999 99999999999776643
No 195
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=47.34 E-value=58 Score=27.59 Aligned_cols=45 Identities=20% Similarity=0.328 Sum_probs=33.1
Q ss_pred hHHHHHHHhhhCHHHHHHHHHhHHHHHHHhcCCCCCCCCcccccccccCCCcccCCHHHHHHH-----HHHHHcC
Q 015999 295 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAI-----ERLEAMG 364 (397)
Q Consensus 295 l~~~Lqqi~~~nP~l~~~I~~n~~~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~Ee~~ai-----~rL~~lG 364 (397)
|..++.++. .|+.++...+|++.++. .-.||+||+++| .+|.++|
T Consensus 16 LN~f~~sL~--~a~~Re~F~aD~eAy~~-----------------------~~gLTeEe~~AV~~rD~~~Li~lG 65 (106)
T cd07921 16 LNKMCMSLN--KAENREAFKADEEAYCD-----------------------KFGLTEEQKQAVLDRDWLRLLELG 65 (106)
T ss_pred HHHHHHHHC--CHHHHHHHHhCHHHHHH-----------------------HcCCCHHHHHHHHhCCHHHHHHhc
Confidence 456666764 78889888888888876 225789999885 4577776
No 196
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=47.08 E-value=1.2e+02 Score=23.77 Aligned_cols=54 Identities=6% Similarity=0.114 Sum_probs=32.3
Q ss_pred EEeCC-CCCHHHHHHHHHHHhCC--CCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 15 IEVKP-EDKVSDVKKNIETVQGS--DVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 15 veV~~-~~TV~dLK~~I~~~~g~--~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
++++. ..||.+|++.|.+++.. ........++..+++...+ +.-|++||.|.++
T Consensus 19 ~~v~~~~~tv~~l~~~L~~~~~~~~~~~~~~~~~~aVN~~~~~~-----~~~l~dgDeVai~ 75 (81)
T PRK11130 19 LELAADFPTVEALRQHLAQKGDRWALALEDGKLLAAVNQTLVSF-----DHPLTDGDEVAFF 75 (81)
T ss_pred EEecCCCCCHHHHHHHHHHhCccHHhhhcCCCEEEEECCEEcCC-----CCCCCCCCEEEEe
Confidence 44443 47999999999887531 0012233344446654433 3358899999876
No 197
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=46.87 E-value=45 Score=26.35 Aligned_cols=41 Identities=22% Similarity=0.369 Sum_probs=30.2
Q ss_pred hhCHHHHHHHHHhHHHHHHHhcCCCCCCCCcccccccccCCCcccCCHHHHHHH-----HHHHHcCCCh
Q 015999 304 KQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAI-----ERLEAMGFDR 367 (397)
Q Consensus 304 ~~nP~l~~~I~~n~~~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~Ee~~ai-----~rL~~lGF~r 367 (397)
..+|++++...+||+.++. .-.||+||+++| .+|.++|=+-
T Consensus 13 ~~~~~~re~f~~dp~a~~~-----------------------~~~Lt~eE~~al~~rD~~~L~~lG~~~ 58 (77)
T cd07321 13 LVKPEVKERFKADPEAVLA-----------------------EYGLTPEEKAALLARDVGALYVLGVNP 58 (77)
T ss_pred hcCHHHHHHHHhCHHHHHH-----------------------HcCCCHHHHHHHHcCCHHHHHHcCCCH
Confidence 4568888888889988876 225799999884 4577777443
No 198
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=46.86 E-value=41 Score=28.96 Aligned_cols=36 Identities=19% Similarity=0.238 Sum_probs=31.4
Q ss_pred HHHHHHHHHc-CCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 015999 168 EATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLY 206 (397)
Q Consensus 168 e~~I~~i~~M-G~~~f~r~~v~~ALrAafnNpdrAveyL~ 206 (397)
++-|.-+++- | -+|+++++||+.+.++.-.|+-||.
T Consensus 79 ~eDI~lV~eq~g---vs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 79 EDDIELVMKQCN---VSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred HHHHHHHHHHhC---cCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 4667777774 6 8999999999999999999999985
No 199
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=46.63 E-value=66 Score=26.35 Aligned_cols=54 Identities=20% Similarity=0.220 Sum_probs=32.8
Q ss_pred EEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe-CC------eecCCCC---ch--hhcccCCCCEEEEE
Q 015999 15 IEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH-QG------KVLKDVT---TL--EENKVAENSFVVVM 73 (397)
Q Consensus 15 veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy-~G------KiL~D~~---tL--~d~gI~~gstI~v~ 73 (397)
++++...||.+|-..|.+.+. ..+-+|+. .| -+|-++. .+ .++-+++||.|.++
T Consensus 23 ~~~~~~~tV~dll~~L~~~~~-----~~~~~lf~~~g~lr~~i~VlvN~~di~~l~g~~t~L~dgD~v~i~ 88 (94)
T cd01764 23 LDGEKPVTVGDLLDYVASNLL-----EERPDLFIEGGSVRPGIIVLINDTDWELLGEEDYILEDGDHVVFI 88 (94)
T ss_pred ccCCCCCcHHHHHHHHHHhCc-----hhhhhhEecCCcccCCEEEEECCccccccCCcccCCCCcCEEEEE
Confidence 344456799999999987753 33334433 22 1232322 23 35679999999876
No 200
>PLN03196 MOC1-like protein; Provisional
Probab=46.03 E-value=1.8e+02 Score=30.98 Aligned_cols=49 Identities=20% Similarity=0.342 Sum_probs=34.9
Q ss_pred CCcccCCHHHH-HHHHHHHHcCCChHHHHHHHHHh-------CCCHHHHHHHHhccC
Q 015999 344 PQAVTVTPEER-EAIERLEAMGFDRALVLEVFFAC-------NKNEELAANYLLDHM 392 (397)
Q Consensus 344 ~~~~~lt~Ee~-~ai~rL~~lGF~r~~~iqAy~ac-------~kne~~Aan~L~~~~ 392 (397)
+....++.+-. ..++=|+.+||+++++..++..| .++.....+||.+.+
T Consensus 330 P~il~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneM 386 (487)
T PLN03196 330 PQIVSLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEM 386 (487)
T ss_pred chhhcccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHh
Confidence 33556666553 56888999999999998887765 356677777777643
No 201
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=44.08 E-value=26 Score=32.51 Aligned_cols=30 Identities=13% Similarity=0.385 Sum_probs=26.1
Q ss_pred cchHHHHHHHHHcCCCCCCHHHHHHHHHHhcCC
Q 015999 165 SNLEATVQQILDMGGGSWDRETVIRALRAAYNN 197 (397)
Q Consensus 165 ~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafnN 197 (397)
+..++.+..|+.+| |.+.++.+|++....+
T Consensus 145 ~~~~e~~~aL~~LG---y~~~e~~~ai~~~~~~ 174 (191)
T TIGR00084 145 AARDELFEALVSLG---YKPQEIQQALKKIKNK 174 (191)
T ss_pred chHHHHHHHHHHcC---CCHHHHHHHHHHHhhc
Confidence 34678999999999 9999999999988653
No 202
>PF12053 DUF3534: Domain of unknown function (DUF3534); InterPro: IPR021922 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 amino acids in length. This domain is found associated with PF00595 from PFAM. This domain has a conserved GILD sequence motif. ; PDB: 2NS5_A.
Probab=43.92 E-value=1.1e+02 Score=27.35 Aligned_cols=74 Identities=16% Similarity=0.085 Sum_probs=37.6
Q ss_pred CEEEEEeCCCcEEEEEeC-CCCCHHHHHHHHHHHhCCC-CCCCCCe----EEEe-CCeecCCCCchhhcccCCCCEEEEE
Q 015999 1 MKVFVKTLKGTHFEIEVK-PEDKVSDVKKNIETVQGSD-VYPASQQ----MLIH-QGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~-~~~TV~dLK~~I~~~~g~~-~ip~~~q----rLiy-~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
|||+|.. ....+.|-+. ...||.+|-++--.++.+- ...++.. +|-| .|-+|+.++.|.+. +.+.+.|+.+
T Consensus 1 mkvtV~f-g~~~vvVPC~dg~~tV~~L~~~A~~RY~K~~~~~~~~~v~V~~l~~~dggiLd~DD~l~dV-~dd~d~liAv 78 (145)
T PF12053_consen 1 MKVTVCF-GRTRVVVPCGDGQLTVRDLIQQALRRYRKAKEKDPDYWVVVHHLEYTDGGILDPDDVLCDV-VDDRDQLIAV 78 (145)
T ss_dssp -EEEEEE-TTEEEEEEESSS---HHHHHHHHHHHHHHHTT--TTS-EEEEEEE-SSS-EE-TTS-HHHH-S-TTEEEEEE
T ss_pred CeEEEEe-CCeEEEEEeCCCCccHHHHHHHHhHhHHHhhccCCCceEEEeeEEecCCceeccccceeEe-ccChhhhhee
Confidence 8999996 3445566555 5689998876554333210 0223322 2332 56688888888876 4567777666
Q ss_pred Eee
Q 015999 74 LTK 76 (397)
Q Consensus 74 v~k 76 (397)
..-
T Consensus 79 ydE 81 (145)
T PF12053_consen 79 YDE 81 (145)
T ss_dssp EEE
T ss_pred ecc
Confidence 554
No 203
>PF02017 CIDE-N: CIDE-N domain; InterPro: IPR003508 This domain consists of caspase-activated (CAD) nucleases, which induce DNA fragmentation and chromatin condensation during apoptosis, and the cell death activator proteins CIDE-A and CIDE-B, which are inhibitors of CAD nuclease. The two proteins interact through the region defined by the method signatures.; GO: 0006915 apoptosis, 0005622 intracellular; PDB: 1IBX_A 2EEL_A 1F2R_I 1C9F_A 1D4B_A.
Probab=41.28 E-value=66 Score=25.74 Aligned_cols=62 Identities=10% Similarity=0.223 Sum_probs=39.7
Q ss_pred EEEeCC-CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecCCCCchhhcccCCCCEEEEE
Q 015999 4 FVKTLK-GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 4 ~Vktl~-gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy--~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
.|++.+ .+.+-|-+ .+..+|+.+.++..+ ++.+..+|+. .|.+++|+.-+.. +.++..+++.
T Consensus 6 kv~~~~r~~k~Gv~A---~sL~eL~~K~~~~l~---~~~~~~~lvL~eDGT~VddEeyF~t--Lp~nT~lm~L 70 (78)
T PF02017_consen 6 KVRNHDRSVKKGVAA---SSLEELLEKACDKLQ---LPEEPVRLVLEEDGTEVDDEEYFQT--LPDNTVLMLL 70 (78)
T ss_dssp EEEETTSSCEEEEEE---SSHHHHHHHHHHHHT----SSSTCEEEETTTTCBESSCHHHCC--SSSSEEEEEE
T ss_pred EEecCCCCceEeEEc---CCHHHHHHHHHHHhC---CCCcCcEEEEeCCCcEEccHHHHhh--CCCCCEEEEE
Confidence 455544 23444544 489999999999999 8877777765 6777776643332 4455555443
No 204
>PF06234 TmoB: Toluene-4-monooxygenase system protein B (TmoB); InterPro: IPR009355 This family consists of several Toluene-4-monooxygenase system protein B (TmoB) sequences. Pseudomonas mendocina KR1 metabolises toluene as a carbon source. The initial step of the pathway is hydroxylation of toluene to form p-cresol by a multicomponent toluene-4-monooxygenase (T4MO) system [].; PDB: 3N1Y_C 3RNG_C 3RNA_C 3RN9_C 3RNC_C 3N1X_C 3RNE_C 3RNF_C 3N1Z_C 3N20_C ....
Probab=41.19 E-value=91 Score=25.38 Aligned_cols=63 Identities=21% Similarity=0.276 Sum_probs=42.9
Q ss_pred EEEEeCCCCCHHHHHHHHHHHh-CCCCCC-CC-CeEEEeCC--eecCCCCchhhcccCCCCEEEEEEe
Q 015999 13 FEIEVKPEDKVSDVKKNIETVQ-GSDVYP-AS-QQMLIHQG--KVLKDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 13 ~~veV~~~~TV~dLK~~I~~~~-g~~~ip-~~-~qrLiy~G--KiL~D~~tL~d~gI~~gstI~v~v~ 75 (397)
.-+-|+..+|+.++-.+++... |...-+ +. ..++-++| ..+..+.++.+-||++-+.|-+...
T Consensus 17 ~Lv~VDt~dTmdqVA~k~A~HsVGrRV~~~pg~~lrVr~~g~~~~~p~~~tVaeagl~P~e~vev~~~ 84 (85)
T PF06234_consen 17 QLVPVDTEDTMDQVAAKVAHHSVGRRVAPRPGAPLRVRRQGDTQPFPRSMTVAEAGLQPMEWVEVRFE 84 (85)
T ss_dssp EEEEEETT-BHHHHHHHHHTTTTTTSS---TTSEEEEEETTTSSEE-TT-BGGGHT--TTEEEEEEEE
T ss_pred EEEEeCCCCcHHHHHHHHhhhhcceecCCCCCCEEEEEecCCCccCCCccEehhcCCCcceEEEEEEc
Confidence 4468999999999999987542 433222 23 45666888 8999999999999999999988753
No 205
>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=40.94 E-value=41 Score=32.44 Aligned_cols=70 Identities=19% Similarity=0.371 Sum_probs=45.5
Q ss_pred EEEEeCC--CcEE----EEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC----Cee--cCCCCchhhcccCCCCEE
Q 015999 3 VFVKTLK--GTHF----EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ----GKV--LKDVTTLEENKVAENSFV 70 (397)
Q Consensus 3 I~Vktl~--gk~~----~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~----GKi--L~D~~tL~d~gI~~gstI 70 (397)
|++|..+ .+++ .+-|..+++|.+|-..|.+..| +|.+.--++|. +++ ++.+.++....|.+||.|
T Consensus 71 lFlK~fDp~~q~L~~iGh~~v~~~~~v~~l~~~i~~~~g---~p~~t~l~lyEEi~~~~ie~i~~~~t~~~~el~~GdIi 147 (249)
T PF12436_consen 71 LFLKYFDPETQTLRYIGHVYVPKNDKVSELVPLINERAG---LPPDTPLLLYEEIKPNMIEPIDPNQTFEKAELQDGDII 147 (249)
T ss_dssp EEEEEEETTTTEEEEEEEEEEETT-BGGGTHHHHHHHHT-----TT--EEEEEEEETTEEEE--SSSBHHHTT--TTEEE
T ss_pred EEEEeeCCCCCEEEEEeEEEECCCCCHHHHHHHHHHHcC---CCCCCceEEEEEeccceeeEcCCCCchhhcccCCCCEE
Confidence 6666543 2332 3568889999999999999999 88876666663 443 677899999999999988
Q ss_pred EEEEe
Q 015999 71 VVMLT 75 (397)
Q Consensus 71 ~v~v~ 75 (397)
++-..
T Consensus 148 ~fQ~~ 152 (249)
T PF12436_consen 148 CFQRA 152 (249)
T ss_dssp EEEE-
T ss_pred EEEec
Confidence 77543
No 206
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=40.59 E-value=43 Score=32.98 Aligned_cols=35 Identities=23% Similarity=0.356 Sum_probs=29.5
Q ss_pred HHHHHcCCCCCCHHHHHHHHHHh-cCChHHHHHHH-HcCC
Q 015999 172 QQILDMGGGSWDRETVIRALRAA-YNNPERAVEYL-YSGI 209 (397)
Q Consensus 172 ~~i~~MG~~~f~r~~v~~ALrAa-fnNpdrAveyL-~~GI 209 (397)
+.+|+|| |++.-+.+||-.. .-+-+-|++|| +.+.
T Consensus 5 ~~l~~mg---fps~k~e~al~~~~n~~~e~al~wl~~d~~ 41 (290)
T KOG2689|consen 5 QSLEEMG---FPSGKAEKALAVYGNRGIEQALDWLEMDHA 41 (290)
T ss_pred HHHHHhc---CchhhhhhHhhhhccccHHHHHHHHHhccc
Confidence 7899999 9999999999766 55778899999 6653
No 207
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=40.21 E-value=1.1e+02 Score=24.21 Aligned_cols=49 Identities=18% Similarity=0.194 Sum_probs=39.0
Q ss_pred EEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC--eecCCC
Q 015999 5 VKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG--KVLKDV 56 (397)
Q Consensus 5 Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~G--KiL~D~ 56 (397)
|--.+|..-.+.+.+..||.++-.++.++.| +..+...++.-| |.|.-+
T Consensus 4 V~LPdg~~T~V~vrpG~ti~d~L~kllekRg---l~~~~~~vf~~g~~k~l~~~ 54 (73)
T cd01817 4 VILPDGSTTVVPTRPGESIRDLLSGLCEKRG---INYAAVDLFLVGGDKPLVLD 54 (73)
T ss_pred EECCCCCeEEEEecCCCCHHHHHHHHHHHcC---CChhHEEEEEecCCcccccC
Confidence 4456788888999999999999999999999 888888776555 455433
No 208
>PF08783 DWNN: DWNN domain; InterPro: IPR014891 The ~75-residue DWNN (Domain With No Name) domain is highly conserved through eukaryotic species but is absent in prokaryotes. The DWNN domain is found only at the N terminus of the RBBP6 family of proteins which includes: Mammalian RBBP6, a splicing-associated protein that plays a role in the induction of apoptosis and regulation of the cell cycle. Drosophila melanogaster (Fruit fly) SNAMA (something that sticks like glue), a protein that appears to play a role in apoptosis. All of the identified RBBP6 homologues include the DWNN domain, a CCHC-type zinc finger (see PDOC50158 from PROSITEDOC) and a RING-type zinc finger (see PDOC00449 from PROSITEDOC). The three domain form is found in plants, protozoa, fungi and microsporidia. The RBBP6 homologues in vertebrates, insects and worms are longer and include additional domains. In addition to forming part of the full-length RBBP6 protein, the DWNN domain is also expressed in vertebrates as a small protein containing a DWNN domain and a short C-terminal tail (RBBP6 variant 3). The DWNN domain adopts a fold similar to the ubiquitin one, characterised by two alpha-helices and four beta-sheets ordered as beta-beta-alpha-beta-alpha-beta along the sequence. The similarity of DWNN domain to ubiquitin and the presence of the RING finger suggest that the DWNN domain may act as an ubiquitin-like modifier, possibly playing a role in the regulation of the splicing machinery [, ]. ; GO: 0008270 zinc ion binding, 0005634 nucleus; PDB: 2C7H_A.
Probab=40.02 E-value=63 Score=25.53 Aligned_cols=32 Identities=19% Similarity=0.081 Sum_probs=21.3
Q ss_pred EEEeCCCcE-EEEEeC-CCCCHHHHHHHHHHHhC
Q 015999 4 FVKTLKGTH-FEIEVK-PEDKVSDVKKNIETVQG 35 (397)
Q Consensus 4 ~Vktl~gk~-~~veV~-~~~TV~dLK~~I~~~~g 35 (397)
+.|..+.+. ..|.++ ...+|.+||..|..+.+
T Consensus 2 ~YKFkS~k~~~~i~fdG~~Isv~dLKr~I~~~~~ 35 (74)
T PF08783_consen 2 HYKFKSQKDYDTITFDGTSISVFDLKREIIEKKK 35 (74)
T ss_dssp EEEETT-SSEEEEEESSSEEEHHHHHHHHHHHHT
T ss_pred eEEecccCCccEEEECCCeeEHHHHHHHHHHHhC
Confidence 444444443 346666 46899999999977766
No 209
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=38.83 E-value=84 Score=26.88 Aligned_cols=61 Identities=8% Similarity=0.118 Sum_probs=41.8
Q ss_pred cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeec--CCCCchhhc--ccCCCCEEEEEE
Q 015999 11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVL--KDVTTLEEN--KVAENSFVVVML 74 (397)
Q Consensus 11 k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL--~D~~tL~d~--gI~~gstI~v~v 74 (397)
|.-...|++++|+..+...|.+..+ ++..++-++|=..-. ..+..++++ +..-++.|+|.-
T Consensus 45 K~~k~~i~~t~tfa~vi~Flkk~Lk---l~as~slflYVN~sFAPsPDq~v~~Ly~cf~~d~~Lvl~Y 109 (116)
T KOG3439|consen 45 KKSKFKINPTQTFAKVILFLKKFLK---LQASDSLFLYVNNSFAPSPDQIVGNLYECFGTDGKLVLNY 109 (116)
T ss_pred ecceEEeCcchhhHHHHHHHHHHhC---CcccCeEEEEEcCccCCCchhHHHHHHHhcCCCCEEEEEE
Confidence 3345678999999999999999999 999999888855544 234444443 233344555543
No 210
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.84 E-value=39 Score=31.73 Aligned_cols=28 Identities=14% Similarity=0.338 Sum_probs=25.1
Q ss_pred cchHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Q 015999 165 SNLEATVQQILDMGGGSWDRETVIRALRAAY 195 (397)
Q Consensus 165 ~~~e~~I~~i~~MG~~~f~r~~v~~ALrAaf 195 (397)
+..++++..|+.+| |.|.++.+|++...
T Consensus 153 ~~~~ea~~AL~~LG---y~~~ea~~av~~~~ 180 (203)
T PRK14602 153 SVFRDALAGLANLG---YGEEEARPVLKEVL 180 (203)
T ss_pred chHHHHHHHHHHcC---CCHHHHHHHHHHHh
Confidence 34688999999999 99999999999885
No 211
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=36.49 E-value=66 Score=32.31 Aligned_cols=42 Identities=21% Similarity=0.239 Sum_probs=35.8
Q ss_pred CcchHHHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 164 GSNLEATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 164 g~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
....++.++-|.+-| .+.+++..+++.+.++|.+|.+|+..+
T Consensus 171 ~~~~~~~~~~L~~~~---~~~~~a~~~~~l~~G~p~~A~~~~~~~ 212 (319)
T PRK08769 171 LPPAHEALAWLLAQG---VSERAAQEALDAARGHPGLAAQWLRED 212 (319)
T ss_pred CcCHHHHHHHHHHcC---CChHHHHHHHHHcCCCHHHHHHHhcCc
Confidence 345577788888889 999999999999999999999999654
No 212
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=36.45 E-value=55 Score=32.99 Aligned_cols=39 Identities=15% Similarity=0.277 Sum_probs=34.6
Q ss_pred HHHHHHHHHHH-cCCChHHHHHHHHHhCCCHHHHHHHHhc
Q 015999 352 EEREAIERLEA-MGFDRALVLEVFFACNKNEELAANYLLD 390 (397)
Q Consensus 352 Ee~~ai~rL~~-lGF~r~~~iqAy~ac~kne~~Aan~L~~ 390 (397)
.+++.|.+|.+ -|++-..|.+|+.-|++|...|..||=+
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k 84 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHK 84 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHH
Confidence 35677999987 4999999999999999999999999965
No 213
>PLN03196 MOC1-like protein; Provisional
Probab=36.40 E-value=83 Score=33.53 Aligned_cols=36 Identities=22% Similarity=0.423 Sum_probs=22.0
Q ss_pred HHHHHHHhCccchH-----------HHHHHHhhhCHHHHHHHHHhHH
Q 015999 283 ALRTMVQANPQILQ-----------PMLQELGKQNPHLMRLIQEHQT 318 (397)
Q Consensus 283 ~lrq~vq~NP~ll~-----------~~Lqqi~~~nP~l~~~I~~n~~ 318 (397)
++..+|..+|.+|. .+|+.++-.+.++..+|..+|.
T Consensus 140 ~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~ 186 (487)
T PLN03196 140 SLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPE 186 (487)
T ss_pred HHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCch
Confidence 66667777777655 3455555666666666665554
No 214
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=35.60 E-value=11 Score=31.27 Aligned_cols=54 Identities=31% Similarity=0.495 Sum_probs=42.4
Q ss_pred HHhhcc----HHHHHHHHHHHhCccchHHHHHHHhhhCHHHHHHHHHhHHHHHHHhcC
Q 015999 273 DFLRNS----QQFQALRTMVQANPQILQPMLQELGKQNPHLMRLIQEHQTDFLRLINE 326 (397)
Q Consensus 273 ~~L~~~----P~f~~lrq~vq~NP~ll~~~Lqqi~~~nP~l~~~I~~n~~~Fl~~l~~ 326 (397)
+||++. -...+|+++++.+-..|.-=+..|..-+|+|++.|..||..++.+|.+
T Consensus 7 ~Fl~~f~~~~~Y~~~l~~~~~~~~~~l~Vd~~dL~~f~~~L~~~l~~~P~~~l~~~~~ 64 (121)
T PF14551_consen 7 EFLREFKEEPKYMDQLREMIQRNKKSLYVDLDDLREFDPDLAEALIENPYRYLPLFEE 64 (121)
T ss_dssp HHCCCH-TS-CCHHHHHHHHHHT-SCEEEEHHHHHHH-HHHHHHHHHCCCCCHHHHHH
T ss_pred HHHHcCCCchHHHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456653 467799999998888888778888889999999999999988887654
No 215
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=34.98 E-value=62 Score=22.87 Aligned_cols=30 Identities=20% Similarity=0.480 Sum_probs=20.0
Q ss_pred HHHHHHHhhhCHHHHHHHHH--hHHHHHHHhcC
Q 015999 296 QPMLQELGKQNPHLMRLIQE--HQTDFLRLINE 326 (397)
Q Consensus 296 ~~~Lqqi~~~nP~l~~~I~~--n~~~Fl~~l~~ 326 (397)
..+|..+ .+||+|++.+.+ ++++|+.+..+
T Consensus 7 ~~Fl~~~-~~d~~l~~~l~~~~~~~e~~~lA~~ 38 (49)
T PF07862_consen 7 KAFLEKV-KSDPELREQLKACQNPEEVVALARE 38 (49)
T ss_pred HHHHHHH-hcCHHHHHHHHhcCCHHHHHHHHHH
Confidence 3445544 567888888876 77788776544
No 216
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=34.70 E-value=44 Score=31.48 Aligned_cols=36 Identities=22% Similarity=0.569 Sum_probs=28.0
Q ss_pred cchHHHHHHHHHcCCCCCCHHHHHHHHHHhcCC-hHHHHH
Q 015999 165 SNLEATVQQILDMGGGSWDRETVIRALRAAYNN-PERAVE 203 (397)
Q Consensus 165 ~~~e~~I~~i~~MG~~~f~r~~v~~ALrAafnN-pdrAve 203 (397)
...+..|..|+.+| |.+.++.+|+....-+ |+--++
T Consensus 154 ~~~~~~v~AL~~LG---y~~~e~~~av~~v~~~~~~~~~~ 190 (201)
T COG0632 154 PALEEAVEALVALG---YKEKEIKKAVKKVLKENPDADVE 190 (201)
T ss_pred hhhhHHHHHHHHcC---CCHHHHHHHHHHHHhcCCCCCHH
Confidence 34556699999999 9999999999888765 444443
No 217
>TIGR03260 met_CoM_red_D methyl-coenzyme M reductase operon protein D. Members of this protein family are protein D, a non-structural protein, of the operon for methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). That enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis; it has several modified sites, so accessory proteins are expected. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes. Proteins in this family are expressed at much lower levels than the methyl-coenzyme M reductase itself and associate and have been shown to form at least transient associations. The precise function is unknown.
Probab=34.51 E-value=66 Score=28.86 Aligned_cols=43 Identities=19% Similarity=0.329 Sum_probs=29.1
Q ss_pred EEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhc
Q 015999 13 FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN 62 (397)
Q Consensus 13 ~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~ 62 (397)
+-|++...+.|..+++...+.+. ++ . -+..||.+.+..|+.||
T Consensus 76 I~le~~~~~~i~~I~eiC~e~~p---F~---y-~i~~g~f~r~~~TvtDY 118 (150)
T TIGR03260 76 IILELEDEDIVEEIEEICKEMLP---FG---Y-EVRVGKFLRTKPTVTDY 118 (150)
T ss_pred EEEEecCHHHHHHHHHHHHhhCC---Cc---e-EeeeeeEeecCCchhhh
Confidence 44566666777777765544433 21 1 14679999999999999
No 218
>PRK01777 hypothetical protein; Validated
Probab=33.29 E-value=1.9e+02 Score=23.87 Aligned_cols=62 Identities=10% Similarity=0.016 Sum_probs=39.4
Q ss_pred CEEEEEeC-CC--cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC--C-----eEEEeCCeecCCCCchhhcccCCCCEE
Q 015999 1 MKVFVKTL-KG--THFEIEVKPEDKVSDVKKNIETVQGSDVYPAS--Q-----QMLIHQGKVLKDVTTLEENKVAENSFV 70 (397)
Q Consensus 1 MkI~Vktl-~g--k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~--~-----qrLiy~GKiL~D~~tL~d~gI~~gstI 70 (397)
|+|.|-.. .. +.+.+++....||.++-... | ++.. . .++.-+||...-+. -+++||.|
T Consensus 4 i~v~V~ya~~~~~~~~~l~vp~GtTv~dal~~s----g---i~~~~pei~~~~~~vgI~Gk~v~~d~-----~L~dGDRV 71 (95)
T PRK01777 4 IRVEVVYALPERQYLQRLTLQEGATVEEAIRAS----G---LLELRTDIDLAKNKVGIYSRPAKLTD-----VLRDGDRV 71 (95)
T ss_pred eEEEEEEECCCceEEEEEEcCCCCcHHHHHHHc----C---CCccCcccccccceEEEeCeECCCCC-----cCCCCCEE
Confidence 46666543 22 33568889999999976554 4 4333 2 35555677665433 47789999
Q ss_pred EEEE
Q 015999 71 VVML 74 (397)
Q Consensus 71 ~v~v 74 (397)
-++-
T Consensus 72 eIyr 75 (95)
T PRK01777 72 EIYR 75 (95)
T ss_pred EEec
Confidence 8874
No 219
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=33.22 E-value=1.5e+02 Score=24.68 Aligned_cols=45 Identities=22% Similarity=0.281 Sum_probs=31.2
Q ss_pred hHHHHHHHhhhCHHHHHHHHHhHHHHHHHhcCCCCCCCCcccccccccCCCcccCCHHHHHHH-----HHHHHcC
Q 015999 295 LQPMLQELGKQNPHLMRLIQEHQTDFLRLINEPVEGGEGNVLGQLASAMPQAVTVTPEEREAI-----ERLEAMG 364 (397)
Q Consensus 295 l~~~Lqqi~~~nP~l~~~I~~n~~~Fl~~l~~~~~~~~g~~~~~~~~~~~~~~~lt~Ee~~ai-----~rL~~lG 364 (397)
|..++-+|. .|+.++...++++.+++ .--||+||+++| .+|.++|
T Consensus 8 LN~f~~sL~--~a~~RerF~~D~ea~~~-----------------------e~gLt~Ee~~av~~rD~~~li~~G 57 (94)
T cd07923 8 INRFLHRLI--EPAHRERFLEDPEALFD-----------------------EAGLTEEERTLIRNRDWIGMIRYG 57 (94)
T ss_pred HHHHHHHHC--CHHHHHHHHhCHHHHHH-----------------------HcCCCHHHHHHHHcchHHHHHHcc
Confidence 445666663 78888888888887765 225789998874 4566776
No 220
>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]
Probab=32.69 E-value=29 Score=39.94 Aligned_cols=66 Identities=8% Similarity=-0.142 Sum_probs=51.6
Q ss_pred EeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEEE
Q 015999 6 KTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVML 74 (397)
Q Consensus 6 ktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~v 74 (397)
+++.-..|...+....++...|.+|..++| |++..++|++-|..++++..+..|+....-..+..+
T Consensus 330 ~~l~~p~~~~~~~~~~~~~~~~p~~~~qtg---ipi~~~~l~~vg~~~n~d~P~s~~~~e~~~~~p~~~ 395 (1143)
T KOG4248|consen 330 CNLACPPPRHLHVVRPMSHYTTPMVLQQTG---IPIQINVLTTVGMTGNGDRPPSTPNAEAPPPGPGQA 395 (1143)
T ss_pred hcccCCCCceeeecchhhhccCceeeeccc---ccccccceeeecccccCCCCCCccccccCCCCCccc
Confidence 344444555556667788888999999999 999999999999999999999988777666555443
No 221
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.33 E-value=56 Score=30.32 Aligned_cols=28 Identities=11% Similarity=0.409 Sum_probs=25.0
Q ss_pred chHHHHHHHHHcCCCCCCHHHHHHHHHHhcC
Q 015999 166 NLEATVQQILDMGGGSWDRETVIRALRAAYN 196 (397)
Q Consensus 166 ~~e~~I~~i~~MG~~~f~r~~v~~ALrAafn 196 (397)
..++++..|+.+| |.+.++.+|++....
T Consensus 142 ~~~e~~~AL~~LG---y~~~ea~~av~~~~~ 169 (188)
T PRK14606 142 IYHESLEALVSLG---YPEKQAREAVKHVYR 169 (188)
T ss_pred cHHHHHHHHHHcC---CCHHHHHHHHHHHhh
Confidence 4678999999999 999999999998854
No 222
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=31.51 E-value=86 Score=25.50 Aligned_cols=41 Identities=22% Similarity=0.383 Sum_probs=35.0
Q ss_pred cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEE-EeCCeecC
Q 015999 11 THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQML-IHQGKVLK 54 (397)
Q Consensus 11 k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrL-iy~GKiL~ 54 (397)
..+++.|+++.|=.++|+.|+..+| +.+...+. ++.||.-.
T Consensus 21 n~~tF~V~~~atK~~Ik~aie~iy~---V~V~~Vnt~~~~gk~kR 62 (91)
T PF00276_consen 21 NQYTFEVDPRATKTEIKEAIEKIYG---VKVKKVNTMNYPGKKKR 62 (91)
T ss_dssp SEEEEEETTTSTHHHHHHHHHHHHT---SEEEEEEEEEETSEEEE
T ss_pred CEEEEEEeCCCCHHHHHHHHHhhcC---CCeeEEEEeEeCCCceE
Confidence 5789999999999999999999999 88877754 67888654
No 223
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.37 E-value=55 Score=30.58 Aligned_cols=28 Identities=11% Similarity=0.214 Sum_probs=24.7
Q ss_pred hHHHHHHHHHcCCCCCCHHHHHHHHHHhcCC
Q 015999 167 LEATVQQILDMGGGSWDRETVIRALRAAYNN 197 (397)
Q Consensus 167 ~e~~I~~i~~MG~~~f~r~~v~~ALrAafnN 197 (397)
.++++..|+.+| |.+.++.+|++....+
T Consensus 149 ~~e~~~aL~~LG---y~~~ea~~ai~~i~~~ 176 (195)
T PRK14604 149 DRELSEILISLG---YSAAEAAAAIAALPSD 176 (195)
T ss_pred HHHHHHHHHHcC---CCHHHHHHHHHHHhhc
Confidence 578999999999 9999999999887543
No 224
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=30.82 E-value=1.5e+02 Score=23.48 Aligned_cols=48 Identities=13% Similarity=0.317 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecCCCCchhhcccCCCCEEEEE
Q 015999 21 DKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 21 ~TV~dLK~~I~~~~g~~~ip~~~qrLiy--~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
.+..+|+.+..++.+ ++....+|+. .|..++|+.-+.. +.++..+++.
T Consensus 19 ~sL~eL~~K~~~~l~---l~~~~~~l~L~eDGT~VddEeyF~t--Lp~nt~l~~L 68 (74)
T smart00266 19 SSLEELLSKVCDKLA---LPDSPVTLVLEEDGTIVDDEEYFQT--LPDNTELMAL 68 (74)
T ss_pred CCHHHHHHHHHHHhC---CCCCCcEEEEecCCcEEccHHHHhc--CCCCcEEEEE
Confidence 479999999999999 8766666643 7888887754443 4455555443
No 225
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.43 E-value=59 Score=30.13 Aligned_cols=27 Identities=7% Similarity=0.352 Sum_probs=24.3
Q ss_pred chHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Q 015999 166 NLEATVQQILDMGGGSWDRETVIRALRAAY 195 (397)
Q Consensus 166 ~~e~~I~~i~~MG~~~f~r~~v~~ALrAaf 195 (397)
..++.+..|+.+| |.|.++.+|++...
T Consensus 144 ~~~e~~~aL~~LG---y~~~ea~~al~~v~ 170 (186)
T PRK14600 144 INDDALAALISLG---YEKTKAFNAIQKIK 170 (186)
T ss_pred cHHHHHHHHHHcC---CCHHHHHHHHHHhh
Confidence 4578999999999 99999999999874
No 226
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=30.41 E-value=95 Score=31.32 Aligned_cols=39 Identities=15% Similarity=0.200 Sum_probs=31.5
Q ss_pred hHHHHHHHHHc-CCCCCCHHHHHHHHHHhcCChHHHHHHHHcC
Q 015999 167 LEATVQQILDM-GGGSWDRETVIRALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 167 ~e~~I~~i~~M-G~~~f~r~~v~~ALrAafnNpdrAveyL~~G 208 (397)
.+...+-|.+- | .+.+++..++|.|-++|.+|.+||..|
T Consensus 169 ~~~~~~~L~~~~~---~~~~~a~~~~~la~G~~~~Al~l~~~~ 208 (334)
T PRK07993 169 EQYALTWLSREVT---MSQDALLAALRLSAGAPGAALALLQPE 208 (334)
T ss_pred HHHHHHHHHHccC---CCHHHHHHHHHHcCCCHHHHHHHhcCc
Confidence 45555556664 7 899999999999999999999999654
No 227
>COG5272 UBI4 Ubiquitin [Posttranslational modification, protein turnover, chaperones]
Probab=30.30 E-value=15 Score=27.22 Aligned_cols=46 Identities=11% Similarity=-0.060 Sum_probs=37.8
Q ss_pred cCCHHHHHHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCC
Q 015999 348 TVTPEEREAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHE 394 (397)
Q Consensus 348 ~lt~Ee~~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~~~~d 394 (397)
.++.+......+++..|+.+.. .+++..|.+..+++..+.+.+.+.
T Consensus 7 ~~~~~~~k~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 52 (57)
T COG5272 7 KATGGAAKPESQLAKAKDTRPE-KQYAEQDSQLNEMALMDCERNLEA 52 (57)
T ss_pred ccccccccccchHHHHhhccch-hhhhhhccChhhhhcccccccccc
Confidence 4455555667788888999999 999999999999999998876554
No 228
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=30.24 E-value=1.2e+02 Score=24.80 Aligned_cols=41 Identities=22% Similarity=0.360 Sum_probs=34.3
Q ss_pred CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeE-EEeCCeec
Q 015999 10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM-LIHQGKVL 53 (397)
Q Consensus 10 gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qr-Liy~GKiL 53 (397)
...+.+.|++..|=.++|+.|+..++ +.+...+ +++.||.-
T Consensus 20 ~n~~~F~V~~~a~K~eIK~aie~lf~---VkV~~VnT~~~~gk~k 61 (92)
T PRK05738 20 QNKYVFEVAPDATKPEIKAAVEKLFG---VKVESVNTLNVKGKTK 61 (92)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHcC---CceeEEEEEEeCCcee
Confidence 46899999999999999999999999 8888774 45677653
No 229
>cd06539 CIDE_N_A CIDE_N domain of CIDE-A proteins. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45, and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, the CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance.
Probab=29.90 E-value=1.4e+02 Score=23.88 Aligned_cols=48 Identities=10% Similarity=0.192 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHhCCCCCCCCCeEE--EeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 21 DKVSDVKKNIETVQGSDVYPASQQML--IHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 21 ~TV~dLK~~I~~~~g~~~ip~~~qrL--iy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
.+..+|+.|.++... ++....+| --.|.+++|+.-+.. +.++..++++
T Consensus 21 ~sL~EL~~K~~~~l~---~~~~~~~lvL~eDGT~Vd~EeyF~~--LpdnT~lm~L 70 (78)
T cd06539 21 SSLQELISKTLDALV---ITSGLVTLVLEEDGTVVDTEEFFQT--LGDNTHFMVL 70 (78)
T ss_pred cCHHHHHHHHHHHhC---CCCCCcEEEEeCCCCEEccHHHHhh--CCCCCEEEEE
Confidence 379999999999999 77655555 447888877754443 4556665554
No 230
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=29.67 E-value=35 Score=23.76 Aligned_cols=22 Identities=41% Similarity=0.520 Sum_probs=9.2
Q ss_pred cCCHHHHHHHHHHHHcCCChHH
Q 015999 348 TVTPEEREAIERLEAMGFDRAL 369 (397)
Q Consensus 348 ~lt~Ee~~ai~rL~~lGF~r~~ 369 (397)
.||++|+..|++|-+.|++-..
T Consensus 4 ~Lt~~eR~~I~~l~~~G~s~~~ 25 (44)
T PF13936_consen 4 HLTPEERNQIEALLEQGMSIRE 25 (44)
T ss_dssp --------HHHHHHCS---HHH
T ss_pred chhhhHHHHHHHHHHcCCCHHH
Confidence 6899999999999999986544
No 231
>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=29.16 E-value=2e+02 Score=24.07 Aligned_cols=67 Identities=16% Similarity=0.150 Sum_probs=41.7
Q ss_pred EEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC-CCeEE-EeCC---eecCC-CC-------chhhcccCCCCEE
Q 015999 4 FVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA-SQQML-IHQG---KVLKD-VT-------TLEENKVAENSFV 70 (397)
Q Consensus 4 ~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~-~~qrL-iy~G---KiL~D-~~-------tL~d~gI~~gstI 70 (397)
.|=..++.--++.+..+.||.+|-..+..+.. ++. ...+| ++.| |+|.. ++ .|...|.++.|-|
T Consensus 6 RIFr~D~Tf~Tls~~l~tTv~eli~~L~rK~~---l~~~~ny~l~l~~~~l~RvL~p~ErPl~IqkrlL~q~GY~~~D~l 82 (97)
T cd01775 6 RVFRSDGTFTTLSCPLNTTVSELIPQLAKKFY---LPSGGNYQLSLKKHDLSRVLRPTEKPLLIQKRLLLQVGYEERDRI 82 (97)
T ss_pred EEEecCCcEEEEEcCCcCcHHHHHHHHHHhhc---CCCCCCeEEEEEECCeeeecCCcCCcHHHHHHHHHHcCCCCCCcH
Confidence 33334555567899999999999999999877 544 44454 3444 45532 32 2445555665555
Q ss_pred EEE
Q 015999 71 VVM 73 (397)
Q Consensus 71 ~v~ 73 (397)
+.+
T Consensus 83 ~~l 85 (97)
T cd01775 83 EDI 85 (97)
T ss_pred HHh
Confidence 544
No 232
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.14 E-value=64 Score=29.87 Aligned_cols=26 Identities=19% Similarity=0.548 Sum_probs=23.7
Q ss_pred chHHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 015999 166 NLEATVQQILDMGGGSWDRETVIRALRAA 194 (397)
Q Consensus 166 ~~e~~I~~i~~MG~~~f~r~~v~~ALrAa 194 (397)
..++++..|+++| |.|.++.+|++..
T Consensus 141 ~~~ea~~AL~~LG---y~~~ea~~a~~~~ 166 (183)
T PRK14601 141 DKSEALAALLTLG---FKQEKIIKVLASC 166 (183)
T ss_pred cHHHHHHHHHHcC---CCHHHHHHHHHhc
Confidence 3578999999999 9999999999876
No 233
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=28.96 E-value=57 Score=25.77 Aligned_cols=24 Identities=33% Similarity=0.624 Sum_probs=18.0
Q ss_pred HHHHHHHHHHhCccchHHHHHHHh
Q 015999 280 QFQALRTMVQANPQILQPMLQELG 303 (397)
Q Consensus 280 ~f~~lrq~vq~NP~ll~~~Lqqi~ 303 (397)
.+|+|+-+|.+||.++..-+..++
T Consensus 45 KLQ~lm~~VMqnP~LikeAv~ELg 68 (82)
T PF11212_consen 45 KLQQLMAQVMQNPALIKEAVEELG 68 (82)
T ss_pred HHHHHHHHHhcChHHHHHHHHHhC
Confidence 477888888888888776666665
No 234
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=28.87 E-value=1.4e+02 Score=22.07 Aligned_cols=59 Identities=15% Similarity=0.159 Sum_probs=38.6
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEEE
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
|+|.+.+|+... +....|+.|+=..|....++ .-.--..+|+..+-+ +-|+++++|.++
T Consensus 1 I~v~lpdG~~~~--~~~g~T~~d~A~~I~~~l~~-----~~~~A~Vng~~vdl~-----~~L~~~d~v~ii 59 (60)
T PF02824_consen 1 IRVYLPDGSIKE--LPEGSTVLDVAYSIHSSLAK-----RAVAAKVNGQLVDLD-----HPLEDGDVVEII 59 (60)
T ss_dssp EEEEETTSCEEE--EETTBBHHHHHHHHSHHHHH-----CEEEEEETTEEEETT-----SBB-SSEEEEEE
T ss_pred CEEECCCCCeee--CCCCCCHHHHHHHHCHHHHh-----heeEEEEcCEECCCC-----CCcCCCCEEEEE
Confidence 567778888766 56778999999999877662 112224577665433 346678877664
No 235
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=28.74 E-value=1.1e+02 Score=21.37 Aligned_cols=24 Identities=21% Similarity=0.335 Sum_probs=20.0
Q ss_pred ChHHHHHHHHHhCCCHHHHHHHHh
Q 015999 366 DRALVLEVFFACNKNEELAANYLL 389 (397)
Q Consensus 366 ~r~~~iqAy~ac~kne~~Aan~L~ 389 (397)
.|+..-..+..|++|+=.|++.++
T Consensus 16 kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 16 KRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred ChHHHHHHHHHcCCcHHHHHHHhC
Confidence 477777788999999999998764
No 236
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=28.67 E-value=1.5e+02 Score=25.01 Aligned_cols=57 Identities=16% Similarity=0.215 Sum_probs=37.0
Q ss_pred EEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCC---CCeEEEeCC--------eecCCCCchhhc
Q 015999 3 VFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPA---SQQMLIHQG--------KVLKDVTTLEEN 62 (397)
Q Consensus 3 I~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~---~~qrLiy~G--------KiL~D~~tL~d~ 62 (397)
|+|-.-+|.+..|.|....+-.++|.++-+++| +.. .-...+..| +.|.|...+.=|
T Consensus 3 i~~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg---~~~~~~~~~~~v~d~~~~~~~~~~~LsD~EL~~IC 70 (105)
T PF14847_consen 3 IRFILEDGSTKTVNVSGCFNAQEIKRRVLKKFG---LPEHPRNYCFYVLDGESPDPSNCRPLSDVELVTIC 70 (105)
T ss_dssp EEEEETTTEEEEEE--S--HHHHHHHHHHHHHT---SS--CCCEEEEEE-S-----SSEEEE-SSHHHHHH
T ss_pred EEEECCCCcEEEEEECCCCCHHHHHHHHHHHcC---CccccccceEEEecccccccccceECcHHHHHHHH
Confidence 667778999999999999999999999999999 444 333445566 455665555544
No 237
>PF09722 DUF2384: Protein of unknown function (DUF2384); InterPro: IPR024467 This domain is found predominantly in proteobacterial proteins. Its function in unknown.
Probab=28.18 E-value=1.3e+02 Score=21.55 Aligned_cols=20 Identities=10% Similarity=0.358 Sum_probs=16.4
Q ss_pred HHHHHhcCChHHHHHHHHcC
Q 015999 189 RALRAAYNNPERAVEYLYSG 208 (397)
Q Consensus 189 ~ALrAafnNpdrAveyL~~G 208 (397)
++++.-|.|+++|..||.+-
T Consensus 2 ~~a~~vfgd~~~a~~Wl~~p 21 (54)
T PF09722_consen 2 KQAEEVFGDEDKARRWLRTP 21 (54)
T ss_pred hHHHHHHCCHHHHHHHHHCh
Confidence 45677889999999999744
No 238
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.93 E-value=76 Score=29.63 Aligned_cols=27 Identities=19% Similarity=0.304 Sum_probs=24.5
Q ss_pred chHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Q 015999 166 NLEATVQQILDMGGGSWDRETVIRALRAAY 195 (397)
Q Consensus 166 ~~e~~I~~i~~MG~~~f~r~~v~~ALrAaf 195 (397)
..++++..|+.+| |.+.++.+|++...
T Consensus 151 ~~~ea~~AL~~LG---y~~~ea~~al~~i~ 177 (197)
T PRK14603 151 AAEDAVLALLALG---FREAQVRSVVAELL 177 (197)
T ss_pred cHHHHHHHHHHcC---CCHHHHHHHHHHHH
Confidence 4688999999999 99999999999874
No 239
>cd01615 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein.
Probab=27.76 E-value=1.7e+02 Score=23.38 Aligned_cols=48 Identities=10% Similarity=0.286 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHhCCCCCCCCCeEEEe--CCeecCCCCchhhcccCCCCEEEEE
Q 015999 21 DKVSDVKKNIETVQGSDVYPASQQMLIH--QGKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 21 ~TV~dLK~~I~~~~g~~~ip~~~qrLiy--~GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
.+..+|+.+..++.+ ++....+|+. .|..++|+.-+.. +.++..++++
T Consensus 21 ~sL~eL~~K~~~~l~---l~~~~~~lvL~eDGTeVddEeYF~t--Lp~nT~l~~l 70 (78)
T cd01615 21 SSLEELLSKACEKLK---LPSAPVTLVLEEDGTEVDDEEYFQT--LPDNTVLMLL 70 (78)
T ss_pred CCHHHHHHHHHHHcC---CCCCCeEEEEeCCCcEEccHHHHhc--CCCCcEEEEE
Confidence 479999999999999 8666666653 7888877754443 4455555443
No 240
>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=27.12 E-value=2e+02 Score=28.98 Aligned_cols=64 Identities=16% Similarity=0.172 Sum_probs=45.1
Q ss_pred EEEeCCCCCHHHHHHHHHHHh----CCC--------CCCCCCeEEEeCCeecCCCCchhhcc---cCCCCEEEEEEeec
Q 015999 14 EIEVKPEDKVSDVKKNIETVQ----GSD--------VYPASQQMLIHQGKVLKDVTTLEENK---VAENSFVVVMLTKV 77 (397)
Q Consensus 14 ~veV~~~~TV~dLK~~I~~~~----g~~--------~ip~~~qrLiy~GKiL~D~~tL~d~g---I~~gstI~v~v~k~ 77 (397)
.|....-.-|..|+..|.++. ... ..|.+.+.|+++|.+|..+.||..+. -|.++-|+|..|.+
T Consensus 251 rL~A~~mLrvkKI~~yV~ek~~~~~~~~~~~~~~~~~~p~e~lEl~C~gqvL~~~mtLaTVr~~~WK~~~di~L~YR~k 329 (331)
T PF11816_consen 251 RLNAPRMLRVKKILEYVAEKLEKTPESKTPEMKPKKLKPEEWLELLCNGQVLPPDMTLATVRTFIWKSSGDIVLHYRRK 329 (331)
T ss_pred eecccchhhhHHHHHHHHHHhccCccccCccccccCCCCCceEEEEeCCeEcCCcCCHHHHHHhhccCCCeEEEEEEec
Confidence 344444566888888888887 100 14567789999999999999988774 36666777766644
No 241
>COG3760 Uncharacterized conserved protein [Function unknown]
Probab=26.96 E-value=94 Score=28.05 Aligned_cols=58 Identities=28% Similarity=0.334 Sum_probs=40.7
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcccCCCCEEEE
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~gI~~gstI~v 72 (397)
.+++|..+++.|-|.|+.. ++-||| .|.+..| .. ||.|+-. ++.++-+|+..|++-.+
T Consensus 47 nLfLkdkK~q~~lv~~~e~-~~vDLk-~ih~~IG-----~~--RlsFg~~----E~l~E~LGv~pG~VT~F 104 (164)
T COG3760 47 NLFLKDKKDQFFLVTVDED-AVVDLK-SIHETIG-----AA--RLSFGSP----ERLMEYLGVIPGSVTVF 104 (164)
T ss_pred eeEeecCCCCEEEEEeccc-ceecHH-HHHHHhc-----ee--eeecCCH----HHHHHHhCCCcCceeEe
Confidence 4789988888888888754 567888 5777777 33 7777542 34455668888886544
No 242
>PF02505 MCR_D: Methyl-coenzyme M reductase operon protein D; InterPro: IPR003901 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. Genes encoding the beta (mcrB) and gamma (mcrG) subunits of MCR are separated by two open reading frames coding for two proteins C and D [, ]. The function of proteins C and D is unknown. This entry represents protein D.; GO: 0015948 methanogenesis
Probab=26.39 E-value=1.2e+02 Score=27.39 Aligned_cols=43 Identities=21% Similarity=0.378 Sum_probs=28.8
Q ss_pred EEEEeCC-CCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhc
Q 015999 13 FEIEVKP-EDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEEN 62 (397)
Q Consensus 13 ~~veV~~-~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~ 62 (397)
+.++++. .+.+..+++...+.+. ++ .. ++.|+.+....|++||
T Consensus 77 i~lele~~~~~ie~I~~iCee~lp---f~---y~-i~~G~f~r~~~TvtDY 120 (153)
T PF02505_consen 77 IILELEDEEDVIEKIREICEEVLP---FG---YD-IKEGKFIRTKPTVTDY 120 (153)
T ss_pred EEEEecCcHHHHHHHHHHHHHhCC---Cc---eE-eeeeEEeccCCchhhh
Confidence 4567776 5666677655544433 22 22 4579999999999999
No 243
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=25.88 E-value=1.7e+02 Score=35.08 Aligned_cols=44 Identities=23% Similarity=0.262 Sum_probs=34.2
Q ss_pred HHHH-HHHHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHhccCCCC
Q 015999 351 PEER-EAIERLEAMGFDRALVLEVFFACNKNEELAANYLLDHMHEF 395 (397)
Q Consensus 351 ~Ee~-~ai~rL~~lGF~r~~~iqAy~ac~kne~~Aan~L~~~~~d~ 395 (397)
|||. ...++... |=+|+..|+-+.-++-|++.|+|-||+...+|
T Consensus 189 PEELInnaQqVLQ-GKSRdVIIRELQRTgLdVNeAVNNLLSRDD~D 233 (3015)
T KOG0943|consen 189 PEELINNAQQVLQ-GKSRDVIIRELQRTGLDVNEAVNNLLSRDDED 233 (3015)
T ss_pred cHHHHHHHHHHHh-CCchhHHHHHHHHhCCcHHHHHHhhhcccccc
Confidence 5554 44444433 89999999999999999999999999864443
No 244
>KOG0514 consensus Ankyrin repeat protein [General function prediction only]
Probab=25.81 E-value=64 Score=33.27 Aligned_cols=34 Identities=29% Similarity=0.589 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHHHcCC-------------------ChHHHHHHHHHhCCCHHH
Q 015999 350 TPEEREAIERLEAMGF-------------------DRALVLEVFFACNKNEEL 383 (397)
Q Consensus 350 t~Ee~~ai~rL~~lGF-------------------~r~~~iqAy~ac~kne~~ 383 (397)
++.|+..|+||..||= .|-+++.+|+||+-|+|.
T Consensus 316 ~~~d~~vV~~LF~mgnVNaKAsQ~gQTALMLAVSHGr~d~vk~LLacgAdVNi 368 (452)
T KOG0514|consen 316 QPADRTVVERLFKMGDVNAKASQHGQTALMLAVSHGRVDMVKALLACGADVNI 368 (452)
T ss_pred chhhHHHHHHHHhccCcchhhhhhcchhhhhhhhcCcHHHHHHHHHccCCCcc
Confidence 5788899999999981 378899999999999874
No 245
>PHA01748 hypothetical protein
Probab=25.59 E-value=1.2e+02 Score=22.74 Aligned_cols=31 Identities=13% Similarity=0.277 Sum_probs=25.5
Q ss_pred cccCCHHHHHHHHHHHH-cCCChHHHHHHHHH
Q 015999 346 AVTVTPEEREAIERLEA-MGFDRALVLEVFFA 376 (397)
Q Consensus 346 ~~~lt~Ee~~ai~rL~~-lGF~r~~~iqAy~a 376 (397)
.+.+++|..+.|++++. .|.+|..+|+..+.
T Consensus 6 SvrLp~el~~eld~~a~~~g~~RSE~Ir~Ai~ 37 (60)
T PHA01748 6 TFKIEEDLLELLDRYAIKHGLNRSEAIRKAIE 37 (60)
T ss_pred EEECCHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 46889999999999874 69999999987654
No 246
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=25.52 E-value=1.5e+02 Score=25.42 Aligned_cols=40 Identities=23% Similarity=0.293 Sum_probs=31.7
Q ss_pred hHHHHHHHHH--cCCCCCCHHHHHHHHHHhcCChHHHHHHHHcCCCCC
Q 015999 167 LEATVQQILD--MGGGSWDRETVIRALRAAYNNPERAVEYLYSGIPEQ 212 (397)
Q Consensus 167 ~e~~I~~i~~--MG~~~f~r~~v~~ALrAafnNpdrAveyL~~GIP~~ 212 (397)
+|..+++|.. .+ |.|++|+.+|.+-+ +..++||++|---+
T Consensus 31 l~~Ia~~i~~~~s~---~t~~di~~vl~~~~---~~~~~~l~~G~sV~ 72 (124)
T PF14848_consen 31 LEDIAEEIAKEGST---LTRADIEAVLNALK---DEMIEALMNGYSVN 72 (124)
T ss_pred HHHHHHHHHHhCCC---CCHHHHHHHHHHHH---HHHHHHHhCCCEEE
Confidence 5677788874 56 99999999998876 67789999995433
No 247
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=25.16 E-value=75 Score=23.84 Aligned_cols=20 Identities=30% Similarity=0.531 Sum_probs=14.8
Q ss_pred HHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 015999 169 ATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY 206 (397)
Q Consensus 169 ~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~ 206 (397)
.+|..+++|| .+|+|.|||.
T Consensus 28 qvI~gllqlg------------------~~~~a~eYi~ 47 (62)
T PF14689_consen 28 QVIYGLLQLG------------------KYEEAKEYIK 47 (62)
T ss_dssp HHHHHHHHTT-------------------HHHHHHHHH
T ss_pred HHHHHHHHCC------------------CHHHHHHHHH
Confidence 3566777777 8999999985
No 248
>PRK09814 beta-1,6-galactofuranosyltransferase; Provisional
Probab=23.91 E-value=85 Score=31.03 Aligned_cols=38 Identities=34% Similarity=0.528 Sum_probs=29.5
Q ss_pred HHHHcCCCCCCHHHHHHHHHH-------------------hcCChHHHHHHHHcCCCCC
Q 015999 173 QILDMGGGSWDRETVIRALRA-------------------AYNNPERAVEYLYSGIPEQ 212 (397)
Q Consensus 173 ~i~~MG~~~f~r~~v~~ALrA-------------------afnNpdrAveyL~~GIP~~ 212 (397)
++.=.| .++++++.+.|+. -||+|....+||..|+|--
T Consensus 208 ~V~f~G--~~~~eel~~~l~~~~gLv~~~~~~~~~~~~y~~~~~P~K~~~ymA~G~PVI 264 (333)
T PRK09814 208 NISYKG--WFDPEELPNELSKGFGLVWDGDTNDGEYGEYYKYNNPHKLSLYLAAGLPVI 264 (333)
T ss_pred CeEEec--CCCHHHHHHHHhcCcCeEEcCCCCCccchhhhhccchHHHHHHHHCCCCEE
Confidence 333355 2488888888876 3899999999999999964
No 249
>KOG2019 consensus Metalloendoprotease HMP1 (insulinase superfamily) [General function prediction only; Posttranslational modification, protein turnover, chaperones]
Probab=23.70 E-value=2e+02 Score=32.41 Aligned_cols=40 Identities=18% Similarity=0.410 Sum_probs=34.3
Q ss_pred CCCchHHhhccHHHHHHHHHHHh-CccchHHHHHHHhhhCH
Q 015999 268 GAGTLDFLRNSQQFQALRTMVQA-NPQILQPMLQELGKQNP 307 (397)
Q Consensus 268 ~~~~l~~L~~~P~f~~lrq~vq~-NP~ll~~~Lqqi~~~nP 307 (397)
+.++++.|.-+.+++.+|+-++. ++.++++++.+..-+||
T Consensus 445 d~DPfE~Lk~~~~L~~lk~~l~ek~~~lfq~lIkkYilnn~ 485 (998)
T KOG2019|consen 445 DMDPFEPLKFEEQLKKLKQRLAEKSKKLFQPLIKKYILNNP 485 (998)
T ss_pred CCCccchhhhhhHHHHHHHHHhhhchhHHHHHHHHHHhcCC
Confidence 35677788889999999999998 99999999998877776
No 250
>PF14483 Cut8_M: Cut8 dimerisation domain; PDB: 3Q5W_A 3Q5X_A.
Probab=23.59 E-value=66 Score=22.07 Aligned_cols=23 Identities=30% Similarity=0.510 Sum_probs=17.1
Q ss_pred ccchHHHHHHHhhhCHHHHHHHH
Q 015999 292 PQILQPMLQELGKQNPHLMRLIQ 314 (397)
Q Consensus 292 P~ll~~~Lqqi~~~nP~l~~~I~ 314 (397)
.+-|+.+|+.+.+.||++.+-|+
T Consensus 12 ~~qL~~lL~~l~~~HPei~~~i~ 34 (38)
T PF14483_consen 12 KDQLQSLLQSLCERHPEIQQEIR 34 (38)
T ss_dssp HHHHHHHHHHHHHHSTHHHHHHH
T ss_pred HHHHHHHHHHHHHhChhHHHHHH
Confidence 34466778888888998887765
No 251
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=23.59 E-value=67 Score=30.18 Aligned_cols=50 Identities=24% Similarity=0.397 Sum_probs=27.9
Q ss_pred CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCC---CeEE--EeCC-----eecCCCC--chhhc
Q 015999 10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPAS---QQML--IHQG-----KVLKDVT--TLEEN 62 (397)
Q Consensus 10 gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~---~qrL--iy~G-----KiL~D~~--tL~d~ 62 (397)
|-.|.+-|.+..|..++|++|.++.| ++.. ..|+ +..+ +.|+|+. .|.+.
T Consensus 132 GiPF~f~v~~gE~f~~tK~Rl~~rlg---v~~keF~K~Kfaiv~~~~~~~~~yl~d~~~~il~~~ 193 (213)
T PF14533_consen 132 GIPFLFVVKPGETFSDTKERLQKRLG---VSDKEFEKWKFAIVQNSRYSKPRYLEDDDDLILFDE 193 (213)
T ss_dssp EEEEEEEEETT--HHHHHHHHHHHH------HHHHTT-EEEEEETTEE---EE--TT-T----GG
T ss_pred CCCEEEEeeCCCcHHHHHHHHHHHhC---CChhhheeEEEEEEecCCcccceeccccchhhhhhh
Confidence 55688899999999999999999998 5433 4444 3444 4566654 45544
No 252
>PF09469 Cobl: Cordon-bleu ubiquitin-like domain; InterPro: IPR019025 The Cordon-bleu protein domain is highly conserved among vertebrates. The sequence contains three repeated lysine, arginine, and proline-rich regions, the KKRAP motif. The exact function of the protein is unknown but it is thought to be involved in mid-brain neural tube closure. It is expressed specifically in the node []. ; PDB: 2DAJ_A.
Probab=23.44 E-value=70 Score=25.63 Aligned_cols=42 Identities=17% Similarity=0.208 Sum_probs=23.7
Q ss_pred HHHHHhCCCCCCCCCeEEEe---CCeecCCCCchhhcccCCCCEEEEEEee
Q 015999 29 NIETVQGSDVYPASQQMLIH---QGKVLKDVTTLEENKVAENSFVVVMLTK 76 (397)
Q Consensus 29 ~I~~~~g~~~ip~~~qrLiy---~GKiL~D~~tL~d~gI~~gstI~v~v~k 76 (397)
.|++++. +.++...|+- ++..|+-+++|.+|||++ |+.+-.+
T Consensus 2 ~IC~KCE---fdp~htvLLrD~~s~e~LdLsKSLndlGirE---LYA~D~~ 46 (79)
T PF09469_consen 2 AICEKCE---FDPEHTVLLRDYQSGEELDLSKSLNDLGIRE---LYAWDTS 46 (79)
T ss_dssp HHHHHTT-----TTSEEEES-SS---B--TTS-HHHHT-SE---EEEEE--
T ss_pred ccccccc---cCcceEEEeecCCCCCcccccccHHHhhHHH---HHhhccc
Confidence 4778866 7788887763 567899999999999984 6555444
No 253
>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=23.39 E-value=3.7e+02 Score=21.34 Aligned_cols=57 Identities=18% Similarity=0.128 Sum_probs=42.7
Q ss_pred EEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeC-CeecCCCCchhhcccCCCCEEEEE
Q 015999 14 EIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQ-GKVLKDVTTLEENKVAENSFVVVM 73 (397)
Q Consensus 14 ~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~-GKiL~D~~tL~d~gI~~gstI~v~ 73 (397)
.+.|..+.....+-+-.++++. +++..--+|.+ |--+....+..+.-+|.|+.|.++
T Consensus 19 v~sVPE~apftaVlkfaAeeF~---vp~~tsaiItndG~GInP~QTag~vflKhGseLrli 76 (76)
T PF03671_consen 19 VISVPEEAPFTAVLKFAAEEFK---VPPATSAIITNDGVGINPQQTAGNVFLKHGSELRLI 76 (76)
T ss_dssp EEEEETTSBHHHHHHHHHHHTT---S-SSSEEEEESSS-EE-TTSBHHHHHHHT-SEEEEE
T ss_pred EEecCCCCchHHHHHHHHHHcC---CCCceEEEEecCCcccccchhhhhhHhhcCcEeeeC
Confidence 3577777777777777888888 88888888865 666788899999999999998764
No 254
>PF09030 Creb_binding: Creb binding; InterPro: IPR014744 This entry represents the interlocking domain of the eukaryotic nuclear receptor coactivators CREBP and p300. The interlocking domain forms a 3-helical non-globular array that forms interlocked heterodimers with its target. Nuclear receptors are ligand-activated transcription factors involved in the regulation of many processes, including development, reproduction and homeostasis. Nuclear receptor coactivators act to modulate the function of nuclear receptors. Coactivators associate with promoters and enhancers primarily through protein-protein contacts to facilitate the interaction between DNA-bound transcription factors and the transcription machinery. Many of these coactivators are structurally related, including CBP (CREB-binding protein) and p300 []. CBP and p300 both have histone acetyltransferase activity (2.3.1.48 from EC). CBP/p300 proteins function synergistically to activate transcription, acting to remodel chromatin and to recruit RNA polymerase II and the basal transcription machinery. CBP is required for proper cell cycle control, differentiation and apoptosis. The interaction of CBP/p300 with transcription factors involves several small domains. The IBiD domain in the C-terminal of CBP is responsible for CBP interaction with IRF-3, as well as with the adenoviral oncoprotein E1A, TIF-2 coactivator, and the IRF homologue KSHV IRF-1 []. ; GO: 0003713 transcription coactivator activity, 0004402 histone acetyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0016573 histone acetylation, 0000123 histone acetyltransferase complex, 0005634 nucleus; PDB: 2KKJ_A 2C52_A 1JJS_A 2L14_A 1KBH_B 1ZOQ_C.
Probab=23.33 E-value=61 Score=27.31 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=11.9
Q ss_pred HHHHHHHHHHhCccchHHHHHH
Q 015999 280 QFQALRTMVQANPQILQPMLQE 301 (397)
Q Consensus 280 ~f~~lrq~vq~NP~ll~~~Lqq 301 (397)
+=+++-.++.+||+||-.||.+
T Consensus 71 QQQQVLnILkSNPqLMAAFIKQ 92 (104)
T PF09030_consen 71 QQQQVLNILKSNPQLMAAFIKQ 92 (104)
T ss_dssp HHHHHHHHHHTSHHHHHHHHHH
T ss_pred HHHHHHHHHhhCHHHHHHHHHH
Confidence 3445555556666655555543
No 255
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=23.11 E-value=1.3e+02 Score=30.01 Aligned_cols=36 Identities=28% Similarity=0.353 Sum_probs=29.2
Q ss_pred HHHHHHHHcCCCCCCHHHHHHHHHHhcCChHHHHHHHH
Q 015999 169 ATVQQILDMGGGSWDRETVIRALRAAYNNPERAVEYLY 206 (397)
Q Consensus 169 ~~I~~i~~MG~~~f~r~~v~~ALrAafnNpdrAveyL~ 206 (397)
..|++|-++-| =.=-+|.+||-.+-+|-|.|+|||-
T Consensus 7 ~~VKeLRe~Tg--AGMmdCKkAL~E~~Gd~EkAie~LR 42 (296)
T COG0264 7 ALVKELREKTG--AGMMDCKKALEEANGDIEKAIEWLR 42 (296)
T ss_pred HHHHHHHHHhC--CcHHHHHHHHHHcCCCHHHHHHHHH
Confidence 46777777632 3346899999999999999999996
No 256
>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].
Probab=22.55 E-value=1e+02 Score=23.95 Aligned_cols=43 Identities=12% Similarity=0.321 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCCchhhcc-cCCCCEEEEE
Q 015999 21 DKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVTTLEENK-VAENSFVVVM 73 (397)
Q Consensus 21 ~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~tL~d~g-I~~gstI~v~ 73 (397)
.|+.+|++..++++| +. ....+. .|..-+.|.. |.+|+.|+++
T Consensus 26 ~SleeLl~ia~~kfg---~~-~~~v~~------~dgaeIdDI~~IRDgD~L~~~ 69 (69)
T PF11834_consen 26 DSLEELLKIASEKFG---FS-ATKVLN------EDGAEIDDIDVIRDGDHLYLV 69 (69)
T ss_pred ccHHHHHHHHHHHhC---CC-ceEEEc------CCCCEEeEEEEEEcCCEEEEC
Confidence 699999999999999 53 222222 2333344443 6788888763
No 257
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=22.48 E-value=87 Score=26.75 Aligned_cols=28 Identities=18% Similarity=0.318 Sum_probs=25.4
Q ss_pred CCChHHHHHHHHHhCCCHHHHHHHHhcc
Q 015999 364 GFDRALVLEVFFACNKNEELAANYLLDH 391 (397)
Q Consensus 364 GF~r~~~iqAy~ac~kne~~Aan~L~~~ 391 (397)
.|..+.||+.++.|+-..-.|+|||.+.
T Consensus 42 ~f~de~vI~~hidaGIs~~~AVN~LVeK 69 (114)
T PF06755_consen 42 PFSDETVIQEHIDAGISPADAVNFLVEK 69 (114)
T ss_pred ccchHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 3779999999999999999999999874
No 258
>PF04126 Cyclophil_like: Cyclophilin-like; InterPro: IPR007256 Proteins of this family have no known function.; PDB: 2KA0_A 1ZX8_C 2NNZ_A.
Probab=22.41 E-value=51 Score=28.21 Aligned_cols=29 Identities=17% Similarity=0.313 Sum_probs=23.7
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHH
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNI 30 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I 30 (397)
|+|.|+. +++.+..++..+.|.++|.+++
T Consensus 1 mkI~i~i-~~~~~~a~L~d~~ta~~~~~~L 29 (120)
T PF04126_consen 1 MKIKITI-GGQEIEAELNDSPTARAFAAQL 29 (120)
T ss_dssp EEEEEEE-TTEEEEEEEETTHHHHHHHHC-
T ss_pred CeEEEEE-CCEEEEEEECCCHHHHHHHHhC
Confidence 7888884 5889999999998888887765
No 259
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=22.13 E-value=1.8e+02 Score=24.16 Aligned_cols=60 Identities=17% Similarity=0.238 Sum_probs=42.2
Q ss_pred CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeE-EEeCCee---------cCCCCchhhcccCCCCEEEE
Q 015999 10 GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQM-LIHQGKV---------LKDVTTLEENKVAENSFVVV 72 (397)
Q Consensus 10 gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qr-Liy~GKi---------L~D~~tL~d~gI~~gstI~v 72 (397)
..++.+.|+++.|=.++|..|++.++ +-+.... |+..|+. +..+..-...-+..|..|.+
T Consensus 21 ~nk~vF~V~~~AtK~~IK~AvE~lF~---VkV~kVNTl~~k~k~KR~~~k~~G~~~~~kka~V~l~~G~~i~~ 90 (94)
T COG0089 21 ENKYVFIVDPDATKPEIKAAVEELFG---VKVEKVNTLNTKGKTKRAGVKRIGLRKDYKKAYVTLKEGQSIDF 90 (94)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHhC---CeEEEEEEEEeCCcceEEeccccccCcccceeEEEccCCCEEee
Confidence 46789999999999999999999999 7777774 4556642 33333444445556665543
No 260
>PF11333 DUF3135: Protein of unknown function (DUF3135); InterPro: IPR021482 This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=21.69 E-value=65 Score=25.99 Aligned_cols=26 Identities=27% Similarity=0.570 Sum_probs=20.8
Q ss_pred ccHHHHHHHHHHHhCccchHHHHHHH
Q 015999 277 NSQQFQALRTMVQANPQILQPMLQEL 302 (397)
Q Consensus 277 ~~P~f~~lrq~vq~NP~ll~~~Lqqi 302 (397)
..|.|..|+.+.+.||+.+..+-+.+
T Consensus 2 ~lp~FD~L~~LA~~dPe~fe~lr~~~ 27 (83)
T PF11333_consen 2 ELPDFDELKELAQNDPEAFEQLRQEL 27 (83)
T ss_pred CCCCHHHHHHHHHhCHHHHHHHHHHH
Confidence 35789999999999999888555444
No 261
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=21.60 E-value=68 Score=23.88 Aligned_cols=32 Identities=22% Similarity=0.367 Sum_probs=21.8
Q ss_pred CEEEEEeCCCcEEEEEeCCCCCHHHHHHHHHH
Q 015999 1 MKVFVKTLKGTHFEIEVKPEDKVSDVKKNIET 32 (397)
Q Consensus 1 MkI~Vktl~gk~~~veV~~~~TV~dLK~~I~~ 32 (397)
|.|++++.+|+.|.++.+.-.--.-||..|..
T Consensus 1 ~~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~~ 32 (62)
T PF03931_consen 1 MYVKLVSSDGQEFEVSREAAKQSKTIKNMLED 32 (62)
T ss_dssp -EEEEEETTSEEEEEEHHHHTTSHHHHHHHHC
T ss_pred CEEEEEcCCCCEEEeeHHHHHHhHHHHHHHhh
Confidence 78999999999999985533334445555643
No 262
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=21.43 E-value=92 Score=23.60 Aligned_cols=32 Identities=19% Similarity=0.215 Sum_probs=27.2
Q ss_pred cCCHHHHHHHHHHHH-cCCChHHHHHHHHHhCC
Q 015999 348 TVTPEEREAIERLEA-MGFDRALVLEVFFACNK 379 (397)
Q Consensus 348 ~lt~Ee~~ai~rL~~-lGF~r~~~iqAy~ac~k 379 (397)
.+|+-|++.|..+.+ .||+-+.++.|+.-|-+
T Consensus 12 ~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~ 44 (73)
T TIGR01446 12 MLSPFEMEDLKYWLDEFGNSPELIKEALKEAVS 44 (73)
T ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 579999988888764 69999999999998854
No 263
>KOG4147 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.75 E-value=2e+02 Score=24.65 Aligned_cols=59 Identities=15% Similarity=0.187 Sum_probs=35.5
Q ss_pred EeCC-CCCHHHHHHHHHHHhCCC-CCC------CCCeEEEeCC-----------------eecC-CCCchhhcccCCCCE
Q 015999 16 EVKP-EDKVSDVKKNIETVQGSD-VYP------ASQQMLIHQG-----------------KVLK-DVTTLEENKVAENSF 69 (397)
Q Consensus 16 eV~~-~~TV~dLK~~I~~~~g~~-~ip------~~~qrLiy~G-----------------KiL~-D~~tL~d~gI~~gst 69 (397)
+++. +.||.+++..|.+....+ +++ -+..|+++.. .+|+ ++++|..|||.+...
T Consensus 28 d~dLad~Tvk~f~~~~~~~Iq~~~sl~pfRn~kfDtLKIy~~Ah~sKT~nLvinldhDd~w~L~d~~ktL~~~GIenETE 107 (127)
T KOG4147|consen 28 DVDLADQTVKEFIVFLKQDIQLRTSLPPFRNYKFDTLKIYHQAHKSKTNNLVINLDHDDRWLLKDEDKTLKAAGIENETE 107 (127)
T ss_pred ccchhHhhHHHHHHHHHHhcccCCCCCccccccccceeeehhhhhcccceEEEeccCCcceeecCccchHHHhccCcchh
Confidence 4554 778998887776553311 122 2334444321 3565 467999999998877
Q ss_pred EEEEE
Q 015999 70 VVVML 74 (397)
Q Consensus 70 I~v~v 74 (397)
|-+..
T Consensus 108 is~F~ 112 (127)
T KOG4147|consen 108 ISFFC 112 (127)
T ss_pred hhhhh
Confidence 76554
No 264
>KOG4598 consensus Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.73 E-value=1.6e+02 Score=33.01 Aligned_cols=59 Identities=19% Similarity=0.288 Sum_probs=44.9
Q ss_pred EEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEe----CCeec--CCCCchhhcccCCCCEEEEEEe
Q 015999 12 HFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIH----QGKVL--KDVTTLEENKVAENSFVVVMLT 75 (397)
Q Consensus 12 ~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy----~GKiL--~D~~tL~d~gI~~gstI~v~v~ 75 (397)
-+.+.|+...++..+|++|+...+ ++.+-.||.- +|..+ .++.+|+. ..++.+|.+-+.
T Consensus 878 ~~kl~Vd~rmr~~AFKkHiE~~i~---V~~~HFKi~R~~~~N~~~~S~~~NetLs~--~~~~~~iTI~LG 942 (1203)
T KOG4598|consen 878 FHKLDVDSRMRVLAFKKHVEEQLE---VDKDHFKIVRHASDNGSEASFMDNETLSG--AFQSCFITIKLG 942 (1203)
T ss_pred heeeeccceeeHHHHHHHHHHHhC---cChhHeEEEEEecCCcchhhhccchhhhh--hcccceEEEEec
Confidence 467899999999999999999999 8899998863 34444 45677775 456777766443
No 265
>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=20.57 E-value=2.9e+02 Score=22.53 Aligned_cols=70 Identities=10% Similarity=0.111 Sum_probs=39.2
Q ss_pred EEEEeCCC----cEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCe-ec-CCCCchhhc--ccCCCCEEEEEE
Q 015999 3 VFVKTLKG----THFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGK-VL-KDVTTLEEN--KVAENSFVVVML 74 (397)
Q Consensus 3 I~Vktl~g----k~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GK-iL-~D~~tL~d~--gI~~gstI~v~v 74 (397)
|.+|..++ +.-.+.|+.++|+..|-.-|.++.+ +...+...+|=.. .- ..|.+++++ ..+.++.|+|.-
T Consensus 4 v~fk~iG~aPilk~~k~kI~~~~~f~~vi~fLrk~Lk---~~~~~slFlYin~sFaPspDe~vg~L~~~f~~~~~Liv~Y 80 (87)
T PF04110_consen 4 VRFKAIGSAPILKQKKFKISASQTFATVIAFLRKKLK---LKPSDSLFLYINNSFAPSPDETVGDLYRCFGTNGELIVSY 80 (87)
T ss_dssp EEEEEETT----S--EEEEETTSBTHHHHHHHHHHCT-------SS-EEEEEEEE---TTSBHHHHHHHH-BTTBEEEEE
T ss_pred EEEEecCCCccccCcEEEECCCCchHHHHHHHHHHhC---CccCCeEEEEEcCccCCCchhHHHHHHHHhCCCCEEEEEE
Confidence 44454443 2345677889999999999999988 6555555555443 32 345666665 334566666654
Q ss_pred e
Q 015999 75 T 75 (397)
Q Consensus 75 ~ 75 (397)
.
T Consensus 81 s 81 (87)
T PF04110_consen 81 S 81 (87)
T ss_dssp E
T ss_pred e
Confidence 3
No 266
>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform
Probab=20.35 E-value=2.4e+02 Score=23.73 Aligned_cols=63 Identities=8% Similarity=0.067 Sum_probs=44.9
Q ss_pred EEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCCeecCCCC-chhhcccCCCCEEEEEEee
Q 015999 13 FEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQGKVLKDVT-TLEENKVAENSFVVVMLTK 76 (397)
Q Consensus 13 ~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~GKiL~D~~-tL~d~gI~~gstI~v~v~k 76 (397)
..|.-..-.|+.++-+++.++.+-..+.+=....|+.|+.|.... .|-.+++..+ ++.+-+|.
T Consensus 23 ~~l~~~~~~t~~~~l~~l~~~l~lh~VevIg~E~I~A~~ll~~~~~~L~H~~~~~~-~l~l~vrs 86 (104)
T PF14807_consen 23 QNLPSSSQRTLPEFLQRLQQKLRLHVVEVIGNEGIFACQLLNSSPVCLLHCRVNAG-TLDLWVRS 86 (104)
T ss_pred EeccccCcCCHHHHHHHHHHhcCceEEEEeCccceeeeeccCCCCeEEEEEEecCC-eEEEEEEc
Confidence 344334567888888888877663223344457899999998776 8999999877 88887763
No 267
>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=20.24 E-value=1.7e+02 Score=28.10 Aligned_cols=43 Identities=7% Similarity=0.089 Sum_probs=31.2
Q ss_pred EEEEEeCC---CcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEE
Q 015999 2 KVFVKTLK---GTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLI 47 (397)
Q Consensus 2 kI~Vktl~---gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLi 47 (397)
.|+|+... +..|++.++...|-.+|-++|++..+ ++++.+||.
T Consensus 178 ~V~f~~~~~~~~~~F~l~ls~~~tY~~la~~Va~~l~---~dP~~lr~~ 223 (249)
T PF12436_consen 178 EVEFKPKDNPNDPEFTLWLSKKMTYDQLAEKVAEHLN---VDPEHLRFF 223 (249)
T ss_dssp EEEEEETTSTT---EEEEEETT--HHHHHHHHHHHHT---S-GGGEEEE
T ss_pred EEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHC---CChHHEEEE
Confidence 45565532 34799999999999999999999999 889998884
No 268
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction 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.
Probab=20.16 E-value=3.5e+02 Score=21.89 Aligned_cols=57 Identities=11% Similarity=0.079 Sum_probs=39.1
Q ss_pred EEEEEeCCCcEEEEEeCCCCCHHHHHHHHHHHhCCCCCCCCCeEEEeCC---e--ecCCCCchhhc
Q 015999 2 KVFVKTLKGTHFEIEVKPEDKVSDVKKNIETVQGSDVYPASQQMLIHQG---K--VLKDVTTLEEN 62 (397)
Q Consensus 2 kI~Vktl~gk~~~veV~~~~TV~dLK~~I~~~~g~~~ip~~~qrLiy~G---K--iL~D~~tL~d~ 62 (397)
+.+|+ .+|.+..+.+...-|-..|+++|...+. +|....-|.|-. - -|.|+.-|.++
T Consensus 2 ~fKv~-~~g~~RRf~~~~~pt~~~L~~kl~~Lf~---lp~~~~~vtYiDeD~D~ITlssd~eL~d~ 63 (82)
T cd06397 2 QFKSS-FLGDTRRIVFPDIPTWEALASKLENLYN---LPEIKVGVTYIDNDNDEITLSSNKELQDF 63 (82)
T ss_pred eEEEE-eCCceEEEecCCCccHHHHHHHHHHHhC---CChhHeEEEEEcCCCCEEEecchHHHHHH
Confidence 34555 3565666667767789999999999999 998777777722 1 24555555554
Done!