Query 031604
Match_columns 156
No_of_seqs 311 out of 1398
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 02:49:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031604hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0004 Ubiquitin/40S ribosoma 100.0 8.7E-49 1.9E-53 282.9 7.5 155 1-155 1-155 (156)
2 PF01599 Ribosomal_S27: Riboso 100.0 8E-31 1.7E-35 154.7 2.5 47 101-147 1-47 (47)
3 COG1998 RPS31 Ribosomal protei 99.9 1.2E-26 2.5E-31 136.6 3.4 49 99-150 1-49 (51)
4 cd01793 Fubi Fubi ubiquitin-li 99.9 3.2E-22 6.9E-27 130.6 9.1 74 1-76 1-74 (74)
5 PTZ00044 ubiquitin; Provisiona 99.9 1E-21 2.3E-26 128.4 9.6 76 1-76 1-76 (76)
6 cd01807 GDX_N ubiquitin-like d 99.9 1.5E-21 3.2E-26 127.4 9.0 73 1-73 1-73 (74)
7 cd01802 AN1_N ubiquitin-like d 99.9 2.5E-21 5.4E-26 134.0 9.2 76 1-76 28-103 (103)
8 cd01803 Ubiquitin Ubiquitin. U 99.9 4.2E-21 9E-26 125.2 9.4 76 1-76 1-76 (76)
9 cd01806 Nedd8 Nebb8-like ubiq 99.8 1.1E-20 2.4E-25 123.1 9.8 76 1-76 1-76 (76)
10 cd01810 ISG15_repeat2 ISG15 ub 99.8 8E-21 1.7E-25 124.0 8.6 74 3-76 1-74 (74)
11 cd01797 NIRF_N amino-terminal 99.8 2.5E-20 5.3E-25 123.0 9.0 74 1-74 1-76 (78)
12 cd01804 midnolin_N Ubiquitin-l 99.8 2.3E-20 5E-25 123.1 8.7 75 1-76 2-76 (78)
13 cd01791 Ubl5 UBL5 ubiquitin-li 99.8 7.8E-20 1.7E-24 119.1 8.1 71 1-71 2-72 (73)
14 cd01805 RAD23_N Ubiquitin-like 99.8 2.7E-19 5.9E-24 117.2 9.5 73 1-73 1-75 (77)
15 cd01800 SF3a120_C Ubiquitin-li 99.8 2.2E-19 4.7E-24 117.8 7.9 72 8-79 5-76 (76)
16 cd01809 Scythe_N Ubiquitin-lik 99.8 5.2E-19 1.1E-23 114.1 8.9 72 1-72 1-72 (72)
17 cd01794 DC_UbP_C dendritic cel 99.8 2.9E-19 6.3E-24 115.5 7.7 69 3-71 1-69 (70)
18 cd01798 parkin_N amino-termina 99.8 3.1E-19 6.7E-24 115.1 7.8 70 3-72 1-70 (70)
19 cd01792 ISG15_repeat1 ISG15 ub 99.8 8.1E-19 1.7E-23 116.2 8.0 73 1-73 3-77 (80)
20 cd01808 hPLIC_N Ubiquitin-like 99.8 2.4E-18 5.3E-23 111.3 8.4 71 1-72 1-71 (71)
21 PF00240 ubiquitin: Ubiquitin 99.8 3.1E-18 6.7E-23 109.8 8.2 68 6-73 1-68 (69)
22 KOG0003 Ubiquitin/60s ribosoma 99.8 9.1E-20 2E-24 124.4 0.7 78 1-78 1-78 (128)
23 cd01796 DDI1_N DNA damage indu 99.7 1.1E-17 2.4E-22 108.3 7.4 68 3-70 1-70 (71)
24 cd01763 Sumo Small ubiquitin-r 99.7 4.2E-17 9.1E-22 109.6 9.6 76 1-76 12-87 (87)
25 cd01812 BAG1_N Ubiquitin-like 99.7 3.2E-17 7E-22 105.5 7.8 70 1-71 1-70 (71)
26 cd01790 Herp_N Homocysteine-re 99.7 4.5E-17 9.7E-22 107.3 7.2 71 1-71 2-78 (79)
27 PRK00432 30S ribosomal protein 99.7 1.2E-17 2.7E-22 100.7 4.1 47 99-149 2-48 (50)
28 cd01813 UBP_N UBP ubiquitin pr 99.7 1.5E-16 3.1E-21 103.9 8.0 69 1-70 1-72 (74)
29 KOG0005 Ubiquitin-like protein 99.7 5E-17 1.1E-21 99.9 4.7 70 1-70 1-70 (70)
30 smart00213 UBQ Ubiquitin homol 99.6 8.5E-16 1.9E-20 96.3 7.5 64 1-65 1-64 (64)
31 cd01814 NTGP5 Ubiquitin-like N 99.6 1.1E-15 2.3E-20 106.1 5.9 90 2-91 6-109 (113)
32 TIGR00601 rad23 UV excision re 99.6 5.4E-15 1.2E-19 122.9 8.9 72 1-72 1-75 (378)
33 cd01799 Hoil1_N Ubiquitin-like 99.6 1.1E-14 2.4E-19 95.3 7.4 64 7-71 9-74 (75)
34 cd01815 BMSC_UbP_N Ubiquitin-l 99.5 1.5E-14 3.2E-19 94.2 4.9 56 16-71 15-74 (75)
35 cd01769 UBL Ubiquitin-like dom 99.5 1E-13 2.2E-18 87.9 7.6 67 5-71 2-68 (69)
36 PF11976 Rad60-SLD: Ubiquitin- 99.4 4E-13 8.7E-18 86.7 7.3 71 1-71 1-72 (72)
37 cd01795 USP48_C USP ubiquitin- 99.4 3.2E-13 7E-18 91.5 6.6 61 12-72 16-77 (107)
38 KOG0010 Ubiquitin-like protein 99.4 2E-13 4.3E-18 114.9 6.4 73 1-74 16-88 (493)
39 KOG0011 Nucleotide excision re 99.3 3.4E-12 7.4E-17 102.8 7.3 74 1-74 1-76 (340)
40 cd01789 Alp11_N Ubiquitin-like 99.3 2.4E-11 5.2E-16 81.1 8.5 70 2-71 3-80 (84)
41 PF14560 Ubiquitin_2: Ubiquiti 99.2 1E-10 2.2E-15 78.4 7.6 70 2-71 3-82 (87)
42 KOG0001 Ubiquitin and ubiquiti 99.2 4.3E-10 9.2E-15 71.0 9.1 73 3-75 2-74 (75)
43 PF13881 Rad60-SLD_2: Ubiquiti 99.2 4.4E-10 9.6E-15 78.7 9.6 78 2-79 4-95 (111)
44 cd01788 ElonginB Ubiquitin-lik 99.1 2.1E-10 4.5E-15 79.6 7.7 77 1-77 1-85 (119)
45 PLN02560 enoyl-CoA reductase 99.1 2E-10 4.3E-15 93.4 8.0 74 1-76 1-85 (308)
46 cd01801 Tsc13_N Ubiquitin-like 98.9 3.8E-09 8.2E-14 69.2 6.8 68 2-69 2-74 (77)
47 KOG4248 Ubiquitin-like protein 98.9 3E-09 6.5E-14 96.1 6.4 73 2-75 4-76 (1143)
48 PF11543 UN_NPL4: Nuclear pore 98.9 6.8E-09 1.5E-13 68.6 6.2 69 1-70 5-78 (80)
49 cd00196 UBQ Ubiquitin-like pro 98.7 7.7E-08 1.7E-12 57.7 7.7 67 5-71 2-68 (69)
50 cd01811 OASL_repeat1 2'-5' oli 98.6 5.3E-07 1.1E-11 58.1 7.5 70 1-71 1-75 (80)
51 KOG1769 Ubiquitin-like protein 98.4 2.3E-06 4.9E-11 58.2 8.8 76 2-77 22-97 (99)
52 KOG3493 Ubiquitin-like protein 98.4 1.2E-07 2.6E-12 59.4 2.1 69 2-70 3-71 (73)
53 KOG0006 E3 ubiquitin-protein l 98.4 6.8E-07 1.5E-11 72.3 6.0 73 1-73 1-77 (446)
54 PF13019 Telomere_Sde2: Telome 98.3 7.2E-06 1.6E-10 60.7 8.9 78 1-78 1-90 (162)
55 KOG1872 Ubiquitin-specific pro 98.3 2.3E-06 4.9E-11 72.3 6.7 71 3-74 6-77 (473)
56 KOG4495 RNA polymerase II tran 98.2 2.1E-06 4.5E-11 58.0 4.2 62 1-62 1-65 (110)
57 PF00789 UBX: UBX domain; Int 97.9 0.00013 2.8E-09 47.8 9.0 69 2-70 8-81 (82)
58 PF08817 YukD: WXG100 protein 97.9 4E-05 8.8E-10 50.2 6.5 68 2-69 4-78 (79)
59 PF11470 TUG-UBL1: GLUT4 regul 97.9 7.2E-05 1.6E-09 47.5 6.6 63 7-69 3-65 (65)
60 smart00166 UBX Domain present 97.8 0.00024 5.1E-09 46.6 7.9 68 2-69 6-78 (80)
61 COG5227 SMT3 Ubiquitin-like pr 97.7 5.8E-05 1.2E-09 50.5 3.7 75 3-77 27-101 (103)
62 PF10302 DUF2407: DUF2407 ubiq 97.6 0.00016 3.4E-09 49.4 5.6 58 2-59 2-64 (97)
63 cd01772 SAKS1_UBX SAKS1-like U 97.6 0.00064 1.4E-08 44.6 8.2 68 2-70 6-78 (79)
64 cd01767 UBX UBX (ubiquitin reg 97.4 0.0017 3.6E-08 42.1 8.1 66 2-69 4-74 (77)
65 cd01773 Faf1_like1_UBX Faf1 ik 97.4 0.0021 4.7E-08 42.5 8.4 69 2-71 7-80 (82)
66 cd01770 p47_UBX p47-like ubiqu 97.3 0.0019 4.1E-08 42.4 7.7 65 2-67 6-74 (79)
67 cd01771 Faf1_UBX Faf1 UBX doma 97.2 0.0037 8.1E-08 41.1 8.0 68 2-70 6-78 (80)
68 KOG0013 Uncharacterized conser 97.2 0.00076 1.6E-08 51.9 5.3 64 9-72 155-218 (231)
69 cd01774 Faf1_like2_UBX Faf1 ik 97.2 0.0047 1E-07 41.1 8.2 68 2-70 6-83 (85)
70 KOG1639 Steroid reductase requ 97.2 0.00094 2E-08 52.7 5.5 75 1-77 1-82 (297)
71 COG5417 Uncharacterized small 96.7 0.016 3.4E-07 37.5 7.5 64 6-69 12-80 (81)
72 KOG3206 Alpha-tubulin folding 96.6 0.0077 1.7E-07 46.4 6.2 71 2-72 3-81 (234)
73 PRK06437 hypothetical protein; 96.6 0.029 6.2E-07 35.6 7.9 63 5-76 5-67 (67)
74 PF15044 CLU_N: Mitochondrial 96.2 0.0085 1.8E-07 39.1 4.1 57 17-73 1-59 (76)
75 PRK06488 sulfur carrier protei 96.1 0.053 1.2E-06 33.9 7.3 65 1-76 1-65 (65)
76 PRK08364 sulfur carrier protei 96.1 0.062 1.3E-06 34.2 7.7 56 12-76 15-70 (70)
77 PLN02799 Molybdopterin synthas 96.1 0.027 5.9E-07 36.7 6.2 71 1-76 2-82 (82)
78 KOG4583 Membrane-associated ER 96.1 0.0029 6.2E-08 51.9 1.5 60 2-61 11-74 (391)
79 PF09379 FERM_N: FERM N-termin 95.9 0.079 1.7E-06 34.0 7.7 62 5-66 1-69 (80)
80 cd06409 PB1_MUG70 The MUG70 pr 95.9 0.034 7.4E-07 37.1 5.9 44 2-45 2-48 (86)
81 cd00754 MoaD Ubiquitin domain 95.8 0.054 1.2E-06 34.8 6.5 60 12-76 17-80 (80)
82 PF12754 Blt1: Cell-cycle cont 95.7 0.0027 5.8E-08 51.6 0.0 77 2-78 80-183 (309)
83 cd06406 PB1_P67 A PB1 domain i 95.7 0.056 1.2E-06 35.6 6.0 38 12-49 12-49 (80)
84 PF14836 Ubiquitin_3: Ubiquiti 95.5 0.13 2.8E-06 34.5 7.4 65 11-76 14-84 (88)
85 PF11620 GABP-alpha: GA-bindin 95.4 0.085 1.8E-06 35.0 6.2 62 12-73 4-65 (88)
86 PHA00626 hypothetical protein 95.1 0.014 3.1E-07 35.6 1.6 30 120-151 2-36 (59)
87 PRK05863 sulfur carrier protei 94.9 0.18 3.9E-06 31.6 6.6 65 1-76 1-65 (65)
88 PF10790 DUF2604: Protein of U 94.9 0.19 4.1E-06 31.7 6.3 65 9-73 4-72 (76)
89 COG5100 NPL4 Nuclear pore prot 94.9 0.12 2.6E-06 43.7 7.1 71 1-72 1-79 (571)
90 PRK05659 sulfur carrier protei 94.6 0.34 7.3E-06 30.1 7.3 66 1-76 1-66 (66)
91 PRK06944 sulfur carrier protei 94.6 0.46 9.9E-06 29.3 7.8 65 1-76 1-65 (65)
92 cd00565 ThiS ThiaminS ubiquiti 94.5 0.2 4.4E-06 31.2 5.9 58 14-76 8-65 (65)
93 TIGR01682 moaD molybdopterin c 94.3 0.37 8E-06 31.1 7.2 60 12-76 17-80 (80)
94 PRK08053 sulfur carrier protei 94.3 0.53 1.1E-05 29.4 7.6 66 1-76 1-66 (66)
95 TIGR01687 moaD_arch MoaD famil 94.1 0.57 1.2E-05 30.7 7.9 62 11-76 16-88 (88)
96 PF14453 ThiS-like: ThiS-like 94.0 0.23 4.9E-06 30.6 5.2 54 1-70 1-54 (57)
97 cd06407 PB1_NLP A PB1 domain i 93.9 0.26 5.7E-06 32.5 5.8 46 1-47 1-47 (82)
98 KOG0012 DNA damage inducible p 93.9 0.11 2.3E-06 43.2 4.8 70 1-70 1-74 (380)
99 PF02597 ThiS: ThiS family; I 93.8 0.31 6.7E-06 30.9 6.0 63 12-76 13-77 (77)
100 TIGR01683 thiS thiamine biosyn 93.7 0.4 8.6E-06 29.7 6.2 57 15-76 8-64 (64)
101 smart00666 PB1 PB1 domain. Pho 93.7 0.39 8.5E-06 30.9 6.3 45 2-47 3-47 (81)
102 PF09855 DUF2082: Nucleic-acid 93.6 0.065 1.4E-06 33.8 2.4 19 137-155 35-53 (64)
103 PRK06083 sulfur carrier protei 93.1 0.63 1.4E-05 30.8 6.7 57 15-76 28-84 (84)
104 PRK07696 sulfur carrier protei 92.9 1.1 2.5E-05 28.1 7.4 66 1-76 1-67 (67)
105 PRK07440 hypothetical protein; 92.9 0.99 2.1E-05 28.7 7.2 61 9-76 10-70 (70)
106 smart00295 B41 Band 4.1 homolo 92.7 1.5 3.3E-05 32.6 9.3 71 2-72 5-83 (207)
107 KOG0009 Ubiquitin-like/40S rib 92.1 0.059 1.3E-06 33.1 0.6 27 76-102 7-33 (62)
108 PF10571 UPF0547: Uncharacteri 92.0 0.057 1.2E-06 27.9 0.4 24 119-148 1-24 (26)
109 cd01760 RBD Ubiquitin-like dom 91.9 1.2 2.7E-05 28.6 6.6 44 3-46 2-45 (72)
110 KOG2689 Predicted ubiquitin re 91.2 0.74 1.6E-05 37.0 6.1 68 2-69 212-284 (290)
111 KOG2086 Protein tyrosine phosp 91.2 0.47 1E-05 39.8 5.1 65 2-66 307-375 (380)
112 smart00647 IBR In Between Ring 91.0 0.14 3.1E-06 31.2 1.6 34 118-151 18-53 (64)
113 smart00455 RBD Raf-like Ras-bi 91.0 1.1 2.3E-05 28.6 5.7 49 3-51 2-52 (70)
114 COG2104 ThiS Sulfur transfer p 90.9 2.3 5.1E-05 27.0 7.1 59 13-76 10-68 (68)
115 TIGR02958 sec_mycoba_snm4 secr 90.9 1.2 2.6E-05 38.4 7.5 69 2-71 4-79 (452)
116 cd06408 PB1_NoxR The PB1 domai 90.6 1.9 4.1E-05 28.8 6.7 46 9-57 10-55 (86)
117 PRK05978 hypothetical protein; 90.4 0.16 3.5E-06 37.3 1.6 33 117-151 32-65 (148)
118 PF01485 IBR: IBR domain; Int 90.2 0.12 2.7E-06 31.5 0.8 33 119-151 19-53 (64)
119 PF00564 PB1: PB1 domain; Int 90.0 1.5 3.2E-05 28.2 5.8 44 3-47 4-48 (84)
120 COG2051 RPS27A Ribosomal prote 89.8 0.6 1.3E-05 29.5 3.6 38 111-150 12-50 (67)
121 COG1997 RPL43A Ribosomal prote 89.5 0.27 5.8E-06 32.8 1.9 32 115-148 32-63 (89)
122 cd05992 PB1 The PB1 domain is 89.3 1.8 3.9E-05 27.6 5.8 45 2-47 2-47 (81)
123 smart00661 RPOL9 RNA polymeras 89.0 0.23 5E-06 29.3 1.3 27 120-150 2-32 (52)
124 PF01780 Ribosomal_L37ae: Ribo 89.0 0.36 7.8E-06 32.5 2.3 31 117-149 34-64 (90)
125 COG1645 Uncharacterized Zn-fin 89.0 0.17 3.8E-06 36.3 0.8 34 115-152 25-58 (131)
126 PF02196 RBD: Raf-like Ras-bin 88.9 4.4 9.5E-05 25.8 8.2 56 3-58 3-60 (71)
127 PRK11840 bifunctional sulfur c 88.6 2.6 5.7E-05 34.8 7.5 68 1-78 1-68 (326)
128 cd06411 PB1_p51 The PB1 domain 88.5 1.2 2.5E-05 29.2 4.3 36 12-47 8-43 (78)
129 PRK00398 rpoP DNA-directed RNA 88.1 0.57 1.2E-05 27.2 2.5 34 118-153 3-36 (46)
130 cd06410 PB1_UP2 Uncharacterize 87.1 3 6.5E-05 28.3 6.0 40 5-45 17-56 (97)
131 TIGR02098 MJ0042_CXXC MJ0042 f 87.0 0.47 1E-05 26.2 1.6 29 118-149 2-36 (38)
132 PTZ00380 microtubule-associate 86.9 0.72 1.6E-05 32.7 2.9 59 13-71 43-104 (121)
133 PF10209 DUF2340: Uncharacteri 86.6 2.2 4.7E-05 30.3 5.2 55 16-70 21-106 (122)
134 PRK11130 moaD molybdopterin sy 86.5 5.3 0.00011 25.8 6.8 57 15-76 19-81 (81)
135 cd06398 PB1_Joka2 The PB1 doma 86.5 4.3 9.3E-05 27.2 6.4 70 3-73 3-88 (91)
136 PF01907 Ribosomal_L37e: Ribos 86.4 0.49 1.1E-05 28.8 1.6 25 117-146 14-38 (55)
137 cd06396 PB1_NBR1 The PB1 domai 85.6 5.4 0.00012 26.3 6.4 40 3-45 3-44 (81)
138 COG1096 Predicted RNA-binding 85.5 0.62 1.3E-05 35.4 2.1 31 119-153 150-180 (188)
139 PRK01777 hypothetical protein; 85.2 6 0.00013 26.8 6.7 69 1-78 4-82 (95)
140 TIGR00280 L37a ribosomal prote 85.1 0.64 1.4E-05 31.3 1.8 32 116-149 33-64 (91)
141 PF04758 Ribosomal_S30: Riboso 84.3 0.19 4.2E-06 31.0 -0.9 26 74-99 3-28 (59)
142 cd01787 GRB7_RA RA (RAS-associ 84.2 4.7 0.0001 26.8 5.6 66 3-68 5-81 (85)
143 PRK03976 rpl37ae 50S ribosomal 83.8 0.75 1.6E-05 30.9 1.7 32 116-149 34-65 (90)
144 PF08825 E2_bind: E2 binding d 83.6 2.4 5.3E-05 28.0 4.1 55 15-70 1-69 (84)
145 PF08792 A2L_zn_ribbon: A2L zi 82.9 1.4 3E-05 24.0 2.2 29 119-149 4-32 (33)
146 PF13248 zf-ribbon_3: zinc-rib 82.8 0.44 9.4E-06 24.4 0.2 24 118-147 2-25 (26)
147 PRK09710 lar restriction allev 82.8 1.1 2.4E-05 28.2 2.0 28 118-147 6-36 (64)
148 smart00154 ZnF_AN1 AN1-like Zi 82.3 0.74 1.6E-05 26.0 1.1 23 118-143 12-36 (39)
149 PF02017 CIDE-N: CIDE-N domain 82.3 5.5 0.00012 26.1 5.3 49 21-72 21-71 (78)
150 PTZ00255 60S ribosomal protein 82.1 0.94 2E-05 30.5 1.7 32 116-149 34-65 (90)
151 PRK09336 30S ribosomal protein 82.0 0.57 1.2E-05 28.0 0.5 24 75-98 5-28 (50)
152 COG5349 Uncharacterized protei 81.4 0.5 1.1E-05 33.5 0.1 34 117-152 20-54 (126)
153 PF14451 Ub-Mut7C: Mut7-C ubiq 81.2 8.7 0.00019 25.2 6.0 52 10-70 22-74 (81)
154 PF14533 USP7_C2: Ubiquitin-sp 80.8 7.5 0.00016 30.0 6.6 48 12-59 35-90 (213)
155 PF08337 Plexin_cytopl: Plexin 80.8 6.1 0.00013 34.9 6.6 64 11-74 202-291 (539)
156 cd01766 Ufm1 Urm1-like ubiquit 80.8 10 0.00022 24.6 5.9 61 14-74 19-80 (82)
157 PF02150 RNA_POL_M_15KD: RNA p 80.8 1.2 2.6E-05 24.5 1.5 27 120-150 3-32 (35)
158 KOG4250 TANK binding protein k 80.7 4.8 0.0001 36.6 6.0 41 9-49 323-363 (732)
159 cd01764 Urm1 Urm1-like ubuitin 80.4 4.6 0.0001 27.1 4.6 60 15-76 23-94 (94)
160 PF13719 zinc_ribbon_5: zinc-r 79.5 1 2.2E-05 25.0 1.0 30 118-149 2-36 (37)
161 PF09538 FYDLN_acid: Protein o 79.4 0.89 1.9E-05 31.6 0.9 32 117-151 8-39 (108)
162 KOG2982 Uncharacterized conser 79.4 3 6.6E-05 34.6 4.1 57 14-70 351-415 (418)
163 COG1571 Predicted DNA-binding 79.2 1.9 4.1E-05 36.8 2.9 31 116-149 348-378 (421)
164 PTZ00467 40S ribosomal protein 79.2 0.63 1.4E-05 29.3 0.1 26 74-99 5-30 (66)
165 PF00276 Ribosomal_L23: Riboso 79.2 6.3 0.00014 26.3 5.0 38 11-48 21-59 (91)
166 KOG2507 Ubiquitin regulatory p 79.2 4.1 8.9E-05 34.9 4.9 72 2-73 316-392 (506)
167 PF00788 RA: Ras association ( 78.9 13 0.00027 23.9 6.4 41 3-43 5-51 (93)
168 PF14803 Nudix_N_2: Nudix N-te 78.4 1.5 3.2E-05 24.1 1.4 27 120-148 2-32 (34)
169 cd01768 RA RA (Ras-associating 77.2 13 0.00029 23.9 6.1 35 10-44 12-48 (87)
170 PF02991 Atg8: Autophagy prote 76.7 5.5 0.00012 27.4 4.2 57 15-71 37-97 (104)
171 PF11069 DUF2870: Protein of u 76.5 3.4 7.4E-05 28.2 3.0 37 42-78 3-40 (98)
172 PF01428 zf-AN1: AN1-like Zinc 76.4 0.83 1.8E-05 26.2 0.0 24 117-143 12-37 (43)
173 COG3478 Predicted nucleic-acid 76.0 0.81 1.8E-05 28.8 -0.1 17 138-154 40-56 (68)
174 PF14732 UAE_UbL: Ubiquitin/SU 75.7 6.8 0.00015 25.9 4.3 56 15-70 2-67 (87)
175 PF08271 TF_Zn_Ribbon: TFIIB z 75.3 2.2 4.7E-05 24.3 1.6 28 120-149 2-30 (43)
176 cd01818 TIAM1_RBD Ubiquitin do 75.0 13 0.00028 24.2 5.2 38 4-41 3-40 (77)
177 PF13717 zinc_ribbon_4: zinc-r 74.7 1.5 3.2E-05 24.2 0.7 29 118-148 2-35 (36)
178 smart00144 PI3K_rbd PI3-kinase 74.0 26 0.00055 24.0 7.7 63 11-73 29-105 (108)
179 cd01777 SNX27_RA Ubiquitin dom 73.4 10 0.00023 25.3 4.7 40 2-41 3-42 (87)
180 PRK05738 rplW 50S ribosomal pr 73.4 10 0.00022 25.4 4.7 33 10-42 20-52 (92)
181 PLN00209 ribosomal protein S27 73.3 3.6 7.8E-05 27.4 2.4 33 115-149 33-66 (86)
182 smart00266 CAD Domains present 73.2 10 0.00022 24.6 4.4 39 21-59 19-59 (74)
183 PRK00420 hypothetical protein; 73.1 2.7 5.8E-05 29.4 1.9 31 117-150 22-52 (112)
184 COG5272 UBI4 Ubiquitin [Posttr 72.9 0.72 1.6E-05 28.1 -0.9 42 80-122 4-45 (57)
185 PTZ00083 40S ribosomal protein 72.8 3.9 8.5E-05 27.1 2.5 33 115-149 32-65 (85)
186 cd01611 GABARAP Ubiquitin doma 72.4 7.4 0.00016 27.1 4.0 57 15-72 45-106 (112)
187 PF14533 USP7_C2: Ubiquitin-sp 72.3 3.8 8.3E-05 31.6 2.8 30 10-39 132-161 (213)
188 cd06397 PB1_UP1 Uncharacterize 72.0 21 0.00046 23.5 5.8 44 2-46 2-45 (82)
189 TIGR02300 FYDLN_acid conserved 72.0 2.2 4.7E-05 30.5 1.2 31 117-150 8-38 (129)
190 KOG0007 Splicing factor 3a, su 71.9 1.9 4.1E-05 35.7 1.1 49 8-56 290-339 (341)
191 KOG4572 Predicted DNA-binding 71.4 6.5 0.00014 36.6 4.3 62 9-70 3-68 (1424)
192 smart00314 RA Ras association 71.3 25 0.00054 22.8 6.3 35 10-44 15-51 (90)
193 PF10407 Cytokin_check_N: Cdc1 70.9 22 0.00047 22.9 5.6 61 11-72 3-70 (73)
194 TIGR03636 L23_arch archaeal ri 70.6 13 0.00028 24.2 4.6 33 11-43 15-47 (77)
195 PF03671 Ufm1: Ubiquitin fold 70.3 25 0.00054 22.7 5.6 59 12-70 16-76 (76)
196 cd01615 CIDE_N CIDE_N domain, 70.3 13 0.00027 24.4 4.5 39 21-59 21-61 (78)
197 PRK04179 rpl37e 50S ribosomal 69.8 2.2 4.7E-05 26.6 0.8 25 117-146 16-40 (62)
198 PF05129 Elf1: Transcription e 68.9 3.8 8.2E-05 26.9 1.8 35 117-153 21-61 (81)
199 PF07754 DUF1610: Domain of un 68.4 2.6 5.6E-05 21.3 0.7 22 125-146 3-24 (24)
200 PF03604 DNA_RNApol_7kD: DNA d 68.4 4.8 0.0001 21.7 1.8 30 120-152 2-31 (32)
201 cd06539 CIDE_N_A CIDE_N domain 68.0 17 0.00036 23.8 4.6 47 21-69 21-69 (78)
202 cd01775 CYR1_RA Ubiquitin doma 67.3 33 0.00071 23.4 6.1 35 4-38 6-40 (97)
203 PRK14548 50S ribosomal protein 66.8 17 0.00038 24.0 4.7 34 10-43 21-54 (84)
204 PRK00415 rps27e 30S ribosomal 66.4 5.6 0.00012 24.6 2.1 33 115-149 8-41 (59)
205 PF06234 TmoB: Toluene-4-monoo 66.4 36 0.00077 22.6 6.4 60 12-71 16-83 (85)
206 cd01817 RGS12_RBD Ubiquitin do 66.2 33 0.00071 22.1 7.7 47 5-51 4-52 (73)
207 PF01783 Ribosomal_L32p: Ribos 65.5 6.2 0.00014 23.9 2.2 22 118-146 26-47 (56)
208 PF12436 USP7_ICP0_bdg: ICP0-b 65.2 8.5 0.00018 30.4 3.5 73 2-74 70-154 (249)
209 COG0089 RplW Ribosomal protein 65.0 17 0.00037 24.6 4.4 34 10-43 21-54 (94)
210 PF09788 Tmemb_55A: Transmembr 64.6 4.9 0.00011 32.0 2.0 62 89-154 98-173 (256)
211 PF12436 USP7_ICP0_bdg: ICP0-b 64.4 22 0.00047 28.1 5.7 35 10-44 189-223 (249)
212 smart00659 RPOLCX RNA polymera 64.2 8.1 0.00018 22.3 2.4 31 119-152 3-33 (44)
213 PRK14892 putative transcriptio 63.8 3.8 8.3E-05 28.0 1.1 32 118-152 21-56 (99)
214 KOG2561 Adaptor protein NUB1, 63.4 2.3 5.1E-05 36.7 -0.0 59 14-72 53-111 (568)
215 PF06677 Auto_anti-p27: Sjogre 63.3 6.6 0.00014 22.4 1.9 26 117-145 16-41 (41)
216 KOG3439 Protein conjugation fa 63.2 28 0.0006 24.4 5.2 38 13-50 47-84 (116)
217 PF07282 OrfB_Zn_ribbon: Putat 62.9 4.2 9.1E-05 25.3 1.1 30 118-149 28-57 (69)
218 COG4888 Uncharacterized Zn rib 62.9 7.6 0.00016 26.6 2.4 37 117-155 21-63 (104)
219 PF05191 ADK_lid: Adenylate ki 62.1 2.7 5.9E-05 23.2 0.1 12 138-149 1-12 (36)
220 PF11834 DUF3354: Domain of un 62.1 15 0.00032 23.4 3.5 43 21-69 26-68 (69)
221 PF09297 zf-NADH-PPase: NADH p 61.7 6.6 0.00014 20.8 1.6 29 118-148 3-31 (32)
222 PF08646 Rep_fac-A_C: Replicat 61.0 5.7 0.00012 28.5 1.6 29 118-148 18-47 (146)
223 PF12760 Zn_Tnp_IS1595: Transp 59.4 6.5 0.00014 22.6 1.4 26 119-146 19-45 (46)
224 cd01612 APG12_C Ubiquitin-like 59.4 18 0.0004 23.9 3.8 58 14-71 19-80 (87)
225 cd06536 CIDE_N_ICAD CIDE_N dom 59.4 22 0.00049 23.3 4.1 39 21-59 21-63 (80)
226 CHL00030 rpl23 ribosomal prote 59.4 24 0.00053 23.7 4.4 32 10-41 19-50 (93)
227 KOG4684 Uncharacterized conser 58.9 5 0.00011 31.4 1.1 37 116-152 136-184 (275)
228 PTZ00073 60S ribosomal protein 57.5 5.1 0.00011 26.9 0.8 25 117-146 15-39 (91)
229 KOG3475 60S ribosomal protein 57.4 2.3 4.9E-05 28.2 -0.8 26 118-148 16-41 (92)
230 PRK01103 formamidopyrimidine/5 57.2 8.1 0.00018 30.9 2.1 28 118-147 245-274 (274)
231 PF09469 Cobl: Cordon-bleu ubi 56.8 8.4 0.00018 25.2 1.7 34 29-62 2-38 (79)
232 PF11706 zf-CGNR: CGNR zinc fi 56.0 4.1 8.8E-05 23.6 0.1 26 119-145 3-32 (44)
233 COG2888 Predicted Zn-ribbon RN 55.8 6.4 0.00014 24.4 1.0 10 136-145 48-57 (61)
234 COG0675 Transposase and inacti 55.3 5.9 0.00013 31.6 1.0 24 119-149 310-333 (364)
235 cd06538 CIDE_N_FSP27 CIDE_N do 55.1 30 0.00065 22.7 4.1 39 21-59 21-60 (79)
236 PF03658 Ub-RnfH: RnfH family 55.1 59 0.0013 21.5 5.7 73 1-78 1-79 (84)
237 PF08783 DWNN: DWNN domain; I 55.1 42 0.00092 21.6 4.8 32 5-36 3-36 (74)
238 PF00794 PI3K_rbd: PI3-kinase 55.0 62 0.0014 21.7 6.3 71 2-72 18-102 (106)
239 cd01776 Rin1_RA Ubiquitin doma 54.8 47 0.001 22.1 5.0 43 12-54 15-62 (87)
240 cd00350 rubredoxin_like Rubred 54.1 6.4 0.00014 21.1 0.7 13 138-150 1-13 (33)
241 COG3677 Transposase and inacti 54.0 13 0.00029 26.5 2.6 32 118-152 30-67 (129)
242 KOG1364 Predicted ubiquitin re 53.8 14 0.00031 30.8 3.0 65 2-66 279-349 (356)
243 cd06537 CIDE_N_B CIDE_N domain 53.7 39 0.00084 22.2 4.5 47 21-69 21-68 (81)
244 KOG0006 E3 ubiquitin-protein l 53.7 3 6.6E-05 34.5 -0.9 33 119-151 316-349 (446)
245 PRK12280 rplW 50S ribosomal pr 53.6 31 0.00066 25.6 4.5 39 10-48 22-61 (158)
246 KOG1779 40s ribosomal protein 53.5 13 0.00028 24.4 2.1 54 86-149 10-64 (84)
247 KOG4598 Putative ubiquitin-spe 52.5 17 0.00038 33.4 3.5 57 12-70 878-940 (1203)
248 PF02192 PI3K_p85B: PI3-kinase 52.4 22 0.00049 23.1 3.2 22 13-34 2-23 (78)
249 PF01667 Ribosomal_S27e: Ribos 52.0 15 0.00032 22.4 2.2 34 115-150 4-38 (55)
250 PRK11827 hypothetical protein; 51.8 9.2 0.0002 23.7 1.3 29 120-150 10-38 (60)
251 PF13240 zinc_ribbon_2: zinc-r 50.6 6.3 0.00014 19.5 0.3 21 120-146 1-21 (23)
252 PRK12286 rpmF 50S ribosomal pr 50.4 8.5 0.00018 23.6 0.9 22 118-146 27-48 (57)
253 PF13453 zf-TFIIB: Transcripti 50.2 9.9 0.00021 21.3 1.1 25 120-148 1-29 (41)
254 TIGR00595 priA primosomal prot 49.8 8.2 0.00018 33.7 1.1 25 120-148 224-250 (505)
255 cd01782 AF6_RA_repeat1 Ubiquit 49.2 89 0.0019 21.8 6.0 37 1-37 24-62 (112)
256 PHA02942 putative transposase; 49.0 9.2 0.0002 32.3 1.2 27 118-148 325-352 (383)
257 PF09151 DUF1936: Domain of un 48.7 12 0.00027 20.0 1.3 14 120-135 3-16 (36)
258 COG1545 Predicted nucleic-acid 48.5 8 0.00017 27.9 0.7 36 104-147 17-52 (140)
259 COG3809 Uncharacterized protei 48.5 14 0.0003 24.3 1.7 26 120-147 3-30 (88)
260 COG2816 NPY1 NTP pyrophosphohy 46.7 7.8 0.00017 31.4 0.4 31 116-148 109-139 (279)
261 smart00143 PI3K_p85B PI3-kinas 46.6 28 0.0006 22.8 2.9 22 13-34 2-23 (78)
262 PF14847 Ras_bdg_2: Ras-bindin 46.0 97 0.0021 21.3 5.8 36 3-38 3-38 (105)
263 PF15616 TerY-C: TerY-C metal 44.9 19 0.00042 25.8 2.2 25 119-152 78-102 (131)
264 COG1977 MoaD Molybdopterin con 44.5 47 0.001 21.6 3.9 60 13-76 19-84 (84)
265 PRK00241 nudC NADH pyrophospha 44.0 12 0.00027 29.7 1.2 30 117-148 98-127 (256)
266 PRK12380 hydrogenase nickel in 43.6 19 0.00042 24.9 2.0 26 117-146 69-94 (113)
267 PRK03681 hypA hydrogenase nick 43.3 18 0.0004 25.1 1.9 26 117-146 69-95 (114)
268 PF11781 RRN7: RNA polymerase 43.3 13 0.00028 20.5 0.8 24 120-146 10-33 (36)
269 PRK14810 formamidopyrimidine-D 42.7 20 0.00043 28.8 2.2 27 118-146 244-272 (272)
270 PF13878 zf-C2H2_3: zinc-finge 41.5 11 0.00023 21.4 0.4 15 137-151 12-26 (41)
271 PRK10445 endonuclease VIII; Pr 41.3 21 0.00046 28.4 2.2 26 118-145 235-262 (263)
272 PF00301 Rubredoxin: Rubredoxi 40.8 9 0.0002 22.5 -0.0 16 138-155 1-16 (47)
273 PTZ00191 60S ribosomal protein 40.7 66 0.0014 23.6 4.4 34 10-43 82-115 (145)
274 PRK14714 DNA polymerase II lar 40.7 19 0.00041 35.1 2.0 18 92-109 618-635 (1337)
275 PLN03086 PRLI-interacting fact 40.5 16 0.00035 32.5 1.5 33 116-149 431-464 (567)
276 PRK14811 formamidopyrimidine-D 40.4 22 0.00048 28.4 2.2 27 118-146 235-263 (269)
277 KOG0466 Translation initiation 40.1 20 0.00043 30.0 1.8 44 95-147 73-118 (466)
278 KOG2906 RNA polymerase III sub 39.8 29 0.00063 23.7 2.3 30 120-151 3-34 (105)
279 PHA00616 hypothetical protein 39.6 4.6 0.0001 23.5 -1.4 10 140-149 3-12 (44)
280 PF09138 Urm1: Urm1 (Ubiquitin 39.6 39 0.00085 22.9 3.0 64 11-76 18-96 (96)
281 PF09567 RE_MamI: MamI restric 39.2 9.8 0.00021 30.5 -0.0 35 103-150 74-108 (314)
282 PHA02768 hypothetical protein; 38.6 17 0.00037 22.1 1.0 30 117-149 4-42 (55)
283 PF00096 zf-C2H2: Zinc finger, 38.5 13 0.00028 17.5 0.4 9 140-148 2-10 (23)
284 KOG2660 Locus-specific chromos 38.4 26 0.00056 29.0 2.3 47 13-59 166-214 (331)
285 PF02824 TGS: TGS domain; Int 38.2 91 0.002 18.8 6.6 59 3-70 1-59 (60)
286 PF04126 Cyclophil_like: Cyclo 38.0 31 0.00066 24.1 2.4 29 1-30 1-29 (120)
287 PRK04023 DNA polymerase II lar 37.9 18 0.00038 34.5 1.3 36 92-129 584-635 (1121)
288 PF01376 Enterotoxin_b: Heat-l 37.7 60 0.0013 21.5 3.5 31 3-33 38-68 (102)
289 PF10263 SprT-like: SprT-like 37.4 31 0.00067 24.7 2.4 32 115-150 120-155 (157)
290 PF13913 zf-C2HC_2: zinc-finge 37.3 23 0.00049 17.7 1.2 10 139-148 3-12 (25)
291 PRK13945 formamidopyrimidine-D 37.3 26 0.00056 28.2 2.1 27 118-146 254-282 (282)
292 TIGR00354 polC DNA polymerase, 37.0 25 0.00055 33.4 2.2 47 92-146 583-645 (1095)
293 COG1594 RPB9 DNA-directed RNA 36.6 52 0.0011 22.9 3.3 31 118-150 72-112 (113)
294 PF13408 Zn_ribbon_recom: Reco 36.6 24 0.00053 20.6 1.5 13 139-151 6-18 (58)
295 TIGR00100 hypA hydrogenase nic 36.3 30 0.00066 24.0 2.1 26 117-146 69-94 (115)
296 TIGR00577 fpg formamidopyrimid 35.9 29 0.00064 27.7 2.2 26 118-145 245-272 (272)
297 PRK13902 alaS alanyl-tRNA synt 35.8 20 0.00044 33.7 1.5 25 116-143 17-41 (900)
298 PF14354 Lar_restr_allev: Rest 35.7 39 0.00084 20.2 2.3 26 119-146 4-37 (61)
299 KOG3173 Predicted Zn-finger pr 35.7 18 0.00039 27.0 0.9 21 118-142 119-141 (167)
300 TIGR01031 rpmF_bact ribosomal 35.1 21 0.00046 21.6 1.0 21 118-145 26-46 (55)
301 PF03931 Skp1_POZ: Skp1 family 35.0 32 0.0007 20.9 1.8 31 1-31 1-31 (62)
302 PF13894 zf-C2H2_4: C2H2-type 35.0 17 0.00037 16.8 0.5 9 140-148 2-10 (24)
303 PF12172 DUF35_N: Rubredoxin-l 34.8 28 0.0006 18.8 1.4 24 118-147 11-34 (37)
304 KOG3183 Predicted Zn-finger pr 34.7 12 0.00025 29.7 -0.2 27 114-143 19-47 (250)
305 PF06827 zf-FPG_IleRS: Zinc fi 34.6 20 0.00044 18.4 0.8 25 119-145 2-28 (30)
306 PF13699 DUF4157: Domain of un 34.1 73 0.0016 20.5 3.5 46 24-69 4-49 (79)
307 PF02505 MCR_D: Methyl-coenzym 34.1 1.1E+02 0.0023 22.6 4.7 44 12-59 76-120 (153)
308 PF13465 zf-H2C2_2: Zinc-finge 33.7 20 0.00044 17.9 0.6 11 138-148 14-24 (26)
309 TIGR01206 lysW lysine biosynth 33.3 53 0.0011 19.8 2.5 30 119-150 3-34 (54)
310 cd00730 rubredoxin Rubredoxin; 32.7 35 0.00076 20.2 1.6 11 138-148 1-11 (50)
311 PRK14890 putative Zn-ribbon RN 32.6 28 0.0006 21.5 1.2 11 136-146 46-56 (59)
312 PF12773 DZR: Double zinc ribb 32.5 20 0.00044 20.6 0.6 27 118-147 12-38 (50)
313 COG3582 Predicted nucleic acid 32.3 92 0.002 23.2 4.1 39 101-142 93-133 (162)
314 KOG3391 Transcriptional co-rep 32.0 40 0.00087 24.5 2.1 27 49-75 113-139 (151)
315 PF14319 Zn_Tnp_IS91: Transpos 32.0 33 0.00073 23.7 1.7 29 117-148 41-70 (111)
316 PF09358 UBA_e1_C: Ubiquitin-a 31.3 71 0.0015 22.5 3.4 25 15-39 37-61 (125)
317 cd00729 rubredoxin_SM Rubredox 31.0 26 0.00056 18.9 0.8 11 139-149 3-13 (34)
318 PRK05580 primosome assembly pr 31.0 26 0.00056 31.8 1.3 25 120-148 392-418 (679)
319 PF13180 PDZ_2: PDZ domain; PD 30.9 81 0.0017 19.8 3.3 55 11-73 15-71 (82)
320 COG2260 Predicted Zn-ribbon RN 30.7 28 0.00061 21.4 1.0 20 117-139 16-35 (59)
321 PF03833 PolC_DP2: DNA polymer 30.6 17 0.00036 34.0 0.0 55 91-147 611-689 (900)
322 PF11816 DUF3337: Domain of un 29.7 1.8E+02 0.0039 23.9 5.9 60 14-73 251-328 (331)
323 TIGR03260 met_CoM_red_D methyl 29.4 1.4E+02 0.003 22.0 4.6 44 12-59 75-118 (150)
324 PF08115 Toxin_28: SFI toxin f 28.8 48 0.001 17.9 1.6 17 129-145 7-23 (35)
325 PF08299 Bac_DnaA_C: Bacterial 28.8 26 0.00057 22.0 0.7 20 22-41 1-20 (70)
326 PF07191 zinc-ribbons_6: zinc- 28.6 51 0.0011 21.1 2.0 27 120-150 3-29 (70)
327 PF07295 DUF1451: Protein of u 28.3 56 0.0012 23.9 2.4 30 118-150 112-142 (146)
328 KOG3483 Uncharacterized conser 27.8 1.8E+02 0.0039 19.0 5.3 62 15-76 31-93 (94)
329 TIGR03831 YgiT_finger YgiT-typ 27.7 71 0.0015 17.5 2.4 12 137-148 31-42 (46)
330 PF10164 DUF2367: Uncharacteri 27.0 40 0.00086 23.0 1.3 13 117-131 48-60 (98)
331 COG5131 URM1 Ubiquitin-like pr 27.0 2E+02 0.0044 19.3 6.4 67 10-76 17-96 (96)
332 COG0375 HybF Zn finger protein 27.0 54 0.0012 23.0 2.0 32 116-151 68-100 (115)
333 COG0333 RpmF Ribosomal protein 26.9 36 0.00079 20.8 1.0 22 118-146 27-48 (57)
334 COG1773 Rubredoxin [Energy pro 26.8 40 0.00086 20.5 1.2 11 138-148 3-13 (55)
335 PRK14873 primosome assembly pr 26.7 32 0.00069 31.3 1.1 26 119-148 393-420 (665)
336 TIGR03655 anti_R_Lar restricti 26.5 41 0.00089 19.8 1.2 28 119-148 2-36 (53)
337 PF13912 zf-C2H2_6: C2H2-type 26.5 27 0.00058 17.1 0.4 10 139-148 2-11 (27)
338 cd06404 PB1_aPKC PB1 domain is 26.3 2E+02 0.0043 19.0 6.0 38 9-46 8-46 (83)
339 PF14599 zinc_ribbon_6: Zinc-r 26.3 47 0.001 20.6 1.5 25 119-145 31-55 (61)
340 PRK14715 DNA polymerase II lar 26.2 48 0.0011 32.8 2.2 47 92-146 632-694 (1627)
341 cd06535 CIDE_N_CAD CIDE_N doma 25.9 1.6E+02 0.0034 19.2 3.9 31 21-51 21-53 (77)
342 COG4530 Uncharacterized protei 25.7 33 0.00071 24.1 0.8 29 117-148 8-36 (129)
343 PHA02998 RNA polymerase subuni 25.6 55 0.0012 24.9 2.0 41 102-148 131-181 (195)
344 smart00760 Bac_DnaA_C Bacteria 25.5 38 0.00082 20.4 1.0 20 22-41 1-20 (60)
345 TIGR00155 pqiA_fam integral me 25.4 40 0.00087 28.7 1.4 30 118-152 215-244 (403)
346 KOG0402 60S ribosomal protein 25.2 18 0.0004 24.0 -0.5 31 116-148 34-64 (92)
347 PF03147 FDX-ACB: Ferredoxin-f 25.2 1.3E+02 0.0029 19.6 3.7 41 11-51 8-50 (94)
348 COG1996 RPC10 DNA-directed RNA 25.2 62 0.0013 19.2 1.8 32 118-151 6-37 (49)
349 PRK00564 hypA hydrogenase nick 24.3 58 0.0013 22.7 1.8 26 117-146 70-96 (117)
350 PF14807 AP4E_app_platf: Adapt 24.3 2.1E+02 0.0046 19.6 4.6 55 18-73 28-86 (104)
351 PF07929 PRiA4_ORF3: Plasmid p 24.1 1.6E+02 0.0034 21.7 4.3 40 2-41 6-48 (179)
352 KOG1973 Chromatin remodeling p 23.7 45 0.00097 26.8 1.3 24 119-145 233-266 (274)
353 COG4919 Ribosomal protein S30 23.7 44 0.00096 19.8 0.9 24 75-98 5-28 (54)
354 KOG2834 Nuclear pore complex, 23.4 1.2E+02 0.0025 26.6 3.7 80 53-148 17-96 (510)
355 cd04476 RPA1_DBD_C RPA1_DBD_C: 23.3 36 0.00079 24.8 0.7 28 117-148 33-61 (166)
356 smart00834 CxxC_CXXC_SSSS Puta 23.3 57 0.0012 17.6 1.4 8 119-128 6-13 (41)
357 PF10083 DUF2321: Uncharacteri 23.3 37 0.0008 25.2 0.7 31 119-151 40-81 (158)
358 PF13439 Glyco_transf_4: Glyco 23.1 92 0.002 21.4 2.8 27 24-51 148-174 (177)
359 TIGR00244 transcriptional regu 22.6 59 0.0013 23.9 1.6 16 111-128 21-36 (147)
360 KOG3456 NADH:ubiquinone oxidor 22.6 24 0.00052 24.5 -0.4 13 137-149 103-115 (120)
361 KOG0956 PHD finger protein AF1 22.5 38 0.00083 31.1 0.8 35 108-146 12-56 (900)
362 PF01396 zf-C4_Topoisom: Topoi 22.5 1.1E+02 0.0024 16.8 2.5 29 119-150 2-36 (39)
363 PRK03824 hypA hydrogenase nick 22.4 76 0.0017 22.6 2.2 10 117-128 69-78 (135)
364 PF01155 HypA: Hydrogenase exp 22.2 40 0.00088 23.2 0.7 29 116-148 68-96 (113)
365 cd01666 TGS_DRG_C TGS_DRG_C: 22.2 2.2E+02 0.0048 18.1 5.9 64 2-70 3-74 (75)
366 KOG3896 Dynactin, subunit p62 22.2 40 0.00086 28.3 0.7 25 118-145 27-52 (449)
367 PRK04351 hypothetical protein; 22.0 87 0.0019 22.9 2.4 33 117-152 111-146 (149)
368 PF00684 DnaJ_CXXCXGXG: DnaJ c 22.0 74 0.0016 19.5 1.8 23 117-145 40-63 (66)
369 PF04060 FeS: Putative Fe-S cl 22.0 32 0.00069 18.7 0.1 10 138-147 4-13 (35)
370 PRK12366 replication factor A; 21.9 43 0.00094 30.3 1.0 26 118-147 532-557 (637)
371 PF01282 Ribosomal_S24e: Ribos 21.0 1.7E+02 0.0038 19.0 3.5 25 19-43 11-35 (84)
372 KOG4842 Protein involved in si 21.0 32 0.0007 27.6 0.0 39 9-47 11-49 (278)
373 KOG4146 Ubiquitin-like protein 20.9 1.1E+02 0.0024 20.7 2.6 57 19-76 34-101 (101)
374 COG0484 DnaJ DnaJ-class molecu 20.7 75 0.0016 26.9 2.1 16 15-30 10-25 (371)
375 PF08154 NLE: NLE (NUC135) dom 20.7 2.2E+02 0.0047 17.4 5.7 40 13-52 18-59 (65)
376 COG3357 Predicted transcriptio 20.6 35 0.00076 23.0 0.1 9 141-149 61-69 (97)
377 PF11305 DUF3107: Protein of u 20.5 2.5E+02 0.0054 18.1 5.1 34 1-35 1-34 (74)
378 COG0266 Nei Formamidopyrimidin 20.4 81 0.0018 25.5 2.2 28 117-146 244-273 (273)
379 PF10276 zf-CHCC: Zinc-finger 20.4 1.1E+02 0.0024 17.2 2.1 10 139-148 30-39 (40)
380 PF09723 Zn-ribbon_8: Zinc rib 20.3 1E+02 0.0023 17.2 2.1 27 118-147 5-35 (42)
381 COG2126 RPL37A Ribosomal prote 20.1 46 0.001 20.5 0.6 26 117-147 15-40 (61)
382 cd04482 RPA2_OBF_like RPA2_OBF 20.1 2.7E+02 0.0058 18.2 6.0 26 100-127 66-91 (91)
No 1
>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.7e-49 Score=282.94 Aligned_cols=155 Identities=86% Similarity=1.312 Sum_probs=152.2
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCCcccc
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAKKR 80 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg~~k~ 80 (156)
|+|+|+.+.++++.+++.+++||..+|+.|+..+|||+++|||+|.|++|+|..+|+||+|+..+||+|+++++||.+++
T Consensus 1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg~kkr 80 (156)
T KOG0004|consen 1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGAKKR 80 (156)
T ss_pred CccchhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEecCCcccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCcccccccceeeeeeeeeEEEcCCCeEEEecccCCCCccCCceEEeEeCCCCccCCceeEEEeecCCC
Q 031604 81 KKKTYTKPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMASHFDRHYCGKCGLTYVYQKAGG 155 (156)
Q Consensus 81 ~kk~~~~pk~~k~~kkk~k~~v~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~~~~ 155 (156)
+++.|++|+++++.++++++++++||++|+||+|++++++||++.|++|||||.|++|+|||+|.+|+.++.+.+
T Consensus 81 kkk~~~~pk~~~~~~kk~~l~~~~y~kvd~ngkiq~l~~~~~~~~~~~~v~~a~~~~r~y~gkc~~~~~~~~~~~ 155 (156)
T KOG0004|consen 81 KKKSYTTPKKIKSKHKKVSLAVLKYYKVDENGKVQRLRRECPNPACGAGVFMASHADRHYCGKCLLTYKFKKAGG 155 (156)
T ss_pred cccccccccccCCCccccccCCccceeeccCcchhhhhhhcCCcccccceecccccccccccccceeehhhhccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999988764
No 2
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=99.96 E-value=8e-31 Score=154.66 Aligned_cols=47 Identities=74% Similarity=1.441 Sum_probs=39.4
Q ss_pred eeeeeEEEcCCCeEEEecccCCCCccCCceEEeEeCCCCccCCceeE
Q 031604 101 AVLQFYKVDDSGKVQRLRKECPNAECGAGTFMASHFDRHYCGKCGLT 147 (156)
Q Consensus 101 ~v~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
|+|+||+||+||+|++++++||+++||+|||||.|+||+||||||+|
T Consensus 1 AvlkyYkvd~~Gkv~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 1 AVLKYYKVDENGKVKRLRKECPSPRCGAGVFMAEHKDRHYCGKCGYT 47 (47)
T ss_dssp S----CEEETTTEEEESSEE-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred CcceEEEECCCCcEEEhhhcCCCcccCCceEeeecCCCccCCCcccC
Confidence 68999999999999999999999999999999999999999999997
No 3
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.2e-26 Score=136.59 Aligned_cols=49 Identities=55% Similarity=1.047 Sum_probs=45.2
Q ss_pred eeeeeeeEEEcCCCeEEEecccCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031604 99 KLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMASHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 99 k~~v~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~ 150 (156)
++++++||+|| +++|+++++.|| +||+|||||.|.||++|||||||++.
T Consensus 1 ~~~~~~yY~v~-~~kv~rk~~~CP--rCG~gvfmA~H~dR~~CGkCgyTe~~ 49 (51)
T COG1998 1 KMAVLKYYEVD-DEKVKRKNRFCP--RCGPGVFMADHKDRWACGKCGYTEFK 49 (51)
T ss_pred CccceeEEEEc-CCcEEEccccCC--CCCCcchhhhcCceeEeccccceEee
Confidence 46899999999 567999999999 99999999999999999999999943
No 4
>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=99.88 E-value=3.2e-22 Score=130.60 Aligned_cols=74 Identities=41% Similarity=0.621 Sum_probs=71.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+||. ++++.++|++++||++||++|++.+|+|+++|+|+|+|++|+|+.+|++|+|+++++|+|+++++||
T Consensus 1 mqi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~GG 74 (74)
T cd01793 1 MQLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLGG 74 (74)
T ss_pred CEEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence 8999997 4789999999999999999999999999999999999999999999999999999999999999987
No 5
>PTZ00044 ubiquitin; Provisional
Probab=99.87 E-value=1e-21 Score=128.44 Aligned_cols=76 Identities=50% Similarity=0.822 Sum_probs=74.5
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+||..+|+++.++|++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+++++++|+|+++++||
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~gg 76 (76)
T PTZ00044 1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRGG 76 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEccCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999886
No 6
>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=99.86 E-value=1.5e-21 Score=127.38 Aligned_cols=73 Identities=36% Similarity=0.653 Sum_probs=71.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEe
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~ 73 (156)
|+|+|+..+|+++.++|++++||++||++|++.+|+|+++|+|+|+|++|+|+.+|++|+|+++++|+|++++
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~ 73 (74)
T cd01807 1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRP 73 (74)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999875
No 7
>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=99.86 E-value=2.5e-21 Score=134.02 Aligned_cols=76 Identities=51% Similarity=0.763 Sum_probs=74.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|+.++|+++.++|++++||++||++|++..|+|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+++++||
T Consensus 28 M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l~GG 103 (103)
T cd01802 28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAMRGG 103 (103)
T ss_pred EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEecCCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999987
No 8
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=99.86 E-value=4.2e-21 Score=125.17 Aligned_cols=76 Identities=96% Similarity=1.322 Sum_probs=74.5
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|+..+|+++.++|++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+++++++|+|+++++||
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~gg 76 (76)
T cd01803 1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76 (76)
T ss_pred CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEccCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999987
No 9
>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=99.85 E-value=1.1e-20 Score=123.14 Aligned_cols=76 Identities=55% Similarity=0.965 Sum_probs=74.3
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|++.+|+++.+++++++||++||++|++..|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+|+++++||
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~gg 76 (76)
T cd01806 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALRGG 76 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEccCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999887
No 10
>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=99.84 E-value=8e-21 Score=123.96 Aligned_cols=74 Identities=32% Similarity=0.618 Sum_probs=72.1
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+||++.|+++.++|++++||++||++|++..|+|+++|+|+|+|+.|+|+.+|++|||+++++|+|++++.||
T Consensus 1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~gg 74 (74)
T cd01810 1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLRGG 74 (74)
T ss_pred CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEccCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999886
No 11
>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=99.83 E-value=2.5e-20 Score=122.98 Aligned_cols=74 Identities=36% Similarity=0.634 Sum_probs=70.9
Q ss_pred CEEEEEeCCCCE-EEEE-ecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEec
Q 031604 1 MQIFVKTLTGKT-ITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 1 M~I~Vk~~~g~~-~~l~-V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~ 74 (156)
|+|+|++.+|++ +.++ +++++||++||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||+++++|+|++++.
T Consensus 1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~~ 76 (78)
T cd01797 1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQD 76 (78)
T ss_pred CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence 899999999997 6895 8999999999999999999999999999999999999999999999999999999875
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=99.83 E-value=2.3e-20 Score=123.10 Aligned_cols=75 Identities=25% Similarity=0.491 Sum_probs=72.9
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|++..|+.+.++|++++||++||++|++..++|+++|+|+|.|+.|+|+ +|++|||+++++|+|+..+.||
T Consensus 2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~~~ 76 (78)
T cd01804 2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVEAG 76 (78)
T ss_pred eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecccc
Confidence 89999999999999999999999999999999999999999999999999999 9999999999999999999887
No 13
>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=99.81 E-value=7.8e-20 Score=119.12 Aligned_cols=71 Identities=24% Similarity=0.378 Sum_probs=68.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
|+|+|++..|+.+.++|++++||++||++|++..|+|+++|||+|.|+.|+|+.+|++|||++|++|||..
T Consensus 2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~ 72 (73)
T cd01791 2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY 72 (73)
T ss_pred EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence 78999999999999999999999999999999999999999999999999999999999999999999863
No 14
>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=99.81 E-value=2.7e-19 Score=117.16 Aligned_cols=73 Identities=38% Similarity=0.705 Sum_probs=70.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCC--CCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEe
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gi--p~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~ 73 (156)
|+|+|++.+|+++.+++++++||++||++|++.+|+ |+++|+|+|+|+.|+|+.+|++|||++|++|+++++.
T Consensus 1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~ 75 (77)
T cd01805 1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSK 75 (77)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEec
Confidence 899999999999999999999999999999999999 9999999999999999999999999999999998763
No 15
>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=99.80 E-value=2.2e-19 Score=117.79 Aligned_cols=72 Identities=35% Similarity=0.676 Sum_probs=68.7
Q ss_pred CCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCCccc
Q 031604 8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAKK 79 (156)
Q Consensus 8 ~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg~~k 79 (156)
++|+++.++|++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|+++++|+|+++++||+++
T Consensus 5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~gg~~~ 76 (76)
T cd01800 5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERGGRKK 76 (76)
T ss_pred cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCCCcCC
Confidence 468999999999999999999999999999999999999999999999999999999999999999998753
No 16
>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=99.79 E-value=5.2e-19 Score=114.08 Aligned_cols=72 Identities=44% Similarity=0.704 Sum_probs=69.7
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
|+|+|+.++|+++.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++||++++++|+|+.+
T Consensus 1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~ 72 (72)
T cd01809 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR 72 (72)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999764
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=99.79 E-value=2.9e-19 Score=115.53 Aligned_cols=69 Identities=36% Similarity=0.587 Sum_probs=66.3
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEE
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
+.|+.++|+++.++|++++||++||++|++.+|+|+++|+|+|+|++|+|+.+|++|+|+++++|||++
T Consensus 1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~ 69 (70)
T cd01794 1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV 69 (70)
T ss_pred CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence 357889999999999999999999999999999999999999999999999999999999999999986
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=99.79 E-value=3.1e-19 Score=115.15 Aligned_cols=70 Identities=39% Similarity=0.733 Sum_probs=67.5
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEE
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
|+|+..+|+++.++|++++||++||++|++.+|+|+++|+|+|+|++|+|+.+|++|+|+++++|||+.|
T Consensus 1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~ 70 (70)
T cd01798 1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR 70 (70)
T ss_pred CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999864
No 19
>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=99.78 E-value=8.1e-19 Score=116.15 Aligned_cols=73 Identities=32% Similarity=0.431 Sum_probs=70.3
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeE--eeCCeecCCCCcccccCcCCCCEEEEEEEe
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL--~~~G~~L~d~~tL~~~gi~~~stv~l~~~~ 73 (156)
|+|+|+..+|+++.+++++++||++||++|++..|+|+++|+| +|+|+.|+|+.+|++|||++|++|+|+++.
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~ 77 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQN 77 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEc
Confidence 7899999999999999999999999999999999999999999 899999999999999999999999999873
No 20
>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=99.77 E-value=2.4e-18 Score=111.26 Aligned_cols=71 Identities=34% Similarity=0.489 Sum_probs=67.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
|.|+|++.+|+ ..+++++++||++||++|++..|+|+++|+|+|+|+.|+|+.+|++|||+++++|+|+++
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-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK 71 (71)
T ss_pred CEEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence 68999999987 589999999999999999999999999999999999999999999999999999999874
No 21
>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=99.76 E-value=3.1e-18 Score=109.79 Aligned_cols=68 Identities=56% Similarity=0.962 Sum_probs=65.3
Q ss_pred EeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEe
Q 031604 6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 6 k~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~ 73 (156)
|+++|+.+.++|++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|||.++++|+|++++
T Consensus 1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~ 68 (69)
T PF00240_consen 1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKP 68 (69)
T ss_dssp EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEec
Confidence 56789999999999999999999999999999999999999999999999999999999999999875
No 22
>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]
Probab=99.76 E-value=9.1e-20 Score=124.44 Aligned_cols=78 Identities=96% Similarity=1.290 Sum_probs=75.8
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCCcc
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAK 78 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg~~ 78 (156)
|+++++.+.|+++++++.|++||..+|+.|....|||++.|+|+|+|++|+|..||++|||+..+||+++++++||--
T Consensus 1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~GG~i 78 (128)
T KOG0003|consen 1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGII 78 (128)
T ss_pred CcEEEEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHhcCCC
Confidence 789999999999999999999999999999999999999999999999999999999999999999999999999953
No 23
>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=99.73 E-value=1.1e-17 Score=108.33 Aligned_cols=68 Identities=35% Similarity=0.543 Sum_probs=64.3
Q ss_pred EEEEeC-CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCC-CcccccCcCCCCEEEEE
Q 031604 3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLV 70 (156)
Q Consensus 3 I~Vk~~-~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~-~tL~~~gi~~~stv~l~ 70 (156)
|+|+.. +|+++.++|++++||++||++|++.+|+|+++|+|+|+|++|+|+ .+|++|||+++++|+|.
T Consensus 1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l~ 70 (71)
T cd01796 1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLR 70 (71)
T ss_pred CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEEe
Confidence 578998 899999999999999999999999999999999999999999987 68999999999999874
No 24
>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=99.73 E-value=4.2e-17 Score=109.60 Aligned_cols=76 Identities=18% Similarity=0.467 Sum_probs=74.2
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|++.+|+.+.++|.+++|++.|+++++++.|+|+++|+|+|+|+.|+++.|+++|+++++++|+++++++||
T Consensus 12 i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~GG 87 (87)
T cd01763 12 INLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTGG 87 (87)
T ss_pred EEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEecccC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999999997
No 25
>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=99.72 E-value=3.2e-17 Score=105.51 Aligned_cols=70 Identities=29% Similarity=0.469 Sum_probs=66.7
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
|+|+|+.. |+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+|+.
T Consensus 1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~ 70 (71)
T cd01812 1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE 70 (71)
T ss_pred CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence 68999996 89999999999999999999999999999999999999999999999999999999999863
No 26
>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=99.70 E-value=4.5e-17 Score=107.26 Aligned_cols=71 Identities=25% Similarity=0.282 Sum_probs=63.4
Q ss_pred CEEEEEeCCCCE--EEEEecCCCcHHHHHHHHHHHhC--CCCCceeEeeCCeecCCCCcccccC--cCCCCEEEEEE
Q 031604 1 MQIFVKTLTGKT--ITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYN--IQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~--~~l~V~~~~TV~~LK~~I~~~~g--ip~~~qrL~~~G~~L~d~~tL~~~g--i~~~stv~l~~ 71 (156)
|.|+||+++++. +.+++++++||.+||++|++..+ .|+++|||+|.|+.|.|+.+|++|. +.++.+|||+.
T Consensus 2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~ 78 (79)
T cd01790 2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC 78 (79)
T ss_pred eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence 579999999988 55566899999999999999874 4579999999999999999999996 99999999975
No 27
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=99.70 E-value=1.2e-17 Score=100.73 Aligned_cols=47 Identities=57% Similarity=1.123 Sum_probs=44.1
Q ss_pred eeeeeeeEEEcCCCeEEEecccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 99 KLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 99 k~~v~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
++++++||+|| +++|.++++.|| +||++ ||+.|.+|++||+||+|+.
T Consensus 2 ~~~~~~~y~v~-~~~v~~~~~fCP--~Cg~~-~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 2 KMAKREYYEVD-GGKVKRKNKFCP--RCGSG-FMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred CcceeeeEEEC-CCEEEEccCcCc--CCCcc-hheccCCcEECCCcCCEEe
Confidence 78999999998 569999999999 89999 9999999999999999993
No 28
>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=99.69 E-value=1.5e-16 Score=103.94 Aligned_cols=69 Identities=23% Similarity=0.427 Sum_probs=65.2
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEee---CCeecCCCCcccccCcCCCCEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~---~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
|.|.|+. +|+++.++|++++||++||++|++.+|+|+++|+|+| .|+.|.|+.+|++|+|.+|+.|+|+
T Consensus 1 ~~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lm 72 (74)
T cd01813 1 VPVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMM 72 (74)
T ss_pred CEEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEE
Confidence 6788986 6889999999999999999999999999999999996 8999999999999999999999986
No 29
>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=99.68 E-value=5e-17 Score=99.86 Aligned_cols=70 Identities=54% Similarity=0.911 Sum_probs=67.8
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
|.|.|++++|+.+.++++|+++|+.+|++|++..||||.+|||+|.|+++.|+.+-++|++.-||++|++
T Consensus 1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv 70 (70)
T KOG0005|consen 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV 70 (70)
T ss_pred CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999974
No 30
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=99.64 E-value=8.5e-16 Score=96.31 Aligned_cols=64 Identities=61% Similarity=0.864 Sum_probs=61.3
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKES 65 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~s 65 (156)
|+|+|+..+ ..+.++|++++||++||++|+..+|+|+++|+|+|+|+.|+|+.+|++|||++|+
T Consensus 1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~ 64 (64)
T smart00213 1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQDGS 64 (64)
T ss_pred CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence 899999998 7899999999999999999999999999999999999999999999999998875
No 31
>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=99.61 E-value=1.1e-15 Score=106.07 Aligned_cols=90 Identities=27% Similarity=0.359 Sum_probs=76.3
Q ss_pred EEEEEeCCCCEE-EEEecCCCcHHHHHHHHHHHh-----CCC--CCceeEeeCCeecCCCCcccccC------cCCCCEE
Q 031604 2 QIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDKE-----GIP--PDQQRLIFAGKQLEDGRTLADYN------IQKESTL 67 (156)
Q Consensus 2 ~I~Vk~~~g~~~-~l~V~~~~TV~~LK~~I~~~~-----gip--~~~qrL~~~G~~L~d~~tL~~~g------i~~~stv 67 (156)
.|.+|..+|..+ .+.+++++||++||++|++.+ ++| +++|+|+|.|++|+|+.+|++|+ +....|+
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 577788888654 578999999999999999555 455 99999999999999999999999 6677999
Q ss_pred EEEEEecCCccccccccccCCccc
Q 031604 68 HLVLRLRGGAKKRKKKTYTKPKKI 91 (156)
Q Consensus 68 ~l~~~~~gg~~k~~kk~~~~pk~~ 91 (156)
||++++....++.+|+....|+..
T Consensus 86 Hvvlr~~~~~~~~~k~~~~~~~~~ 109 (113)
T cd01814 86 HVVVQPPLADKKTEKKVDKAPKAV 109 (113)
T ss_pred EEEecCCCCCccccccccCCcccC
Confidence 999999888887777777767654
No 32
>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=99.59 E-value=5.4e-15 Score=122.87 Aligned_cols=72 Identities=31% Similarity=0.618 Sum_probs=69.8
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC---CCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~g---ip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
|+|+||+++|+++.|+|++++||.+||++|+...| +|+++|+|+|+|++|+|+.+|++|+|+++++|++++.
T Consensus 1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~ 75 (378)
T TIGR00601 1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVS 75 (378)
T ss_pred CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEec
Confidence 89999999999999999999999999999999998 9999999999999999999999999999999999875
No 33
>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=99.57 E-value=1.1e-14 Score=95.27 Aligned_cols=64 Identities=30% Similarity=0.372 Sum_probs=58.4
Q ss_pred eCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecC-CCCcccccCcC-CCCEEEEEE
Q 031604 7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQ-KESTLHLVL 71 (156)
Q Consensus 7 ~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~-d~~tL~~~gi~-~~stv~l~~ 71 (156)
...|.++.++|++++||++||++|++.+|+|++.|+| |+|+.|. |+.+|++||++ +|++|+|.+
T Consensus 9 ~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~ 74 (75)
T cd01799 9 QSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI 74 (75)
T ss_pred ccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence 3467899999999999999999999999999999999 9999885 66899999998 889999864
No 34
>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=99.52 E-value=1.5e-14 Score=94.18 Aligned_cols=56 Identities=32% Similarity=0.555 Sum_probs=50.2
Q ss_pred Eec-CCCcHHHHHHHHHHHh--CCC-CCceeEeeCCeecCCCCcccccCcCCCCEEEEEE
Q 031604 16 EVE-SSDTIDNVKAKIQDKE--GIP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 16 ~V~-~~~TV~~LK~~I~~~~--gip-~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
+|+ .++||.+||++|++.. |++ +++|+|+|.|++|+|+.+|++|||+++++|||+.
T Consensus 15 ~~~~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~ 74 (75)
T cd01815 15 DVSPGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR 74 (75)
T ss_pred CcCCccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence 344 4789999999999995 575 8999999999999999999999999999999874
No 35
>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=99.50 E-value=1e-13 Score=87.90 Aligned_cols=67 Identities=67% Similarity=0.992 Sum_probs=63.6
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEE
Q 031604 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
|+..+|+.+.+++++++||.+||++|+..+|+|+++|+|+|+|+.|+|+.+|++|++.++++|++..
T Consensus 2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~ 68 (69)
T cd01769 2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL 68 (69)
T ss_pred eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence 6777899999999999999999999999999999999999999999999999999999999999864
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=99.45 E-value=4e-13 Score=86.69 Aligned_cols=71 Identities=34% Similarity=0.633 Sum_probs=66.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC-CceeEeeCCeecCCCCcccccCcCCCCEEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~-~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
|+|+|++.+|+.+.+.|.++++++.|.+.+++..++|+ +.++|+|+|+.|+++.|++++|++++++|+|.+
T Consensus 1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I 72 (72)
T PF11976_consen 1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII 72 (72)
T ss_dssp EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence 78999999999999999999999999999999999999 999999999999999999999999999999864
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=99.44 E-value=3.2e-13 Score=91.50 Aligned_cols=61 Identities=28% Similarity=0.335 Sum_probs=56.7
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCC-CCcccccCcCCCCEEEEEEE
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED-GRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d-~~tL~~~gi~~~stv~l~~~ 72 (156)
...++|++++||.+||.+|++.+++||++|+|+++|..|.| ..+|++|||.++|+|.|.+.
T Consensus 16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llid 77 (107)
T cd01795 16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKAD 77 (107)
T ss_pred CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEec
Confidence 56789999999999999999999999999999999999975 57999999999999999864
No 38
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=99.43 E-value=2e-13 Score=114.87 Aligned_cols=73 Identities=37% Similarity=0.592 Sum_probs=69.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEec
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~ 74 (156)
++|+||+.++ .+.|.|..+.||.+||+.|+..+++++++++|||.|++|.|+.+|..|||++|.||||+++..
T Consensus 16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~ 88 (493)
T KOG0010|consen 16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQ 88 (493)
T ss_pred eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccC
Confidence 4689999876 899999999999999999999999999999999999999999999999999999999998754
No 39
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=99.33 E-value=3.4e-12 Score=102.82 Aligned_cols=74 Identities=38% Similarity=0.657 Sum_probs=70.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC--CCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEec
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~g--ip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~ 74 (156)
|+|+||++.+++|++++.|++||.++|..|+...| .|++.|+|||+|+.|.|+.++.+|+|.++.-|.|++.-.
T Consensus 1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~ 76 (340)
T KOG0011|consen 1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKD 76 (340)
T ss_pred CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhccccCceEEEEEecC
Confidence 89999999999999999999999999999999999 999999999999999999999999999999998887643
No 40
>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=99.29 E-value=2.4e-11 Score=81.07 Aligned_cols=70 Identities=21% Similarity=0.379 Sum_probs=58.5
Q ss_pred EEEEEeCC-CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe-eCCe-----ec-CCCCcccccCcCCCCEEEEEE
Q 031604 2 QIFVKTLT-GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGK-----QL-EDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 2 ~I~Vk~~~-g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~-----~L-~d~~tL~~~gi~~~stv~l~~ 71 (156)
.|+|.+.. ....+..+++++||++||++|+..+|+||+.|+|. |.++ .| +|+.+|++||+++|++|||+-
T Consensus 3 ~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVvD 80 (84)
T cd01789 3 TVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVID 80 (84)
T ss_pred EEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEEe
Confidence 56676643 33455669999999999999999999999999995 7887 46 577899999999999999864
No 41
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=99.19 E-value=1e-10 Score=78.37 Aligned_cols=70 Identities=27% Similarity=0.544 Sum_probs=57.4
Q ss_pred EEEEEeCCC--CEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeC----C---eec-CCCCcccccCcCCCCEEEEEE
Q 031604 2 QIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA----G---KQL-EDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 2 ~I~Vk~~~g--~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~----G---~~L-~d~~tL~~~gi~~~stv~l~~ 71 (156)
.|+|.+... ...+..+++++||++||++|+..+|+|++.|+|.+. + ..+ +|+.+|++||+++|.+|++.-
T Consensus 3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~D 82 (87)
T PF14560_consen 3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVVD 82 (87)
T ss_dssp EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEEE
T ss_pred EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEEe
Confidence 577877654 488899999999999999999999999999999865 1 123 467899999999999999863
No 42
>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=99.16 E-value=4.3e-10 Score=70.99 Aligned_cols=73 Identities=84% Similarity=1.145 Sum_probs=68.4
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecC
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG 75 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~g 75 (156)
+++....|+.+.+++.+..+|..+|.+|+...++|++.|++.+.|+.|+|+.+|.+|+|..++++++..++.+
T Consensus 2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~~ 74 (75)
T KOG0001|consen 2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLRG 74 (75)
T ss_pred EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecCC
Confidence 5677788999999999999999999999999999999999999999999999999999999999999987753
No 43
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=99.15 E-value=4.4e-10 Score=78.68 Aligned_cols=78 Identities=28% Similarity=0.464 Sum_probs=58.3
Q ss_pred EEEEEeCCCC-EEEEEecCCCcHHHHHHHHHHHhC-------CCCCceeEeeCCeecCCCCcccccCcCCCC------EE
Q 031604 2 QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEG-------IPPDQQRLIFAGKQLEDGRTLADYNIQKES------TL 67 (156)
Q Consensus 2 ~I~Vk~~~g~-~~~l~V~~~~TV~~LK~~I~~~~g-------ip~~~qrL~~~G~~L~d~~tL~~~gi~~~s------tv 67 (156)
.|.++..+|. +..+.+++++||++||+.|...+- ..++.+||+|.|+.|+|+.+|+++.+..+. ++
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 5667777998 788999999999999999987652 234679999999999999999999887655 68
Q ss_pred EEEEEecCCccc
Q 031604 68 HLVLRLRGGAKK 79 (156)
Q Consensus 68 ~l~~~~~gg~~k 79 (156)
||++++......
T Consensus 84 Hlvvrp~~~~~~ 95 (111)
T PF13881_consen 84 HLVVRPNAPEPN 95 (111)
T ss_dssp EEEE-SSSSSSS
T ss_pred EEEecCCCCCcc
Confidence 888887655443
No 44
>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=99.15 E-value=2.1e-10 Score=79.61 Aligned_cols=77 Identities=30% Similarity=0.437 Sum_probs=65.7
Q ss_pred CEEEEEeCCCC-EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCc-------CCCCEEEEEEE
Q 031604 1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-------QKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~-~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi-------~~~stv~l~~~ 72 (156)
|.+|++....+ ++.+++.++.||.+||+.|+.....||++|+|+-.+..|+|+.+|+|||+ ++.++|-|.+|
T Consensus 1 MdvFlmIrR~KTTiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r 80 (119)
T cd01788 1 MDVFLMIRRHKTTIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFR 80 (119)
T ss_pred CceEEEEEecceEEEeecCCcccHHHHHHHHHHHhcCChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEEe
Confidence 56777665444 68889999999999999999999999999999977789999999999999 66888888887
Q ss_pred ecCCc
Q 031604 73 LRGGA 77 (156)
Q Consensus 73 ~~gg~ 77 (156)
...|.
T Consensus 81 ~~d~~ 85 (119)
T cd01788 81 SSDDT 85 (119)
T ss_pred cCCCC
Confidence 54343
No 45
>PLN02560 enoyl-CoA reductase
Probab=99.13 E-value=2e-10 Score=93.45 Aligned_cols=74 Identities=31% Similarity=0.529 Sum_probs=63.9
Q ss_pred CEEEEEeCCCCEE---EEEecCCCcHHHHHHHHHHHhCC-CCCceeEeeC---C----eecCCCCcccccCcCCCCEEEE
Q 031604 1 MQIFVKTLTGKTI---TLEVESSDTIDNVKAKIQDKEGI-PPDQQRLIFA---G----KQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 1 M~I~Vk~~~g~~~---~l~V~~~~TV~~LK~~I~~~~gi-p~~~qrL~~~---G----~~L~d~~tL~~~gi~~~stv~l 69 (156)
|+|+|+..+|+.+ ++++++++||+|||++|++..++ ++++|||.+. | ..|+|+.+|+++|++++++|++
T Consensus 1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~ 80 (308)
T PLN02560 1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF 80 (308)
T ss_pred CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence 8999998888886 79999999999999999999986 8999999973 3 3789999999999999998764
Q ss_pred EEEecCC
Q 031604 70 VLRLRGG 76 (156)
Q Consensus 70 ~~~~~gg 76 (156)
+.+|-
T Consensus 81 --kDLGp 85 (308)
T PLN02560 81 --KDLGP 85 (308)
T ss_pred --EeCCC
Confidence 55543
No 46
>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=98.94 E-value=3.8e-09 Score=69.17 Aligned_cols=68 Identities=26% Similarity=0.318 Sum_probs=54.4
Q ss_pred EEEEEeCC-CCEEEEEe-cCCCcHHHHHHHHHHHhC-CCCCceeEe--eCCeecCCCCcccccCcCCCCEEEE
Q 031604 2 QIFVKTLT-GKTITLEV-ESSDTIDNVKAKIQDKEG-IPPDQQRLI--FAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~-g~~~~l~V-~~~~TV~~LK~~I~~~~g-ip~~~qrL~--~~G~~L~d~~tL~~~gi~~~stv~l 69 (156)
+|.++..+ .....+++ +++.||++||..|+...+ +++++|+|. +.|+.|.|+.+|.++|+.+|++|++
T Consensus 2 ~i~~~~~~~k~~~~~~~~~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv 74 (77)
T cd01801 2 EILDAKRSDKPIGKLKVSSGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV 74 (77)
T ss_pred eeeccccCcCceeecccCCCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence 46666554 33333444 588999999999999876 578999885 8899999999999999999999876
No 47
>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]
Probab=98.88 E-value=3e-09 Score=96.10 Aligned_cols=73 Identities=34% Similarity=0.592 Sum_probs=69.1
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecC
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG 75 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~g 75 (156)
.|+||+++.++.++.|...+||.+||.+|.+..+|+.+.|||||.|+.|.|++++.+|+| +|-+|||+-|+.-
T Consensus 4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlverppp 76 (1143)
T KOG4248|consen 4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVERPPP 76 (1143)
T ss_pred ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC-CCeEEEeeccCCC
Confidence 478999999999999999999999999999999999999999999999999999999999 8999999987543
No 48
>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=98.87 E-value=6.8e-09 Score=68.63 Aligned_cols=69 Identities=29% Similarity=0.434 Sum_probs=43.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCC---eec--CCCCcccccCcCCCCEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQL--EDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G---~~L--~d~~tL~~~gi~~~stv~l~ 70 (156)
|-|.|++.+| ++.|++++++|+.+|+++|++..++|.+.|.|..+. ..| .++.+|+++||+.|+.|+|.
T Consensus 5 milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~ 78 (80)
T PF11543_consen 5 MILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK 78 (80)
T ss_dssp -EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred EEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence 5678888765 678899999999999999999999999999886432 244 46789999999999999874
No 49
>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=98.75 E-value=7.7e-08 Score=57.67 Aligned_cols=67 Identities=46% Similarity=0.666 Sum_probs=60.3
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEE
Q 031604 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
|+..++....+.+++++|+.+|++.|....|++++.+.|+++|..+.+...+.++++.++++|++..
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 68 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP 68 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence 3444678889999999999999999999999999999999999999999888899999999998863
No 50
>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=98.55 E-value=5.3e-07 Score=58.13 Aligned_cols=70 Identities=29% Similarity=0.407 Sum_probs=60.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeC---C--eecCCCCcccccCcCCCCEEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA---G--KQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~---G--~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
++|+|+-.....+.+.|+|..+|..||++|....+++- .|||.|. | ..|.+..+|++|||-....|-|+-
T Consensus 1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lle 75 (80)
T cd01811 1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLE 75 (80)
T ss_pred CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEeecCCcccccccccccHhhhcceeccEEEEEe
Confidence 68999998888999999999999999999999999976 8999873 3 367899999999998776666653
No 51
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=98.45 E-value=2.3e-06 Score=58.20 Aligned_cols=76 Identities=17% Similarity=0.427 Sum_probs=69.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCCc
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGA 77 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg~ 77 (156)
+|.|..-++....+.|..++++..|+..-+.+.|++.+.+|++|+|+.+.+..|-++++.++++.|.++....||.
T Consensus 22 ~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q~gG~ 97 (99)
T KOG1769|consen 22 NLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQTGGF 97 (99)
T ss_pred EEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeecccCC
Confidence 4556665667889999999999999999999999999999999999999999999999999999999999888875
No 52
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.43 E-value=1.2e-07 Score=59.39 Aligned_cols=69 Identities=26% Similarity=0.398 Sum_probs=62.0
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
++.+...-|+...+.+.+++||.++|..|++++|..++.+.|--.+..+.|+-+|++|.|.+|..+.|.
T Consensus 3 ev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely 71 (73)
T KOG3493|consen 3 EVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY 71 (73)
T ss_pred eehhhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence 566666678999999999999999999999999999999888877888999999999999999888775
No 53
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=98.39 E-value=6.8e-07 Score=72.32 Aligned_cols=73 Identities=32% Similarity=0.604 Sum_probs=61.7
Q ss_pred CEEEEEeC---CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEE-EEe
Q 031604 1 MQIFVKTL---TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV-LRL 73 (156)
Q Consensus 1 M~I~Vk~~---~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~-~~~ 73 (156)
|.++|+.. ....++|+|+.+.+|.+||+.++.+.|+|+++.+++|.|+.|.++.++..+.+.--+.+|++ +|+
T Consensus 1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~lRP 77 (446)
T KOG0006|consen 1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIMLLRP 77 (446)
T ss_pred CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCceeecccccccchhhhhccCc
Confidence 67777754 22358889999999999999999999999999999999999999999997777666777766 554
No 54
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=98.28 E-value=7.2e-06 Score=60.73 Aligned_cols=78 Identities=29% Similarity=0.480 Sum_probs=60.4
Q ss_pred CEEEEEeCCC----CEEEEEecCCCcHHHHHHHHHHHhCCCCCce-eEee-CCeec--CCCCcccccCcCC----CCEEE
Q 031604 1 MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLIF-AGKQL--EDGRTLADYNIQK----ESTLH 68 (156)
Q Consensus 1 M~I~Vk~~~g----~~~~l~V~~~~TV~~LK~~I~~~~gip~~~q-rL~~-~G~~L--~d~~tL~~~gi~~----~stv~ 68 (156)
|+|+|.+++| .++.+.+++++||++|+..|.+..++++..| .|.+ .+..| .++..++++.-.+ -.+|+
T Consensus 1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~~~~~l~ 80 (162)
T PF13019_consen 1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDSDFITLR 80 (162)
T ss_pred CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhccCcCCCCceEEE
Confidence 7899999999 5888999999999999999999999998874 3443 34444 4555566654333 24688
Q ss_pred EEEEecCCcc
Q 031604 69 LVLRLRGGAK 78 (156)
Q Consensus 69 l~~~~~gg~~ 78 (156)
|.+++.||+-
T Consensus 81 l~~rl~GGKG 90 (162)
T PF13019_consen 81 LSLRLRGGKG 90 (162)
T ss_pred EEEeccCCCc
Confidence 9999999875
No 55
>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.27 E-value=2.3e-06 Score=72.34 Aligned_cols=71 Identities=24% Similarity=0.414 Sum_probs=64.1
Q ss_pred EEEEeCCCCEEEEE-ecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEec
Q 031604 3 IFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 3 I~Vk~~~g~~~~l~-V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~ 74 (156)
|.|+. .|+.+.++ ++.++|+..||+++...+|+||++|++++.|..+.|+..+..++|+++.+|+++-...
T Consensus 6 v~VKW-~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e 77 (473)
T KOG1872|consen 6 VIVKW-GGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAE 77 (473)
T ss_pred Eeeee-cCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccccccccccCCCCEEEeecccc
Confidence 56664 68889887 9999999999999999999999999999999999999889999999999999875543
No 56
>KOG4495 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription]
Probab=98.20 E-value=2.1e-06 Score=57.96 Aligned_cols=62 Identities=29% Similarity=0.435 Sum_probs=51.2
Q ss_pred CEEEEEeCCC-CEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEee-CC-eecCCCCcccccCcC
Q 031604 1 MQIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AG-KQLEDGRTLADYNIQ 62 (156)
Q Consensus 1 M~I~Vk~~~g-~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~-~G-~~L~d~~tL~~~gi~ 62 (156)
|.++++.... .++.++..++.||.+||.+++....-|++.|+|+. .- +.|+|..+|+|+|..
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 MDVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTEQLLDDGKTLGDCGFT 65 (110)
T ss_pred CceeeeeeecceeEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHHHHhhccchhhhcccc
Confidence 4556554433 46888999999999999999999999999999986 33 578999999999763
No 57
>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=97.95 E-value=0.00013 Score=47.81 Aligned_cols=69 Identities=23% Similarity=0.347 Sum_probs=58.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCc-eeEe--eCCeecCCC--CcccccCcCCCCEEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLI--FAGKQLEDG--RTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~-qrL~--~~G~~L~d~--~tL~~~gi~~~stv~l~ 70 (156)
.|.||.++|+.+...+.+++||.+|.+.|......+... ..|+ |-.+.|.++ .+|++.|+.++++|+|.
T Consensus 8 ~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v~ 81 (82)
T PF00789_consen 8 RIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIVE 81 (82)
T ss_dssp EEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEEE
T ss_pred EEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEEE
Confidence 588999999999999999999999999999887766654 6775 667777644 69999999999998873
No 58
>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=97.95 E-value=4e-05 Score=50.21 Aligned_cols=68 Identities=24% Similarity=0.405 Sum_probs=49.2
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCC------ceeEe-eCCeecCCCCcccccCcCCCCEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD------QQRLI-FAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~------~qrL~-~~G~~L~d~~tL~~~gi~~~stv~l 69 (156)
.|+|...+++.+.+.++.+.+|.+|...|.+..+.+.. ...|. -+|..|+++.+|+++||.+|+.+.|
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 46666645688999999999999999999998876442 24555 6789999999999999999999986
No 59
>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=97.88 E-value=7.2e-05 Score=47.45 Aligned_cols=63 Identities=19% Similarity=0.252 Sum_probs=46.9
Q ss_pred eCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEE
Q 031604 7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 7 ~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l 69 (156)
..+++.+.+.|.|++++.++-++..+.+++++++-.|.|+++.|+-+.++.-.|+.+|+.+.|
T Consensus 3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlslp~R~snL~n~akLeL 65 (65)
T PF11470_consen 3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSLPFRLSNLPNNAKLEL 65 (65)
T ss_dssp -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-BHHHH---SS-EEEE
T ss_pred ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEeccccceeecCCCCCCEEeC
Confidence 357889999999999999999999999999999999999999999999999999999999875
No 60
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=97.77 E-value=0.00024 Score=46.59 Aligned_cols=68 Identities=22% Similarity=0.260 Sum_probs=56.3
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--eCCeecCC---CCcccccCcCCCCEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d---~~tL~~~gi~~~stv~l 69 (156)
+|.||.++|+.+...+..++||++|.+.|....+.......|+ |-.+.+.+ +.+|.+.|+.++++|.|
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 RLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL 78 (80)
T ss_pred EEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence 5889999999999999999999999999976666666667776 66677753 47999999988888876
No 61
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=97.67 E-value=5.8e-05 Score=50.50 Aligned_cols=75 Identities=19% Similarity=0.387 Sum_probs=66.9
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCCc
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGA 77 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg~ 77 (156)
+.|-..++.++.+.|..+++...|....+.+.|-..++.|++|+|+.++.+++-++++.++++.|.++....||.
T Consensus 27 Lkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~eQvGG~ 101 (103)
T COG5227 27 LKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVTEQVGGA 101 (103)
T ss_pred eEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCCChhhcCCccchHHHHHHHHhcCc
Confidence 445455678899999999999999999999999999999999999999999999999999999998877777775
No 62
>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=97.63 E-value=0.00016 Score=49.45 Aligned_cols=58 Identities=21% Similarity=0.352 Sum_probs=45.2
Q ss_pred EEEEEeCCC-CEEEEEec--CCCcHHHHHHHHHHHhC--CCCCceeEeeCCeecCCCCccccc
Q 031604 2 QIFVKTLTG-KTITLEVE--SSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADY 59 (156)
Q Consensus 2 ~I~Vk~~~g-~~~~l~V~--~~~TV~~LK~~I~~~~g--ip~~~qrL~~~G~~L~d~~tL~~~ 59 (156)
.|+||..++ ....++++ .+.||..||+.|.+... ..-.++||+|+|+.|.|+..|+..
T Consensus 2 ~l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~~~ 64 (97)
T PF10302_consen 2 YLTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSE 64 (97)
T ss_pred eEEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhh
Confidence 467777653 34677777 78999999999999873 333568999999999999877654
No 63
>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=97.62 E-value=0.00064 Score=44.58 Aligned_cols=68 Identities=16% Similarity=0.320 Sum_probs=55.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--eCCeecCC---CCcccccCcCCCCEEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d---~~tL~~~gi~~~stv~l~ 70 (156)
+|.||.++|+.+...++.++||++|.+.|....+.+ ....|+ |-.+.+.+ +.+|.+.|+.+.++|.|.
T Consensus 6 ~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~~-~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v~ 78 (79)
T cd01772 6 RIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNG-GPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIVT 78 (79)
T ss_pred EEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCCC-CCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEEe
Confidence 578999999999999999999999999998765433 445665 67788853 479999999999888763
No 64
>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=97.42 E-value=0.0017 Score=42.13 Aligned_cols=66 Identities=17% Similarity=0.303 Sum_probs=51.6
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--eCCeecCC---CCcccccCcCCCCEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d---~~tL~~~gi~~~stv~l 69 (156)
.|.||.++|+.+...++.++||++|.+-|.....- .....|+ |-.+.+.+ +.+|.+.|+.+ +++.+
T Consensus 4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~~-s~~~~ 74 (77)
T cd01767 4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMTSFPRRVLTDLDYELTLQEAGLVN-EVVFQ 74 (77)
T ss_pred EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEeCCCCccCCCCCccCcHHHcCCcc-ceEEE
Confidence 57899999999999999999999999999876433 4456666 56677754 68999999984 45444
No 65
>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=97.39 E-value=0.0021 Score=42.54 Aligned_cols=69 Identities=16% Similarity=0.316 Sum_probs=58.8
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--eCCeecC---CCCcccccCcCCCCEEEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~---d~~tL~~~gi~~~stv~l~~ 71 (156)
+|.||.++|+...-.+..++++++|-..+.. .|.+++...|+ |--+.+. .+.+|.+.|+.+.++|.|.-
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-KGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE 80 (82)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEec
Confidence 5889999999999999999999999999988 57788888887 6666663 34799999999999998753
No 66
>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=97.34 E-value=0.0019 Score=42.39 Aligned_cols=65 Identities=23% Similarity=0.326 Sum_probs=51.6
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCC-CCceeEe--eCCeecCC-CCcccccCcCCCCEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP-PDQQRLI--FAGKQLED-GRTLADYNIQKESTL 67 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip-~~~qrL~--~~G~~L~d-~~tL~~~gi~~~stv 67 (156)
+|.||..+|+.+...++.++||++|.+.|....+-+ .....|. |-.+.|.| +.||.|.|+.+ +.|
T Consensus 6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~-s~v 74 (79)
T cd01770 6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPVKELSDESLTLKEANLLN-AVI 74 (79)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCCcccCCCCCcHHHCCCcC-cEE
Confidence 588999999999999999999999999999865432 2456665 67777754 68999999985 444
No 67
>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=97.21 E-value=0.0037 Score=41.13 Aligned_cols=68 Identities=21% Similarity=0.329 Sum_probs=57.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--eCCeecC---CCCcccccCcCCCCEEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~---d~~tL~~~gi~~~stv~l~ 70 (156)
+|.||.++|+...-.+..++++++|-.-|... |.++...+|+ |--+.+. .+.+|.+.|+.+..+|.|-
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-GYPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLILE 78 (80)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-CCCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEEE
Confidence 68899999999999999999999999999875 7777788887 6666663 3579999999999888774
No 68
>KOG0013 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.21 E-value=0.00076 Score=51.87 Aligned_cols=64 Identities=28% Similarity=0.428 Sum_probs=57.5
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEE
Q 031604 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
.++.+.+.+..-+|+.+++.++.+..|+.+-.|+++|+|..|-|...|.+++|+.|+...|.+.
T Consensus 155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqvi 218 (231)
T KOG0013|consen 155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQVI 218 (231)
T ss_pred hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCCCEEEEEEE
Confidence 3567888999999999999999999999999999999999999999999999999977665544
No 69
>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=97.16 E-value=0.0047 Score=41.10 Aligned_cols=68 Identities=12% Similarity=0.183 Sum_probs=54.8
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEee--CCeecC--------CCCcccccCcCCCCEEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLE--------DGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~--~G~~L~--------d~~tL~~~gi~~~stv~l~ 70 (156)
+|.||.++|+.+.-.+..++||++|.+-|... +..++...|+. --+.+. .+.||.+.||.+.++|.|.
T Consensus 6 ~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~~-~~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L~V~ 83 (85)
T cd01774 6 KIVFKLPNGTRVERRFLFTQSLRVIHDFLFSL-KETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLFVQ 83 (85)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhC-CCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEEEe
Confidence 68899999999999999999999999999654 45567788874 346775 3579999999988877663
No 70
>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]
Probab=97.16 E-value=0.00094 Score=52.70 Aligned_cols=75 Identities=28% Similarity=0.369 Sum_probs=55.3
Q ss_pred CEEEEEeCCCC-EEE-EEecCCCcHHHHHHHHHHHh-CCCCCceeE----eeCCeecCCCCcccccCcCCCCEEEEEEEe
Q 031604 1 MQIFVKTLTGK-TIT-LEVESSDTIDNVKAKIQDKE-GIPPDQQRL----IFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 1 M~I~Vk~~~g~-~~~-l~V~~~~TV~~LK~~I~~~~-gip~~~qrL----~~~G~~L~d~~tL~~~gi~~~stv~l~~~~ 73 (156)
|.|++.+.++. ... ...+...|+.|++..|.... .+.+..+|+ .-.|++|-|+.+|++|++.++++|. ++.
T Consensus 1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~--vKD 78 (297)
T KOG1639|consen 1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIY--VKD 78 (297)
T ss_pred CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhccCccchhheeeccCCCccccchhHHHHhccCCCCEEE--Eec
Confidence 78999887663 333 56788999999998887654 566644443 3578999999999999998886665 455
Q ss_pred cCCc
Q 031604 74 RGGA 77 (156)
Q Consensus 74 ~gg~ 77 (156)
+|-.
T Consensus 79 LGpQ 82 (297)
T KOG1639|consen 79 LGPQ 82 (297)
T ss_pred cCCc
Confidence 5543
No 71
>COG5417 Uncharacterized small protein [Function unknown]
Probab=96.74 E-value=0.016 Score=37.54 Aligned_cols=64 Identities=19% Similarity=0.264 Sum_probs=53.2
Q ss_pred EeCCCCEEEEEecCCCcHHHHHHHHHHHhCCC--C---CceeEeeCCeecCCCCcccccCcCCCCEEEE
Q 031604 6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIP--P---DQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 6 k~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip--~---~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l 69 (156)
+..+|.++.+.++.-.++..|-..+.+...+. + ..+++.-.++.|.++..|.+|+|.+|+.+.+
T Consensus 12 t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei 80 (81)
T COG5417 12 TNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI 80 (81)
T ss_pred EecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence 55678999999999999999988877665433 2 3468888999999999999999999998875
No 72
>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]
Probab=96.58 E-value=0.0077 Score=46.35 Aligned_cols=71 Identities=15% Similarity=0.297 Sum_probs=54.6
Q ss_pred EEEEEeCCCC-EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe-eCC-----eecC-CCCcccccCcCCCCEEEEEEE
Q 031604 2 QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAG-----KQLE-DGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 2 ~I~Vk~~~g~-~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G-----~~L~-d~~tL~~~gi~~~stv~l~~~ 72 (156)
.|+|.+.... ......++++||++||.+++..+|.+++.+.|. |.| ..|+ ++..|..|...+|-.||++-.
T Consensus 3 ~v~Iss~~~~~~~Ekr~~~~ltl~q~K~KLe~~~G~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihviD~ 81 (234)
T KOG3206|consen 3 RVVISSSLNDFRTEKRLSNSLTLAQFKDKLELLTGTEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVIDS 81 (234)
T ss_pred EEEEecccccchhhhhcCCcCcHHHHHhhhhhhhCCCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEEec
Confidence 4556543222 244578899999999999999999999999886 655 2455 457899999999999998743
No 73
>PRK06437 hypothetical protein; Provisional
Probab=96.57 E-value=0.029 Score=35.56 Aligned_cols=63 Identities=19% Similarity=0.383 Sum_probs=46.6
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+-..++...++++...||++|-++ .+++++..-+..+|..+.. +.-+++|+.|.++--..||
T Consensus 5 ~~v~g~~~~~~~i~~~~tv~dLL~~----Lgi~~~~vaV~vNg~iv~~-----~~~L~dgD~Veiv~~V~GG 67 (67)
T PRK06437 5 IRVKGHINKTIEIDHELTVNDIIKD----LGLDEEEYVVIVNGSPVLE-----DHNVKKEDDVLILEVFSGG 67 (67)
T ss_pred EEecCCcceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCEECCC-----ceEcCCCCEEEEEecccCC
Confidence 3333456688888999999998866 4888888888899999974 4455679999876444443
No 74
>PF15044 CLU_N: Mitochondrial function, CLU-N-term
Probab=96.24 E-value=0.0085 Score=39.05 Aligned_cols=57 Identities=23% Similarity=0.312 Sum_probs=45.6
Q ss_pred ecCCCcHHHHHHHHHHHhC-CCCCceeEeeCCeecCCCCccccc-CcCCCCEEEEEEEe
Q 031604 17 VESSDTIDNVKAKIQDKEG-IPPDQQRLIFAGKQLEDGRTLADY-NIQKESTLHLVLRL 73 (156)
Q Consensus 17 V~~~~TV~~LK~~I~~~~g-ip~~~qrL~~~G~~L~d~~tL~~~-gi~~~stv~l~~~~ 73 (156)
|+++++|.+|++.+..... ..-....|.++|..|++...|+++ |+.++++|.|+..+
T Consensus 1 v~~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lve~p 59 (76)
T PF15044_consen 1 VSPTDTVQDVRQVLAESPETCYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELVEEP 59 (76)
T ss_pred CChhhHHHHHHHHHHhCccccceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEEecC
Confidence 5789999999999987654 233567888999999988888887 57889999987543
No 75
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=96.14 E-value=0.053 Score=33.86 Aligned_cols=65 Identities=18% Similarity=0.391 Sum_probs=44.2
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+| +|+.+.+ + ..||.+|.+.+ +++++...+..+++.+..+ ..++.-+++|+.|.++-...||
T Consensus 1 m~i~~---Ng~~~~~--~-~~tl~~Ll~~l----~~~~~~vavavN~~iv~~~-~~~~~~L~dgD~Ieiv~~V~GG 65 (65)
T PRK06488 1 MKLFV---NGETLQT--E-ATTLALLLAEL----DYEGNWLATAVNGELVHKE-ARAQFVLHEGDRIEILSPMQGG 65 (65)
T ss_pred CEEEE---CCeEEEc--C-cCcHHHHHHHc----CCCCCeEEEEECCEEcCHH-HcCccccCCCCEEEEEEeccCC
Confidence 66766 4666666 3 46899998765 5666666677899888632 2345567789999986555554
No 76
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=96.13 E-value=0.062 Score=34.21 Aligned_cols=56 Identities=13% Similarity=0.238 Sum_probs=42.1
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
...+++++..||.+|-+++ ++++....+..+|+.+.. +.-+++|+.|.+.--..||
T Consensus 15 ~~~~~~~~~~tv~~ll~~l----~~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii~~V~GG 70 (70)
T PRK08364 15 EKEIEWRKGMKVADILRAV----GFNTESAIAKVNGKVALE-----DDPVKDGDYVEVIPVVSGG 70 (70)
T ss_pred ceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECCC-----CcCcCCCCEEEEEccccCC
Confidence 5678888999999998776 677777777899999864 3445679999886544444
No 77
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=96.12 E-value=0.027 Score=36.74 Aligned_cols=71 Identities=18% Similarity=0.285 Sum_probs=47.6
Q ss_pred CEEEEEeCC------C-CEEEEEecCCCcHHHHHHHHHHHh-CCCC--CceeEeeCCeecCCCCcccccCcCCCCEEEEE
Q 031604 1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKE-GIPP--DQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~~------g-~~~~l~V~~~~TV~~LK~~I~~~~-gip~--~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
|+|.|+... | ....++++...||++|.+.+.... ++.. ....+..+++...++. -+++|++|.+.
T Consensus 2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~~v~~~~-----~l~dgDeVai~ 76 (82)
T PLN02799 2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYTTESA-----ALKDGDELAII 76 (82)
T ss_pred eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEcCCCc-----CcCCCCEEEEe
Confidence 678887653 4 467788888999999999997664 1111 1124567888765443 45679999886
Q ss_pred EEecCC
Q 031604 71 LRLRGG 76 (156)
Q Consensus 71 ~~~~gg 76 (156)
-...||
T Consensus 77 PpvsGG 82 (82)
T PLN02799 77 PPISGG 82 (82)
T ss_pred CCCCCC
Confidence 555554
No 78
>KOG4583 consensus Membrane-associated ER protein involved in stress response (contains ubiquitin-like domain) [Posttranslational modification, protein turnover, chaperones]
Probab=96.08 E-value=0.0029 Score=51.91 Aligned_cols=60 Identities=23% Similarity=0.398 Sum_probs=47.1
Q ss_pred EEEEEeCCCC--EEEEEecCCCcHHHHHHHHHHHhCC-C-CCceeEeeCCeecCCCCcccccCc
Q 031604 2 QIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEGI-P-PDQQRLIFAGKQLEDGRTLADYNI 61 (156)
Q Consensus 2 ~I~Vk~~~g~--~~~l~V~~~~TV~~LK~~I~~~~gi-p-~~~qrL~~~G~~L~d~~tL~~~gi 61 (156)
.++|++.+.+ ...|..+..+||++||..++...-- | ..+|||+|.|+.|.|+..|.|.-+
T Consensus 11 ~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~qcl~d~lr 74 (391)
T KOG4583|consen 11 TLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQCLTDWLR 74 (391)
T ss_pred EEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccchhHHHHHH
Confidence 4677887765 4566777889999999999887632 2 257999999999999998888754
No 79
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=95.93 E-value=0.079 Score=34.03 Aligned_cols=62 Identities=24% Similarity=0.337 Sum_probs=47.1
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC-CceeEee----CC--eecCCCCcccccCcCCCCE
Q 031604 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIF----AG--KQLEDGRTLADYNIQKEST 66 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~-~~qrL~~----~G--~~L~d~~tL~~~gi~~~st 66 (156)
|+.++|....++|++++|+.+|-+.|....++.. +-.-|.+ +| .-|+.+.+|.+........
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~~~~~ 69 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKKNNPP 69 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBTSSSS
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCCCCCC
Confidence 5778999999999999999999999999999875 3356666 22 2467778888887663333
No 80
>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=95.92 E-value=0.034 Score=37.13 Aligned_cols=44 Identities=14% Similarity=0.278 Sum_probs=38.0
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC---CceeEee
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP---DQQRLIF 45 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~---~~qrL~~ 45 (156)
.+.++.+.|+++.+.+.|++++.+|++.|+++.|+.. +...|.|
T Consensus 2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Y 48 (86)
T cd06409 2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSY 48 (86)
T ss_pred cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEE
Confidence 3567888999999999999999999999999999886 3556666
No 81
>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=95.82 E-value=0.054 Score=34.77 Aligned_cols=60 Identities=13% Similarity=0.228 Sum_probs=44.5
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCC----CCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGI----PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gi----p~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
...++++...||.+|.+.+....+- ......+..+|+.... +.-|.+|+.|.++-...||
T Consensus 17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~~-----~~~l~~gD~v~i~ppv~GG 80 (80)
T cd00754 17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVRL-----DTPLKDGDEVAIIPPVSGG 80 (80)
T ss_pred eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcCC-----CcccCCCCEEEEeCCCCCC
Confidence 4677888889999999999887532 2345567789988873 3456789999987666665
No 82
>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=95.73 E-value=0.0027 Score=51.60 Aligned_cols=77 Identities=19% Similarity=0.434 Sum_probs=0.0
Q ss_pred EEEEEeCCCCEEEEEec---C--CCcHHHHHHHHHH----------HhCCCCCcee-----EeeCCeecCCCCcccccCc
Q 031604 2 QIFVKTLTGKTITLEVE---S--SDTIDNVKAKIQD----------KEGIPPDQQR-----LIFAGKQLEDGRTLADYNI 61 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~---~--~~TV~~LK~~I~~----------~~gip~~~qr-----L~~~G~~L~d~~tL~~~gi 61 (156)
.|+++++....+.+.++ + +.||.+||..+++ ..++|.+.++ |+|+-+++.|..+|.+..-
T Consensus 80 tV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~vp~dKik~~~~~lL~~kkPv~~~ktl~e~l~ 159 (309)
T PF12754_consen 80 TVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETRVPLDKIKNFRCRLLYKKKPVGDSKTLAEVLA 159 (309)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred EEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhcccccccccccCCHHHhhhhhhhheecCccCCCcCcHHHHHh
Confidence 45566665554444322 3 6899999999999 8899999888 9999999988888887754
Q ss_pred C-------CCCEEEEEEEecCCcc
Q 031604 62 Q-------KESTLHLVLRLRGGAK 78 (156)
Q Consensus 62 ~-------~~stv~l~~~~~gg~~ 78 (156)
. .+.+|.+.+...||..
T Consensus 160 ~~~~~l~~~~~~vE~gvMVlGGa~ 183 (309)
T PF12754_consen 160 DSESRLLSGGKEVEFGVMVLGGAA 183 (309)
T ss_dssp ------------------------
T ss_pred cccchhccCCceEEEEEEEECCcc
Confidence 3 3677888888788875
No 83
>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=95.66 E-value=0.056 Score=35.58 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=35.2
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCee
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ 49 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~ 49 (156)
++.|.|++..+.++|.++|.++..+|++...|.|....
T Consensus 12 tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~ 49 (80)
T cd06406 12 TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEA 49 (80)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCC
Confidence 88999999999999999999999999999999997653
No 84
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=95.51 E-value=0.13 Score=34.49 Aligned_cols=65 Identities=20% Similarity=0.251 Sum_probs=46.1
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEee--C--C-eecC-CCCcccccCcCCCCEEEEEEEecCC
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--A--G-KQLE-DGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~--~--G-~~L~-d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
..++..++..+||..+...+...+.| ..+.||.- . + ..|. .+.||.+.+|.+|.+|.+-.+...|
T Consensus 14 ~~~t~~FSk~DTI~~v~~~~rklf~i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn~DG 84 (88)
T PF14836_consen 14 SVLTKQFSKTDTIGFVEKEMRKLFNI-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERNEDG 84 (88)
T ss_dssp EEEEEEE-TTSBHHHHHHHHHHHCT--TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--TTS
T ss_pred cHhHhhccccChHHHHHHHHHHHhCC-CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeeccCC
Confidence 46778899999999999999999999 66678862 2 2 2564 4579999999999999888876555
No 85
>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=95.41 E-value=0.085 Score=35.05 Aligned_cols=62 Identities=19% Similarity=0.337 Sum_probs=44.8
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEe
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~ 73 (156)
.+...++-.++++.||..++.+.+++.+.-.+...+..|+++.+|.+-+++-..+|.+.+..
T Consensus 4 vI~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQi 65 (88)
T PF11620_consen 4 VIMQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQI 65 (88)
T ss_dssp EEEEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEEE
T ss_pred eEEEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccceecCCccHHHhhccccCEEEEEEEE
Confidence 35567788899999999999999999888888888888999999999999988888887764
No 86
>PHA00626 hypothetical protein
Probab=95.09 E-value=0.014 Score=35.64 Aligned_cols=30 Identities=30% Similarity=0.758 Sum_probs=22.6
Q ss_pred cCCCCccCCceEEe-----EeCCCCccCCceeEEEee
Q 031604 120 ECPNAECGAGTFMA-----SHFDRHYCGKCGLTYVYQ 151 (156)
Q Consensus 120 ~cp~~~c~~g~fma-----~h~~r~~cg~c~~t~~~~ 151 (156)
.|| .||.+-.+- .|.+|+-|-.|||+|+.+
T Consensus 2 ~CP--~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCP--KCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCC--CCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 588 898753332 567999999999998654
No 87
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=94.95 E-value=0.18 Score=31.56 Aligned_cols=65 Identities=20% Similarity=0.316 Sum_probs=44.9
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|. |+.+ ++++..||.+|-+. .++++...-+..++..+..+.- +.+ +++|+.|.+.--..||
T Consensus 1 m~i~vN---G~~~--~~~~~~tl~~ll~~----l~~~~~~vav~~N~~iv~r~~~-~~~-L~~gD~ieIv~~VgGG 65 (65)
T PRK05863 1 MIVVVN---EEQV--EVDEQTTVAALLDS----LGFPEKGIAVAVDWSVLPRSDW-ATK-LRDGARLEVVTAVQGG 65 (65)
T ss_pred CEEEEC---CEEE--EcCCCCcHHHHHHH----cCCCCCcEEEEECCcCcChhHh-hhh-cCCCCEEEEEeeccCC
Confidence 666664 5544 44567888888765 5888888888999998764431 234 7899999986544443
No 88
>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function.
Probab=94.88 E-value=0.19 Score=31.75 Aligned_cols=65 Identities=23% Similarity=0.473 Sum_probs=51.7
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHh---CCCCCceeEe-eCCeecCCCCcccccCcCCCCEEEEEEEe
Q 031604 9 TGKTITLEVESSDTIDNVKAKIQDKE---GIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~---gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stv~l~~~~ 73 (156)
+|+...++.+++..+--..++--+.. |-|++.-.|- -+|..|+-+..++|||+.++.++.|.++-
T Consensus 4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLKA 72 (76)
T PF10790_consen 4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLKA 72 (76)
T ss_pred CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEeec
Confidence 58888899988888777776655444 4677766665 67889999999999999999999887763
No 89
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=94.87 E-value=0.12 Score=43.71 Aligned_cols=71 Identities=23% Similarity=0.267 Sum_probs=53.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHh--CCCCCceeEeeC----Cee--cCCCCcccccCcCCCCEEEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE--GIPPDQQRLIFA----GKQ--LEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~--gip~~~qrL~~~----G~~--L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
|-+.+|+..| ...+++.++++++.|-.+|-..+ +..|+.+.+.-+ |.. +..++++.++|+..|.+++|...
T Consensus 1 Mi~rfRsk~G-~~Rve~qe~d~lg~l~~kll~~~~~n~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~ys 79 (571)
T COG5100 1 MIFRFRSKEG-QRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEYS 79 (571)
T ss_pred CeEEEecCCC-ceeeeccccchhhhhhHHHHhhhccCCCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEec
Confidence 6778887654 57899999999999999887665 455666665532 232 45678899999999999999874
No 90
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=94.64 E-value=0.34 Score=30.09 Aligned_cols=66 Identities=20% Similarity=0.388 Sum_probs=45.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|. |+. ++++...||.+|-.. .++++...-+..+|..+.-+. -.+.-+++|+.|.+.--..||
T Consensus 1 m~i~vN---G~~--~~~~~~~tl~~lL~~----l~~~~~~vav~vNg~iv~r~~-~~~~~l~~gD~vei~~~vgGG 66 (66)
T PRK05659 1 MNIQLN---GEP--RELPDGESVAALLAR----EGLAGRRVAVEVNGEIVPRSQ-HASTALREGDVVEIVHALGGG 66 (66)
T ss_pred CEEEEC---CeE--EEcCCCCCHHHHHHh----cCCCCCeEEEEECCeEeCHHH-cCcccCCCCCEEEEEEEecCC
Confidence 666664 554 466677898888765 578888888889998876332 223346789999986555444
No 91
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=94.59 E-value=0.46 Score=29.35 Aligned_cols=65 Identities=20% Similarity=0.253 Sum_probs=41.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|. |+. +++++..||.+|-+.+. ++ ....+..+|..+..+. -.+.-+++|++|.++-...||
T Consensus 1 m~i~vN---g~~--~~~~~~~tl~~ll~~l~----~~-~~~~v~vN~~~v~~~~-~~~~~L~~gD~vei~~~v~GG 65 (65)
T PRK06944 1 MDIQLN---QQT--LSLPDGATVADALAAYG----AR-PPFAVAVNGDFVARTQ-HAARALAAGDRLDLVQPVAGG 65 (65)
T ss_pred CEEEEC---CEE--EECCCCCcHHHHHHhhC----CC-CCeEEEECCEEcCchh-cccccCCCCCEEEEEeeccCC
Confidence 566664 443 45667889999988763 33 2456678888875322 223336789999987655554
No 92
>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=94.48 E-value=0.2 Score=31.18 Aligned_cols=58 Identities=21% Similarity=0.393 Sum_probs=41.4
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
.++++...||.+|.+++ +++++...+..+|+.+..+. -.+.-|++|+.|.+.-...||
T Consensus 8 ~~~~~~~~tv~~ll~~l----~~~~~~i~V~vNg~~v~~~~-~~~~~L~~gD~V~ii~~v~GG 65 (65)
T cd00565 8 PREVEEGATLAELLEEL----GLDPRGVAVALNGEIVPRSE-WASTPLQDGDRIEIVTAVGGG 65 (65)
T ss_pred EEEcCCCCCHHHHHHHc----CCCCCcEEEEECCEEcCHHH-cCceecCCCCEEEEEEeccCC
Confidence 34566788999998775 46777888889999886542 223456789999987655554
No 93
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=94.33 E-value=0.37 Score=31.15 Aligned_cols=60 Identities=15% Similarity=0.268 Sum_probs=43.2
Q ss_pred EEEEEecCC-CcHHHHHHHHHHHhC-C-C-CCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 12 TITLEVESS-DTIDNVKAKIQDKEG-I-P-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 12 ~~~l~V~~~-~TV~~LK~~I~~~~g-i-p-~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
...++++.. .||.+|.+.+.+... + . .....+..+++...++ .-|++|++|.+.-...||
T Consensus 17 ~~~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~~~-----~~l~dgDevai~PpvsGG 80 (80)
T TIGR01682 17 EETLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVTDD-----ALLNEGDEVAFIPPVSGG 80 (80)
T ss_pred eEEEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcCCC-----cCcCCCCEEEEeCCCCCC
Confidence 457888877 899999999988763 1 1 1234666888887753 456789999987666665
No 94
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=94.32 E-value=0.53 Score=29.42 Aligned_cols=66 Identities=15% Similarity=0.265 Sum_probs=43.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|. |+.+ +++...||.+|-+.+ +++.....+-.++..+..+. -++.-+++|+.|.+.--..||
T Consensus 1 m~i~vN---g~~~--~~~~~~tl~~ll~~l----~~~~~~vaVavN~~iv~r~~-w~~~~L~~gD~Ieii~~v~GG 66 (66)
T PRK08053 1 MQILFN---DQPM--QCAAGQTVHELLEQL----NQLQPGAALAINQQIIPREQ-WAQHIVQDGDQILLFQVIAGG 66 (66)
T ss_pred CEEEEC---CeEE--EcCCCCCHHHHHHHc----CCCCCcEEEEECCEEeChHH-cCccccCCCCEEEEEEEccCC
Confidence 667774 5554 446678999988764 55555677788999885321 233346789999986555554
No 95
>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=94.13 E-value=0.57 Score=30.71 Aligned_cols=62 Identities=13% Similarity=0.286 Sum_probs=43.4
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCC------C-----CCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKEGI------P-----PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gi------p-----~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
....++++ ..||.+|.+.+.+...- . -....+..+|+..+.+.. ..|++|+.|.++-...||
T Consensus 16 ~~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~PpvsGG 88 (88)
T TIGR01687 16 KSEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIFPPVSGG 88 (88)
T ss_pred ceEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEeCCCcCC
Confidence 35677776 89999999999877531 0 123566678887765431 457889999987776665
No 96
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=93.97 E-value=0.23 Score=30.61 Aligned_cols=54 Identities=19% Similarity=0.295 Sum_probs=40.1
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEE
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
|+|+|. | ..+++....|+.+|+.++... .-.++++|-+..++..|. +|+.|.+.
T Consensus 1 M~I~vN---~--k~~~~~~~~tl~~lr~~~k~~------~DI~I~NGF~~~~d~~L~-----e~D~v~~I 54 (57)
T PF14453_consen 1 MKIKVN---E--KEIETEENTTLFELRKESKPD------ADIVILNGFPTKEDIELK-----EGDEVFLI 54 (57)
T ss_pred CEEEEC---C--EEEEcCCCcCHHHHHHhhCCC------CCEEEEcCcccCCccccC-----CCCEEEEE
Confidence 677774 2 457788889999999987553 226789999988776664 68888775
No 97
>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=93.92 E-value=0.26 Score=32.50 Aligned_cols=46 Identities=11% Similarity=0.140 Sum_probs=36.7
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC-CceeEeeCC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAG 47 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~-~~qrL~~~G 47 (156)
|.|.+.. ++..+.+.++++.+..+|++.|+.+.++.. ....|.|-.
T Consensus 1 ~~vK~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~D 47 (82)
T cd06407 1 VRVKATY-GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLD 47 (82)
T ss_pred CEEEEEe-CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEEC
Confidence 4455543 677899999999999999999999999875 567777744
No 98
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=93.91 E-value=0.11 Score=43.24 Aligned_cols=70 Identities=21% Similarity=0.323 Sum_probs=58.6
Q ss_pred CEEEEEeC--CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCC--CcccccCcCCCCEEEEE
Q 031604 1 MQIFVKTL--TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG--RTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~--~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~--~tL~~~gi~~~stv~l~ 70 (156)
|.++|-.. ....+.++|.....+.+|+..+....|++.+..-|+|+++++.+. ..|.++|+..++++.+-
T Consensus 1 M~~tvs~~l~~~~~~~i~v~~dg~L~nl~aL~~~d~g~~~~~~~li~n~~~l~s~~s~~l~Q~g~~~~dsl~lr 74 (380)
T KOG0012|consen 1 MSLTVSVALNFEKKFPIPVTTDGELNNLAALCWKDTGIVYDPSDLIYNPRPLVSNESQGLTQIGLKDGDSLALR 74 (380)
T ss_pred CeEEEEEEecceeeeccccccccchhhHHHHHHHHhCcccchhhcccCCCccccchhhhhhhcccccceeEecc
Confidence 55665443 456788999999999999999999999999999999999999754 67999999988887653
No 99
>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=93.82 E-value=0.31 Score=30.87 Aligned_cols=63 Identities=14% Similarity=0.248 Sum_probs=47.3
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCC--CCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gi--p~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
...+.+....||.+|.+.+.....- ......+..+|+...+ . -.+.-+++|++|.++-...||
T Consensus 13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~~v~~-~-~~~~~l~~gD~V~i~ppvsGG 77 (77)
T PF02597_consen 13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGEIVPD-D-GLDTPLKDGDEVAILPPVSGG 77 (77)
T ss_dssp EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEEEGG-G-TTTSBEETTEEEEEEESTSTS
T ss_pred CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEEcCC-c-cCCcCcCCCCEEEEECCCCCC
Confidence 5678889999999999999877521 2256778899999888 2 445556789999987655555
No 100
>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=93.73 E-value=0.4 Score=29.74 Aligned_cols=57 Identities=19% Similarity=0.372 Sum_probs=39.8
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
++++...||.+|.+.+ +++++...+..+|+.+..+. -.++-|++|+.|.+.-...||
T Consensus 8 ~~~~~~~tv~~ll~~l----~~~~~~v~v~vN~~iv~~~~-~~~~~L~~gD~veii~~V~GG 64 (64)
T TIGR01683 8 VEVEDGLTLAALLESL----GLDPRRVAVAVNGEIVPRSE-WDDTILKEGDRIEIVTFVGGG 64 (64)
T ss_pred EEcCCCCcHHHHHHHc----CCCCCeEEEEECCEEcCHHH-cCceecCCCCEEEEEEeccCC
Confidence 4456778999998864 56777777789999885332 233457789999986555554
No 101
>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=93.67 E-value=0.39 Score=30.87 Aligned_cols=45 Identities=16% Similarity=0.334 Sum_probs=37.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCC
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG 47 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G 47 (156)
.|.++. ++..+.+.++++.|..+|..+|...++++.....|.|..
T Consensus 3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~D 47 (81)
T smart00666 3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQD 47 (81)
T ss_pred cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEEC
Confidence 345554 567889999999999999999999999987778888864
No 102
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=93.62 E-value=0.065 Score=33.79 Aligned_cols=19 Identities=26% Similarity=0.578 Sum_probs=15.3
Q ss_pred CCCccCCceeEEEeecCCC
Q 031604 137 DRHYCGKCGLTYVYQKAGG 155 (156)
Q Consensus 137 ~r~~cg~c~~t~~~~~~~~ 155 (156)
.-.+|-+||||+.|+...+
T Consensus 35 ~~v~C~~CGYTE~Y~~~~~ 53 (64)
T PF09855_consen 35 TTVSCTNCGYTEFYKAKTS 53 (64)
T ss_pred EEEECCCCCCEEEEeecCc
Confidence 4568999999999986643
No 103
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=93.11 E-value=0.63 Score=30.82 Aligned_cols=57 Identities=12% Similarity=0.245 Sum_probs=40.0
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
.++++..||.+|-+. .++++...-+-.+|..+.-+ .-++.-+++|+.|.++--..||
T Consensus 28 ~~~~~~~tl~~LL~~----l~~~~~~vAVevNg~iVpr~-~w~~t~L~egD~IEIv~~VgGG 84 (84)
T PRK06083 28 IQVDISSSLAQIIAQ----LSLPELGCVFAINNQVVPRS-EWQSTVLSSGDAISLFQAIAGG 84 (84)
T ss_pred EEcCCCCcHHHHHHH----cCCCCceEEEEECCEEeCHH-HcCcccCCCCCEEEEEEEecCC
Confidence 345667788888765 47788777888999988533 2445567889999986554444
No 104
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=92.94 E-value=1.1 Score=28.12 Aligned_cols=66 Identities=18% Similarity=0.255 Sum_probs=44.3
Q ss_pred CEEEEEeCCCCEEEEEecCC-CcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 1 MQIFVKTLTGKTITLEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~-~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
|+|+|. |+.+ +++.. .||.+|-+. .++++...-+-.++..+.-+. -++.-+++|+.|.++--..||
T Consensus 1 m~I~vN---G~~~--~~~~~~~tv~~lL~~----l~~~~~~vav~vN~~iv~r~~-w~~~~L~~gD~iEIv~~VgGG 67 (67)
T PRK07696 1 MNLKIN---GNQI--EVPESVKTVAELLTH----LELDNKIVVVERNKDILQKDD-HTDTSVFDGDQIEIVTFVGGG 67 (67)
T ss_pred CEEEEC---CEEE--EcCCCcccHHHHHHH----cCCCCCeEEEEECCEEeCHHH-cCceecCCCCEEEEEEEecCC
Confidence 666663 5654 44554 678877764 577777777889999886442 344557889999986544443
No 105
>PRK07440 hypothetical protein; Provisional
Probab=92.91 E-value=0.99 Score=28.69 Aligned_cols=61 Identities=20% Similarity=0.329 Sum_probs=42.2
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
+|+. ++++...||.+|-+. .++++...-+-.+|..+.-+. -.+.-+++|+.|.++--..||
T Consensus 10 NG~~--~~~~~~~tl~~lL~~----l~~~~~~vav~~N~~iv~r~~-w~~~~L~~gD~IEIv~~v~GG 70 (70)
T PRK07440 10 NGET--RTCSSGTSLPDLLQQ----LGFNPRLVAVEYNGEILHRQF-WEQTQVQPGDRLEIVTIVGGG 70 (70)
T ss_pred CCEE--EEcCCCCCHHHHHHH----cCCCCCeEEEEECCEEeCHHH-cCceecCCCCEEEEEEEecCC
Confidence 4554 556778899988764 477777788889999886332 334456789999986555444
No 106
>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=92.75 E-value=1.5 Score=32.63 Aligned_cols=71 Identities=28% Similarity=0.368 Sum_probs=49.5
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCC-ceeEeeC---C---eecCCCCcccccCcC-CCCEEEEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFA---G---KQLEDGRTLADYNIQ-KESTLHLVLR 72 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~-~qrL~~~---G---~~L~d~~tL~~~gi~-~~stv~l~~~ 72 (156)
.|.|..++|....+.+++++|+.++-..++...|++.. ..-|.+- + .-|+...+|.+.... ....+++..+
T Consensus 5 ~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~l~fr~r 83 (207)
T smart00295 5 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVKSEPLTLYFRVK 83 (207)
T ss_pred EEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHhcCCCCCcEEEEEEE
Confidence 57788889999999999999999999999999999642 2344421 1 235556666666544 2344555444
No 107
>KOG0009 consensus Ubiquitin-like/40S ribosomal S30 protein fusion [Translation, ribosomal structure and biogenesis; Posttranslational modification, protein turnover, chaperones]
Probab=92.07 E-value=0.059 Score=33.10 Aligned_cols=27 Identities=30% Similarity=0.207 Sum_probs=22.4
Q ss_pred CccccccccccCCcccccccceeeeee
Q 031604 76 GAKKRKKKTYTKPKKIKHKKKKVKLAV 102 (156)
Q Consensus 76 g~~k~~kk~~~~pk~~k~~kkk~k~~v 102 (156)
.-.+++|+..+|||+++++++|.|...
T Consensus 7 slarAGKVr~QTPKv~kqeK~kkk~GR 33 (62)
T KOG0009|consen 7 SLARAGKVRGQTPKVEKQEKKKKKRGR 33 (62)
T ss_pred ehhhcccccccCCcchhhhhcccccch
Confidence 345778899999999999999988753
No 108
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=92.00 E-value=0.057 Score=27.89 Aligned_cols=24 Identities=42% Similarity=1.096 Sum_probs=17.4
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 119 KECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
+.|| .|++-|-. +-..|..|||.|
T Consensus 1 K~CP--~C~~~V~~----~~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCP--ECGAEVPE----SAKFCPHCGYDF 24 (26)
T ss_pred CcCC--CCcCCchh----hcCcCCCCCCCC
Confidence 4799 89865533 446799999877
No 109
>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=91.88 E-value=1.2 Score=28.59 Aligned_cols=44 Identities=20% Similarity=0.272 Sum_probs=38.6
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeC
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 46 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~ 46 (156)
+.|-.++|+.-.+.|.|.+||.|+-+.+.++.|+.++.--|+..
T Consensus 2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~ 45 (72)
T cd01760 2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLL 45 (72)
T ss_pred EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEe
Confidence 45677899999999999999999999999999999987766644
No 110
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=91.25 E-value=0.74 Score=37.04 Aligned_cols=68 Identities=18% Similarity=0.283 Sum_probs=53.2
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--eCCeecC-C--CCcccccCcCCCCEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE-D--GRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~-d--~~tL~~~gi~~~stv~l 69 (156)
.|.||..+|+++..++++..|+.+++..+....+..+....|. |--..+. | ..+|..+++.+.++|.+
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 RLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRGDGLDPYSFHTGFPRVTFTEDDELKPLQELDLVPSAVLIL 284 (290)
T ss_pred EEEEEcCCCCeeeeecCchhhHHHHHHHHHHhccCCCCCeeeecCCCceecccccccccHHHhccccchheec
Confidence 4778999999999999999999999999998887665444443 3334443 2 37899999998888765
No 111
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=91.18 E-value=0.47 Score=39.82 Aligned_cols=65 Identities=20% Similarity=0.314 Sum_probs=50.8
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC-CCCCceeEe--eCCeecCC-CCcccccCcCCCCE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG-IPPDQQRLI--FAGKQLED-GRTLADYNIQKEST 66 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~g-ip~~~qrL~--~~G~~L~d-~~tL~~~gi~~~st 66 (156)
.|.||..+|..+...++.+.||.+|+..|...-. -+...+.|+ |--+.|.| +.||++-||.+...
T Consensus 307 sIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsvl 375 (380)
T KOG2086|consen 307 SIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSVL 375 (380)
T ss_pred eEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceeeeecCCCcccCCcchhHHhccchhhhh
Confidence 4788999999999999999999999999987653 333456665 67788865 57999999875543
No 112
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=91.01 E-value=0.14 Score=31.22 Aligned_cols=34 Identities=29% Similarity=0.816 Sum_probs=27.2
Q ss_pred cccCCCCccCCceEEeE--eCCCCccCCceeEEEee
Q 031604 118 RKECPNAECGAGTFMAS--HFDRHYCGKCGLTYVYQ 151 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~--h~~r~~cg~c~~t~~~~ 151 (156)
.+-||.+.|+..+.... ......|.+|++.|++.
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence 56899999987777653 45688899999999875
No 113
>smart00455 RBD Raf-like Ras-binding domain.
Probab=91.01 E-value=1.1 Score=28.61 Aligned_cols=49 Identities=22% Similarity=0.322 Sum_probs=41.7
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCC--eecC
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG--KQLE 51 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G--~~L~ 51 (156)
+.|-.++|+...+.+.|..||.|+-..+.++.|+.++...++..| ++|+
T Consensus 2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~ld 52 (70)
T smart00455 2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLD 52 (70)
T ss_pred eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccee
Confidence 346677899999999999999999999999999999988888755 3454
No 114
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=90.94 E-value=2.3 Score=26.97 Aligned_cols=59 Identities=19% Similarity=0.371 Sum_probs=41.6
Q ss_pred EEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
-.++++...|+++|-+. .+++++..-+..+|..+..+. -.+.-+++++.|.++--..||
T Consensus 10 ~~~e~~~~~tv~dLL~~----l~~~~~~vav~vNg~iVpr~~-~~~~~l~~gD~ievv~~v~GG 68 (68)
T COG2104 10 KEVEIAEGTTVADLLAQ----LGLNPEGVAVAVNGEIVPRSQ-WADTILKEGDRIEVVRVVGGG 68 (68)
T ss_pred EEEEcCCCCcHHHHHHH----hCCCCceEEEEECCEEccchh-hhhccccCCCEEEEEEeecCC
Confidence 34566666999998775 578888888889999887433 234556778999876444443
No 115
>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=90.85 E-value=1.2 Score=38.38 Aligned_cols=69 Identities=14% Similarity=0.165 Sum_probs=53.6
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCC----CC--CceeEe-eCCeecCCCCcccccCcCCCCEEEEEE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI----PP--DQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gi----p~--~~qrL~-~~G~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
+|+|... .+...+-++.+.+|.||--.|-+..+- +. ..-.|. .+|.+|+.+.+|.+.||.+|+.++|.-
T Consensus 4 RVtV~~~-~~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L~p 79 (452)
T TIGR02958 4 RVTVLAG-RRAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVLVP 79 (452)
T ss_pred EEEEeeC-CeeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEEee
Confidence 4677654 345788899999999999999887753 11 223443 578899999999999999999999874
No 116
>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=90.57 E-value=1.9 Score=28.76 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=36.3
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCccc
Q 031604 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLA 57 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~ 57 (156)
.|..+.+.|+++.+..+|.++|..++++. ....|-|... .|-.+|+
T Consensus 10 ~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE--GD~iti~ 55 (86)
T cd06408 10 QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD--GDMITMG 55 (86)
T ss_pred cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC--CCCcccc
Confidence 67899999999999999999999999985 5566666555 4444443
No 117
>PRK05978 hypothetical protein; Provisional
Probab=90.38 E-value=0.16 Score=37.29 Aligned_cols=33 Identities=27% Similarity=0.779 Sum_probs=26.2
Q ss_pred ecccCCCCccCCceEEeEe-CCCCccCCceeEEEee
Q 031604 117 LRKECPNAECGAGTFMASH-FDRHYCGKCGLTYVYQ 151 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h-~~r~~cg~c~~t~~~~ 151 (156)
++..|| +||.|-+...- .-+..|..||..|...
T Consensus 32 l~grCP--~CG~G~LF~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCP--ACGEGKLFRAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCC--CCCCCcccccccccCCCccccCCccccC
Confidence 689999 99988876544 3588999999988544
No 118
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=90.22 E-value=0.12 Score=31.47 Aligned_cols=33 Identities=21% Similarity=0.575 Sum_probs=20.8
Q ss_pred ccCCCCccCCceEEeEeCCC--CccCCceeEEEee
Q 031604 119 KECPNAECGAGTFMASHFDR--HYCGKCGLTYVYQ 151 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r--~~cg~c~~t~~~~ 151 (156)
+-||++.|+..+......+. ..|..|+..|++.
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~ 53 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFK 53 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSS
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccc
Confidence 59998899866555554444 7899999999875
No 119
>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=89.97 E-value=1.5 Score=28.16 Aligned_cols=44 Identities=20% Similarity=0.397 Sum_probs=35.0
Q ss_pred EEEEeCCCCEEE-EEecCCCcHHHHHHHHHHHhCCCCCceeEeeCC
Q 031604 3 IFVKTLTGKTIT-LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG 47 (156)
Q Consensus 3 I~Vk~~~g~~~~-l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G 47 (156)
|.+.. ++.... +.++++.|..+|..+|+..++.+.....|.|..
T Consensus 4 vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D 48 (84)
T PF00564_consen 4 VKVRY-GGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKD 48 (84)
T ss_dssp EEEEE-TTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEE
T ss_pred EEEEE-CCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeC
Confidence 44443 445555 899999999999999999999998888888853
No 120
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=89.85 E-value=0.6 Score=29.55 Aligned_cols=38 Identities=32% Similarity=0.581 Sum_probs=31.4
Q ss_pred CCeEEEecccCCCCccCCceEEeEe-CCCCccCCceeEEEe
Q 031604 111 SGKVQRLRKECPNAECGAGTFMASH-FDRHYCGKCGLTYVY 150 (156)
Q Consensus 111 ~g~~~~~~~~cp~~~c~~g~fma~h-~~r~~cg~c~~t~~~ 150 (156)
+.+-.+++-+|| .|+.---...| .....|.-||.|...
T Consensus 12 ~p~s~Fl~VkCp--dC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 12 EPRSRFLRVKCP--DCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred CCCceEEEEECC--CCCCEEEEeccCceEEEecccccEEEe
Confidence 455688899999 89988788888 478999999998853
No 121
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=89.51 E-value=0.27 Score=32.82 Aligned_cols=32 Identities=34% Similarity=0.684 Sum_probs=21.9
Q ss_pred EEecccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 115 QRLRKECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 115 ~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
.+-...|| .|+.-..=-.-..=|.|.+||++|
T Consensus 32 ~~~~~~Cp--~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 32 QRAKHVCP--FCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HhcCCcCC--CCCCcceeeeccCeEEcCCCCCee
Confidence 34478999 897532111124789999999998
No 122
>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=89.27 E-value=1.8 Score=27.57 Aligned_cols=45 Identities=22% Similarity=0.335 Sum_probs=35.2
Q ss_pred EEEEEeCCCCEEEEEec-CCCcHHHHHHHHHHHhCCCCCceeEeeCC
Q 031604 2 QIFVKTLTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAG 47 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~-~~~TV~~LK~~I~~~~gip~~~qrL~~~G 47 (156)
.|.++. +|....+.++ .+.|..+|+++|.+.++++.....|.|..
T Consensus 2 ~vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D 47 (81)
T cd05992 2 RVKVKY-GGEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPD 47 (81)
T ss_pred cEEEEe-cCCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeC
Confidence 455554 3678888888 89999999999999999886666666644
No 123
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.04 E-value=0.23 Score=29.29 Aligned_cols=27 Identities=33% Similarity=0.797 Sum_probs=18.6
Q ss_pred cCCCCccCCceEEeEeC----CCCccCCceeEEEe
Q 031604 120 ECPNAECGAGTFMASHF----DRHYCGKCGLTYVY 150 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~----~r~~cg~c~~t~~~ 150 (156)
-|| .||. +|.... +|+.|..||+.+-.
T Consensus 2 FCp--~Cg~--~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCP--KCGN--MLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCC--CCCC--ccccccCCCCCEEECCcCCCeEEC
Confidence 488 8976 333321 37899999998744
No 124
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=89.02 E-value=0.36 Score=32.45 Aligned_cols=31 Identities=26% Similarity=0.607 Sum_probs=22.7
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
....|| .||.-.+=-.--.=|.|.+|+++|.
T Consensus 34 ~ky~Cp--~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCP--FCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEES--SSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CCCcCC--CCCCceeEEeeeEEeecCCCCCEEe
Confidence 367899 9986654444456799999999984
No 125
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=88.99 E-value=0.17 Score=36.28 Aligned_cols=34 Identities=32% Similarity=0.733 Sum_probs=26.9
Q ss_pred EEecccCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031604 115 QRLRKECPNAECGAGTFMASHFDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 115 ~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~ 152 (156)
+.|...|| .||.=-| .|-.+.+|.-||+++....
T Consensus 25 kML~~hCp--~Cg~PLF--~KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 25 KMLAKHCP--KCGTPLF--RKDGEVFCPVCGYREVVVE 58 (131)
T ss_pred HHHHhhCc--ccCCcce--eeCCeEECCCCCceEEEee
Confidence 55789999 9976444 6889999999998885543
No 126
>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=88.85 E-value=4.4 Score=25.78 Aligned_cols=56 Identities=20% Similarity=0.242 Sum_probs=40.4
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeC--CeecCCCCcccc
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GKQLEDGRTLAD 58 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~--G~~L~d~~tL~~ 58 (156)
+.|..++|+...+.+.|..||.|+-..+.+..|+.++...+... .+.|+-+...+.
T Consensus 3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~~~k~l~~~~d~~~ 60 (71)
T PF02196_consen 3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVGEKKPLDWDQDSSS 60 (71)
T ss_dssp EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEEEEEEE-TTSBGGG
T ss_pred EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccccCCCceee
Confidence 45777899999999999999999999999999999987665533 446655544433
No 127
>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional
Probab=88.59 E-value=2.6 Score=34.82 Aligned_cols=68 Identities=19% Similarity=0.292 Sum_probs=49.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCCcc
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAK 78 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg~~ 78 (156)
|+|+|. |+. +++++..||.+|-+. .+++++..-+..||+.+.-+. -.++-|++|+.|.++--..||.-
T Consensus 1 M~I~VN---Gk~--~el~e~~TL~dLL~~----L~i~~~~VAVeVNgeIVpr~~-w~~t~LkeGD~IEII~~VgGGs~ 68 (326)
T PRK11840 1 MRIRLN---GEP--RQVPAGLTIAALLAE----LGLAPKKVAVERNLEIVPRSE-YGQVALEEGDELEIVHFVGGGSD 68 (326)
T ss_pred CEEEEC---CEE--EecCCCCcHHHHHHH----cCCCCCeEEEEECCEECCHHH-cCccccCCCCEEEEEEEecCCCC
Confidence 666664 554 556677889888765 588888888889999986332 34556788999998766666654
No 128
>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=88.50 E-value=1.2 Score=29.24 Aligned_cols=36 Identities=11% Similarity=0.250 Sum_probs=32.7
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCC
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG 47 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G 47 (156)
++.+.+++..+.++|.++|+++...+++...|.|..
T Consensus 8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~ 43 (78)
T cd06411 8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRA 43 (78)
T ss_pred EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecC
Confidence 566789999999999999999999999999999854
No 129
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.14 E-value=0.57 Score=27.17 Aligned_cols=34 Identities=18% Similarity=0.481 Sum_probs=22.7
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeEEEeecC
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLTYVYQKA 153 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~~ 153 (156)
...|| .||+-+-.-.......|..||..+.++..
T Consensus 3 ~y~C~--~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 3 EYKCA--RCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EEECC--CCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 46799 89864333332337889999988876543
No 130
>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=87.10 E-value=3 Score=28.34 Aligned_cols=40 Identities=18% Similarity=0.249 Sum_probs=33.7
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEee
Q 031604 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 45 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~ 45 (156)
++..+|++..+.|+.+.|..+|+.++++..+++.. +.|-|
T Consensus 17 l~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~-~~lky 56 (97)
T cd06410 17 LRYVGGETRIVSVDRSISFKELVSKLSELFGAGVV-VTLKY 56 (97)
T ss_pred EEEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCc-eEEEE
Confidence 45567889999999999999999999999998876 55544
No 131
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=87.02 E-value=0.47 Score=26.23 Aligned_cols=29 Identities=34% Similarity=0.872 Sum_probs=19.0
Q ss_pred cccCCCCccCCceEEeEe------CCCCccCCceeEEE
Q 031604 118 RKECPNAECGAGTFMASH------FDRHYCGKCGLTYV 149 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h------~~r~~cg~c~~t~~ 149 (156)
+-.|| +|++ .|...- .....|++||..|.
T Consensus 2 ~~~CP--~C~~-~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCP--NCKT-SFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECC--CCCC-EEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 45799 8985 343331 12468999998873
No 132
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=86.90 E-value=0.72 Score=32.72 Aligned_cols=59 Identities=15% Similarity=0.213 Sum_probs=41.8
Q ss_pred EEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCc---CCCCEEEEEE
Q 031604 13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI---QKESTLHLVL 71 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi---~~~stv~l~~ 71 (156)
..+-|+.+.||+++...|..+.+++++..-|+.++..+..+.+++++=- .++.-|++..
T Consensus 43 KfllVP~d~tV~qF~~iIRkrl~l~~~k~flfVnn~lp~~s~~mg~lYe~~KDeDGFLYi~Y 104 (121)
T PTZ00380 43 HFLALPRDATVAELEAAVRQALGTSAKKVTLAIEGSTPAVTATVGDIADACKRDDGFLYVSV 104 (121)
T ss_pred EEEEcCCCCcHHHHHHHHHHHcCCChhHEEEEECCccCCccchHHHHHHHhcCCCCeEEEEE
Confidence 3346999999999999999999999988666667766666666655411 1244566543
No 133
>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown.
Probab=86.57 E-value=2.2 Score=30.29 Aligned_cols=55 Identities=20% Similarity=0.466 Sum_probs=38.8
Q ss_pred EecC-CCcHHHHHHHHHHHh----CCCCC------ceeEee----------------CC-eec---CCCCcccccCcCCC
Q 031604 16 EVES-SDTIDNVKAKIQDKE----GIPPD------QQRLIF----------------AG-KQL---EDGRTLADYNIQKE 64 (156)
Q Consensus 16 ~V~~-~~TV~~LK~~I~~~~----gip~~------~qrL~~----------------~G-~~L---~d~~tL~~~gi~~~ 64 (156)
.|+. ++||.+|++.+.+.. |++|- .++|.. +. ..| +++.+|.++||.++
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 4887 999999998887654 55542 233332 11 356 67789999999999
Q ss_pred CEEEEE
Q 031604 65 STLHLV 70 (156)
Q Consensus 65 stv~l~ 70 (156)
..|.+.
T Consensus 101 TEiSfF 106 (122)
T PF10209_consen 101 TEISFF 106 (122)
T ss_pred ceeeee
Confidence 888765
No 134
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=86.54 E-value=5.3 Score=25.80 Aligned_cols=57 Identities=12% Similarity=0.220 Sum_probs=34.7
Q ss_pred EEecC-CCcHHHHHHHHHHHhC-----CCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 15 LEVES-SDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 15 l~V~~-~~TV~~LK~~I~~~~g-----ip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
+++++ ..||.+|++.+.++.. ......++..+++...+ +.-|++|+.|-+.-...||
T Consensus 19 ~~v~~~~~tv~~l~~~L~~~~~~~~~~~~~~~~~~aVN~~~~~~-----~~~l~dgDeVai~PPVsGG 81 (81)
T PRK11130 19 LELAADFPTVEALRQHLAQKGDRWALALEDGKLLAAVNQTLVSF-----DHPLTDGDEVAFFPPVTGG 81 (81)
T ss_pred EEecCCCCCHHHHHHHHHHhCccHHhhhcCCCEEEEECCEEcCC-----CCCCCCCCEEEEeCCCCCC
Confidence 44443 4799999999987752 11122344455544333 2346789999887665555
No 135
>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=86.46 E-value=4.3 Score=27.24 Aligned_cols=70 Identities=17% Similarity=0.290 Sum_probs=44.7
Q ss_pred EEEEeCCCCEEEEEecC-----CCcHHHHHHHHHHHhCCCC-CceeEeeCCe-----ecCCCCccccc-----CcCCCCE
Q 031604 3 IFVKTLTGKTITLEVES-----SDTIDNVKAKIQDKEGIPP-DQQRLIFAGK-----QLEDGRTLADY-----NIQKEST 66 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~-----~~TV~~LK~~I~~~~gip~-~~qrL~~~G~-----~L~d~~tL~~~-----gi~~~st 66 (156)
|.|.. +|....+.++. +.+..+|+++|++.+.+++ ....|.|... .|.++.-|.+. .-....+
T Consensus 3 vKv~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~~~~~~~~~~ 81 (91)
T cd06398 3 VKVKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYFCSGSRLNP 81 (91)
T ss_pred EEEEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHHhccCCCce
Confidence 34433 56677777774 7999999999999999998 5667777543 23333333222 2234667
Q ss_pred EEEEEEe
Q 031604 67 LHLVLRL 73 (156)
Q Consensus 67 v~l~~~~ 73 (156)
+.|.++.
T Consensus 82 lrl~v~~ 88 (91)
T cd06398 82 LRIDVTV 88 (91)
T ss_pred EEEEEEE
Confidence 7666654
No 136
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=86.40 E-value=0.49 Score=28.84 Aligned_cols=25 Identities=28% Similarity=0.842 Sum_probs=19.4
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
..-.|. +||.-. -|.-...|+.|||
T Consensus 14 tH~~Cr--RCG~~s---yH~qK~~CasCGy 38 (55)
T PF01907_consen 14 THTLCR--RCGRRS---YHIQKKTCASCGY 38 (55)
T ss_dssp SEEE-T--TTSSEE---EETTTTEETTTBT
T ss_pred cEeeec--ccCCee---eecCCCcccccCC
Confidence 356788 999655 4999999999997
No 137
>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=85.62 E-value=5.4 Score=26.27 Aligned_cols=40 Identities=18% Similarity=0.303 Sum_probs=31.3
Q ss_pred EEEEeCCCCEEEEEecC--CCcHHHHHHHHHHHhCCCCCceeEee
Q 031604 3 IFVKTLTGKTITLEVES--SDTIDNVKAKIQDKEGIPPDQQRLIF 45 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~--~~TV~~LK~~I~~~~gip~~~qrL~~ 45 (156)
|.+. .+|.+..+.+++ +.+..+|++.|+.+++++ .+.|-|
T Consensus 3 vKat-y~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKY 44 (81)
T cd06396 3 LKVT-YNGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKY 44 (81)
T ss_pred EEEE-ECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEE
Confidence 4443 367888999998 779999999999999998 444444
No 138
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=85.46 E-value=0.62 Score=35.44 Aligned_cols=31 Identities=26% Similarity=0.433 Sum_probs=23.8
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEEeecC
Q 031604 119 KECPNAECGAGTFMASHFDRHYCGKCGLTYVYQKA 153 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~~ 153 (156)
-.|+ +|++ +|-.-.+-++|.+||.|+..+-+
T Consensus 150 A~Cs--rC~~--~L~~~~~~l~Cp~Cg~tEkRKia 180 (188)
T COG1096 150 ARCS--RCRA--PLVKKGNMLKCPNCGNTEKRKIA 180 (188)
T ss_pred EEcc--CCCc--ceEEcCcEEECCCCCCEEeeeec
Confidence 4688 9975 44446688999999999987654
No 139
>PRK01777 hypothetical protein; Validated
Probab=85.18 E-value=6 Score=26.75 Aligned_cols=69 Identities=9% Similarity=0.084 Sum_probs=45.7
Q ss_pred CEEEEEeC-CC--CEEEEEecCCCcHHHHHHHHHHHhCCCCC--c-----eeEeeCCeecCCCCcccccCcCCCCEEEEE
Q 031604 1 MQIFVKTL-TG--KTITLEVESSDTIDNVKAKIQDKEGIPPD--Q-----QRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~-~g--~~~~l~V~~~~TV~~LK~~I~~~~gip~~--~-----qrL~~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
|+|.|-.. .. ....+++++.+||.++-.++ ||+.+ + -.+.-+|+....+. -+++|++|.+.
T Consensus 4 i~v~V~ya~~~~~~~~~l~vp~GtTv~dal~~s----gi~~~~pei~~~~~~vgI~Gk~v~~d~-----~L~dGDRVeIy 74 (95)
T PRK01777 4 IRVEVVYALPERQYLQRLTLQEGATVEEAIRAS----GLLELRTDIDLAKNKVGIYSRPAKLTD-----VLRDGDRVEIY 74 (95)
T ss_pred eEEEEEEECCCceEEEEEEcCCCCcHHHHHHHc----CCCccCcccccccceEEEeCeECCCCC-----cCCCCCEEEEe
Confidence 46666543 22 24668899999999987764 55544 2 24556777665544 44679999998
Q ss_pred EEecCCcc
Q 031604 71 LRLRGGAK 78 (156)
Q Consensus 71 ~~~~gg~~ 78 (156)
-.+.-..+
T Consensus 75 rPL~~DPk 82 (95)
T PRK01777 75 RPLLADPK 82 (95)
T ss_pred cCCCCCHH
Confidence 77666554
No 140
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=85.13 E-value=0.64 Score=31.31 Aligned_cols=32 Identities=28% Similarity=0.641 Sum_probs=22.6
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
.-...|| .|+..-+=-.--.=|.|.+|+++|.
T Consensus 33 ~a~y~Cp--fCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 33 KAKYVCP--FCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred hcCccCC--CCCCCceEEEeeEEEEcCCCCCEEe
Confidence 3468999 9975433333346799999999984
No 141
>PF04758 Ribosomal_S30: Ribosomal protein S30; InterPro: IPR006846 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 entry is for the ribosomal protein S30.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_X 2XZM_X 3IZB_Z 3U5G_e 3U5C_e 3J16_E 3IZ6_Z.
Probab=84.34 E-value=0.19 Score=31.02 Aligned_cols=26 Identities=31% Similarity=0.305 Sum_probs=19.6
Q ss_pred cCCccccccccccCCcccccccceee
Q 031604 74 RGGAKKRKKKTYTKPKKIKHKKKKVK 99 (156)
Q Consensus 74 ~gg~~k~~kk~~~~pk~~k~~kkk~k 99 (156)
.|.-.+++|+..+|||++++++++.+
T Consensus 3 HGSLarAGKVR~QTPKV~k~~k~k~~ 28 (59)
T PF04758_consen 3 HGSLARAGKVRGQTPKVEKQEKKKKP 28 (59)
T ss_dssp CCCCTTTTHHHHHSSSSS--HHHHHH
T ss_pred ccchhhcccccccCCCcCccccccCC
Confidence 45667889999999999999987654
No 142
>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=84.17 E-value=4.7 Score=26.81 Aligned_cols=66 Identities=23% Similarity=0.276 Sum_probs=45.5
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCc-eeEe-e-----CCeecCCCCcc----cccCcCCCCEEE
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLI-F-----AGKQLEDGRTL----ADYNIQKESTLH 68 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~-qrL~-~-----~G~~L~d~~tL----~~~gi~~~stv~ 68 (156)
|.|-+.+|.+..|.|+..+|+.++-+.+..+.+...+. -.|+ . --+.++|+..| +..+..+++.+.
T Consensus 5 vkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~LvE~~P~l~lER~~EDHE~vvdvl~~W~~~~~n~l~ 81 (85)
T cd01787 5 VKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLVEHLPHLQLERLFEDHELVVEVLSTWHSAGNSVLF 81 (85)
T ss_pred EEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEEEecchhhhhhhccchHHHHHHHHhcccCCCcEEE
Confidence 45666789999999999999999999999999876643 3333 1 13456777554 444443344443
No 143
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=83.84 E-value=0.75 Score=30.94 Aligned_cols=32 Identities=28% Similarity=0.643 Sum_probs=22.8
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
.-...|| .|+..-+=-.--.=|.|.+|+++|.
T Consensus 34 ~a~y~Cp--fCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 34 RAKHVCP--VCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred hcCccCC--CCCCCceEEEEEEEEEcCCCCCEEe
Confidence 3468999 9965444333346799999999983
No 144
>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=83.60 E-value=2.4 Score=28.03 Aligned_cols=55 Identities=16% Similarity=0.282 Sum_probs=37.0
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCC-------ceeEeeCCe-ecC------CCCcccccCcCCCCEEEEE
Q 031604 15 LEVESSDTIDNVKAKIQDKEGIPPD-------QQRLIFAGK-QLE------DGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~-------~qrL~~~G~-~L~------d~~tL~~~gi~~~stv~l~ 70 (156)
|+|++++|+++|-+.+.+...+... .-.|++.+- .|+ -+.+|.++ +.+|..|.|.
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 6799999999999999887433222 234443332 232 24678998 8889988875
No 145
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=82.90 E-value=1.4 Score=23.98 Aligned_cols=29 Identities=28% Similarity=0.694 Sum_probs=21.4
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 119 KECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
+.|+ -|+....+-.=.+...|..||.+|.
T Consensus 4 ~~C~--~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 4 KKCS--KCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred eEcC--CCCCCeEEEecCCeEEcccCCcEee
Confidence 5688 6976665544467788999999884
No 146
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.82 E-value=0.44 Score=24.36 Aligned_cols=24 Identities=38% Similarity=0.888 Sum_probs=17.4
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeE
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLT 147 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
...|| .||+ . ...+-.+|..||..
T Consensus 2 ~~~Cp--~Cg~--~--~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCP--NCGA--E--IDPDAKFCPNCGAK 25 (26)
T ss_pred cCCCc--ccCC--c--CCcccccChhhCCC
Confidence 36799 8986 2 23477889999963
No 147
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=82.76 E-value=1.1 Score=28.17 Aligned_cols=28 Identities=29% Similarity=0.698 Sum_probs=22.4
Q ss_pred cccCCCCccCCceEEeEeCCCCc---cCCceeE
Q 031604 118 RKECPNAECGAGTFMASHFDRHY---CGKCGLT 147 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~---cg~c~~t 147 (156)
-+-|| .||.-+....|.++++ |.+|+-.
T Consensus 6 lKPCP--FCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCP--FCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCC--CCCCceeEEEecCceEEEEcCCCCcC
Confidence 46799 9998888888887665 9999854
No 148
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=82.32 E-value=0.74 Score=25.96 Aligned_cols=23 Identities=30% Similarity=0.703 Sum_probs=19.2
Q ss_pred cccCCCCccCCceEEeEe--CCCCccCC
Q 031604 118 RKECPNAECGAGTFMASH--FDRHYCGK 143 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h--~~r~~cg~ 143 (156)
...|+ .|+ ++|...| .+.|.|.+
T Consensus 12 ~f~C~--~C~-~~FC~~HR~~e~H~C~~ 36 (39)
T smart00154 12 GFKCR--HCG-NLFCGEHRLPEDHDCPG 36 (39)
T ss_pred CeECC--ccC-CccccccCCccccCCcc
Confidence 67898 897 8999999 58888864
No 149
>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=82.30 E-value=5.5 Score=26.06 Aligned_cols=49 Identities=20% Similarity=0.424 Sum_probs=34.5
Q ss_pred CcHHHHHHHHHHHhCCCCCceeEe--eCCeecCCCCcccccCcCCCCEEEEEEE
Q 031604 21 DTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
.|+.+|+.+..+.++++.+..+|. -+|..++|+.-+..+ +..|+.+.+.
T Consensus 21 ~sL~eL~~K~~~~l~~~~~~~~lvL~eDGT~VddEeyF~tL---p~nT~lm~L~ 71 (78)
T PF02017_consen 21 SSLEELLEKACDKLQLPEEPVRLVLEEDGTEVDDEEYFQTL---PDNTVLMLLE 71 (78)
T ss_dssp SSHHHHHHHHHHHHT-SSSTCEEEETTTTCBESSCHHHCCS---SSSEEEEEEE
T ss_pred CCHHHHHHHHHHHhCCCCcCcEEEEeCCCcEEccHHHHhhC---CCCCEEEEEC
Confidence 689999999999999997766665 488888887554443 2445544443
No 150
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=82.14 E-value=0.94 Score=30.45 Aligned_cols=32 Identities=22% Similarity=0.418 Sum_probs=22.2
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
.-...|| .|+..-+=-.--.=|.|.+|+++|.
T Consensus 34 ~a~y~Cp--fCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 34 HAKYFCP--FCGKHAVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred hCCccCC--CCCCCceeeeeeEEEEcCCCCCEEe
Confidence 3468999 9974333222236699999999984
No 151
>PRK09336 30S ribosomal protein S30e; Provisional
Probab=81.99 E-value=0.57 Score=27.98 Aligned_cols=24 Identities=29% Similarity=0.248 Sum_probs=19.2
Q ss_pred CCccccccccccCCccccccccee
Q 031604 75 GGAKKRKKKTYTKPKKIKHKKKKV 98 (156)
Q Consensus 75 gg~~k~~kk~~~~pk~~k~~kkk~ 98 (156)
|.-.+++|+..+|||++++++++.
T Consensus 5 GSLarAGKVr~qTPkv~k~ekkk~ 28 (50)
T PRK09336 5 GSLTKAGKVRSQTPKIPPKPKKNE 28 (50)
T ss_pred hhhhhcccccCCCCCcchhhhccC
Confidence 455678899999999998887553
No 152
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.38 E-value=0.5 Score=33.47 Aligned_cols=34 Identities=35% Similarity=0.844 Sum_probs=25.4
Q ss_pred ecccCCCCccCCceEEeEe-CCCCccCCceeEEEeec
Q 031604 117 LRKECPNAECGAGTFMASH-FDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h-~~r~~cg~c~~t~~~~~ 152 (156)
++..|| +||.|-..-.- .-+..|.-||+.|-+-.
T Consensus 20 l~grCP--~CGeGrLF~gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 20 LRGRCP--RCGEGRLFRGFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred hcCCCC--CCCCchhhhhhcccCchhhhccccccCCc
Confidence 689999 99988643322 46888999999886653
No 153
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=81.22 E-value=8.7 Score=25.18 Aligned_cols=52 Identities=19% Similarity=0.408 Sum_probs=40.0
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe-eCCeecCCCCcccccCcCCCCEEEEE
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
+..+.+.+++..||.++-+. .|+|..+.-++ -||+..+-+ |-+++|+.|.+.
T Consensus 22 ~~~~~~~~~~~~tvkd~IEs----LGVP~tEV~~i~vNG~~v~~~-----~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 22 GGPFTHPFDGGATVKDVIES----LGVPHTEVGLILVNGRPVDFD-----YRLKDGDRVAVY 74 (81)
T ss_pred CCceEEecCCCCcHHHHHHH----cCCChHHeEEEEECCEECCCc-----ccCCCCCEEEEE
Confidence 34677889999999988765 69999888665 688877654 455679998875
No 154
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=80.84 E-value=7.5 Score=29.98 Aligned_cols=48 Identities=21% Similarity=0.329 Sum_probs=29.1
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCC---ceeEe--eCCee---cCCCCccccc
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIPPD---QQRLI--FAGKQ---LEDGRTLADY 59 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~---~qrL~--~~G~~---L~d~~tL~~~ 59 (156)
.+.+-|+.+.||+||.+.++...+++.+ .+||+ ++++. +..+..|.++
T Consensus 35 ~~~~~vpk~~tV~Dll~~l~~k~~~~~~~~~~lrl~ev~~~ki~~~~~~d~~i~~l 90 (213)
T PF14533_consen 35 EYELLVPKTGTVSDLLEELQKKVGFSEEGTGKLRLWEVSNHKIYKILSEDEPISSL 90 (213)
T ss_dssp EEEE--BTT-BHHHHHHHHHTT----TT----EEEEEEETTEEEEEE-TTSBGGGS
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCcCCcCcEEEEEeECCEEEeecCCCCchhhc
Confidence 5778899999999999999999998765 45554 56653 5566666554
No 155
>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=80.82 E-value=6.1 Score=34.95 Aligned_cols=64 Identities=36% Similarity=0.532 Sum_probs=41.8
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHh--CCC------CCceeEee--C--Ce-ecCCC-------------CcccccCcCCC
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF--A--GK-QLEDG-------------RTLADYNIQKE 64 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~--gip------~~~qrL~~--~--G~-~L~d~-------------~tL~~~gi~~~ 64 (156)
..+.+.|-..+||.++|++|-... +.| +++.-|.+ + |+ .|.|. .||.+|+|.+|
T Consensus 202 ~~i~VkVLdCDTItQVKeKiLDavyk~~p~S~rp~~~d~dLEwr~~~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg 281 (539)
T PF08337_consen 202 EEIPVKVLDCDTITQVKEKILDAVYKNTPYSQRPRADDVDLEWRQGRGGRLILQDEDSTSKVEGGWKRLNTLAHYKVPDG 281 (539)
T ss_dssp TCEEEEEETTSBHHHHHHHHHHHHTTTS-GGGS--GGGEEEEEEETTSEEEEESSSSTTSEEETTEEE--BHHHHT--TT
T ss_pred ceEEEEEEecCcccHHHHHHHHHHHcCCCCCCCCCccccceeeecCCCCcccccCCCCCcccCCCceEeccHhhcCCCCC
Confidence 458889999999999999996553 333 24444432 2 23 45443 36999999999
Q ss_pred CEEEEEEEec
Q 031604 65 STLHLVLRLR 74 (156)
Q Consensus 65 stv~l~~~~~ 74 (156)
++|-|+.+..
T Consensus 282 a~vaLv~k~~ 291 (539)
T PF08337_consen 282 ATVALVPKQH 291 (539)
T ss_dssp EEEEEEES--
T ss_pred ceEEEeeccc
Confidence 9999987653
No 156
>cd01766 Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-fold modifier 1) is a post-translational UBL (ubiquitin-like) modifier with a tertiary structure similar to that of ubiquitin. Ufm1 is initially expressed as a precursor which undergoes C-terminal cleavage to expose a conserved glycine residue that is required for the conjugation reactions involving Ufm1.
Probab=80.77 E-value=10 Score=24.59 Aligned_cols=61 Identities=21% Similarity=0.268 Sum_probs=48.0
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceeEe-eCCeecCCCCcccccCcCCCCEEEEEEEec
Q 031604 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stv~l~~~~~ 74 (156)
.+.|+++.....+-.-.++++.+|+..--++ -+|--+...++-...=++.|+.+.|+-|.+
T Consensus 19 vlsVpE~aPftAvlkfaAEeFkv~~~TsAiiTndGvGINP~qtAGnvflkhgselrliPRDr 80 (82)
T cd01766 19 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRLIPRDR 80 (82)
T ss_pred EEeccccCchHHHHHHHHHhcCCCccceeEEecCccccChhhcccceeeecCCEeeeccccc
Confidence 4689888888888888889999998765555 556667777888888888899998886654
No 157
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=80.76 E-value=1.2 Score=24.46 Aligned_cols=27 Identities=33% Similarity=0.806 Sum_probs=16.0
Q ss_pred cCCCCccCCceEEeEeCCCC---ccCCceeEEEe
Q 031604 120 ECPNAECGAGTFMASHFDRH---YCGKCGLTYVY 150 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~~r~---~cg~c~~t~~~ 150 (156)
-|| .|+. +|..-.++. .|-+|+|.+-.
T Consensus 3 FCp--~C~n--lL~p~~~~~~~~~C~~C~Y~~~~ 32 (35)
T PF02150_consen 3 FCP--ECGN--LLYPKEDKEKRVACRTCGYEEPI 32 (35)
T ss_dssp BET--TTTS--BEEEEEETTTTEEESSSS-EEE-
T ss_pred eCC--CCCc--cceEcCCCccCcCCCCCCCccCC
Confidence 488 8975 443333333 49999998743
No 158
>KOG4250 consensus TANK binding protein kinase TBK1 [Signal transduction mechanisms]
Probab=80.72 E-value=4.8 Score=36.58 Aligned_cols=41 Identities=24% Similarity=0.488 Sum_probs=36.6
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCee
Q 031604 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ 49 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~ 49 (156)
+...+.+-++++.|+..+++.|+..+|+|.+.|-|+|.|..
T Consensus 323 ~~~~~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~~ 363 (732)
T KOG4250|consen 323 QATSHEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGGL 363 (732)
T ss_pred cceEEEEecChhhhHHHHHHHHHHhhCCCCccceeeeecCc
Confidence 34567888999999999999999999999999999998764
No 159
>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=80.37 E-value=4.6 Score=27.13 Aligned_cols=60 Identities=20% Similarity=0.356 Sum_probs=35.8
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCceeEeeC-Ce------ecCCCC---cc--cccCcCCCCEEEEEEEecCC
Q 031604 15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA-GK------QLEDGR---TL--ADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~-G~------~L~d~~---tL--~~~gi~~~stv~l~~~~~gg 76 (156)
+++....||.+|-+.|.+.. +....+|+.. |. .|-++. .| .++-+++|++|.+.....||
T Consensus 23 ~~~~~~~tV~dll~~L~~~~--~~~~~~lf~~~g~lr~~i~VlvN~~di~~l~g~~t~L~dgD~v~i~P~v~GG 94 (94)
T cd01764 23 LDGEKPVTVGDLLDYVASNL--LEERPDLFIEGGSVRPGIIVLINDTDWELLGEEDYILEDGDHVVFISTLHGG 94 (94)
T ss_pred ccCCCCCcHHHHHHHHHHhC--chhhhhhEecCCcccCCEEEEECCccccccCCcccCCCCcCEEEEECCCCCC
Confidence 34445679999999998776 2333333322 21 122221 23 35668899999987766665
No 160
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=79.49 E-value=1 Score=24.99 Aligned_cols=30 Identities=23% Similarity=0.542 Sum_probs=19.4
Q ss_pred cccCCCCccCCceEEeEe-----CCCCccCCceeEEE
Q 031604 118 RKECPNAECGAGTFMASH-----FDRHYCGKCGLTYV 149 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h-----~~r~~cg~c~~t~~ 149 (156)
+-.|| .|++.--...- .-+..|++|+..|.
T Consensus 2 ~i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 2 IITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EEECC--CCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 34688 78753333322 34788999998874
No 161
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=79.44 E-value=0.89 Score=31.59 Aligned_cols=32 Identities=31% Similarity=0.742 Sum_probs=21.8
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCceeEEEee
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGLTYVYQ 151 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~ 151 (156)
..+.|| .||+.-+=.. .+--.|.+||.+|...
T Consensus 8 tKR~Cp--~CG~kFYDLn-k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCP--SCGAKFYDLN-KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCC--CCcchhccCC-CCCccCCCCCCccCcc
Confidence 468999 8996443222 2556799999887543
No 162
>KOG2982 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.43 E-value=3 Score=34.60 Aligned_cols=57 Identities=12% Similarity=0.199 Sum_probs=45.4
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceeEee---CCee-----cCCCCcccccCcCCCCEEEEE
Q 031604 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQ-----LEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~---~G~~-----L~d~~tL~~~gi~~~stv~l~ 70 (156)
..-|+-+-||.|++..+....|+.+.+++|++ +|+. .+.+..|-.|.|++|+.+.+-
T Consensus 351 s~~I~~~~TV~D~~~~Ld~~VGvk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~lvq 415 (418)
T KOG2982|consen 351 SGLICMTRTVLDFMKILDPKVGVKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFLVQ 415 (418)
T ss_pred ceEEEeehHHHHHHHHhccccccccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEeeee
Confidence 34566678999999999999999999999986 3443 234567899999999988663
No 163
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=79.24 E-value=1.9 Score=36.81 Aligned_cols=31 Identities=32% Similarity=0.768 Sum_probs=22.1
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
+.+-.|| +|| |-|=++=.+.+-|-|||+++-
T Consensus 348 ~~~p~Cp--~Cg-~~m~S~G~~g~rC~kCg~~~~ 378 (421)
T COG1571 348 RVNPVCP--RCG-GRMKSAGRNGFRCKKCGTRAR 378 (421)
T ss_pred EcCCCCC--ccC-CchhhcCCCCcccccccccCC
Confidence 3467999 998 444444344799999999873
No 164
>PTZ00467 40S ribosomal protein S30; Provisional
Probab=79.20 E-value=0.63 Score=29.32 Aligned_cols=26 Identities=27% Similarity=0.321 Sum_probs=21.0
Q ss_pred cCCccccccccccCCcccccccceee
Q 031604 74 RGGAKKRKKKTYTKPKKIKHKKKKVK 99 (156)
Q Consensus 74 ~gg~~k~~kk~~~~pk~~k~~kkk~k 99 (156)
.|.-.+++|+..+||+++++++++.+
T Consensus 5 HGSLarAGKVr~QTPkv~k~eKkk~~ 30 (66)
T PTZ00467 5 HGSLARAGKVKNQTPKVAKQEKPKQP 30 (66)
T ss_pred hhhhhhcccccCCCCCchhhhcccCC
Confidence 45556788999999999999977755
No 165
>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=79.20 E-value=6.3 Score=26.31 Aligned_cols=38 Identities=24% Similarity=0.416 Sum_probs=32.0
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe-eCCe
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGK 48 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~ 48 (156)
..+++.|++.+|=.++|+.|+..+|+++...+.+ +.|+
T Consensus 21 n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk 59 (91)
T PF00276_consen 21 NQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGK 59 (91)
T ss_dssp SEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSE
T ss_pred CEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCC
Confidence 6789999999999999999999999998766443 5554
No 166
>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]
Probab=79.18 E-value=4.1 Score=34.93 Aligned_cols=72 Identities=14% Similarity=0.284 Sum_probs=58.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--eCCeecCC---CCcccccCcCCCCEEEEEEEe
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d---~~tL~~~gi~~~stv~l~~~~ 73 (156)
+|.||.++|..++-.++.++-+..+++.+.+..++......|- |--+...+ +++|.++.+.+...|.|+-+-
T Consensus 316 rLqiRLPdGssfte~Fps~~vL~~vr~yvrq~~~i~~g~f~LatpyPRReft~eDy~KtllEl~L~psaalvvlpk~ 392 (506)
T KOG2507|consen 316 RLQIRLPDGSSFTEKFPSTSVLRMVRDYVRQNQTIGLGAFDLATPYPRREFTDEDYDKTLLELRLFPSAALVVLPKK 392 (506)
T ss_pred EEEEecCCccchhhcCCcchHHHHHHHHHHhcccccccceeeccccccccccchhhhhhHHHhccCCcceEEEEecC
Confidence 5789999999999999999999999999998888877766664 77776643 378999999988887766443
No 167
>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=78.89 E-value=13 Score=23.95 Aligned_cols=41 Identities=29% Similarity=0.272 Sum_probs=31.6
Q ss_pred EEEEeCCCC----EEEEEecCCCcHHHHHHHHHHHhCC--CCCceeE
Q 031604 3 IFVKTLTGK----TITLEVESSDTIDNVKAKIQDKEGI--PPDQQRL 43 (156)
Q Consensus 3 I~Vk~~~g~----~~~l~V~~~~TV~~LK~~I~~~~gi--p~~~qrL 43 (156)
|.|-..++. ...|.|++++|+.++-+++..++++ .++...|
T Consensus 5 lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L 51 (93)
T PF00788_consen 5 LRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCL 51 (93)
T ss_dssp EEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEE
T ss_pred EEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEE
Confidence 344444555 7889999999999999999999998 3344566
No 168
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=78.39 E-value=1.5 Score=24.08 Aligned_cols=27 Identities=30% Similarity=0.683 Sum_probs=14.3
Q ss_pred cCCCCccCCceEEe----EeCCCCccCCceeEE
Q 031604 120 ECPNAECGAGTFMA----SHFDRHYCGKCGLTY 148 (156)
Q Consensus 120 ~cp~~~c~~g~fma----~h~~r~~cg~c~~t~ 148 (156)
-|| .||.-+-.. .+..|+.|..||...
T Consensus 2 fC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCP--QCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-T--TT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccc--cccChhhhhcCCCCCccceECCCCCCEE
Confidence 488 787554332 335699999998653
No 169
>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=77.15 E-value=13 Score=23.89 Aligned_cols=35 Identities=29% Similarity=0.448 Sum_probs=29.2
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCC--CCceeEe
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIP--PDQQRLI 44 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip--~~~qrL~ 44 (156)
+...+|.|+.++|..++-..+.+++++. ++...|+
T Consensus 12 ~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~ 48 (87)
T cd01768 12 GTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALV 48 (87)
T ss_pred ccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEE
Confidence 5568899999999999999999999987 4445554
No 170
>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=76.75 E-value=5.5 Score=27.42 Aligned_cols=57 Identities=14% Similarity=0.173 Sum_probs=38.5
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCc-eeEeeCCeecCCCCcccccCc---CCCCEEEEEE
Q 031604 15 LEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADYNI---QKESTLHLVL 71 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~-qrL~~~G~~L~d~~tL~~~gi---~~~stv~l~~ 71 (156)
+-|+.+.||++|...|..+..++++. +-|+.++..+..+.++++.=- .++.-|++..
T Consensus 37 fLvp~~~tv~qf~~~ir~rl~l~~~~alfl~Vn~~lp~~s~tm~elY~~~kdeDGFLY~~Y 97 (104)
T PF02991_consen 37 FLVPKDLTVGQFVYIIRKRLQLSPEQALFLFVNNTLPSTSSTMGELYEKYKDEDGFLYMTY 97 (104)
T ss_dssp EEEETTSBHHHHHHHHHHHTT--TTS-EEEEBTTBESSTTSBHHHHHHHHB-TTSSEEEEE
T ss_pred EEEcCCCchhhHHHHhhhhhcCCCCceEEEEEcCcccchhhHHHHHHHHhCCCCCeEEEEe
Confidence 34889999999999999999998764 556677766677777765411 2344565543
No 171
>PF11069 DUF2870: Protein of unknown function (DUF2870); InterPro: IPR021298 This is a eukaryotic family of proteins with unknown function.
Probab=76.52 E-value=3.4 Score=28.18 Aligned_cols=37 Identities=32% Similarity=0.639 Sum_probs=27.4
Q ss_pred eEeeCCeecCCCCccccc-CcCCCCEEEEEEEecCCcc
Q 031604 42 RLIFAGKQLEDGRTLADY-NIQKESTLHLVLRLRGGAK 78 (156)
Q Consensus 42 rL~~~G~~L~d~~tL~~~-gi~~~stv~l~~~~~gg~~ 78 (156)
.|.|.|+.|..+.+|++| |-.+-+.|.|-+...|.+.
T Consensus 3 ~LW~aGK~l~~~k~l~dy~GkNEKtKiivKl~~~g~g~ 40 (98)
T PF11069_consen 3 QLWWAGKELQRGKKLSDYIGKNEKTKIIVKLQKRGQGP 40 (98)
T ss_pred eEEeccccccCCCcHHHhcCCCcceeEEEEeccCCCCC
Confidence 588999999999999999 3344455666666666654
No 172
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=76.44 E-value=0.83 Score=26.16 Aligned_cols=24 Identities=38% Similarity=0.834 Sum_probs=16.6
Q ss_pred ecccCCCCccCCceEEeEe--CCCCccCC
Q 031604 117 LRKECPNAECGAGTFMASH--FDRHYCGK 143 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h--~~r~~cg~ 143 (156)
+...|+ .|+ +.|+..| .+.|.|..
T Consensus 12 ~~~~C~--~C~-~~FC~~Hr~~e~H~C~~ 37 (43)
T PF01428_consen 12 LPFKCK--HCG-KSFCLKHRLPEDHNCSK 37 (43)
T ss_dssp SHEE-T--TTS--EE-TTTHSTTTCT-SS
T ss_pred CCeECC--CCC-cccCccccCccccCCcc
Confidence 678899 898 9999999 58888874
No 173
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=76.03 E-value=0.81 Score=28.80 Aligned_cols=17 Identities=29% Similarity=0.507 Sum_probs=13.9
Q ss_pred CCccCCceeEEEeecCC
Q 031604 138 RHYCGKCGLTYVYQKAG 154 (156)
Q Consensus 138 r~~cg~c~~t~~~~~~~ 154 (156)
-.+|-+||||+.|+...
T Consensus 40 ~itCk~CgYtEfY~a~~ 56 (68)
T COG3478 40 VITCKNCGYTEFYSAKI 56 (68)
T ss_pred EEEeccCCchhheeccc
Confidence 46899999999888653
No 174
>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B.
Probab=75.72 E-value=6.8 Score=25.94 Aligned_cols=56 Identities=16% Similarity=0.289 Sum_probs=29.2
Q ss_pred EEec-CCCcHHHHHHHHH-HHhCCCCCc----eeEeeCCee----cCCCCcccccCcCCCCEEEEE
Q 031604 15 LEVE-SSDTIDNVKAKIQ-DKEGIPPDQ----QRLIFAGKQ----LEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 15 l~V~-~~~TV~~LK~~I~-~~~gip~~~----qrL~~~G~~----L~d~~tL~~~gi~~~stv~l~ 70 (156)
+.++ ..+|+.+|-+.|- ...|...-. .+++|.... -..+++|+++||.+|+.|.+.
T Consensus 2 v~~d~~~~TL~~lv~~Vlk~~Lg~~~P~v~~~~~ilyd~de~~~~~~l~k~L~elgi~~gs~L~v~ 67 (87)
T PF14732_consen 2 VKVDTKKMTLGDLVEKVLKKKLGMNEPDVSVGGTILYDSDEEEYDDNLPKKLSELGIVNGSILTVD 67 (87)
T ss_dssp EEE-TTT-BHHHHHHHCCCCCS--SSEEEEES-EEEE-SSSSSSTTCTTSBGGGGT--TT-EEEEE
T ss_pred EEEechhCcHHHHHHHHHHhccCCCCCEEEeCCCEEEcCCcchhhhcccCChhHcCCCCCCEEEEE
Confidence 3444 4689999999874 355544322 233343322 112478999999999988765
No 175
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=75.32 E-value=2.2 Score=24.29 Aligned_cols=28 Identities=29% Similarity=0.755 Sum_probs=19.1
Q ss_pred cCCCCccCCceEEeEeC-CCCccCCceeEEE
Q 031604 120 ECPNAECGAGTFMASHF-DRHYCGKCGLTYV 149 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~-~r~~cg~c~~t~~ 149 (156)
.|| .||...+...+. .-..|..||+..-
T Consensus 2 ~Cp--~Cg~~~~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp SBT--TTSSSEEEEETTTTEEEETTT-BBEE
T ss_pred CCc--CCcCCceEEcCCCCeEECCCCCCEee
Confidence 599 898876555543 4558999998653
No 176
>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor. Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.
Probab=75.01 E-value=13 Score=24.23 Aligned_cols=38 Identities=5% Similarity=0.158 Sum_probs=33.6
Q ss_pred EEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031604 4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ 41 (156)
Q Consensus 4 ~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~q 41 (156)
.|-.++|+...+.|.|++|+.|+-+.+....++.|++-
T Consensus 3 ~V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh 40 (77)
T cd01818 3 WVCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEH 40 (77)
T ss_pred EEECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHh
Confidence 35567899999999999999999999999999998764
No 177
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=74.72 E-value=1.5 Score=24.24 Aligned_cols=29 Identities=28% Similarity=0.624 Sum_probs=17.4
Q ss_pred cccCCCCccCCceEEeEe-----CCCCccCCceeEE
Q 031604 118 RKECPNAECGAGTFMASH-----FDRHYCGKCGLTY 148 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h-----~~r~~cg~c~~t~ 148 (156)
+-.|| .|++---.++. .-...|++|+.+|
T Consensus 2 ~i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 34688 78743222222 2357799999887
No 178
>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=73.98 E-value=26 Score=24.04 Aligned_cols=63 Identities=29% Similarity=0.307 Sum_probs=42.3
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHh------CCCCC-ceeEeeCCe--ecCCCCcccccC-----cCCCCEEEEEEEe
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKE------GIPPD-QQRLIFAGK--QLEDGRTLADYN-----IQKESTLHLVLRL 73 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~------gip~~-~qrL~~~G~--~L~d~~tL~~~g-----i~~~stv~l~~~~ 73 (156)
..+++.+++++|+.+|.+.+-... .-+++ +..|--.|+ -|..+..|.+|. +..+..++|++..
T Consensus 29 ~~~t~~v~~~~~p~~li~~~l~k~~~~~~~~~~~~~dyvLkV~G~~Eyl~~~~~L~~~~yIr~cl~~~~~~~L~L~~ 105 (108)
T smart00144 29 QTKTLKVNPNCTPDSVLAQAFTKMLSLHDQVDPTSEDYILKVCGRDEYLLGDHPLGSFEYIRNCLKNGREPHLVLMT 105 (108)
T ss_pred eeEEEEECCCCCHHHHHHHHHHHHHhccccccCCCCcEEEEecCcEEEEeCCeeeechHHHHHHHhcCCCceEEEEe
Confidence 568999999999999999886651 12222 445555564 355666676663 4667788887654
No 179
>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27). SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.
Probab=73.41 E-value=10 Score=25.29 Aligned_cols=40 Identities=23% Similarity=0.290 Sum_probs=35.7
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ 41 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~q 41 (156)
+|.|-.++|..+.+++..+++.+++=+.+..+.|+|.+-+
T Consensus 3 ~L~V~Lpdg~~i~V~v~~s~~a~~Vleav~~kl~L~~e~~ 42 (87)
T cd01777 3 ELRIALPDKATVTVRVRKNATTDQVYQALVAKAGMDSYTQ 42 (87)
T ss_pred EEEEEccCCCEEEEEEEEcccHHHHHHHHHHHhCCCHHHH
Confidence 5667778999999999999999999999999999997654
No 180
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=73.35 E-value=10 Score=25.44 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=29.8
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCcee
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQR 42 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qr 42 (156)
.+.+.+.|++.+|=.++|+.|+..+++++...+
T Consensus 20 ~n~~~F~V~~~a~K~eIK~aie~lf~VkV~~Vn 52 (92)
T PRK05738 20 QNKYVFEVAPDATKPEIKAAVEKLFGVKVESVN 52 (92)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHcCCceeEEE
Confidence 468999999999999999999999999987664
No 181
>PLN00209 ribosomal protein S27; Provisional
Probab=73.35 E-value=3.6 Score=27.37 Aligned_cols=33 Identities=24% Similarity=0.360 Sum_probs=27.1
Q ss_pred EEecccCCCCccCCceEEeEeC-CCCccCCceeEEE
Q 031604 115 QRLRKECPNAECGAGTFMASHF-DRHYCGKCGLTYV 149 (156)
Q Consensus 115 ~~~~~~cp~~~c~~g~fma~h~-~r~~cg~c~~t~~ 149 (156)
.++.-.|| .|+.--....|. .-..|..||.+..
T Consensus 33 ~Fm~VkCp--~C~n~q~VFShA~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 33 FFMDVKCQ--GCFNITTVFSHSQTVVVCGSCQTVLC 66 (86)
T ss_pred EEEEEECC--CCCCeeEEEecCceEEEccccCCEee
Confidence 56778999 898877788884 6788999998874
No 182
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=73.20 E-value=10 Score=24.59 Aligned_cols=39 Identities=18% Similarity=0.372 Sum_probs=30.7
Q ss_pred CcHHHHHHHHHHHhCCCCCceeEe--eCCeecCCCCccccc
Q 031604 21 DTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLEDGRTLADY 59 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d~~tL~~~ 59 (156)
.|+.+|+.+..+.++++....+|. -+|..++|+.-+..+
T Consensus 19 ~sL~eL~~K~~~~l~l~~~~~~l~L~eDGT~VddEeyF~tL 59 (74)
T smart00266 19 SSLEELLSKVCDKLALPDSPVTLVLEEDGTIVDDEEYFQTL 59 (74)
T ss_pred CCHHHHHHHHHHHhCCCCCCcEEEEecCCcEEccHHHHhcC
Confidence 579999999999999996555554 589999887655544
No 183
>PRK00420 hypothetical protein; Validated
Probab=73.14 E-value=2.7 Score=29.44 Aligned_cols=31 Identities=32% Similarity=0.614 Sum_probs=23.4
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~ 150 (156)
+...|| .||+=.|.. .....+|..||..+..
T Consensus 22 l~~~CP--~Cg~pLf~l-k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 22 LSKHCP--VCGLPLFEL-KDGEVVCPVHGKVYIV 52 (112)
T ss_pred ccCCCC--CCCCcceec-CCCceECCCCCCeeee
Confidence 568999 898654443 6678999999986644
No 184
>COG5272 UBI4 Ubiquitin [Posttranslational modification, protein turnover, chaperones]
Probab=72.95 E-value=0.72 Score=28.07 Aligned_cols=42 Identities=12% Similarity=-0.077 Sum_probs=33.4
Q ss_pred cccccccCCcccccccceeeeeeeeeEEEcCCCeEEEecccCC
Q 031604 80 RKKKTYTKPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECP 122 (156)
Q Consensus 80 ~~kk~~~~pk~~k~~kkk~k~~v~k~y~vd~~g~~~~~~~~cp 122 (156)
+.++.+++|++++++..+..+.++. +.+++.+.-.+....||
T Consensus 4 ~~~~~~~~~~k~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 45 (57)
T COG5272 4 PIKKATGGAAKPESQLAKAKDTRPE-KQYAEQDSQLNEMALMD 45 (57)
T ss_pred cccccccccccccchHHHHhhccch-hhhhhhccChhhhhccc
Confidence 4578899999999999999999999 88876555555555566
No 185
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=72.84 E-value=3.9 Score=27.14 Aligned_cols=33 Identities=27% Similarity=0.515 Sum_probs=27.1
Q ss_pred EEecccCCCCccCCceEEeEeC-CCCccCCceeEEE
Q 031604 115 QRLRKECPNAECGAGTFMASHF-DRHYCGKCGLTYV 149 (156)
Q Consensus 115 ~~~~~~cp~~~c~~g~fma~h~-~r~~cg~c~~t~~ 149 (156)
.++.-.|| .|+.---...|. ....|..||.++.
T Consensus 32 ~Fm~VkCp--~C~n~q~VFShA~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 32 YFMDVKCP--GCSQITTVFSHAQTVVLCGGCSSQLC 65 (85)
T ss_pred eEEEEECC--CCCCeeEEEecCceEEEccccCCEee
Confidence 56678999 898877778884 6888999998874
No 186
>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=72.37 E-value=7.4 Score=27.13 Aligned_cols=57 Identities=14% Similarity=0.146 Sum_probs=39.3
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCc-eeEeeCCeecCCCCccccc----CcCCCCEEEEEEE
Q 031604 15 LEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADY----NIQKESTLHLVLR 72 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~-qrL~~~G~~L~d~~tL~~~----gi~~~stv~l~~~ 72 (156)
+-|+.+.||+++...|.....+++++ .-|+.++.....+.+++++ .. ++.-|+|...
T Consensus 45 flVp~~~tv~~f~~~irk~l~l~~~~slfl~Vn~~~p~~~~~~~~lY~~~kd-~DGfLyl~Ys 106 (112)
T cd01611 45 YLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNSLPPTSATMSQLYEEHKD-EDGFLYMTYS 106 (112)
T ss_pred EEecCCCCHHHHHHHHHHHhCCCccceEEEEECCccCCchhHHHHHHHHhCC-CCCEEEEEEe
Confidence 45999999999999999999988865 4455566544555666543 32 2446666543
No 187
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=72.31 E-value=3.8 Score=31.60 Aligned_cols=30 Identities=20% Similarity=0.450 Sum_probs=22.2
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCC
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPD 39 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~ 39 (156)
|-+|.+.|.+.+|..++|++|+.++|++..
T Consensus 132 GiPF~f~v~~gE~f~~tK~Rl~~rlgv~~k 161 (213)
T PF14533_consen 132 GIPFLFVVKPGETFSDTKERLQKRLGVSDK 161 (213)
T ss_dssp EEEEEEEEETT--HHHHHHHHHHHH---HH
T ss_pred CCCEEEEeeCCCcHHHHHHHHHHHhCCChh
Confidence 557888999999999999999999999864
No 188
>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=72.05 E-value=21 Score=23.51 Aligned_cols=44 Identities=14% Similarity=0.178 Sum_probs=35.3
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeC
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 46 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~ 46 (156)
+..|+. +|.+..+.++..-|-+.|.++|...+.+|+...-|.|-
T Consensus 2 ~fKv~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYi 45 (82)
T cd06397 2 QFKSSF-LGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYI 45 (82)
T ss_pred eEEEEe-CCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEE
Confidence 445543 56777888888889999999999999999877777763
No 189
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=71.99 E-value=2.2 Score=30.52 Aligned_cols=31 Identities=13% Similarity=0.227 Sum_probs=21.4
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~ 150 (156)
..+.|| .||+.-+=. -.+--.|.+||.+|..
T Consensus 8 tKr~Cp--~cg~kFYDL-nk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICP--NTGSKFYDL-NRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCC--CcCcccccc-CCCCccCCCcCCccCc
Confidence 468999 898643322 2366789999988743
No 190
>KOG0007 consensus Splicing factor 3a, subunit 1 [RNA processing and modification]
Probab=71.88 E-value=1.9 Score=35.75 Aligned_cols=49 Identities=35% Similarity=0.575 Sum_probs=42.8
Q ss_pred CCCCEEEEEec-CCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcc
Q 031604 8 LTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL 56 (156)
Q Consensus 8 ~~g~~~~l~V~-~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL 56 (156)
.+|+...+.+. .+..+..||.++....+|+++-|.+.+.|..|.|..++
T Consensus 290 ~dg~~~~~~~~~~~~~~~~~k~k~~~~~~i~~~~q~~~~~~~~l~d~~~~ 339 (341)
T KOG0007|consen 290 ADGQVIKITVQSLSENVASLKEKIADESQIPANKQKLRGEGAFLKDNRSL 339 (341)
T ss_pred CCCceeeeccccccccccccccccccccccchhheeeccCCcccCccccc
Confidence 46778787777 78899999999999999999999999999999887444
No 191
>KOG4572 consensus Predicted DNA-binding transcription factor, interacts with stathmin [Transcription; General function prediction only; Signal transduction mechanisms]
Probab=71.45 E-value=6.5 Score=36.60 Aligned_cols=62 Identities=18% Similarity=0.386 Sum_probs=47.1
Q ss_pred CCCEEEEEec-CCCcHHHHHHHHHHHhCCCCCceeEe-eCCeecCCCCcccccCc--CCCCEEEEE
Q 031604 9 TGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNI--QKESTLHLV 70 (156)
Q Consensus 9 ~g~~~~l~V~-~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi--~~~stv~l~ 70 (156)
.|+..+++.. .++|+.+||.+|+...|+...+|.++ -+|..+..+..|..|.- .+.+-|++.
T Consensus 3 rGqaltFDleaetqT~adLk~aiqke~~~aIq~~tfl~egGecmaadkrl~e~StaGTdTnPiffF 68 (1424)
T KOG4572|consen 3 RGQALTFDLEAETQTFADLKDAIQKEVGHAIQDLTFLDEGGECMAADKRLAEISTAGTDTNPIFFF 68 (1424)
T ss_pred CCceeEEeecceeehHHHHHHHHHHHhchhhceeeeeecCCcCcccccchhhhccccCCCCceEEe
Confidence 4777888776 46799999999999999999998887 45667887887877762 233445554
No 192
>smart00314 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)
Probab=71.27 E-value=25 Score=22.75 Aligned_cols=35 Identities=26% Similarity=0.318 Sum_probs=29.1
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCC--CceeEe
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPP--DQQRLI 44 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~--~~qrL~ 44 (156)
+...+|.|++++|+.++-..+.++++++. +...|+
T Consensus 15 ~~~kti~v~~~tTa~~Vi~~~l~k~~l~~~~~~y~L~ 51 (90)
T smart00314 15 GTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLV 51 (90)
T ss_pred CcEEEEEECCCCCHHHHHHHHHHHhCCCCCcccEEEE
Confidence 56788999999999999999999999875 344554
No 193
>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=70.87 E-value=22 Score=22.93 Aligned_cols=61 Identities=16% Similarity=0.317 Sum_probs=37.7
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhC-CCCCceeEe------eCCeecCCCCcccccCcCCCCEEEEEEE
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKEG-IPPDQQRLI------FAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~g-ip~~~qrL~------~~G~~L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
+.|..-.+++.|+++|+..|.+++. +.|....+. -.|-.|+.+-.++|.= ..+++|.++++
T Consensus 3 kKFLhlt~~~~tl~~L~~eI~~~f~kLYP~~~~~~I~~LQD~~~cDLD~d~~V~DVf-~~~~~vrvi~~ 70 (73)
T PF10407_consen 3 KKFLHLTDPNNTLSQLKEEIEERFKKLYPNEPELEILSLQDSDGCDLDPDFLVKDVF-NSNNVVRVILK 70 (73)
T ss_pred cEEEEEeCCCCcHHHHHHHHHHHHHHHCCCCCCceEEEeecCCCCCCCcccEeeeee-ccCCEEEEEec
Confidence 3455567899999999999998874 344332221 1333455555555542 35777777664
No 194
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=70.60 E-value=13 Score=24.19 Aligned_cols=33 Identities=12% Similarity=0.214 Sum_probs=29.9
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceeE
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL 43 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL 43 (156)
+.+.+.|++..|=.++|+.|+..+++.+...+.
T Consensus 15 n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt 47 (77)
T TIGR03636 15 NKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNT 47 (77)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHhCCceEEEEe
Confidence 689999999999999999999999999877654
No 195
>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=70.31 E-value=25 Score=22.71 Aligned_cols=59 Identities=17% Similarity=0.272 Sum_probs=42.6
Q ss_pred EE-EEEecCCCcHHHHHHHHHHHhCCCCCceeEe-eCCeecCCCCcccccCcCCCCEEEEE
Q 031604 12 TI-TLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 12 ~~-~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
++ .+.|+++.....+-...++++.+|+..--++ -+|--+...++..+.-++.|+.|.|+
T Consensus 16 p~kv~sVPE~apftaVlkfaAeeF~vp~~tsaiItndG~GInP~QTag~vflKhGseLrli 76 (76)
T PF03671_consen 16 PYKVISVPEEAPFTAVLKFAAEEFKVPPATSAIITNDGVGINPQQTAGNVFLKHGSELRLI 76 (76)
T ss_dssp -EEEEEEETTSBHHHHHHHHHHHTTS-SSSEEEEESSS-EE-TTSBHHHHHHHT-SEEEEE
T ss_pred cceEEecCCCCchHHHHHHHHHHcCCCCceEEEEecCCcccccchhhhhhHhhcCcEeeeC
Confidence 44 4689999988888888899999999766666 56777778888877777888888763
No 196
>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=70.26 E-value=13 Score=24.36 Aligned_cols=39 Identities=15% Similarity=0.342 Sum_probs=30.2
Q ss_pred CcHHHHHHHHHHHhCCCCCceeEe--eCCeecCCCCccccc
Q 031604 21 DTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLEDGRTLADY 59 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d~~tL~~~ 59 (156)
.|+.+|+.+..+.++++....+|+ -+|..++|+.-+..+
T Consensus 21 ~sL~eL~~K~~~~l~l~~~~~~lvL~eDGTeVddEeYF~tL 61 (78)
T cd01615 21 SSLEELLSKACEKLKLPSAPVTLVLEEDGTEVDDEEYFQTL 61 (78)
T ss_pred CCHHHHHHHHHHHcCCCCCCeEEEEeCCCcEEccHHHHhcC
Confidence 579999999999999976555554 589999887655443
No 197
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=69.79 E-value=2.2 Score=26.62 Aligned_cols=25 Identities=28% Similarity=0.902 Sum_probs=20.2
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
..-.|. +||.- +-|.-..+|..|||
T Consensus 16 tHt~Cr--RCG~~---syh~qK~~CasCGy 40 (62)
T PRK04179 16 THIRCR--RCGRH---SYNVRKKYCAACGF 40 (62)
T ss_pred ccchhc--ccCcc---cccccccchhhcCC
Confidence 356798 99864 45888999999998
No 198
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=68.95 E-value=3.8 Score=26.90 Aligned_cols=35 Identities=17% Similarity=0.390 Sum_probs=15.6
Q ss_pred ecccCCCCccC-CceEEeEe-----CCCCccCCceeEEEeecC
Q 031604 117 LRKECPNAECG-AGTFMASH-----FDRHYCGKCGLTYVYQKA 153 (156)
Q Consensus 117 ~~~~cp~~~c~-~g~fma~h-----~~r~~cg~c~~t~~~~~~ 153 (156)
....|| .|+ ....-... .....|+.||+.|.+.-.
T Consensus 21 ~~F~CP--fC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~ 61 (81)
T PF05129_consen 21 KVFDCP--FCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKIN 61 (81)
T ss_dssp S----T--TT--SS-EEEEEETTTTEEEEEESSS--EEEEE--
T ss_pred ceEcCC--cCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccC
Confidence 368899 897 22222111 136789999999987654
No 199
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=68.36 E-value=2.6 Score=21.28 Aligned_cols=22 Identities=23% Similarity=0.502 Sum_probs=11.8
Q ss_pred ccCCceEEeEeCCCCccCCcee
Q 031604 125 ECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 125 ~c~~g~fma~h~~r~~cg~c~~ 146 (156)
+|+....=..+..++.|.+||.
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCcccCceEeCCCCCC
Confidence 4643222223356777888873
No 200
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=68.35 E-value=4.8 Score=21.71 Aligned_cols=30 Identities=37% Similarity=0.702 Sum_probs=20.1
Q ss_pred cCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031604 120 ECPNAECGAGTFMASHFDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~ 152 (156)
.|. +||+-+-+. ..|-..|..||+...|++
T Consensus 2 ~C~--~Cg~~~~~~-~~~~irC~~CG~RIlyK~ 31 (32)
T PF03604_consen 2 ICG--ECGAEVELK-PGDPIRCPECGHRILYKK 31 (32)
T ss_dssp BES--SSSSSE-BS-TSSTSSBSSSS-SEEBE-
T ss_pred CCC--cCCCeeEcC-CCCcEECCcCCCeEEEec
Confidence 477 788766633 467788999998887764
No 201
>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=67.98 E-value=17 Score=23.82 Aligned_cols=47 Identities=11% Similarity=0.130 Sum_probs=33.7
Q ss_pred CcHHHHHHHHHHHhCCCCCceeE--eeCCeecCCCCcccccCcCCCCEEEE
Q 031604 21 DTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~qrL--~~~G~~L~d~~tL~~~gi~~~stv~l 69 (156)
.|+.+|+.+..+..+++....+| .-+|..++|+.-+..+ .+++.+.+
T Consensus 21 ~sL~EL~~K~~~~l~~~~~~~~lvL~eDGT~Vd~EeyF~~L--pdnT~lm~ 69 (78)
T cd06539 21 SSLQELISKTLDALVITSGLVTLVLEEDGTVVDTEEFFQTL--GDNTHFMV 69 (78)
T ss_pred cCHHHHHHHHHHHhCCCCCCcEEEEeCCCCEEccHHHHhhC--CCCCEEEE
Confidence 57999999999999998655554 5689999887655543 24444443
No 202
>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=67.26 E-value=33 Score=23.40 Aligned_cols=35 Identities=20% Similarity=0.204 Sum_probs=28.6
Q ss_pred EEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC
Q 031604 4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP 38 (156)
Q Consensus 4 ~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~ 38 (156)
.|=-.++.-.++.++.++||+||-..+..++.++.
T Consensus 6 RIFr~D~Tf~Tls~~l~tTv~eli~~L~rK~~l~~ 40 (97)
T cd01775 6 RVFRSDGTFTTLSCPLNTTVSELIPQLAKKFYLPS 40 (97)
T ss_pred EEEecCCcEEEEEcCCcCcHHHHHHHHHHhhcCCC
Confidence 33334566678999999999999999999998877
No 203
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=66.80 E-value=17 Score=23.99 Aligned_cols=34 Identities=12% Similarity=0.211 Sum_probs=30.5
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeE
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL 43 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL 43 (156)
.+.+.+.|++..+=.++|+.|+..+++.+...+.
T Consensus 21 ~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT 54 (84)
T PRK14548 21 ENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNT 54 (84)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEe
Confidence 3689999999999999999999999999877654
No 204
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=66.41 E-value=5.6 Score=24.62 Aligned_cols=33 Identities=33% Similarity=0.675 Sum_probs=27.4
Q ss_pred EEecccCCCCccCCceEEeEeC-CCCccCCceeEEE
Q 031604 115 QRLRKECPNAECGAGTFMASHF-DRHYCGKCGLTYV 149 (156)
Q Consensus 115 ~~~~~~cp~~~c~~g~fma~h~-~r~~cg~c~~t~~ 149 (156)
.+++-.|| .|+.-.....|. .-..|..||.+..
T Consensus 8 ~F~~VkCp--~C~n~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 8 RFLKVKCP--DCGNEQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred eEEEEECC--CCCCeEEEEecCCcEEECcccCCCcc
Confidence 56778999 899888888895 6788999998873
No 205
>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=66.38 E-value=36 Score=22.64 Aligned_cols=60 Identities=23% Similarity=0.379 Sum_probs=42.5
Q ss_pred EEEEEecCCCcHHHHHHHHHHHh-C--CCC--C-ceeEeeCC--eecCCCCcccccCcCCCCEEEEEE
Q 031604 12 TITLEVESSDTIDNVKAKIQDKE-G--IPP--D-QQRLIFAG--KQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~-g--ip~--~-~qrL~~~G--~~L~d~~tL~~~gi~~~stv~l~~ 71 (156)
...+.|+..+|+.++=++++... | +++ . ..++-.+| +.+..+.++++-||.+-..|.+..
T Consensus 16 ~~Lv~VDt~dTmdqVA~k~A~HsVGrRV~~~pg~~lrVr~~g~~~~~p~~~tVaeagl~P~e~vev~~ 83 (85)
T PF06234_consen 16 LQLVPVDTEDTMDQVAAKVAHHSVGRRVAPRPGAPLRVRRQGDTQPFPRSMTVAEAGLQPMEWVEVRF 83 (85)
T ss_dssp EEEEEEETT-BHHHHHHHHHTTTTTTSS---TTSEEEEEETTTSSEE-TT-BGGGHT--TTEEEEEEE
T ss_pred EEEEEeCCCCcHHHHHHHHhhhhcceecCCCCCCEEEEEecCCCccCCCccEehhcCCCcceEEEEEE
Confidence 45678999999999999997653 3 333 2 45666888 899999999999999999888764
No 206
>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=66.24 E-value=33 Score=22.15 Aligned_cols=47 Identities=23% Similarity=0.345 Sum_probs=39.0
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCC--eecC
Q 031604 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG--KQLE 51 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G--~~L~ 51 (156)
|-.++|+.-.+.+.|.+||.|+-..+.++-|++++..-++.-| ++|+
T Consensus 4 V~LPdg~~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~ 52 (73)
T cd01817 4 VILPDGSTTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLV 52 (73)
T ss_pred EECCCCCeEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCcccc
Confidence 4457889999999999999999999999999999887776545 3554
No 207
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=65.53 E-value=6.2 Score=23.90 Aligned_cols=22 Identities=32% Similarity=0.998 Sum_probs=15.8
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
-..|| .||+ .+...+.|..||+
T Consensus 26 l~~c~--~cg~-----~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 26 LVKCP--NCGE-----PKLPHRVCPSCGY 47 (56)
T ss_dssp EEESS--SSSS-----EESTTSBCTTTBB
T ss_pred eeeec--cCCC-----EecccEeeCCCCe
Confidence 36799 8985 4555678999983
No 208
>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=65.19 E-value=8.5 Score=30.40 Aligned_cols=73 Identities=18% Similarity=0.418 Sum_probs=47.3
Q ss_pred EEEEEeCCC--CEEE----EEecCCCcHHHHHHHHHHHhCCCCCceeEeeC----C--eecCCCCcccccCcCCCCEEEE
Q 031604 2 QIFVKTLTG--KTIT----LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA----G--KQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~g--~~~~----l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~----G--~~L~d~~tL~~~gi~~~stv~l 69 (156)
-||+|..+- +++. +-|+.+++|++|-..|.+..|+|++..-++|. + ..++...++....|++|+.|.+
T Consensus 70 LlFlK~fDp~~q~L~~iGh~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~~~ie~i~~~~t~~~~el~~GdIi~f 149 (249)
T PF12436_consen 70 LLFLKYFDPETQTLRYIGHVYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKPNMIEPIDPNQTFEKAELQDGDIICF 149 (249)
T ss_dssp EEEEEEEETTTTEEEEEEEEEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEETTEEEE--SSSBHHHTT--TTEEEEE
T ss_pred EEEEEeeCCCCCEEEEEeEEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEeccceeeEcCCCCchhhcccCCCCEEEE
Confidence 467776542 3332 46899999999999999999999976555553 2 3577889999999999999987
Q ss_pred EEEec
Q 031604 70 VLRLR 74 (156)
Q Consensus 70 ~~~~~ 74 (156)
-....
T Consensus 150 Q~~~~ 154 (249)
T PF12436_consen 150 QRAPS 154 (249)
T ss_dssp EE--G
T ss_pred Eeccc
Confidence 76554
No 209
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=64.96 E-value=17 Score=24.59 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=29.8
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeE
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL 43 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL 43 (156)
.+.+.+.|++.+|=.++|+.+++.+|+-+.....
T Consensus 21 ~nk~vF~V~~~AtK~~IK~AvE~lF~VkV~kVNT 54 (94)
T COG0089 21 ENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNT 54 (94)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEE
Confidence 4689999999999999999999999988776543
No 210
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=64.57 E-value=4.9 Score=32.04 Aligned_cols=62 Identities=19% Similarity=0.358 Sum_probs=36.7
Q ss_pred cccccccceeeeeeeeeEEEcCCCeEEEecccCCCCccCCceEEeEe--------------CCCCccCCceeEEEeecCC
Q 031604 89 KKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMASH--------------FDRHYCGKCGLTYVYQKAG 154 (156)
Q Consensus 89 k~~k~~kkk~k~~v~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h--------------~~r~~cg~c~~t~~~~~~~ 154 (156)
+...-.||-+.+.-.-+---. ++-.|-.||.+.|..=.-++.- .-|..||.|..||.|+...
T Consensus 98 r~aPpGKKYVRCPCNCLLICk----~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~ 173 (256)
T PF09788_consen 98 RNAPPGKKYVRCPCNCLLICK----SSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLT 173 (256)
T ss_pred cCCCCCCeeEecCCceEEEee----cccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCC
Confidence 344445555655443333222 1335899998889742222221 1388999999999998543
No 211
>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=64.44 E-value=22 Score=28.08 Aligned_cols=35 Identities=20% Similarity=0.358 Sum_probs=27.8
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 44 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~ 44 (156)
...|.++++..+|-.+|-++|++..+++|+.+||+
T Consensus 189 ~~~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~ 223 (249)
T PF12436_consen 189 DPEFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFF 223 (249)
T ss_dssp ---EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE
T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHCCChHHEEEE
Confidence 34799999999999999999999999999999886
No 212
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=64.24 E-value=8.1 Score=22.31 Aligned_cols=31 Identities=32% Similarity=0.674 Sum_probs=23.4
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031604 119 KECPNAECGAGTFMASHFDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~ 152 (156)
+.|. +||.-+-+- -.+-..|..||+-..|++
T Consensus 3 Y~C~--~Cg~~~~~~-~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 3 YICG--ECGRENEIK-SKDVVRCRECGYRILYKK 33 (44)
T ss_pred EECC--CCCCEeecC-CCCceECCCCCceEEEEe
Confidence 5688 898655543 568888999999887775
No 213
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=63.79 E-value=3.8 Score=28.01 Aligned_cols=32 Identities=31% Similarity=0.736 Sum_probs=19.5
Q ss_pred cccCCCCccCCceEEeE----eCCCCccCCceeEEEeec
Q 031604 118 RKECPNAECGAGTFMAS----HFDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~----h~~r~~cg~c~~t~~~~~ 152 (156)
...|| .|+. .-+.. ......|..||+-+-.+-
T Consensus 21 ~f~CP--~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~~V 56 (99)
T PRK14892 21 IFECP--RCGK-VSISVKIKKNIAIITCGNCGLYTEFEV 56 (99)
T ss_pred EeECC--CCCC-eEeeeecCCCcceEECCCCCCccCEEC
Confidence 46799 8984 22220 113567999998765543
No 214
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=63.35 E-value=2.3 Score=36.69 Aligned_cols=59 Identities=24% Similarity=0.264 Sum_probs=50.1
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEE
Q 031604 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~ 72 (156)
.++.+..-|-++|...|+...||+-+..+.+.+|++|.-..||.+-|+..+..+.+.+.
T Consensus 53 l~k~sL~i~Gselqa~iakklgi~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~~ 111 (568)
T KOG2561|consen 53 LKKCSLHITGSELQALIAKKLGIKENHVKCIINGKILSCRKTLAEQGLKINQELMVAVG 111 (568)
T ss_pred hhhcccccccHHHHHHHHHHcCCchhhhheeeccceeecccchhhhhhhhhhHHHHHhc
Confidence 34555667789999999999999999999999999999999999999987776665543
No 215
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=63.32 E-value=6.6 Score=22.41 Aligned_cols=26 Identities=38% Similarity=1.041 Sum_probs=19.8
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCce
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCG 145 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~ 145 (156)
+...|| .|+ ...|-.+..+.+|-.|+
T Consensus 16 L~~~Cp--~C~-~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCP--DCG-TPLMRDKDGKIYCVSCG 41 (41)
T ss_pred hcCccC--CCC-CeeEEecCCCEECCCCC
Confidence 578899 796 45565577788998885
No 216
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=63.25 E-value=28 Score=24.38 Aligned_cols=38 Identities=5% Similarity=0.198 Sum_probs=32.5
Q ss_pred EEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeec
Q 031604 13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL 50 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L 50 (156)
-...|++++|++.+-..|....+++++++-.+|=....
T Consensus 47 ~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sF 84 (116)
T KOG3439|consen 47 SKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSF 84 (116)
T ss_pred ceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCcc
Confidence 44689999999999999999999999998887765544
No 217
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=62.94 E-value=4.2 Score=25.27 Aligned_cols=30 Identities=23% Similarity=0.555 Sum_probs=20.7
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
-+.|| .||.-.--......+.|..||+++-
T Consensus 28 Sq~C~--~CG~~~~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCP--RCGHRNKKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCcc--CcccccccccccceEEcCCCCCEEC
Confidence 47899 8975333222456889999998763
No 218
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=62.90 E-value=7.6 Score=26.65 Aligned_cols=37 Identities=24% Similarity=0.624 Sum_probs=23.7
Q ss_pred ecccCCCCccCCceEE---eEe---CCCCccCCceeEEEeecCCC
Q 031604 117 LRKECPNAECGAGTFM---ASH---FDRHYCGKCGLTYVYQKAGG 155 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fm---a~h---~~r~~cg~c~~t~~~~~~~~ 155 (156)
....|| +|+.-..- ..- -.-..||.||+.|-+..+++
T Consensus 21 k~FtCp--~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l 63 (104)
T COG4888 21 KTFTCP--RCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPEL 63 (104)
T ss_pred ceEecC--ccCCeeeeEEEEEecCceeEEEcccCcceEEEecccc
Confidence 467899 99753332 111 12457999999987765543
No 219
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=62.06 E-value=2.7 Score=23.24 Aligned_cols=12 Identities=50% Similarity=1.076 Sum_probs=8.8
Q ss_pred CCccCCceeEEE
Q 031604 138 RHYCGKCGLTYV 149 (156)
Q Consensus 138 r~~cg~c~~t~~ 149 (156)
|+.|.+||.+|-
T Consensus 1 Rr~C~~Cg~~Yh 12 (36)
T PF05191_consen 1 RRICPKCGRIYH 12 (36)
T ss_dssp EEEETTTTEEEE
T ss_pred CcCcCCCCCccc
Confidence 567888887773
No 220
>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=62.05 E-value=15 Score=23.40 Aligned_cols=43 Identities=19% Similarity=0.306 Sum_probs=29.5
Q ss_pred CcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEE
Q 031604 21 DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l 69 (156)
.|+++|....++++|+++. ..+.-+|...+|=..+ .+|+.|++
T Consensus 26 ~SleeLl~ia~~kfg~~~~-~v~~~dgaeIdDI~~I-----RDgD~L~~ 68 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFSAT-KVLNEDGAEIDDIDVI-----RDGDHLYL 68 (69)
T ss_pred ccHHHHHHHHHHHhCCCce-EEEcCCCCEEeEEEEE-----EcCCEEEE
Confidence 7999999999999999743 3344556555554433 45777765
No 221
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=61.65 E-value=6.6 Score=20.78 Aligned_cols=29 Identities=31% Similarity=0.443 Sum_probs=15.4
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
.+-|| +||+-...+.-.-.-.|..|+..+
T Consensus 3 ~rfC~--~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCG--RCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-T--TT--BEEE-SSSS-EEESSSS-EE
T ss_pred CcccC--cCCccccCCCCcCEeECCCCcCEe
Confidence 46788 898765555444455688888765
No 222
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=60.97 E-value=5.7 Score=28.50 Aligned_cols=29 Identities=28% Similarity=0.582 Sum_probs=18.8
Q ss_pred cccCCCCccCCceEEeEe-CCCCccCCceeEE
Q 031604 118 RKECPNAECGAGTFMASH-FDRHYCGKCGLTY 148 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h-~~r~~cg~c~~t~ 148 (156)
=..||++.|+..+ ..- .+.+.|.+|+.+.
T Consensus 18 Y~aC~~~~C~kKv--~~~~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 18 YPACPNEKCNKKV--TENGDGSYRCEKCNKTV 47 (146)
T ss_dssp EEE-TSTTTS-B---EEETTTEEEETTTTEEE
T ss_pred ECCCCCccCCCEe--ecCCCcEEECCCCCCcC
Confidence 3579988897543 333 3579999999764
No 223
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=59.44 E-value=6.5 Score=22.65 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=16.7
Q ss_pred ccCCCCccCCc-eEEeEeCCCCccCCcee
Q 031604 119 KECPNAECGAG-TFMASHFDRHYCGKCGL 146 (156)
Q Consensus 119 ~~cp~~~c~~g-~fma~h~~r~~cg~c~~ 146 (156)
..|| +||.- ++-.....++.|..|++
T Consensus 19 ~~CP--~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCP--HCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCC--CCCCeeeEEeCCCCeEECCCCCC
Confidence 5699 99752 22222247888999975
No 224
>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=59.39 E-value=18 Score=23.94 Aligned_cols=58 Identities=5% Similarity=0.127 Sum_probs=37.7
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCc-eeEeeCCeec-CCCCcccccC--cCCCCEEEEEE
Q 031604 14 TLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQL-EDGRTLADYN--IQKESTLHLVL 71 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~-qrL~~~G~~L-~d~~tL~~~g--i~~~stv~l~~ 71 (156)
.+-|+.+.|++++...|..+.++.+++ +-|..+...+ ..+.+++++= -.++..|++..
T Consensus 19 kflv~~~~tv~~~~~~lrk~L~l~~~~slflyvnn~f~p~~d~~~g~LY~~~~~dGfLyi~Y 80 (87)
T cd01612 19 VFKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPDENVGNLYRCFGTNGELIVSY 80 (87)
T ss_pred EEEeCCCCCHHHHHHHHHHHhCCCccCeEEEEECCccCCCchhHHHHHHHhcCCCCEEEEEE
Confidence 356999999999999999999988765 4444555423 3444544331 03455666654
No 225
>cd06536 CIDE_N_ICAD CIDE_N domain of ICAD. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the 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 the CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease.
Probab=59.38 E-value=22 Score=23.31 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=29.4
Q ss_pred CcHHHHHHHHHHHhCCCCC--ceeE--eeCCeecCCCCccccc
Q 031604 21 DTIDNVKAKIQDKEGIPPD--QQRL--IFAGKQLEDGRTLADY 59 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~--~qrL--~~~G~~L~d~~tL~~~ 59 (156)
.|+.+|+.+..+.+.++.+ ..+| .-+|..++|+.-+..+
T Consensus 21 ~sL~eL~~K~~~~l~l~~~~~~~~lvL~eDGT~VddEeyF~tL 63 (80)
T cd06536 21 SSLEELRIKACESLGFDSSSAPITLVLAEDGTIVEDEDYFLCL 63 (80)
T ss_pred CCHHHHHHHHHHHhCCCCCCCceEEEEecCCcEEccHHHHhhC
Confidence 5799999999999999843 2444 4689999887655544
No 226
>CHL00030 rpl23 ribosomal protein L23
Probab=59.37 E-value=24 Score=23.74 Aligned_cols=32 Identities=22% Similarity=0.158 Sum_probs=28.2
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ 41 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~q 41 (156)
.+.+.+.|++++|=.++|+.|+..+++.+...
T Consensus 19 ~n~y~F~V~~~anK~eIK~avE~lf~VkV~~V 50 (93)
T CHL00030 19 KNQYTFDVDSGSTKTEIKHWIELFFGVKVIAV 50 (93)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHhCCeEEEE
Confidence 46899999999999999999999999876544
No 227
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=58.86 E-value=5 Score=31.41 Aligned_cols=37 Identities=24% Similarity=0.532 Sum_probs=26.2
Q ss_pred EecccCCCCccCCceEEeE-e-----------CCCCccCCceeEEEeec
Q 031604 116 RLRKECPNAECGAGTFMAS-H-----------FDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~-h-----------~~r~~cg~c~~t~~~~~ 152 (156)
..|-.||.+.|..=.-++- | .=|..||.|..||.|+.
T Consensus 136 SqRIACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tFLfnt 184 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETFLFNT 184 (275)
T ss_pred cceeccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCccceeehhh
Confidence 3678999999974332221 1 12889999999998874
No 228
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=57.46 E-value=5.1 Score=26.88 Aligned_cols=25 Identities=32% Similarity=0.953 Sum_probs=20.3
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
..-.|. +||.-.| |.-..+|+.|||
T Consensus 15 tHtlCr--RCG~~sy---H~qK~~CasCGy 39 (91)
T PTZ00073 15 THTLCR--RCGKRSF---HVQKKRCASCGY 39 (91)
T ss_pred Ccchhc--ccCcccc---ccccccchhcCC
Confidence 356798 9996554 888899999998
No 229
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=57.37 E-value=2.3 Score=28.19 Aligned_cols=26 Identities=27% Similarity=0.878 Sum_probs=20.8
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
...|- +||...| |.-.-.|+.|||.-
T Consensus 16 htlC~--RCG~~sy---H~QKstC~~CGYpa 41 (92)
T KOG3475|consen 16 HTLCR--RCGRRSY---HIQKSTCSSCGYPA 41 (92)
T ss_pred hHHHH--HhCchhh---hhhcccccccCCcc
Confidence 45677 8987655 98999999999864
No 230
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=57.17 E-value=8.1 Score=30.94 Aligned_cols=28 Identities=18% Similarity=0.511 Sum_probs=20.8
Q ss_pred cccCCCCccCCceEEeEeCC--CCccCCceeE
Q 031604 118 RKECPNAECGAGTFMASHFD--RHYCGKCGLT 147 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~--r~~cg~c~~t 147 (156)
...|| +||.-+-.....+ -++|..|+.+
T Consensus 245 g~pC~--~Cg~~I~~~~~~gR~t~~CP~CQ~~ 274 (274)
T PRK01103 245 GEPCR--RCGTPIEKIKQGGRSTFFCPRCQKR 274 (274)
T ss_pred CCCCC--CCCCeeEEEEECCCCcEECcCCCCc
Confidence 36799 8997776666654 5899999853
No 231
>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=56.75 E-value=8.4 Score=25.17 Aligned_cols=34 Identities=26% Similarity=0.486 Sum_probs=20.6
Q ss_pred HHHHHhCCCCCceeEe---eCCeecCCCCcccccCcC
Q 031604 29 KIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQ 62 (156)
Q Consensus 29 ~I~~~~gip~~~qrL~---~~G~~L~d~~tL~~~gi~ 62 (156)
.|.+...+.|+...|+ ..+.+|+-+.+|.++||.
T Consensus 2 ~IC~KCEfdp~htvLLrD~~s~e~LdLsKSLndlGir 38 (79)
T PF09469_consen 2 AICEKCEFDPEHTVLLRDYQSGEELDLSKSLNDLGIR 38 (79)
T ss_dssp HHHHHTT--TTSEEEES-SS---B--TTS-HHHHT-S
T ss_pred ccccccccCcceEEEeecCCCCCcccccccHHHhhHH
Confidence 4677788888888887 356789999999999997
No 232
>PF11706 zf-CGNR: CGNR zinc finger; InterPro: IPR021005 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family. ; PDB: 3H0N_A.
Probab=55.98 E-value=4.1 Score=23.65 Aligned_cols=26 Identities=31% Similarity=0.982 Sum_probs=11.5
Q ss_pred ccCCCCccCCceEE--eEeCCCCccC--Cce
Q 031604 119 KECPNAECGAGTFM--ASHFDRHYCG--KCG 145 (156)
Q Consensus 119 ~~cp~~~c~~g~fm--a~h~~r~~cg--~c~ 145 (156)
+.|.++.|+ .+|+ ..+..|-+|. .||
T Consensus 3 r~C~~~~C~-~~F~D~sr~~~RrwCsm~~Cg 32 (44)
T PF11706_consen 3 RRCANPDCR-WVFLDTSRNGRRRWCSMERCG 32 (44)
T ss_dssp EE--STT----EEE--SSS-----SS-HHHH
T ss_pred cccCCCCCc-eEEEeCCCCCCceecCccccc
Confidence 578888997 7888 5566777787 665
No 233
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.80 E-value=6.4 Score=24.39 Aligned_cols=10 Identities=40% Similarity=0.776 Sum_probs=5.9
Q ss_pred CCCCccCCce
Q 031604 136 FDRHYCGKCG 145 (156)
Q Consensus 136 ~~r~~cg~c~ 145 (156)
.+.+.|.+||
T Consensus 48 g~~Y~Cp~CG 57 (61)
T COG2888 48 GNPYRCPKCG 57 (61)
T ss_pred CCceECCCcC
Confidence 4556666665
No 234
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=55.34 E-value=5.9 Score=31.57 Aligned_cols=24 Identities=33% Similarity=0.721 Sum_probs=18.2
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031604 119 KECPNAECGAGTFMASHFDRHYCGKCGLTYV 149 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~ 149 (156)
+.|| .||. -+...+.|..||++.-
T Consensus 310 ~~C~--~cg~-----~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 310 KTCP--CCGH-----LSGRLFKCPRCGFVHD 333 (364)
T ss_pred cccc--ccCC-----ccceeEECCCCCCeeh
Confidence 7788 8986 3445689999998763
No 235
>cd06538 CIDE_N_FSP27 CIDE_N domain of FSP27 proteins. The CIDE-N (cell death-inducing DFF45-like effector, N-terminal) domain is found in the FSP27/CIDE-C protein, which has been identified as a n adipocyte lipid droplet protein that negatively regulates lipolysis and promotes triglyceride accumulation. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. The CIDE-N domain of FSP27 is sufficient to increase apoptosis in vitro when overexpressed.
Probab=55.13 E-value=30 Score=22.68 Aligned_cols=39 Identities=13% Similarity=0.141 Sum_probs=29.3
Q ss_pred CcHHHHHHHHHHHhCCCC-CceeEeeCCeecCCCCccccc
Q 031604 21 DTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADY 59 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~-~~qrL~~~G~~L~d~~tL~~~ 59 (156)
.|+.+|+.+..+.++++. ....|.-+|..++|+.-+..+
T Consensus 21 ~sL~eL~~K~~~~l~l~~~~~lvL~eDGT~Vd~EeyF~tL 60 (79)
T cd06538 21 DSLEDLLNKVLDALLLDCISSLVLDEDGTGVDTEEFFQAL 60 (79)
T ss_pred CCHHHHHHHHHHHcCCCCccEEEEecCCcEEccHHHHhhC
Confidence 589999999999999963 224455789999887655544
No 236
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=55.11 E-value=59 Score=21.50 Aligned_cols=73 Identities=15% Similarity=0.190 Sum_probs=35.4
Q ss_pred CEEEEEeC--CCC-EEEEEecCCCcHHHHHHHHH---HHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEEEEec
Q 031604 1 MQIFVKTL--TGK-TITLEVESSDTIDNVKAKIQ---DKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 1 M~I~Vk~~--~g~-~~~l~V~~~~TV~~LK~~I~---~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~ 74 (156)
|+|.|-.. ..+ .+.++|+..+||.+--++-- ..-.+..+..++=-.|+....+.. +++|+.|.+.-.+.
T Consensus 1 i~VeV~yA~p~~q~~~~l~vp~GtTv~~Ai~~Sgi~~~~p~idl~~~~vGIfGk~~~~d~~-----L~~GDRVEIYRPL~ 75 (84)
T PF03658_consen 1 IRVEVAYALPERQVILTLEVPEGTTVAQAIEASGILEQFPEIDLEKNKVGIFGKLVKLDTV-----LRDGDRVEIYRPLT 75 (84)
T ss_dssp EEEEEEEEETTCEEEEEEEEETT-BHHHHHHHHTHHHH-TT--TTTSEEEEEE-S--TT-B-------TT-EEEEE-S--
T ss_pred CEEEEEEECCCeEEEEEEECCCcCcHHHHHHHcCchhhCcccCcccceeeeeeeEcCCCCc-----CCCCCEEEEeccCc
Confidence 56666543 222 46789999999998766432 222455566666555666554444 45799999886665
Q ss_pred CCcc
Q 031604 75 GGAK 78 (156)
Q Consensus 75 gg~~ 78 (156)
-..+
T Consensus 76 ~DPk 79 (84)
T PF03658_consen 76 ADPK 79 (84)
T ss_dssp ----
T ss_pred cChh
Confidence 4443
No 237
>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=55.10 E-value=42 Score=21.61 Aligned_cols=32 Identities=22% Similarity=0.225 Sum_probs=21.5
Q ss_pred EEeCCCC-EEEEEecC-CCcHHHHHHHHHHHhCC
Q 031604 5 VKTLTGK-TITLEVES-SDTIDNVKAKIQDKEGI 36 (156)
Q Consensus 5 Vk~~~g~-~~~l~V~~-~~TV~~LK~~I~~~~gi 36 (156)
-|..+.+ ...|.++. ..+|.+||..|.+..++
T Consensus 3 YKFkS~k~~~~i~fdG~~Isv~dLKr~I~~~~~l 36 (74)
T PF08783_consen 3 YKFKSQKDYDTITFDGTSISVFDLKREIIEKKKL 36 (74)
T ss_dssp EEETT-SSEEEEEESSSEEEHHHHHHHHHHHHT-
T ss_pred EEecccCCccEEEECCCeeEHHHHHHHHHHHhCC
Confidence 3444443 45677774 57999999999887765
No 238
>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=54.99 E-value=62 Score=21.73 Aligned_cols=71 Identities=23% Similarity=0.393 Sum_probs=42.1
Q ss_pred EEEEEeC-CCCEEEEEecCCCcHHHHHHHHHHH--hCCCC---C-ceeEeeCCe--ecCCCCcccccC-----cCCCCEE
Q 031604 2 QIFVKTL-TGKTITLEVESSDTIDNVKAKIQDK--EGIPP---D-QQRLIFAGK--QLEDGRTLADYN-----IQKESTL 67 (156)
Q Consensus 2 ~I~Vk~~-~g~~~~l~V~~~~TV~~LK~~I~~~--~gip~---~-~qrL~~~G~--~L~d~~tL~~~g-----i~~~stv 67 (156)
.|.|... ....+++.++.++|+.+|-+++... .+..+ . +..|--.|+ -|..+..|.+|. +..+..+
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 3556655 3457999999999999999988766 22222 1 345545554 456777788774 2446666
Q ss_pred EEEEE
Q 031604 68 HLVLR 72 (156)
Q Consensus 68 ~l~~~ 72 (156)
+|++-
T Consensus 98 ~L~Lv 102 (106)
T PF00794_consen 98 HLVLV 102 (106)
T ss_dssp EEEEE
T ss_pred EEEEE
Confidence 66653
No 239
>cd01776 Rin1_RA Ubiquitin domain of RIN1 RAS effector. Rin1_RA RIN1 is a RAS effector that binds with specificity and high affinity to activated RAS via its carboxy-terminal RA (RAS-associated) domain. RIN1 competes directly with RAF1 for RAS binding and is thought to divert signaling away from RAF and the MAPK pathway while also shunting RAS signals through alternate pathways. In addition, Rin1 and Rin2 are Rab5-binding proteins, binding preferentially to the GTP-bound form, that enhance the GDP-GTP exchange reaction on Rab5 that regulate the docking and fusion processes of endocytic vesicles. In addition to the RA domain, RIN1 and RIN2 have an SH2 (Src homology 2) domain, a proline-rich SH3 domain, and a Vps9 domain.
Probab=54.78 E-value=47 Score=22.06 Aligned_cols=43 Identities=23% Similarity=0.213 Sum_probs=33.3
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCC-CCceeEe--eCCe--ecCCCC
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIP-PDQQRLI--FAGK--QLEDGR 54 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip-~~~qrL~--~~G~--~L~d~~ 54 (156)
.-+|.|.|..|+++|-+.++.++.|. |+...|+ -+|. +|.|+.
T Consensus 15 ~KTL~V~P~~tt~~vc~lcA~Kf~V~qPe~y~LFl~vdg~~~qLadd~ 62 (87)
T cd01776 15 GKTLLVRPYITTEDVCQLCAEKFKVTQPEEYSLFLFVEETWQQLAPDT 62 (87)
T ss_pred eeeeecCCCCcHHHHHHHHHHHhccCChhheeEEEEECCcEEEcCccc
Confidence 46799999999999999999999875 4666665 3443 676653
No 240
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=54.13 E-value=6.4 Score=21.08 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=10.0
Q ss_pred CCccCCceeEEEe
Q 031604 138 RHYCGKCGLTYVY 150 (156)
Q Consensus 138 r~~cg~c~~t~~~ 150 (156)
+|.|..||++|.-
T Consensus 1 ~~~C~~CGy~y~~ 13 (33)
T cd00350 1 KYVCPVCGYIYDG 13 (33)
T ss_pred CEECCCCCCEECC
Confidence 4679999998743
No 241
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=54.00 E-value=13 Score=26.46 Aligned_cols=32 Identities=25% Similarity=0.723 Sum_probs=22.6
Q ss_pred cccCCCCccCCceEEeEe------CCCCccCCceeEEEeec
Q 031604 118 RKECPNAECGAGTFMASH------FDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h------~~r~~cg~c~~t~~~~~ 152 (156)
...|| .|+..- .-.+ .-|+-|-.|+.||...-
T Consensus 30 ~~~cP--~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 30 KVNCP--RCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred cCcCC--CCCccc-eeeECCccccccccccCCcCcceeeec
Confidence 57899 897633 1233 35899999999997653
No 242
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=53.78 E-value=14 Score=30.81 Aligned_cols=65 Identities=17% Similarity=0.173 Sum_probs=50.0
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHh-CCCCCceeEeeCC---eecC--CCCcccccCcCCCCE
Q 031604 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE-GIPPDQQRLIFAG---KQLE--DGRTLADYNIQKEST 66 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~-gip~~~qrL~~~G---~~L~--d~~tL~~~gi~~~st 66 (156)
.|-||.++|+.....+..+++|.-|-.-+.... |.+-....|+.+- +.|+ .+.||.++||.+..+
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 SIQVRFPDGRRKQRKFLKSEPVQLLWSFCYSHMDGSDKKRFKLVQAIPASKTLDYGADATFKEAGLANSET 349 (356)
T ss_pred EEEEecCCccHHHHhhccccHHHHHHHHHHHhhcccccccceeeecccchhhhhccccchHHHhccCcccc
Confidence 377899999887777788999999888776554 5666778888665 5554 468999999987765
No 243
>cd06537 CIDE_N_B CIDE_N domain of CIDE-B 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, 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=53.68 E-value=39 Score=22.25 Aligned_cols=47 Identities=11% Similarity=0.087 Sum_probs=32.2
Q ss_pred CcHHHHHHHHHHHhCCCC-CceeEeeCCeecCCCCcccccCcCCCCEEEE
Q 031604 21 DTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~-~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l 69 (156)
.|+.+|+.+..+...++. ....|.-+|..++++.-+..+ .+++.+.+
T Consensus 21 ~sL~EL~~K~~~~L~~~~~~~lvLeeDGT~Vd~EeyF~tL--pdnT~lm~ 68 (81)
T cd06537 21 ASLQELLAKALETLLLSGVLTLVLEEDGTAVDSEDFFELL--EDDTCLMV 68 (81)
T ss_pred cCHHHHHHHHHHHhCCCCceEEEEecCCCEEccHHHHhhC--CCCCEEEE
Confidence 579999999999999873 334444689999887655443 24444443
No 244
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=53.65 E-value=3 Score=34.47 Aligned_cols=33 Identities=27% Similarity=0.725 Sum_probs=25.3
Q ss_pred ccCCCCccCCceEEeEeCCCCccCC-ceeEEEee
Q 031604 119 KECPNAECGAGTFMASHFDRHYCGK-CGLTYVYQ 151 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~-c~~t~~~~ 151 (156)
.-||++-||+|.+----.-+..|.. ||+.|+.+
T Consensus 316 VlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~ 349 (446)
T KOG0006|consen 316 VLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRE 349 (446)
T ss_pred EecCCCCCCcccccCCCCCcccCCCCchhHhHHH
Confidence 5689999999887655455788876 98888765
No 245
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=53.62 E-value=31 Score=25.64 Aligned_cols=39 Identities=10% Similarity=0.062 Sum_probs=32.8
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe-eCCe
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGK 48 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~ 48 (156)
.+.+.|.|++.+|=.++|..|+..+++.+...+.+ ..|+
T Consensus 22 ~N~ytF~V~~~anK~eIK~AVE~iF~VkV~~VNT~~~~~K 61 (158)
T PRK12280 22 KNVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKK 61 (158)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEecCCc
Confidence 46799999999999999999999999998776544 4443
No 246
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=53.49 E-value=13 Score=24.39 Aligned_cols=54 Identities=26% Similarity=0.359 Sum_probs=32.8
Q ss_pred cCCcccccccceeeeeeeeeEEEcCCCeEEEecccCCCCccCCceEEeEe-CCCCccCCceeEEE
Q 031604 86 TKPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMASH-FDRHYCGKCGLTYV 149 (156)
Q Consensus 86 ~~pk~~k~~kkk~k~~v~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h-~~r~~cg~c~~t~~ 149 (156)
.+|++++.++|+..|-- -. |+ -++...|| .|-.=.....| .....|+.|+..++
T Consensus 10 Ps~e~e~r~hK~krLvq-----~~-ns--yFm~VkC~--gc~~iT~vfSHaqtvVvc~~c~~il~ 64 (84)
T KOG1779|consen 10 PSPEKEKRKHKLKRLVQ-----SP-NS--YFMDVKCP--GCFKITTVFSHAQTVVVCEGCSTILC 64 (84)
T ss_pred CCHHHHhhhhhhhhhee-----CC-Cc--eEEEEEcC--CceEEEEEeecCceEEEcCCCceEEE
Confidence 34555666655444321 11 22 44557899 78555566788 57889999986664
No 247
>KOG4598 consensus Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=52.48 E-value=17 Score=33.43 Aligned_cols=57 Identities=16% Similarity=0.253 Sum_probs=42.7
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--e--CCeec--CCCCcccccCcCCCCEEEEE
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--F--AGKQL--EDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~--~G~~L--~d~~tL~~~gi~~~stv~l~ 70 (156)
-+.+.|+..+++..+|+.|++..+++.+..+|+ + +|..+ .++.+|+.+ .++.+|.+-
T Consensus 878 ~~kl~Vd~rmr~~AFKkHiE~~i~V~~~HFKi~R~~~~N~~~~S~~~NetLs~~--~~~~~iTI~ 940 (1203)
T KOG4598|consen 878 FHKLDVDSRMRVLAFKKHVEEQLEVDKDHFKIVRHASDNGSEASFMDNETLSGA--FQSCFITIK 940 (1203)
T ss_pred heeeeccceeeHHHHHHHHHHHhCcChhHeEEEEEecCCcchhhhccchhhhhh--cccceEEEE
Confidence 356889999999999999999999999988886 2 33333 356677754 356666553
No 248
>PF02192 PI3K_p85B: PI3-kinase family, p85-binding domain; InterPro: IPR003113 This is the region of the p110 phosphatidylinositol 3-kinase (PI3-Kinase) that binds the p85 subunit.; GO: 0046934 phosphatidylinositol-4,5-bisphosphate 3-kinase activity, 0007165 signal transduction, 0005942 phosphatidylinositol 3-kinase complex; PDB: 3HIZ_A 3HHM_A 2RD0_A 4A55_A 2Y3A_A 2V1Y_A.
Probab=52.36 E-value=22 Score=23.12 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=17.5
Q ss_pred EEEEecCCCcHHHHHHHHHHHh
Q 031604 13 ITLEVESSDTIDNVKAKIQDKE 34 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~ 34 (156)
+.++++.++|+.+||+.+-+..
T Consensus 2 i~l~~~~~~Tl~~iK~~lw~~A 23 (78)
T PF02192_consen 2 IPLRVSRDATLSEIKEELWEEA 23 (78)
T ss_dssp EEEEEETT-BHHHHHHHHHHHG
T ss_pred eEEEccCcCcHHHHHHHHHHHH
Confidence 5688999999999999985543
No 249
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=52.00 E-value=15 Score=22.37 Aligned_cols=34 Identities=24% Similarity=0.358 Sum_probs=23.3
Q ss_pred EEecccCCCCccCCceEEeEe-CCCCccCCceeEEEe
Q 031604 115 QRLRKECPNAECGAGTFMASH-FDRHYCGKCGLTYVY 150 (156)
Q Consensus 115 ~~~~~~cp~~~c~~g~fma~h-~~r~~cg~c~~t~~~ 150 (156)
.+++-+|| .|+.--....| .....|..||.+...
T Consensus 4 ~Fm~VkCp--~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 4 YFMDVKCP--GCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp -EEEEE-T--TT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred cEEEEECC--CCCCeeEEEecCCeEEEcccCCCEecC
Confidence 35778999 89888778888 468889999988743
No 250
>PRK11827 hypothetical protein; Provisional
Probab=51.76 E-value=9.2 Score=23.71 Aligned_cols=29 Identities=17% Similarity=0.457 Sum_probs=19.9
Q ss_pred cCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031604 120 ECPNAECGAGTFMASHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~ 150 (156)
.|| .|+.-...-...+...|..|++.|-.
T Consensus 10 aCP--~ckg~L~~~~~~~~Lic~~~~laYPI 38 (60)
T PRK11827 10 ACP--VCNGKLWYNQEKQELICKLDNLAFPL 38 (60)
T ss_pred ECC--CCCCcCeEcCCCCeEECCccCeeccc
Confidence 499 89743333333567899999998854
No 251
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=50.58 E-value=6.3 Score=19.47 Aligned_cols=21 Identities=43% Similarity=1.176 Sum_probs=13.3
Q ss_pred cCCCCccCCceEEeEeCCCCccCCcee
Q 031604 120 ECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
.|| .||+.+ .. +-..|..||.
T Consensus 1 ~Cp--~CG~~~--~~--~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCP--NCGAEI--ED--DAKFCPNCGT 21 (23)
T ss_pred CCc--ccCCCC--CC--cCcchhhhCC
Confidence 378 787633 22 5566888875
No 252
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=50.39 E-value=8.5 Score=23.55 Aligned_cols=22 Identities=36% Similarity=0.892 Sum_probs=13.8
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
-..|| .||. +.- .-+.|+.||+
T Consensus 27 l~~C~--~CG~--~~~---~H~vC~~CG~ 48 (57)
T PRK12286 27 LVECP--NCGE--PKL---PHRVCPSCGY 48 (57)
T ss_pred ceECC--CCCC--ccC---CeEECCCCCc
Confidence 46799 8974 322 3356888873
No 253
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=50.16 E-value=9.9 Score=21.28 Aligned_cols=25 Identities=28% Similarity=0.848 Sum_probs=13.7
Q ss_pred cCCCCccCCceEEeEe----CCCCccCCceeEE
Q 031604 120 ECPNAECGAGTFMASH----FDRHYCGKCGLTY 148 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h----~~r~~cg~c~~t~ 148 (156)
.|| +|+. -|... ..-++|.+|+-.+
T Consensus 1 ~CP--~C~~--~l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCP--RCGT--ELEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcC--CCCc--ccceEEECCEEEEECCCCCeEE
Confidence 377 7754 33332 1345677777554
No 254
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.85 E-value=8.2 Score=33.73 Aligned_cols=25 Identities=28% Similarity=0.700 Sum_probs=18.3
Q ss_pred cCCCCccCCceEEeEeC--CCCccCCceeEE
Q 031604 120 ECPNAECGAGTFMASHF--DRHYCGKCGLTY 148 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~--~r~~cg~c~~t~ 148 (156)
.|| +|. +-|..|. ++..|..||++.
T Consensus 224 ~C~--~C~--~~l~~h~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 224 CCP--NCD--VSLTYHKKEGKLRCHYCGYQE 250 (505)
T ss_pred CCC--CCC--CceEEecCCCeEEcCCCcCcC
Confidence 499 894 5788884 677788887765
No 255
>cd01782 AF6_RA_repeat1 Ubiquitin domain of AT-6, first repeat. The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
Probab=49.25 E-value=89 Score=21.81 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=29.6
Q ss_pred CEEEEEeCCCCE--EEEEecCCCcHHHHHHHHHHHhCCC
Q 031604 1 MQIFVKTLTGKT--ITLEVESSDTIDNVKAKIQDKEGIP 37 (156)
Q Consensus 1 M~I~Vk~~~g~~--~~l~V~~~~TV~~LK~~I~~~~gip 37 (156)
|+.+....+++. -.|.|+.++|+.++.+.+-+++.+.
T Consensus 24 mrf~~qd~~~k~atK~VrVsS~~tt~eVI~~LLeKFk~d 62 (112)
T cd01782 24 MRFYFQDGGEKVATKCIRVSSTATTRDVIDTLSEKFRPD 62 (112)
T ss_pred EEEEEEcCCCcEEEEEEEEecCCCHHHHHHHHHHHhccc
Confidence 667777766553 4589999999999999999998754
No 256
>PHA02942 putative transposase; Provisional
Probab=48.98 E-value=9.2 Score=32.27 Aligned_cols=27 Identities=33% Similarity=0.767 Sum_probs=18.2
Q ss_pred cccCCCCccCCceEEeEeCCC-CccCCceeEE
Q 031604 118 RKECPNAECGAGTFMASHFDR-HYCGKCGLTY 148 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r-~~cg~c~~t~ 148 (156)
-+.|| .||. .+....+| +.|..||++.
T Consensus 325 Sq~Cs--~CG~--~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCP--KCGH--KMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CccCC--CCCC--ccCcCCCCEEECCCCCCEe
Confidence 36799 8975 32222334 8899999876
No 257
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=48.72 E-value=12 Score=20.04 Aligned_cols=14 Identities=36% Similarity=0.937 Sum_probs=10.5
Q ss_pred cCCCCccCCceEEeEe
Q 031604 120 ECPNAECGAGTFMASH 135 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h 135 (156)
-|| .||.||.....
T Consensus 3 lcp--kcgvgvl~pvy 16 (36)
T PF09151_consen 3 LCP--KCGVGVLEPVY 16 (36)
T ss_dssp B-T--TTSSSBEEEEE
T ss_pred cCC--ccCceEEEEee
Confidence 589 99999987654
No 258
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=48.48 E-value=8 Score=27.93 Aligned_cols=36 Identities=36% Similarity=0.841 Sum_probs=23.8
Q ss_pred eeEEEcCCCeEEEecccCCCCccCCceEEeEeCCCCccCCceeE
Q 031604 104 QFYKVDDSGKVQRLRKECPNAECGAGTFMASHFDRHYCGKCGLT 147 (156)
Q Consensus 104 k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
.+|+.-..|++. ...|+ .|| -+| |..|.+|.+|+..
T Consensus 17 ~f~~~l~~~kl~--g~kC~--~CG-~v~---~PPr~~Cp~C~~~ 52 (140)
T COG1545 17 KFFKGLKEGKLL--GTKCK--KCG-RVY---FPPRAYCPKCGSE 52 (140)
T ss_pred HHhhhhhhCcEE--EEEcC--CCC-eEE---cCCcccCCCCCCC
Confidence 344333346666 48899 898 444 5678888888764
No 259
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.46 E-value=14 Score=24.28 Aligned_cols=26 Identities=31% Similarity=0.759 Sum_probs=18.9
Q ss_pred cCCCCccCCceEEeEeC--CCCccCCceeE
Q 031604 120 ECPNAECGAGTFMASHF--DRHYCGKCGLT 147 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~--~r~~cg~c~~t 147 (156)
-|| .|++...|..-. +-.+|.+|.-.
T Consensus 3 lCP--~C~v~l~~~~rs~vEiD~CPrCrGV 30 (88)
T COG3809 3 LCP--ICGVELVMSVRSGVEIDYCPRCRGV 30 (88)
T ss_pred ccC--cCCceeeeeeecCceeeeCCccccE
Confidence 488 788777777664 46789999643
No 260
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=46.68 E-value=7.8 Score=31.40 Aligned_cols=31 Identities=29% Similarity=0.525 Sum_probs=27.6
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
+.++-|| +||.-.++..|.....|.+|+..+
T Consensus 109 ~~~RFCg--~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCG--RCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCC--CCCCcCccccCceeeeCCCCCCcc
Confidence 3578999 999999999999999999999866
No 261
>smart00143 PI3K_p85B PI3-kinase family, p85-binding domain. Region of p110 PI3K that binds the p85 subunit.
Probab=46.56 E-value=28 Score=22.76 Aligned_cols=22 Identities=23% Similarity=0.388 Sum_probs=18.3
Q ss_pred EEEEecCCCcHHHHHHHHHHHh
Q 031604 13 ITLEVESSDTIDNVKAKIQDKE 34 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~ 34 (156)
+.+.|+.+.|+++||+.+-+..
T Consensus 2 i~l~v~~~aTl~~IK~~lw~~A 23 (78)
T smart00143 2 VTLRVLREATLSTIKHELFKQA 23 (78)
T ss_pred eeEEccccccHHHHHHHHHHHH
Confidence 4678999999999999996543
No 262
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=45.98 E-value=97 Score=21.29 Aligned_cols=36 Identities=25% Similarity=0.319 Sum_probs=28.1
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP 38 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~ 38 (156)
|+|-..+|++..|+|..-.+-.+++.++-.++|++.
T Consensus 3 i~~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~ 38 (105)
T PF14847_consen 3 IRFILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPE 38 (105)
T ss_dssp EEEEETTTEEEEEE--S--HHHHHHHHHHHHHTSS-
T ss_pred EEEECCCCcEEEEEECCCCCHHHHHHHHHHHcCCcc
Confidence 566677899999999999999999999999999987
No 263
>PF15616 TerY-C: TerY-C metal binding domain
Probab=44.92 E-value=19 Score=25.84 Aligned_cols=25 Identities=32% Similarity=0.840 Sum_probs=14.8
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031604 119 KECPNAECGAGTFMASHFDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~ 152 (156)
..|| .||+-..+|. | .||..++++.
T Consensus 78 PgCP--~CGn~~~fa~------C-~CGkl~Ci~g 102 (131)
T PF15616_consen 78 PGCP--HCGNQYAFAV------C-GCGKLFCIDG 102 (131)
T ss_pred CCCC--CCcChhcEEE------e-cCCCEEEeCC
Confidence 7899 8987644443 4 2555555444
No 264
>COG1977 MoaD Molybdopterin converting factor, small subunit [Coenzyme metabolism]
Probab=44.54 E-value=47 Score=21.58 Aligned_cols=60 Identities=12% Similarity=0.195 Sum_probs=34.0
Q ss_pred EEEE-ecCCCcHHHHHHHHHHHhC---CCCCcee-E-eeCCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 13 ITLE-VESSDTIDNVKAKIQDKEG---IPPDQQR-L-IFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 13 ~~l~-V~~~~TV~~LK~~I~~~~g---ip~~~qr-L-~~~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
..+. ...-.||++|.+.+.++.. ....... + ..+...+.+. +..|++|++|.+.-+..||
T Consensus 19 ~~~~~~~~~~tv~~L~~~l~~~~~~~~~~~~~~~~v~~~~~~~~~~~----~t~L~dGDeVa~~PPVsGG 84 (84)
T COG1977 19 EELEGLTVGATVGELEELLPKEGERWLLALEDNIVVNAANNEFLVGL----DTPLKDGDEVAFFPPVSGG 84 (84)
T ss_pred eeeecccHHHHHHHHHHHHHhhhhhHHhccCccceEEeeeceeeccc----cccCCCCCEEEEeCCCCCC
Confidence 3344 3446799999999866653 1111112 1 1333444332 2345679999987766665
No 265
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=43.99 E-value=12 Score=29.67 Aligned_cols=30 Identities=20% Similarity=0.366 Sum_probs=22.3
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
..+-|| +||.-.......-+..|+.|+..+
T Consensus 98 ~~~fC~--~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 98 SHRFCG--YCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred cCcccc--ccCCCCeecCCceeEECCCCCCEE
Confidence 368899 998755554445678899999876
No 266
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=43.64 E-value=19 Score=24.94 Aligned_cols=26 Identities=19% Similarity=0.432 Sum_probs=16.8
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
.+..|+ .||. ..+.+...+.|++||-
T Consensus 69 ~~~~C~--~Cg~--~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCW--DCSQ--VVEIHQHDAQCPHCHG 94 (113)
T ss_pred cEEEcc--cCCC--EEecCCcCccCcCCCC
Confidence 578899 8973 3233334455999983
No 267
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.30 E-value=18 Score=25.10 Aligned_cols=26 Identities=19% Similarity=0.461 Sum_probs=16.9
Q ss_pred ecccCCCCccCCceEEeEeCCC-CccCCcee
Q 031604 117 LRKECPNAECGAGTFMASHFDR-HYCGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r-~~cg~c~~ 146 (156)
.+-.|+ .||. +.+..... ..|++||-
T Consensus 69 ~~~~C~--~Cg~--~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCE--TCQQ--YVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcc--cCCC--eeecCCccCCcCcCcCC
Confidence 578899 8974 33332222 56999993
No 268
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=43.26 E-value=13 Score=20.51 Aligned_cols=24 Identities=38% Similarity=0.957 Sum_probs=17.6
Q ss_pred cCCCCccCCceEEeEeCCCCccCCcee
Q 031604 120 ECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
.|+ -|++- +...--.++||-.||.
T Consensus 10 ~C~--~C~~~-~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCP--VCGSR-WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCC--CCCCe-EeEccCCEEEhhhCce
Confidence 488 69865 5555567899999985
No 269
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.68 E-value=20 Score=28.75 Aligned_cols=27 Identities=22% Similarity=0.513 Sum_probs=20.2
Q ss_pred cccCCCCccCCceEEeEeC--CCCccCCcee
Q 031604 118 RKECPNAECGAGTFMASHF--DRHYCGKCGL 146 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~--~r~~cg~c~~ 146 (156)
...|| +||.-+-..... .-++|..|+.
T Consensus 244 g~pCp--rCG~~I~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 244 GEPCL--NCKTPIRRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CCcCC--CCCCeeEEEEECCCccEECcCCcC
Confidence 46899 999777666554 4689999973
No 270
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=41.54 E-value=11 Score=21.37 Aligned_cols=15 Identities=27% Similarity=0.658 Sum_probs=9.9
Q ss_pred CCCccCCceeEEEee
Q 031604 137 DRHYCGKCGLTYVYQ 151 (156)
Q Consensus 137 ~r~~cg~c~~t~~~~ 151 (156)
....|..||.+|...
T Consensus 12 ~~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 12 GATTCPTCGMLYSPG 26 (41)
T ss_pred CCcCCCCCCCEECCC
Confidence 345788888777544
No 271
>PRK10445 endonuclease VIII; Provisional
Probab=41.33 E-value=21 Score=28.43 Aligned_cols=26 Identities=19% Similarity=0.443 Sum_probs=19.6
Q ss_pred cccCCCCccCCceEEeEeC--CCCccCCce
Q 031604 118 RKECPNAECGAGTFMASHF--DRHYCGKCG 145 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~--~r~~cg~c~ 145 (156)
...|| +||.-+-..... .-++|..|+
T Consensus 235 g~~Cp--~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACE--RCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCC--CCCCEeEEEEECCCCcEECCCCc
Confidence 46799 898776666665 458899997
No 272
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=40.81 E-value=9 Score=22.49 Aligned_cols=16 Identities=31% Similarity=0.806 Sum_probs=10.2
Q ss_pred CCccCCceeEEEeecCCC
Q 031604 138 RHYCGKCGLTYVYQKAGG 155 (156)
Q Consensus 138 r~~cg~c~~t~~~~~~~~ 155 (156)
|+.|..|||.| +...|
T Consensus 1 ky~C~~CgyvY--d~~~G 16 (47)
T PF00301_consen 1 KYQCPVCGYVY--DPEKG 16 (47)
T ss_dssp EEEETTTSBEE--ETTTB
T ss_pred CcCCCCCCEEE--cCCcC
Confidence 46788898655 44444
No 273
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=40.70 E-value=66 Score=23.55 Aligned_cols=34 Identities=9% Similarity=0.135 Sum_probs=29.9
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeE
Q 031604 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL 43 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL 43 (156)
.+.+.|.|+...+=.++|+.|+..+++.+....-
T Consensus 82 ~N~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNT 115 (145)
T PTZ00191 82 NNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNT 115 (145)
T ss_pred CCEEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEe
Confidence 4689999999999999999999999998876643
No 274
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=40.67 E-value=19 Score=35.08 Aligned_cols=18 Identities=28% Similarity=0.473 Sum_probs=11.1
Q ss_pred ccccceeeeeeeeeEEEc
Q 031604 92 KHKKKKVKLAVLQFYKVD 109 (156)
Q Consensus 92 k~~kkk~k~~v~k~y~vd 109 (156)
|.+.++.|.+++..|-+.
T Consensus 618 Ks~~R~mkP~~h~LFPig 635 (1337)
T PRK14714 618 KSKPRKMKPPVHTLFPIG 635 (1337)
T ss_pred cccccccCCCCccccccc
Confidence 344455777777777554
No 275
>PLN03086 PRLI-interacting factor K; Provisional
Probab=40.55 E-value=16 Score=32.52 Aligned_cols=33 Identities=27% Similarity=0.632 Sum_probs=22.1
Q ss_pred EecccCCCCccCCceEEeEeCC-CCccCCceeEEE
Q 031604 116 RLRKECPNAECGAGTFMASHFD-RHYCGKCGLTYV 149 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~-r~~cg~c~~t~~ 149 (156)
|....||++.|| -+|+-...+ -+.|..|+..|.
T Consensus 431 r~~V~Cp~~~Cg-~v~~r~el~~H~~C~~Cgk~f~ 464 (567)
T PLN03086 431 RHNVVCPHDGCG-IVLRVEEAKNHVHCEKCGQAFQ 464 (567)
T ss_pred CcceeCCccccc-ceeeccccccCccCCCCCCccc
Confidence 455678865687 566666554 446899988763
No 276
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.41 E-value=22 Score=28.43 Aligned_cols=27 Identities=26% Similarity=0.646 Sum_probs=21.0
Q ss_pred cccCCCCccCCceEEeEeCC--CCccCCcee
Q 031604 118 RKECPNAECGAGTFMASHFD--RHYCGKCGL 146 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~--r~~cg~c~~ 146 (156)
.+.|| +||.-+-.....+ -++|..|+.
T Consensus 235 g~pC~--~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCP--RCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred cCCCC--cCCCeeEEEEECCCCcEECCCCcC
Confidence 36799 9998777666654 589999985
No 277
>KOG0466 consensus Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=40.12 E-value=20 Score=30.00 Aligned_cols=44 Identities=32% Similarity=0.602 Sum_probs=30.2
Q ss_pred cceeeeee--eeeEEEcCCCeEEEecccCCCCccCCceEEeEeCCCCccCCceeE
Q 031604 95 KKKVKLAV--LQFYKVDDSGKVQRLRKECPNAECGAGTFMASHFDRHYCGKCGLT 147 (156)
Q Consensus 95 kkk~k~~v--~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
.-.+||.. .+.|+-| ..+||.|-| +..|-..-.||..|-+||.+
T Consensus 73 NITIKLGYANAKIYkc~--------~~kCprP~c-y~s~gS~k~d~~~c~~~g~~ 118 (466)
T KOG0466|consen 73 NITIKLGYANAKIYKCD--------DPKCPRPGC-YRSFGSSKEDRPPCDRPGCE 118 (466)
T ss_pred ceeEEeccccceEEecC--------CCCCCCcch-hhccCCCCCCCCCcccCCCC
Confidence 33455533 3446665 368998888 45666667899999999865
No 278
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=39.80 E-value=29 Score=23.74 Aligned_cols=30 Identities=27% Similarity=0.620 Sum_probs=20.4
Q ss_pred cCCCCccCCceEEeEeC--CCCccCCceeEEEee
Q 031604 120 ECPNAECGAGTFMASHF--DRHYCGKCGLTYVYQ 151 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~--~r~~cg~c~~t~~~~ 151 (156)
-|| .||.......-. +|..|-.|.|.|-+.
T Consensus 3 FCP--~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCP--TCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccC--CCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 488 898544333322 689999999987554
No 279
>PHA00616 hypothetical protein
Probab=39.63 E-value=4.6 Score=23.48 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=6.8
Q ss_pred ccCCceeEEE
Q 031604 140 YCGKCGLTYV 149 (156)
Q Consensus 140 ~cg~c~~t~~ 149 (156)
.|+.||.+|.
T Consensus 3 qC~~CG~~F~ 12 (44)
T PHA00616 3 QCLRCGGIFR 12 (44)
T ss_pred ccchhhHHHh
Confidence 5777777764
No 280
>PF09138 Urm1: Urm1 (Ubiquitin related modifier); InterPro: IPR015221 Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway []. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily []. ; GO: 0034227 tRNA thio-modification, 0005737 cytoplasm; PDB: 2AX5_A 2QJL_A 2PKO_A 1WGK_A 1XO3_A 2K9X_A.
Probab=39.58 E-value=39 Score=22.91 Aligned_cols=64 Identities=20% Similarity=0.382 Sum_probs=34.6
Q ss_pred CEEEEEec---CCCcHHHHHHHHHHHhCCCCCceeEeeCCe-------ecCCC--Ccc---cccCcCCCCEEEEEEEecC
Q 031604 11 KTITLEVE---SSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLEDG--RTL---ADYNIQKESTLHLVLRLRG 75 (156)
Q Consensus 11 ~~~~l~V~---~~~TV~~LK~~I~~~~gip~~~qrL~~~G~-------~L~d~--~tL---~~~gi~~~stv~l~~~~~g 75 (156)
+.+.++++ ...|+++|-..|....- .++.-|+..+. .|=++ .-| .+|-++++++|.++-.+.|
T Consensus 18 k~h~v~l~~~~~~~ti~~Li~~l~~nll--~~r~elF~~~~~vrPGILvLINd~DwEl~g~~~y~l~~~D~I~FiSTLHG 95 (96)
T PF09138_consen 18 KKHKVSLPSDGEPATIKDLIDYLRDNLL--KERPELFLEGGSVRPGILVLINDADWELLGEEDYVLKDGDNITFISTLHG 95 (96)
T ss_dssp SEEEEEE-SSCSC-BHHHHHHHHCCCT---SSGHHHHBSSSSB-TTEEEEETTCEHHHHTCCCSB--TTEEEEEEETTT-
T ss_pred eeEEEEcCCCCCCcCHHHHHHHHHHhcc--CCCHhHEecCCeEcCcEEEEEcCccceeecCcceEcCCCCEEEEEccCCC
Confidence 56778877 67899999988876431 11222322221 12111 112 3688999999999888887
Q ss_pred C
Q 031604 76 G 76 (156)
Q Consensus 76 g 76 (156)
|
T Consensus 96 G 96 (96)
T PF09138_consen 96 G 96 (96)
T ss_dssp -
T ss_pred C
Confidence 6
No 281
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=39.23 E-value=9.8 Score=30.49 Aligned_cols=35 Identities=31% Similarity=0.656 Sum_probs=24.9
Q ss_pred eeeEEEcCCCeEEEecccCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031604 103 LQFYKVDDSGKVQRLRKECPNAECGAGTFMASHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 103 ~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~ 150 (156)
..+|+||. -+.|. .||++|...+ ..|..|+-|-+.
T Consensus 74 KsC~rvDQ-------l~~C~--~CGa~V~~~e----~~Cp~C~StnI~ 108 (314)
T PF09567_consen 74 KSCYRVDQ-------LGKCN--NCGANVSRLE----ESCPNCGSTNIK 108 (314)
T ss_pred hhhhhhhh-------hhhhc--cccceeeehh----hcCCCCCccccc
Confidence 34788994 57788 7988886554 568888876543
No 282
>PHA02768 hypothetical protein; Provisional
Probab=38.58 E-value=17 Score=22.10 Aligned_cols=30 Identities=27% Similarity=0.571 Sum_probs=20.6
Q ss_pred ecccCCCCccCCceEEe---------EeCCCCccCCceeEEE
Q 031604 117 LRKECPNAECGAGTFMA---------SHFDRHYCGKCGLTYV 149 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma---------~h~~r~~cg~c~~t~~ 149 (156)
+..+|| .|| -.|.- .|...+.|.+|+..|.
T Consensus 4 ~~y~C~--~CG-K~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~ 42 (55)
T PHA02768 4 LGYECP--ICG-EIYIKRKSMITHLRKHNTNLKLSNCKRISL 42 (55)
T ss_pred cccCcc--hhC-CeeccHHHHHHHHHhcCCcccCCcccceec
Confidence 567999 998 45532 2345778999998664
No 283
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=38.50 E-value=13 Score=17.53 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=6.9
Q ss_pred ccCCceeEE
Q 031604 140 YCGKCGLTY 148 (156)
Q Consensus 140 ~cg~c~~t~ 148 (156)
.|..|+.+|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 578888877
No 284
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=38.36 E-value=26 Score=29.04 Aligned_cols=47 Identities=19% Similarity=0.262 Sum_probs=38.8
Q ss_pred EEEEecCCCcHHHHHHHHHHHhC-CC-CCceeEeeCCeecCCCCccccc
Q 031604 13 ITLEVESSDTIDNVKAKIQDKEG-IP-PDQQRLIFAGKQLEDGRTLADY 59 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~g-ip-~~~qrL~~~G~~L~d~~tL~~~ 59 (156)
-.+.++...||.+|+.-+..+.+ ++ ..++-+++++..|.+..||.+.
T Consensus 166 ~fvrcsa~~Tv~hlkkfl~~k~~~~~~~~~idi~~~d~~l~~~~TLk~i 214 (331)
T KOG2660|consen 166 RFLRCSAAATVNHLKKFLRKKMDNLSNKSEIDILCEEELLGDYYTLKDI 214 (331)
T ss_pred ceEeccHHHHHHHHHHHHHHHhccccchhhheeecCCccccchhhhhhh
Confidence 45678889999999999999988 43 3567888999999999888754
No 285
>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=38.24 E-value=91 Score=18.76 Aligned_cols=59 Identities=14% Similarity=0.149 Sum_probs=37.8
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEEE
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
|.|..++|+... ++...|+.|+=..|....+-. -.--..+|+..+-+..| +++++|.+.
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--LPEGSTVLDVAYSIHSSLAKR--AVAAKVNGQLVDLDHPL-----EDGDVVEII 59 (60)
T ss_dssp EEEEETTSCEEE--EETTBBHHHHHHHHSHHHHHC--EEEEEETTEEEETTSBB------SSEEEEEE
T ss_pred CEEECCCCCeee--CCCCCCHHHHHHHHCHHHHhh--eeEEEEcCEECCCCCCc-----CCCCEEEEE
Confidence 456667888766 778899999999998765311 11223677766555444 457777663
No 286
>PF04126 Cyclophil_like: Cyclophilin-like; InterPro: IPR007256 Proteins of this family have no known function.; PDB: 2KA0_A 1ZX8_C 2NNZ_A.
Probab=38.03 E-value=31 Score=24.14 Aligned_cols=29 Identities=28% Similarity=0.398 Sum_probs=24.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHH
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKI 30 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I 30 (156)
|+|.|.. +++.+..++..+.|..+|.+++
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 7888876 5788999999999999988765
No 287
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.86 E-value=18 Score=34.52 Aligned_cols=36 Identities=33% Similarity=0.735 Sum_probs=23.1
Q ss_pred ccccceeeeeeeeeEEEcCCC----------------eEEEecccCCCCccCCc
Q 031604 92 KHKKKKVKLAVLQFYKVDDSG----------------KVQRLRKECPNAECGAG 129 (156)
Q Consensus 92 k~~kkk~k~~v~k~y~vd~~g----------------~~~~~~~~cp~~~c~~g 129 (156)
|.+.++.|.+++-.|-+.+-| .|.--.+.|| .||..
T Consensus 584 Ka~~RkMkP~~h~LFPiG~~GG~~R~i~~A~~~~g~~eVEVg~RfCp--sCG~~ 635 (1121)
T PRK04023 584 KAKERKMKPPVHVLFPIGNAGGSTRDINKAAKYKGTIEVEIGRRKCP--SCGKE 635 (1121)
T ss_pred ccccccCCCCCcccccccccCcccccHHHHHhcCCceeecccCccCC--CCCCc
Confidence 344556778888888665322 2445567899 79864
No 288
>PF01376 Enterotoxin_b: Heat-labile enterotoxin beta chain; InterPro: IPR001835 Escherichia coli heat-labile enterotoxin is a bacterial protein toxin with an AB5 multimer structure, in which the B pentamer has a membrane-binding function and the A chain (IPR001144 from INTERPRO) is needed for enzymatic activity []. The B subunits are arranged as a donut-shaped pentamer, each subunit participating in ~30 hydrogen bonds and 6 salt bridges with its two neighbours []. The A subunit has a less well-defined secondary structure. It predominantly interacts with the pentamer via the C-terminal A2 fragment, which runs through the charged central pore of the B subunits. A putative catalytic residue in the A1 fragment (Glu112) lies close to a hydrophobic region, which packs two loops together. It is thought that this region might be important for catalysis and membrane translocation [].; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1LTA_D 2XRS_O 1LTS_E 1LTT_H 1TET_P 1JQY_Y 1PZI_D 1DJR_E 1EEF_D 1LTB_E ....
Probab=37.73 E-value=60 Score=21.52 Aligned_cols=31 Identities=29% Similarity=0.423 Sum_probs=21.0
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHH
Q 031604 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDK 33 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~ 33 (156)
+.|...+|.+|.++|+.+.-+..-|..|+..
T Consensus 38 ~iitf~ngatfqvevpgsqhi~sqkk~ierm 68 (102)
T PF01376_consen 38 VIITFKNGATFQVEVPGSQHIDSQKKAIERM 68 (102)
T ss_dssp EEEEETTS-EEEE--SSTTSTTTHHHHHHHH
T ss_pred EEEEecCCcEEEEecCCccchhhhHHHHHHH
Confidence 4555668999999999998877777776644
No 289
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=37.37 E-value=31 Score=24.67 Aligned_cols=32 Identities=34% Similarity=0.774 Sum_probs=21.9
Q ss_pred EEecccCCCCccCCceEEeEeC----CCCccCCceeEEEe
Q 031604 115 QRLRKECPNAECGAGTFMASHF----DRHYCGKCGLTYVY 150 (156)
Q Consensus 115 ~~~~~~cp~~~c~~g~fma~h~----~r~~cg~c~~t~~~ 150 (156)
.+....|+ .|+..+ ..|. .++.||.|+-.+..
T Consensus 120 ~~~~~~C~--~C~~~~--~r~~~~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCP--SCGREY--KRHRRSKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcC--CCCCEe--eeecccchhhEECCCCCCEEEE
Confidence 34578998 897432 3442 36789999987754
No 290
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=37.32 E-value=23 Score=17.69 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=7.4
Q ss_pred CccCCceeEE
Q 031604 139 HYCGKCGLTY 148 (156)
Q Consensus 139 ~~cg~c~~t~ 148 (156)
..|..||.+|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 4577888877
No 291
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.26 E-value=26 Score=28.19 Aligned_cols=27 Identities=26% Similarity=0.605 Sum_probs=20.1
Q ss_pred cccCCCCccCCceEEeEeC--CCCccCCcee
Q 031604 118 RKECPNAECGAGTFMASHF--DRHYCGKCGL 146 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~--~r~~cg~c~~ 146 (156)
...|| +||.-+-..... .-++|..|+.
T Consensus 254 g~pC~--~Cg~~I~~~~~~gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCR--KCGTPIERIKLAGRSTHWCPNCQK 282 (282)
T ss_pred cCCCC--cCCCeeEEEEECCCccEECCCCcC
Confidence 46899 998777666555 4588999973
No 292
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=36.98 E-value=25 Score=33.35 Aligned_cols=47 Identities=23% Similarity=0.499 Sum_probs=31.9
Q ss_pred ccccceeeeeeeeeEEEcCC-------------C---eEEEecccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 92 KHKKKKVKLAVLQFYKVDDS-------------G---KVQRLRKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 92 k~~kkk~k~~v~k~y~vd~~-------------g---~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
|.+.++.|.+++-.|-+.+- | .|+--++.|| .||.-. -...|.+||-
T Consensus 583 Ka~~RkMkPp~h~LFPiG~aGG~~R~i~~A~~~g~~i~vev~~RKCP--kCG~yT------lk~rCP~CG~ 645 (1095)
T TIGR00354 583 KAKERKMSPPPHILFPIGMAGGNTRDIKNAINYTKEIEVEIAIRKCP--QCGKES------FWLKCPVCGE 645 (1095)
T ss_pred ccccccCCCCCcccccccccCcchhhHHHHhccCCeeEEEEEEEECC--CCCccc------ccccCCCCCC
Confidence 34455678888887765432 3 3666689999 898533 4567999984
No 293
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=36.60 E-value=52 Score=22.86 Aligned_cols=31 Identities=26% Similarity=0.682 Sum_probs=20.6
Q ss_pred cccCCCCccCCceEEeEe-CCC---------CccCCceeEEEe
Q 031604 118 RKECPNAECGAGTFMASH-FDR---------HYCGKCGLTYVY 150 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h-~~r---------~~cg~c~~t~~~ 150 (156)
...|| .||..=.+..- ..| ..|-+||+++.+
T Consensus 72 ~~~Cp--kCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCP--KCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCC--CCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 46899 99854333322 244 789999998854
No 294
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=36.60 E-value=24 Score=20.59 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=7.2
Q ss_pred CccCCceeEEEee
Q 031604 139 HYCGKCGLTYVYQ 151 (156)
Q Consensus 139 ~~cg~c~~t~~~~ 151 (156)
.+||.||.++...
T Consensus 6 l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 6 LRCGHCGSKMTRR 18 (58)
T ss_pred EEcccCCcEeEEE
Confidence 3466666655544
No 295
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=36.34 E-value=30 Score=24.00 Aligned_cols=26 Identities=27% Similarity=0.626 Sum_probs=16.3
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
.+-.|+ .||. .| +.......|++||-
T Consensus 69 ~~~~C~--~Cg~-~~-~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECE--DCSE-EV-SPEIDLYRCPKCHG 94 (115)
T ss_pred cEEEcc--cCCC-EE-ecCCcCccCcCCcC
Confidence 578899 8973 22 22223456999984
No 296
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.90 E-value=29 Score=27.72 Aligned_cols=26 Identities=23% Similarity=0.602 Sum_probs=19.7
Q ss_pred cccCCCCccCCceEEeEeCC--CCccCCce
Q 031604 118 RKECPNAECGAGTFMASHFD--RHYCGKCG 145 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~--r~~cg~c~ 145 (156)
...|| +||.-+-.....+ -++|..|+
T Consensus 245 g~pC~--~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCR--RCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCC--CCCCeeEEEEECCCCCEECCCCC
Confidence 35899 8988777766654 57899996
No 297
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=35.77 E-value=20 Score=33.71 Aligned_cols=25 Identities=40% Similarity=0.798 Sum_probs=20.7
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCC
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGK 143 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~ 143 (156)
+.|+.|| .|| --|-..+.+|.+||-
T Consensus 17 ~~r~~c~--~cg-~~fwt~~~~r~~cgd 41 (900)
T PRK13902 17 FERKQCK--KCG-SYFWTLDPDRETCGD 41 (900)
T ss_pred ceEeECC--ccC-CceecCCCCcCCCCC
Confidence 3579999 998 567777789999997
No 298
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=35.66 E-value=39 Score=20.23 Aligned_cols=26 Identities=31% Similarity=0.782 Sum_probs=16.2
Q ss_pred ccCCCCccCCceEEeEeCCC--------CccCCcee
Q 031604 119 KECPNAECGAGTFMASHFDR--------HYCGKCGL 146 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r--------~~cg~c~~ 146 (156)
+-|| .||........... ..|..||-
T Consensus 4 kPCP--FCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCP--FCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCC--CCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5699 99865555444221 34888875
No 299
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=35.66 E-value=18 Score=27.02 Aligned_cols=21 Identities=38% Similarity=0.942 Sum_probs=17.1
Q ss_pred cccCCCCccCCceEEeEe--CCCCccC
Q 031604 118 RKECPNAECGAGTFMASH--FDRHYCG 142 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h--~~r~~cg 142 (156)
...| +|| .+|++.| .++|.|-
T Consensus 119 gf~C---rCG-~~fC~~HRy~e~H~C~ 141 (167)
T KOG3173|consen 119 GFKC---RCG-NTFCGTHRYPEQHDCS 141 (167)
T ss_pred cccc---ccC-CcccccccCCcccccc
Confidence 3567 699 8999999 6999874
No 300
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=35.05 E-value=21 Score=21.57 Aligned_cols=21 Identities=43% Similarity=1.121 Sum_probs=13.1
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCce
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCG 145 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~ 145 (156)
-..|| .||. +.-.| +.|..||
T Consensus 26 l~~C~--~cG~--~~~~H---~vc~~cG 46 (55)
T TIGR01031 26 LVVCP--NCGE--FKLPH---RVCPSCG 46 (55)
T ss_pred ceECC--CCCC--cccCe---eECCccC
Confidence 35699 8975 43333 4577777
No 301
>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=34.96 E-value=32 Score=20.87 Aligned_cols=31 Identities=13% Similarity=0.275 Sum_probs=20.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHH
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQ 31 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~ 31 (156)
|.|.+.+.+|+.|.++...-.--.-|+..++
T Consensus 1 ~~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~ 31 (62)
T PF03931_consen 1 MYVKLVSSDGQEFEVSREAAKQSKTIKNMLE 31 (62)
T ss_dssp -EEEEEETTSEEEEEEHHHHTTSHHHHHHHH
T ss_pred CEEEEEcCCCCEEEeeHHHHHHhHHHHHHHh
Confidence 7799999999999998543333333444444
No 302
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=34.95 E-value=17 Score=16.75 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=5.2
Q ss_pred ccCCceeEE
Q 031604 140 YCGKCGLTY 148 (156)
Q Consensus 140 ~cg~c~~t~ 148 (156)
.|..|+.+|
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 577888776
No 303
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=34.78 E-value=28 Score=18.84 Aligned_cols=24 Identities=29% Similarity=0.782 Sum_probs=13.2
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeE
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLT 147 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
-..|+ .||. + .|..|..|..|+-+
T Consensus 11 ~~rC~--~Cg~-~---~~pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 11 GQRCR--DCGR-V---QFPPRPVCPHCGSD 34 (37)
T ss_dssp EEE-T--TT---E---EES--SEETTTT--
T ss_pred EEEcC--CCCC-E---ecCCCcCCCCcCcc
Confidence 47798 7974 3 46689999999744
No 304
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=34.70 E-value=12 Score=29.70 Aligned_cols=27 Identities=33% Similarity=0.790 Sum_probs=22.0
Q ss_pred EEEecccCCCCccCCceEEeEe--CCCCccCC
Q 031604 114 VQRLRKECPNAECGAGTFMASH--FDRHYCGK 143 (156)
Q Consensus 114 ~~~~~~~cp~~~c~~g~fma~h--~~r~~cg~ 143 (156)
+-+|--.|- .|. |+|++.| +..|.|++
T Consensus 19 lDFLPf~Cd--~C~-~~FC~eHrsye~H~Cp~ 47 (250)
T KOG3183|consen 19 LDFLPFKCD--GCS-GIFCLEHRSYESHHCPK 47 (250)
T ss_pred ccccceeeC--Ccc-chhhhccchHhhcCCCc
Confidence 456788898 897 9999999 57888875
No 305
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=34.59 E-value=20 Score=18.44 Aligned_cols=25 Identities=20% Similarity=0.442 Sum_probs=12.7
Q ss_pred ccCCCCccCCceEEeEeC--CCCccCCce
Q 031604 119 KECPNAECGAGTFMASHF--DRHYCGKCG 145 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~--~r~~cg~c~ 145 (156)
..|| +|+.-.-...+. .-++|.+|+
T Consensus 2 ~~C~--rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCP--RCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-T--TT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCc--cCCCcceEeEecCCCCeECcCCc
Confidence 4688 897544444443 356788886
No 306
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=34.07 E-value=73 Score=20.55 Aligned_cols=46 Identities=7% Similarity=0.138 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhCCCCCceeEeeCCeecCCCCcccccCcCCCCEEEE
Q 031604 24 DNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 24 ~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stv~l 69 (156)
..++..++..+|.+.+..++..+...=.-...+..--+.-|..|++
T Consensus 4 ~~~r~~~e~~~G~dl~~Vrvh~~~~a~~~~~~~~A~A~T~G~~I~f 49 (79)
T PF13699_consen 4 ESIRSRLERAFGADLSDVRVHTGPAASRAAAALGARAFTVGNDIYF 49 (79)
T ss_pred HHHHHHHHHHhCCCccceEEEeCCchhhhhhccCCeEEEECCEEEE
Confidence 3688999999999999999887743222222233334456788877
No 307
>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=34.05 E-value=1.1e+02 Score=22.62 Aligned_cols=44 Identities=30% Similarity=0.437 Sum_probs=30.3
Q ss_pred EEEEEecC-CCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCccccc
Q 031604 12 TITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY 59 (156)
Q Consensus 12 ~~~l~V~~-~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~ 59 (156)
.+.+++.. .+.+..+++...+.+-++-+ +.-|+-+....|++||
T Consensus 76 ri~lele~~~~~ie~I~~iCee~lpf~y~----i~~G~f~r~~~TvtDY 120 (153)
T PF02505_consen 76 RIILELEDEEDVIEKIREICEEVLPFGYD----IKEGKFIRTKPTVTDY 120 (153)
T ss_pred EEEEEecCcHHHHHHHHHHHHHhCCCceE----eeeeEEeccCCchhhh
Confidence 35667777 67777777766665533221 3468889999999988
No 308
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=33.67 E-value=20 Score=17.85 Aligned_cols=11 Identities=27% Similarity=0.763 Sum_probs=8.5
Q ss_pred CCccCCceeEE
Q 031604 138 RHYCGKCGLTY 148 (156)
Q Consensus 138 r~~cg~c~~t~ 148 (156)
.+.|..|+++|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 56788888877
No 309
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=33.28 E-value=53 Score=19.82 Aligned_cols=30 Identities=30% Similarity=0.657 Sum_probs=18.1
Q ss_pred ccCCCCccCCceEEeEe--CCCCccCCceeEEEe
Q 031604 119 KECPNAECGAGTFMASH--FDRHYCGKCGLTYVY 150 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h--~~r~~cg~c~~t~~~ 150 (156)
.+|| .||+-+-+..- ..-..|+-||-.+-.
T Consensus 3 ~~CP--~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECP--DCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred cCCC--CCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 4788 88874433221 245678888876643
No 310
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=32.74 E-value=35 Score=20.23 Aligned_cols=11 Identities=36% Similarity=0.954 Sum_probs=8.0
Q ss_pred CCccCCceeEE
Q 031604 138 RHYCGKCGLTY 148 (156)
Q Consensus 138 r~~cg~c~~t~ 148 (156)
++-|.-|||.|
T Consensus 1 ~y~C~~CgyiY 11 (50)
T cd00730 1 KYECRICGYIY 11 (50)
T ss_pred CcCCCCCCeEE
Confidence 46788888655
No 311
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=32.60 E-value=28 Score=21.52 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=6.4
Q ss_pred CCCCccCCcee
Q 031604 136 FDRHYCGKCGL 146 (156)
Q Consensus 136 ~~r~~cg~c~~ 146 (156)
.+.+.|.+||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 45566666663
No 312
>PF12773 DZR: Double zinc ribbon
Probab=32.54 E-value=20 Score=20.57 Aligned_cols=27 Identities=30% Similarity=0.732 Sum_probs=16.8
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeE
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLT 147 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
...|| .||.-+. .......+|.+||..
T Consensus 12 ~~fC~--~CG~~l~-~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCP--HCGTPLP-PPDQSKKICPNCGAE 38 (50)
T ss_pred ccCCh--hhcCChh-hccCCCCCCcCCcCC
Confidence 46788 7865333 233455678888865
No 313
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=32.28 E-value=92 Score=23.24 Aligned_cols=39 Identities=28% Similarity=0.461 Sum_probs=29.6
Q ss_pred eeeeeEEEcCCCeEEEecccCCCCccCCceEEeEeC--CCCccC
Q 031604 101 AVLQFYKVDDSGKVQRLRKECPNAECGAGTFMASHF--DRHYCG 142 (156)
Q Consensus 101 ~v~k~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~--~r~~cg 142 (156)
.+..++...-.|+-..+-..|+ .|+ |-|++.|. ..|.|+
T Consensus 93 ~t~~~a~~~~~g~~s~l~~~c~--~c~-g~fc~~h~lp~nhdc~ 133 (162)
T COG3582 93 ITDRCATPQCTGKGSTLAGKCN--YCT-GYFCAEHRLPENHDCN 133 (162)
T ss_pred cceeeecceeccCCcccccccc--CCC-Ccceeceecccccccc
Confidence 3445666667788888999999 797 88999994 556564
No 314
>KOG3391 consensus Transcriptional co-repressor component [Transcription]
Probab=31.98 E-value=40 Score=24.51 Aligned_cols=27 Identities=15% Similarity=0.284 Sum_probs=23.4
Q ss_pred ecCCCCcccccCcCCCCEEEEEEEecC
Q 031604 49 QLEDGRTLADYNIQKESTLHLVLRLRG 75 (156)
Q Consensus 49 ~L~d~~tL~~~gi~~~stv~l~~~~~g 75 (156)
..+|+.+|.+.+++-|+-|.+.+.+.-
T Consensus 113 g~ddnktL~~~kf~iGD~lDVaI~~p~ 139 (151)
T KOG3391|consen 113 GIDDNKTLQQTKFEIGDYLDVAITPPN 139 (151)
T ss_pred cCCccchhhhCCccccceEEEEecCcc
Confidence 457889999999999999999988654
No 315
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=31.97 E-value=33 Score=23.67 Aligned_cols=29 Identities=24% Similarity=0.588 Sum_probs=19.7
Q ss_pred ecccCCCCccCCceEEeEe-CCCCccCCceeEE
Q 031604 117 LRKECPNAECGAGTFMASH-FDRHYCGKCGLTY 148 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h-~~r~~cg~c~~t~ 148 (156)
.+..|+ .||.-.+.+.- .+| .|.+||...
T Consensus 41 ~~~~C~--~Cg~~~~~~~SCk~R-~CP~C~~~~ 70 (111)
T PF14319_consen 41 HRYRCE--DCGHEKIVYNSCKNR-HCPSCQAKA 70 (111)
T ss_pred ceeecC--CCCceEEecCcccCc-CCCCCCChH
Confidence 457899 69865544432 578 699998643
No 316
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=31.34 E-value=71 Score=22.50 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=18.8
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCC
Q 031604 15 LEVESSDTIDNVKAKIQDKEGIPPD 39 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~ 39 (156)
++|+.+.|+++|-+.+++..|+.+.
T Consensus 37 ~~v~~~~Tl~~li~~~~~~~~lev~ 61 (125)
T PF09358_consen 37 IEVNGDMTLQELIDYFKEKYGLEVT 61 (125)
T ss_dssp EEEES--BHHHHHHHHHHTTS-EEE
T ss_pred EEEcCCCCHHHHHHHHHHHhCceEE
Confidence 5677789999999999999988664
No 317
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.04 E-value=26 Score=18.89 Aligned_cols=11 Identities=27% Similarity=0.597 Sum_probs=7.1
Q ss_pred CccCCceeEEE
Q 031604 139 HYCGKCGLTYV 149 (156)
Q Consensus 139 ~~cg~c~~t~~ 149 (156)
|-|..||+++.
T Consensus 3 ~~C~~CG~i~~ 13 (34)
T cd00729 3 WVCPVCGYIHE 13 (34)
T ss_pred EECCCCCCEeE
Confidence 55777777653
No 318
>PRK05580 primosome assembly protein PriA; Validated
Probab=31.00 E-value=26 Score=31.81 Aligned_cols=25 Identities=36% Similarity=0.845 Sum_probs=16.2
Q ss_pred cCCCCccCCceEEeEeC--CCCccCCceeEE
Q 031604 120 ECPNAECGAGTFMASHF--DRHYCGKCGLTY 148 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~--~r~~cg~c~~t~ 148 (156)
.|| +|. +-|..|. +...|-.||+++
T Consensus 392 ~C~--~C~--~~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 392 ECP--HCD--ASLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred CCC--CCC--CceeEECCCCeEECCCCcCCC
Confidence 688 784 4777785 444566666654
No 319
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=30.87 E-value=81 Score=19.78 Aligned_cols=55 Identities=18% Similarity=0.291 Sum_probs=37.7
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCccccc--CcCCCCEEEEEEEe
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY--NIQKESTLHLVLRL 73 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~--gi~~~stv~l~~~~ 73 (156)
...-.+|.+... ++..|+.+.++-+-.+|..+.+...|..+ ...+|++|.|.+.-
T Consensus 15 g~~V~~V~~~sp--------A~~aGl~~GD~I~~ing~~v~~~~~~~~~l~~~~~g~~v~l~v~R 71 (82)
T PF13180_consen 15 GVVVVSVIPGSP--------AAKAGLQPGDIILAINGKPVNSSEDLVNILSKGKPGDTVTLTVLR 71 (82)
T ss_dssp SEEEEEESTTSH--------HHHTTS-TTEEEEEETTEESSSHHHHHHHHHCSSTTSEEEEEEEE
T ss_pred eEEEEEeCCCCc--------HHHCCCCCCcEEEEECCEEcCCHHHHHHHHHhCCCCCEEEEEEEE
Confidence 344456766653 45678999999999999999665444333 45679999888754
No 320
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=30.74 E-value=28 Score=21.45 Aligned_cols=20 Identities=40% Similarity=0.899 Sum_probs=12.5
Q ss_pred ecccCCCCccCCceEEeEeCCCC
Q 031604 117 LRKECPNAECGAGTFMASHFDRH 139 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~ 139 (156)
|...|| .|| |.--..|..|+
T Consensus 16 Lke~Cp--~CG-~~t~~~~PprF 35 (59)
T COG2260 16 LKEKCP--VCG-GDTKVPHPPRF 35 (59)
T ss_pred ecccCC--CCC-CccccCCCCCC
Confidence 457888 888 44445575443
No 321
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=30.63 E-value=17 Score=33.97 Aligned_cols=55 Identities=33% Similarity=0.686 Sum_probs=0.0
Q ss_pred cccccceeeeeeeeeEEEcCCC-----------------eEEEecccCCCCccCCceEE------eEeC-CCCccCCcee
Q 031604 91 IKHKKKKVKLAVLQFYKVDDSG-----------------KVQRLRKECPNAECGAGTFM------ASHF-DRHYCGKCGL 146 (156)
Q Consensus 91 ~k~~kkk~k~~v~k~y~vd~~g-----------------~~~~~~~~cp~~~c~~g~fm------a~h~-~r~~cg~c~~ 146 (156)
+|.+.++.+.+++-.|=+.+.| .|+--++.|| .||.-.|. ..|- ..++|..|+.
T Consensus 611 EKa~~RkM~P~~h~LFPIG~~GG~~R~i~~A~~~~~g~i~vei~~r~Cp--~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 611 EKAKERKMKPPPHVLFPIGEAGGSRRDIQKAAKKGKGTIEVEIGRRRCP--KCGKETFYNRCPECGSHTEPVYVCPDCGI 688 (900)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CccccccCCCCCceeccccccCcccccHHHHHhcCCCeeEEeeecccCc--ccCCcchhhcCcccCCccccceecccccc
Confidence 3455566888888888765432 1334467899 78765543 3332 3556666664
Q ss_pred E
Q 031604 147 T 147 (156)
Q Consensus 147 t 147 (156)
-
T Consensus 689 ~ 689 (900)
T PF03833_consen 689 E 689 (900)
T ss_dssp -
T ss_pred c
Confidence 3
No 322
>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=29.71 E-value=1.8e+02 Score=23.92 Aligned_cols=60 Identities=18% Similarity=0.218 Sum_probs=42.7
Q ss_pred EEEecCCCcHHHHHHHHHHHh--------------C-CCCCceeEeeCCeecCCCCcccccCc---CCCCEEEEEEEe
Q 031604 14 TLEVESSDTIDNVKAKIQDKE--------------G-IPPDQQRLIFAGKQLEDGRTLADYNI---QKESTLHLVLRL 73 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~--------------g-ip~~~qrL~~~G~~L~d~~tL~~~gi---~~~stv~l~~~~ 73 (156)
.|..+.-.-|.-+...|.+++ . .|.+.+.|+++|+.|+.+.+|+..-- +.+.-|.|..|.
T Consensus 251 rL~A~~mLrvkKI~~yV~ek~~~~~~~~~~~~~~~~~~p~e~lEl~C~gqvL~~~mtLaTVr~~~WK~~~di~L~YR~ 328 (331)
T PF11816_consen 251 RLNAPRMLRVKKILEYVAEKLEKTPESKTPEMKPKKLKPEEWLELLCNGQVLPPDMTLATVRTFIWKSSGDIVLHYRR 328 (331)
T ss_pred eecccchhhhHHHHHHHHHHhccCccccCccccccCCCCCceEEEEeCCeEcCCcCCHHHHHHhhccCCCeEEEEEEe
Confidence 455555667888888888887 2 34456789999999999998876542 456666676654
No 323
>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=29.44 E-value=1.4e+02 Score=21.96 Aligned_cols=44 Identities=25% Similarity=0.404 Sum_probs=29.4
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCCeecCCCCccccc
Q 031604 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY 59 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~ 59 (156)
.+.+++...+.+.++++...+.+-++-+ +.-|+-+....|++||
T Consensus 75 rI~le~~~~~~i~~I~eiC~e~~pF~y~----i~~g~f~r~~~TvtDY 118 (150)
T TIGR03260 75 RIILELEDEDIVEEIEEICKEMLPFGYE----VRVGKFLRTKPTVTDY 118 (150)
T ss_pred EEEEEecCHHHHHHHHHHHHhhCCCceE----eeeeeEeecCCchhhh
Confidence 3556666777788887766665533321 3467778888888887
No 324
>PF08115 Toxin_28: SFI toxin family; InterPro: IPR012633 This family consists of the SFI family of spider toxins. This family of toxins might share structural, evolutionary and functional relationships with other small, highly structurally constrained spider neurotoxins. These toxins are highly selective agonists/antagonists of different voltage-dependent calcium channels and are extremely valuable reagents in the analysis of neuromuscular function.; GO: 0009405 pathogenesis, 0005576 extracellular region
Probab=28.83 E-value=48 Score=17.92 Aligned_cols=17 Identities=29% Similarity=0.505 Sum_probs=13.2
Q ss_pred ceEEeEeCCCCccCCce
Q 031604 129 GTFMASHFDRHYCGKCG 145 (156)
Q Consensus 129 g~fma~h~~r~~cg~c~ 145 (156)
+..+..|-...-||+|-
T Consensus 7 etvcyi~n~n~~~G~CL 23 (35)
T PF08115_consen 7 ETVCYIHNHNDCCGSCL 23 (35)
T ss_pred CcEEEEecCCCccccee
Confidence 45677888888899983
No 325
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=28.76 E-value=26 Score=21.96 Aligned_cols=20 Identities=15% Similarity=0.361 Sum_probs=14.6
Q ss_pred cHHHHHHHHHHHhCCCCCce
Q 031604 22 TIDNVKAKIQDKEGIPPDQQ 41 (156)
Q Consensus 22 TV~~LK~~I~~~~gip~~~q 41 (156)
|++++.+.+++.+|++++++
T Consensus 1 t~~~Ii~~Va~~~~v~~~~i 20 (70)
T PF08299_consen 1 TIEDIIEAVAEYFGVSVEDI 20 (70)
T ss_dssp -HHHHHHHHHHHTT--HHHH
T ss_pred CHHHHHHHHHHHHCCCHHHH
Confidence 68899999999999987654
No 326
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=28.60 E-value=51 Score=21.10 Aligned_cols=27 Identities=22% Similarity=0.508 Sum_probs=16.1
Q ss_pred cCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031604 120 ECPNAECGAGTFMASHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~ 150 (156)
.|| .|.. -|..-.++.+|..|+..|..
T Consensus 3 ~CP--~C~~--~L~~~~~~~~C~~C~~~~~~ 29 (70)
T PF07191_consen 3 TCP--KCQQ--ELEWQGGHYHCEACQKDYKK 29 (70)
T ss_dssp B-S--SS-S--BEEEETTEEEETTT--EEEE
T ss_pred cCC--CCCC--ccEEeCCEEECcccccccee
Confidence 578 7865 36666678888888877643
No 327
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=28.26 E-value=56 Score=23.86 Aligned_cols=30 Identities=30% Similarity=0.561 Sum_probs=21.3
Q ss_pred cccCCCCccCCceEEeEeCC-CCccCCceeEEEe
Q 031604 118 RKECPNAECGAGTFMASHFD-RHYCGKCGLTYVY 150 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~-r~~cg~c~~t~~~ 150 (156)
...|- .||.-+-. .|.+ =-.|.+||.+++.
T Consensus 112 ~l~C~--~Cg~~~~~-~~~~~l~~Cp~C~~~~F~ 142 (146)
T PF07295_consen 112 TLVCE--NCGHEVEL-THPERLPPCPKCGHTEFT 142 (146)
T ss_pred eEecc--cCCCEEEe-cCCCcCCCCCCCCCCeee
Confidence 56788 89865544 3554 4579999999844
No 328
>KOG3483 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.80 E-value=1.8e+02 Score=19.00 Aligned_cols=62 Identities=21% Similarity=0.280 Sum_probs=42.4
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCceeEee-CCeecCCCCcccccCcCCCCEEEEEEEecCC
Q 031604 15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~-~G~~L~d~~tL~~~gi~~~stv~l~~~~~gg 76 (156)
++|+.+.....+-..-++++.+|+.---++- +|--+...++-...=++.||.+.++-|.+-|
T Consensus 31 ~svpestpftavlkfaaeefkvpaatsaiitndgiginpaq~agnvflkhgselr~iprdrvg 93 (94)
T KOG3483|consen 31 LSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVG 93 (94)
T ss_pred ecCCCCCchHHHHHHHHHHccCCccceeEEecCccccCccccccceeeccCCEEEeccccccC
Confidence 4666677666666666778889887665554 4555555666666667889999888765543
No 329
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=27.71 E-value=71 Score=17.55 Aligned_cols=12 Identities=33% Similarity=0.836 Sum_probs=5.7
Q ss_pred CCCccCCceeEE
Q 031604 137 DRHYCGKCGLTY 148 (156)
Q Consensus 137 ~r~~cg~c~~t~ 148 (156)
.-++|..||..|
T Consensus 31 p~~~C~~CGE~~ 42 (46)
T TIGR03831 31 PALVCPQCGEEY 42 (46)
T ss_pred CccccccCCCEe
Confidence 344455555444
No 330
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=27.03 E-value=40 Score=23.00 Aligned_cols=13 Identities=31% Similarity=0.928 Sum_probs=10.4
Q ss_pred ecccCCCCccCCceE
Q 031604 117 LRKECPNAECGAGTF 131 (156)
Q Consensus 117 ~~~~cp~~~c~~g~f 131 (156)
..+.|| .|..|+.
T Consensus 48 vvggCp--~CrvG~l 60 (98)
T PF10164_consen 48 VVGGCP--ACRVGVL 60 (98)
T ss_pred EecCCC--CCceeee
Confidence 358899 8988876
No 331
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=26.96 E-value=2e+02 Score=19.34 Aligned_cols=67 Identities=18% Similarity=0.297 Sum_probs=38.9
Q ss_pred CCEEEEEec--CCCcHHHHHHHHHHHhCCCCCceeEeeCCee------cCCC---Cccc--ccCcCCCCEEEEEEEecCC
Q 031604 10 GKTITLEVE--SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ------LEDG---RTLA--DYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 10 g~~~~l~V~--~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~------L~d~---~tL~--~~gi~~~stv~l~~~~~gg 76 (156)
.+.+.+.++ ...+|..+-..+.....-|...--++.+|.. |-++ ..|+ +|.+.+|+.|.++-.+.||
T Consensus 17 qR~~el~~~~~e~~~vg~liD~~~~~i~~p~~~sifie~g~lrpGiI~LINd~DWeLleke~y~ledgDiIvfistlHGg 96 (96)
T COG5131 17 QREIELTREEVEGSSVGTLIDALRYFIYAPTRDSIFIEHGELRPGIICLINDMDWELLEKERYPLEDGDIIVFISTLHGG 96 (96)
T ss_pred ceeeEEEEcccCCcchhhHHHHHHHHHhCCccceeeecCCCCcccEEEEEcCccHhhhhcccccCCCCCEEEEEecccCC
Confidence 444555554 4567888888877732222222222234432 2121 2343 4889999999998888776
No 332
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=26.95 E-value=54 Score=23.03 Aligned_cols=32 Identities=22% Similarity=0.363 Sum_probs=18.4
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCCce-eEEEee
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGKCG-LTYVYQ 151 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~c~-~t~~~~ 151 (156)
+..-.|. .|+. +.....-+++|++|| .++...
T Consensus 68 p~~~~C~--~C~~--~~~~e~~~~~CP~C~s~~~~i~ 100 (115)
T COG0375 68 PAECWCL--DCGQ--EVELEELDYRCPKCGSINLRII 100 (115)
T ss_pred ccEEEec--cCCC--eecchhheeECCCCCCCceEEe
Confidence 3456777 6753 333344566699998 444333
No 333
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=26.93 E-value=36 Score=20.84 Aligned_cols=22 Identities=36% Similarity=0.901 Sum_probs=13.9
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
-.+|| .||. ..+ .-+.|..||+
T Consensus 27 ~~~c~--~cG~-~~l----~Hrvc~~cg~ 48 (57)
T COG0333 27 LSVCP--NCGE-YKL----PHRVCLKCGY 48 (57)
T ss_pred ceecc--CCCC-ccc----CceEcCCCCC
Confidence 46788 7973 333 3456777774
No 334
>COG1773 Rubredoxin [Energy production and conversion]
Probab=26.84 E-value=40 Score=20.53 Aligned_cols=11 Identities=45% Similarity=1.156 Sum_probs=8.1
Q ss_pred CCccCCceeEE
Q 031604 138 RHYCGKCGLTY 148 (156)
Q Consensus 138 r~~cg~c~~t~ 148 (156)
|+.|--|||.|
T Consensus 3 ~~~C~~CG~vY 13 (55)
T COG1773 3 RWRCSVCGYVY 13 (55)
T ss_pred ceEecCCceEe
Confidence 67788888655
No 335
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.68 E-value=32 Score=31.30 Aligned_cols=26 Identities=19% Similarity=0.413 Sum_probs=18.1
Q ss_pred ccCCCCccCCceEEeEeC--CCCccCCceeEE
Q 031604 119 KECPNAECGAGTFMASHF--DRHYCGKCGLTY 148 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~--~r~~cg~c~~t~ 148 (156)
-.|| +|. +.|.-|. ++..|-.||+..
T Consensus 393 ~~C~--~C~--~~L~~h~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 393 ARCR--HCT--GPLGLPSAGGTPRCRWCGRAA 420 (665)
T ss_pred eECC--CCC--CceeEecCCCeeECCCCcCCC
Confidence 4588 784 4778885 367788888754
No 336
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=26.54 E-value=41 Score=19.83 Aligned_cols=28 Identities=29% Similarity=0.574 Sum_probs=14.5
Q ss_pred ccCCCCccCCceEEeE--eC---CC-C-ccCCceeEE
Q 031604 119 KECPNAECGAGTFMAS--HF---DR-H-YCGKCGLTY 148 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~--h~---~r-~-~cg~c~~t~ 148 (156)
+-|| .||.-..+.. +. .+ . .|..||...
T Consensus 2 kPCP--fCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCP--FCGGADVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCC--CCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence 4578 8864444222 21 11 2 488887654
No 337
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=26.54 E-value=27 Score=17.11 Aligned_cols=10 Identities=40% Similarity=1.119 Sum_probs=7.8
Q ss_pred CccCCceeEE
Q 031604 139 HYCGKCGLTY 148 (156)
Q Consensus 139 ~~cg~c~~t~ 148 (156)
+.|..|+.+|
T Consensus 2 ~~C~~C~~~F 11 (27)
T PF13912_consen 2 FECDECGKTF 11 (27)
T ss_dssp EEETTTTEEE
T ss_pred CCCCccCCcc
Confidence 3588898887
No 338
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles 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,
Probab=26.35 E-value=2e+02 Score=19.01 Aligned_cols=38 Identities=13% Similarity=0.261 Sum_probs=31.2
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCC-ceeEeeC
Q 031604 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFA 46 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~-~qrL~~~ 46 (156)
+|..+...++++.|.++|.+++.+....+.+ ...+.|-
T Consensus 8 ~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~ 46 (83)
T cd06404 8 NGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWI 46 (83)
T ss_pred cCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEE
Confidence 6788888999999999999999999987664 4555553
No 339
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=26.28 E-value=47 Score=20.57 Aligned_cols=25 Identities=36% Similarity=0.810 Sum_probs=13.9
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCce
Q 031604 119 KECPNAECGAGTFMASHFDRHYCGKCG 145 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~ 145 (156)
--|. .|++-.-...|.=.+.|+.|+
T Consensus 31 IlCN--DC~~~s~v~fH~lg~KC~~C~ 55 (61)
T PF14599_consen 31 ILCN--DCNAKSEVPFHFLGHKCSHCG 55 (61)
T ss_dssp EEES--SS--EEEEE--TT----TTTS
T ss_pred EECC--CCCCccceeeeHhhhcCCCCC
Confidence 4477 788888888999999999997
No 340
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=26.18 E-value=48 Score=32.77 Aligned_cols=47 Identities=28% Similarity=0.576 Sum_probs=32.1
Q ss_pred ccccceeeeeeeeeEEEcCC-C---------------eEEEecccCCCCccCCceEEeEeCCCCccCCcee
Q 031604 92 KHKKKKVKLAVLQFYKVDDS-G---------------KVQRLRKECPNAECGAGTFMASHFDRHYCGKCGL 146 (156)
Q Consensus 92 k~~kkk~k~~v~k~y~vd~~-g---------------~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
|.+.++.|.+++..|-+.+- | .|+--.+.|| .||.-. -.+.|..||-
T Consensus 632 Ka~~RkMkPpvh~LFPIG~aGG~~R~i~~A~~~g~~~~vei~~~~Cp--~Cg~~~------~~~~Cp~CG~ 694 (1627)
T PRK14715 632 KAAPRKMKPPVNVLFPIGNAGGQVRLINKAVEENKTDDIEIAFFKCP--KCGKVG------LYHVCPFCGT 694 (1627)
T ss_pred ccccccCCCCCcccccccccCcchhhHHHHhhcCCcceEEEEeeeCC--CCCCcc------ccccCcccCC
Confidence 34455688888888876532 2 2556678999 898543 3456999984
No 341
>cd06535 CIDE_N_CAD CIDE_N domain of CAD nuclease. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of 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 CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and the release of active DFF40/CAD nuclease.
Probab=25.86 E-value=1.6e+02 Score=19.18 Aligned_cols=31 Identities=13% Similarity=0.065 Sum_probs=24.3
Q ss_pred CcHHHHHHHHHHHhCCCCCc--eeEeeCCeecC
Q 031604 21 DTIDNVKAKIQDKEGIPPDQ--QRLIFAGKQLE 51 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~--qrL~~~G~~L~ 51 (156)
.|+.+|+.+..+.+.++... ..|--+|..+.
T Consensus 21 ~sL~eL~~K~~~~l~l~~~~~~l~L~eDGTeVt 53 (77)
T cd06535 21 KNLKELLRKGCRLLQLPCAGSRLCLYEDGTEVT 53 (77)
T ss_pred CCHHHHHHHHHHHhCCCCCCcEEEEecCCcEeh
Confidence 57999999999999998654 44456788874
No 342
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.72 E-value=33 Score=24.06 Aligned_cols=29 Identities=24% Similarity=0.313 Sum_probs=18.6
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
..+.|| .|| ..|---.-+--.|.+||.+|
T Consensus 8 tKridP--etg-~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 8 TKRIDP--ETG-KKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccccCc--ccc-chhhccCCCccccCcccccc
Confidence 367899 787 44533323445688888876
No 343
>PHA02998 RNA polymerase subunit; Provisional
Probab=25.60 E-value=55 Score=24.92 Aligned_cols=41 Identities=29% Similarity=0.669 Sum_probs=25.4
Q ss_pred eeeeEEEcCCCeEEEecccCCCCccCCc--eEEeEe---CC-----CCccCCceeEE
Q 031604 102 VLQFYKVDDSGKVQRLRKECPNAECGAG--TFMASH---FD-----RHYCGKCGLTY 148 (156)
Q Consensus 102 v~k~y~vd~~g~~~~~~~~cp~~~c~~g--~fma~h---~~-----r~~cg~c~~t~ 148 (156)
.-+||+|-. +.....|| .|+.+ .||..+ .| .+.|-+||+++
T Consensus 131 y~~yfnvlp----kkt~v~CP--kCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~w 181 (195)
T PHA02998 131 YDDYFNVLD----EKYNTPCP--NCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHF 181 (195)
T ss_pred chhheeccC----cccCCCCC--CCCCCceEEEEEeeccCCCCceEEEEcCCCCCcc
Confidence 345788853 22468999 89643 233333 12 56899999876
No 344
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=25.53 E-value=38 Score=20.37 Aligned_cols=20 Identities=20% Similarity=0.484 Sum_probs=16.8
Q ss_pred cHHHHHHHHHHHhCCCCCce
Q 031604 22 TIDNVKAKIQDKEGIPPDQQ 41 (156)
Q Consensus 22 TV~~LK~~I~~~~gip~~~q 41 (156)
|+.+|.+.+++.+||+++++
T Consensus 1 ~~~~I~~~Va~~~~i~~~~i 20 (60)
T smart00760 1 TIEEIIEAVAEYFGVKPEDL 20 (60)
T ss_pred CHHHHHHHHHHHhCCCHHHH
Confidence 57889999999999987654
No 345
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=25.37 E-value=40 Score=28.67 Aligned_cols=30 Identities=17% Similarity=0.509 Sum_probs=20.7
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~ 152 (156)
-..|| .|+. +. .+..+..|.+||.+....+
T Consensus 215 ~~~C~--~Cd~-~~--~~~~~a~CpRC~~~L~~~~ 244 (403)
T TIGR00155 215 LRSCS--ACHT-TI--LPAQEPVCPRCSTPLYVRR 244 (403)
T ss_pred CCcCC--CCCC-cc--CCCCCcCCcCCCCcccCCC
Confidence 34599 8986 22 3567888999998874433
No 346
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=25.22 E-value=18 Score=23.95 Aligned_cols=31 Identities=23% Similarity=0.482 Sum_probs=20.3
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
+-++.|+ .||--.+=-.--.-|.|+.|..++
T Consensus 34 haky~Cs--fCGK~~vKR~AvGiW~C~~C~kv~ 64 (92)
T KOG0402|consen 34 HAKYTCS--FCGKKTVKRKAVGIWKCGSCKKVV 64 (92)
T ss_pred hhhhhhh--hcchhhhhhhceeEEecCCcccee
Confidence 3468899 886432211123679999999876
No 347
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=25.21 E-value=1.3e+02 Score=19.64 Aligned_cols=41 Identities=17% Similarity=0.350 Sum_probs=30.1
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEe--eCCeecC
Q 031604 11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE 51 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~ 51 (156)
+.+.+.++...+..+|.+.|....+--..+..|+ |.|..+.
T Consensus 8 RDiS~~v~~~~~~~~i~~~i~~~~~~~l~~v~l~D~y~~~~l~ 50 (94)
T PF03147_consen 8 RDISFVVPEDVPFADIEEVIRSAGGPLLESVELFDVYRGEKLP 50 (94)
T ss_dssp EEEEEEEETTS-HHHHHHHHHHHHTTTEEEEEEEEEEESTTSG
T ss_pred ccEEEEECCCCCHHHHHHHHHHhCccceeEEEEEEEEcCCCCC
Confidence 3577889999999999999988876555666665 7665443
No 348
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=25.20 E-value=62 Score=19.21 Aligned_cols=32 Identities=19% Similarity=0.472 Sum_probs=17.5
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeEEEee
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLTYVYQ 151 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~ 151 (156)
.+.|- +||.-+-.-.-.+..-|..||+-..++
T Consensus 6 ~Y~C~--~Cg~~~~~~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 6 EYKCA--RCGREVELDQETRGIRCPYCGSRILVK 37 (49)
T ss_pred EEEhh--hcCCeeehhhccCceeCCCCCcEEEEe
Confidence 45566 666544222234556677777666554
No 349
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.34 E-value=58 Score=22.66 Aligned_cols=26 Identities=23% Similarity=0.519 Sum_probs=14.8
Q ss_pred ecccCCCCccCCceEEeEeCCCCc-cCCcee
Q 031604 117 LRKECPNAECGAGTFMASHFDRHY-CGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~-cg~c~~ 146 (156)
.+-.|+ .||. ........+. |++||-
T Consensus 70 ~~~~C~--~Cg~--~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECK--DCSH--VFKPNALDYGVCEKCHS 96 (117)
T ss_pred CEEEhh--hCCC--ccccCCccCCcCcCCCC
Confidence 467888 7873 2222212333 999984
No 350
>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform
Probab=24.28 E-value=2.1e+02 Score=19.59 Aligned_cols=55 Identities=24% Similarity=0.244 Sum_probs=38.6
Q ss_pred cCCCcHHHHHHHHHHHhCCCC---CceeEeeCCeecCCCC-cccccCcCCCCEEEEEEEe
Q 031604 18 ESSDTIDNVKAKIQDKEGIPP---DQQRLIFAGKQLEDGR-TLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 18 ~~~~TV~~LK~~I~~~~gip~---~~qrL~~~G~~L~d~~-tL~~~gi~~~stv~l~~~~ 73 (156)
.+-.|+.++-..+.+..++-. =.+-.++.++.+..+. .|-.+.+..+ ++.+.+|-
T Consensus 28 ~~~~t~~~~l~~l~~~l~lh~VevIg~E~I~A~~ll~~~~~~L~H~~~~~~-~l~l~vrs 86 (104)
T PF14807_consen 28 SSQRTLPEFLQRLQQKLRLHVVEVIGNEGIFACQLLNSSPVCLLHCRVNAG-TLDLWVRS 86 (104)
T ss_pred cCcCCHHHHHHHHHHhcCceEEEEeCccceeeeeccCCCCeEEEEEEecCC-eEEEEEEc
Confidence 466788888888888776432 1235678888887766 7777777655 77777663
No 351
>PF07929 PRiA4_ORF3: Plasmid pRiA4b ORF-3-like protein; InterPro: IPR012912 Members of this family are similar to the protein product of ORF-3 (Q44206 from SWISSPROT) found on plasmid pRiA4 in the bacterium Agrobacterium rhizogenes. This plasmid is responsible for tumourigenesis at wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process []. Other proteins found in this family are annotated as being putative TnpR resolvases (Q9LCU7 from SWISSPROT, Q50439 from SWISSPROT), but no further evidence was found to back this. Moreover, another member of this family is described as a probable lexA repressor (Q7UEI4 from SWISSPROT) and in fact carries a LexA DNA binding domain (IPR006199 from INTERPRO), but no references were found to expand on this. ; PDB: 2I1S_A.
Probab=24.12 E-value=1.6e+02 Score=21.69 Aligned_cols=40 Identities=23% Similarity=0.190 Sum_probs=25.0
Q ss_pred EEEEEeCCC--CE-EEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031604 2 QIFVKTLTG--KT-ITLEVESSDTIDNVKAKIQDKEGIPPDQQ 41 (156)
Q Consensus 2 ~I~Vk~~~g--~~-~~l~V~~~~TV~~LK~~I~~~~gip~~~q 41 (156)
+|.|...+- .. ..|.|+.+.|+.+|=..|+..+|......
T Consensus 6 ~lkV~L~~~~p~iwRri~Vp~~~tl~~Lh~~Iq~afgw~~~HL 48 (179)
T PF07929_consen 6 QLKVSLKGSKPPIWRRIEVPADITLADLHEVIQAAFGWDDDHL 48 (179)
T ss_dssp EEEEEETT-SS-EEEEEEEETT-BHHHHHHHHHHHTT----S-
T ss_pred EEEEEEcCCCCCeEEEEEECCCCCHHHHHHHHHHHhCcCCCEe
Confidence 455554332 22 56899999999999999999999876544
No 352
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=23.72 E-value=45 Score=26.78 Aligned_cols=24 Identities=38% Similarity=0.955 Sum_probs=17.0
Q ss_pred ccCCCCccCCceEEeEeC----------CCCccCCce
Q 031604 119 KECPNAECGAGTFMASHF----------DRHYCGKCG 145 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~----------~r~~cg~c~ 145 (156)
..|-++.|...-| |+ +-|||..|-
T Consensus 233 i~CDn~~C~~eWF---H~~CVGL~~~PkgkWyC~~C~ 266 (274)
T KOG1973|consen 233 IGCDNPGCPIEWF---HFTCVGLKTKPKGKWYCPRCK 266 (274)
T ss_pred cccCCCCCCcceE---EEeccccccCCCCcccchhhh
Confidence 4566667776666 63 689999995
No 353
>COG4919 Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]
Probab=23.68 E-value=44 Score=19.77 Aligned_cols=24 Identities=29% Similarity=0.288 Sum_probs=18.1
Q ss_pred CCccccccccccCCccccccccee
Q 031604 75 GGAKKRKKKTYTKPKKIKHKKKKV 98 (156)
Q Consensus 75 gg~~k~~kk~~~~pk~~k~~kkk~ 98 (156)
|.-.+++|+..+|||-..+.+++-
T Consensus 5 GSLTKAGKVR~QTPkipaK~kkn~ 28 (54)
T COG4919 5 GSLTKAGKVRKQTPKIPAKQKKNY 28 (54)
T ss_pred cccccccchhccCCCCCccccccC
Confidence 445678889999999887777654
No 354
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=23.43 E-value=1.2e+02 Score=26.62 Aligned_cols=80 Identities=18% Similarity=0.212 Sum_probs=44.1
Q ss_pred CCcccccCcCCCCEEEEEEEecCCccccccccccCCcccccccceeeeeeeeeEEEcCCCeEEEecccCCCCccCCceEE
Q 031604 53 GRTLADYNIQKESTLHLVLRLRGGAKKRKKKTYTKPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFM 132 (156)
Q Consensus 53 ~~tL~~~gi~~~stv~l~~~~~gg~~k~~kk~~~~pk~~k~~kkk~k~~v~k~y~vd~~g~~~~~~~~cp~~~c~~g~fm 132 (156)
+.+|.+.+++.|..+.|... |...-. +..-.-+|... ...-+...+..+-+.+ +|.|.| ..-| .|
T Consensus 17 ~~~~~~~~~~hG~ml~l~~~--~~~e~~-~sv~~~~~~~~-~~~vr~~dvde~ls~e-dg~I~r--sk~~--lc------ 81 (510)
T KOG2834|consen 17 DGTLLLAGLKHGQMLVLSAP--GNGELD-KSVAPGAKGLR-GQRVRSRDVDERLSKE-DGLITR--SKDK--LC------ 81 (510)
T ss_pred cchhHhhccccccEEEEecC--CCCCcC-cccCCCccccC-CCceecccccchhhhc-CCceee--ccCc--cc------
Confidence 35677888888988887743 222211 11111122222 1122233555554444 788987 3334 56
Q ss_pred eEeCCCCccCCceeEE
Q 031604 133 ASHFDRHYCGKCGLTY 148 (156)
Q Consensus 133 a~h~~r~~cg~c~~t~ 148 (156)
.|..+..|-.|.--.
T Consensus 82 -rh~~~~mc~~c~pL~ 96 (510)
T KOG2834|consen 82 -RHDPLQMCTHCSPLD 96 (510)
T ss_pred -ccCccccCCcCCCCC
Confidence 488999999997433
No 355
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=23.32 E-value=36 Score=24.76 Aligned_cols=28 Identities=21% Similarity=0.490 Sum_probs=19.6
Q ss_pred ecccCCCCccCCceEEeEeC-CCCccCCceeEE
Q 031604 117 LRKECPNAECGAGTFMASHF-DRHYCGKCGLTY 148 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~-~r~~cg~c~~t~ 148 (156)
.=..|| .|...+ .... +.+.|.+|+.+.
T Consensus 33 ~Y~aC~--~C~kkv--~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 33 WYPACP--GCNKKV--VEEGNGTYRCEKCNKSV 61 (166)
T ss_pred EEcccc--ccCccc--EeCCCCcEECCCCCCcC
Confidence 356799 896543 3333 789999999763
No 356
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=23.29 E-value=57 Score=17.61 Aligned_cols=8 Identities=38% Similarity=1.219 Sum_probs=5.3
Q ss_pred ccCCCCccCC
Q 031604 119 KECPNAECGA 128 (156)
Q Consensus 119 ~~cp~~~c~~ 128 (156)
..|| .||.
T Consensus 6 y~C~--~Cg~ 13 (41)
T smart00834 6 YRCE--DCGH 13 (41)
T ss_pred EEcC--CCCC
Confidence 4677 6764
No 357
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.27 E-value=37 Score=25.16 Aligned_cols=31 Identities=35% Similarity=1.039 Sum_probs=20.7
Q ss_pred ccCCCCccCC---------ceEEe-EeC-CCCccCCceeEEEee
Q 031604 119 KECPNAECGA---------GTFMA-SHF-DRHYCGKCGLTYVYQ 151 (156)
Q Consensus 119 ~~cp~~~c~~---------g~fma-~h~-~r~~cg~c~~t~~~~ 151 (156)
..|| .|++ |||-. .|+ --.||-+||..|-+.
T Consensus 40 ~~Cp--~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 40 TSCP--NCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWT 81 (158)
T ss_pred HHCc--CCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchH
Confidence 5688 6764 55544 343 367899999988654
No 358
>PF13439 Glyco_transf_4: Glycosyltransferase Family 4; PDB: 2JJM_E 3MBO_C 2GEJ_A 2GEK_A.
Probab=23.13 E-value=92 Score=21.39 Aligned_cols=27 Identities=26% Similarity=0.634 Sum_probs=14.3
Q ss_pred HHHHHHHHHHhCCCCCceeEeeCCeecC
Q 031604 24 DNVKAKIQDKEGIPPDQQRLIFAGKQLE 51 (156)
Q Consensus 24 ~~LK~~I~~~~gip~~~qrL~~~G~~L~ 51 (156)
..+++.+.+ .|++++...++++|-.++
T Consensus 148 ~~~~~~l~~-~~~~~~ki~vI~ngid~~ 174 (177)
T PF13439_consen 148 ESTKDELIK-FGIPPEKIHVIYNGIDTD 174 (177)
T ss_dssp HHHHHHHHH-HT--SS-EEE----B-CC
T ss_pred HHHHHHHHH-hCCcccCCEEEECCccHH
Confidence 356777777 899999999999987654
No 359
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=22.64 E-value=59 Score=23.85 Aligned_cols=16 Identities=44% Similarity=0.877 Sum_probs=12.7
Q ss_pred CCeEEEecccCCCCccCC
Q 031604 111 SGKVQRLRKECPNAECGA 128 (156)
Q Consensus 111 ~g~~~~~~~~cp~~~c~~ 128 (156)
+|...|-|++|+ .|+.
T Consensus 21 dg~~IRRRReC~--~C~~ 36 (147)
T TIGR00244 21 DGQSIRRRRECL--ECHE 36 (147)
T ss_pred CCCeeeecccCC--ccCC
Confidence 676666699999 8984
No 360
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=22.59 E-value=24 Score=24.51 Aligned_cols=13 Identities=54% Similarity=1.303 Sum_probs=10.8
Q ss_pred CCCccCCceeEEE
Q 031604 137 DRHYCGKCGLTYV 149 (156)
Q Consensus 137 ~r~~cg~c~~t~~ 149 (156)
..+.||-||+.|.
T Consensus 103 ~~~~CgYCGlrf~ 115 (120)
T KOG3456|consen 103 GPHICGYCGLRFV 115 (120)
T ss_pred CCcccccchhhhh
Confidence 4689999999883
No 361
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=22.52 E-value=38 Score=31.06 Aligned_cols=35 Identities=26% Similarity=0.462 Sum_probs=26.1
Q ss_pred EcCCCeEEEecccCCCCccCCceEEeEeC----------CCCccCCcee
Q 031604 108 VDDSGKVQRLRKECPNAECGAGTFMASHF----------DRHYCGKCGL 146 (156)
Q Consensus 108 vd~~g~~~~~~~~cp~~~c~~g~fma~h~----------~r~~cg~c~~ 146 (156)
-||.||.+.=-..|- |.+|-.|.|. .-|+|-||.-
T Consensus 12 SDErGWaeNPLVYCD----G~nCsVAVHQaCYGIvqVPtGpWfCrKCes 56 (900)
T KOG0956|consen 12 SDERGWAENPLVYCD----GHNCSVAVHQACYGIVQVPTGPWFCRKCES 56 (900)
T ss_pred cCcCCCccCceeeec----CCCceeeeehhcceeEecCCCchhhhhhhh
Confidence 478899887444444 6677888894 5899999974
No 362
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=22.45 E-value=1.1e+02 Score=16.83 Aligned_cols=29 Identities=28% Similarity=0.734 Sum_probs=15.6
Q ss_pred ccCCCCccCCceEEeEeCCC---CccC---CceeEEEe
Q 031604 119 KECPNAECGAGTFMASHFDR---HYCG---KCGLTYVY 150 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r---~~cg---~c~~t~~~ 150 (156)
..|| .|| +-+....... +.|- .|.+|+..
T Consensus 2 ~~CP--~Cg-~~lv~r~~k~g~F~~Cs~yP~C~~~~~~ 36 (39)
T PF01396_consen 2 EKCP--KCG-GPLVLRRGKKGKFLGCSNYPECKYTEPL 36 (39)
T ss_pred cCCC--CCC-ceeEEEECCCCCEEECCCCCCcCCeEeC
Confidence 5799 898 4444433211 1343 47777644
No 363
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.42 E-value=76 Score=22.65 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=7.8
Q ss_pred ecccCCCCccCC
Q 031604 117 LRKECPNAECGA 128 (156)
Q Consensus 117 ~~~~cp~~~c~~ 128 (156)
....|+ .||.
T Consensus 69 ~~~~C~--~CG~ 78 (135)
T PRK03824 69 AVLKCR--NCGN 78 (135)
T ss_pred eEEECC--CCCC
Confidence 578899 7983
No 364
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=22.25 E-value=40 Score=23.24 Aligned_cols=29 Identities=31% Similarity=0.803 Sum_probs=16.2
Q ss_pred EecccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031604 116 RLRKECPNAECGAGTFMASHFDRHYCGKCGLTY 148 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
+.+..|+ .||. .|-.... +..|+.||-..
T Consensus 68 p~~~~C~--~Cg~-~~~~~~~-~~~CP~Cgs~~ 96 (113)
T PF01155_consen 68 PARARCR--DCGH-EFEPDEF-DFSCPRCGSPD 96 (113)
T ss_dssp --EEEET--TTS--EEECHHC-CHH-SSSSSS-
T ss_pred CCcEECC--CCCC-EEecCCC-CCCCcCCcCCC
Confidence 3578898 7983 4433333 36799998653
No 365
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=22.21 E-value=2.2e+02 Score=18.12 Aligned_cols=64 Identities=11% Similarity=0.168 Sum_probs=35.6
Q ss_pred EEEEEeCCCC---EEEEEecCCCcHHHHHHHHHHHhCCCCCceeE-----eeCCeecCCCCcccccCcCCCCEEEEE
Q 031604 2 QIFVKTLTGK---TITLEVESSDTIDNVKAKIQDKEGIPPDQQRL-----IFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~---~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL-----~~~G~~L~d~~tL~~~gi~~~stv~l~ 70 (156)
+|+-|..++. .-.+.++..+||.|+-.+|....+-....-.+ -++|+...-+.. ++++++|.+.
T Consensus 3 rvytk~~g~~~d~~~~liL~~GaTV~D~a~~iH~di~~~f~~A~v~g~s~~~~gq~Vgl~~~-----L~d~DvVeI~ 74 (75)
T cd01666 3 RVYTKPKGQEPDFDEPVILRRGSTVEDVCNKIHKDLVKQFKYALVWGSSVKHSPQRVGLDHV-----LEDEDVVQIV 74 (75)
T ss_pred EEEeCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHhCCeeEEeccCCcCCCeECCCCCE-----ecCCCEEEEe
Confidence 4555544332 24577888999999999998643211110111 145555544433 4567777764
No 366
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=22.16 E-value=40 Score=28.33 Aligned_cols=25 Identities=28% Similarity=0.681 Sum_probs=18.0
Q ss_pred cccCCCCccCCceEEeEe-CCCCccCCce
Q 031604 118 RKECPNAECGAGTFMASH-FDRHYCGKCG 145 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h-~~r~~cg~c~ 145 (156)
=+.|+--+|+ |+..| -|.|+|.+|-
T Consensus 27 CRyC~klrc~---~Cv~hEvdshfCp~CL 52 (449)
T KOG3896|consen 27 CRYCFKLRCD---DCVLHEVDSHFCPRCL 52 (449)
T ss_pred eecccccccc---cccccccccccchhhc
Confidence 4667777777 66677 4888888884
No 367
>PRK04351 hypothetical protein; Provisional
Probab=22.00 E-value=87 Score=22.86 Aligned_cols=33 Identities=27% Similarity=0.582 Sum_probs=22.4
Q ss_pred ecccCCCCccCCceEEeE--e-CCCCccCCceeEEEeec
Q 031604 117 LRKECPNAECGAGTFMAS--H-FDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~--h-~~r~~cg~c~~t~~~~~ 152 (156)
..+.|. .||. .+... | ..++-||+|+-.+.+..
T Consensus 111 y~Y~C~--~Cg~-~~~r~Rr~n~~~yrCg~C~g~L~~~~ 146 (149)
T PRK04351 111 YLYECQ--SCGQ-QYLRKRRINTKRYRCGKCRGKLKLIN 146 (149)
T ss_pred EEEECC--CCCC-EeeeeeecCCCcEEeCCCCcEeeecc
Confidence 568897 6974 33221 1 46899999998886653
No 368
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=21.98 E-value=74 Score=19.55 Aligned_cols=23 Identities=30% Similarity=1.136 Sum_probs=12.8
Q ss_pred ecccCCCCcc-CCceEEeEeCCCCccCCce
Q 031604 117 LRKECPNAEC-GAGTFMASHFDRHYCGKCG 145 (156)
Q Consensus 117 ~~~~cp~~~c-~~g~fma~h~~r~~cg~c~ 145 (156)
....|| .| |.|.+. +.+.|..|+
T Consensus 40 ~~~~C~--~C~G~G~~i----~~~~C~~C~ 63 (66)
T PF00684_consen 40 MQQTCP--KCGGTGKII----EKDPCKTCK 63 (66)
T ss_dssp EEEE-T--TTSSSSEE-----TSSB-SSST
T ss_pred EEEECC--CCcceeeEE----CCCCCCCCC
Confidence 456777 77 556542 566777774
No 369
>PF04060 FeS: Putative Fe-S cluster; InterPro: IPR007202 These proteins contain a domain with four conserved cysteines that probably form an Fe-S redox cluster.; GO: 0051536 iron-sulfur cluster binding; PDB: 2YCL_A 4DJF_E 4DJD_C 4DJE_C.
Probab=21.95 E-value=32 Score=18.70 Aligned_cols=10 Identities=40% Similarity=1.105 Sum_probs=4.3
Q ss_pred CCccCCceeE
Q 031604 138 RHYCGKCGLT 147 (156)
Q Consensus 138 r~~cg~c~~t 147 (156)
...||.||+.
T Consensus 4 ~~nCg~CG~~ 13 (35)
T PF04060_consen 4 GTNCGACGYP 13 (35)
T ss_dssp S----TTSSS
T ss_pred CCcCCCCCCc
Confidence 3468889874
No 370
>PRK12366 replication factor A; Reviewed
Probab=21.94 E-value=43 Score=30.25 Aligned_cols=26 Identities=23% Similarity=0.483 Sum_probs=19.3
Q ss_pred cccCCCCccCCceEEeEeCCCCccCCceeE
Q 031604 118 RKECPNAECGAGTFMASHFDRHYCGKCGLT 147 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
=..|| .|..- |....+.|.|-+|+.+
T Consensus 532 y~aCp--~CnkK--v~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCP--NCRKR--VEEVDGEYICEFCGEV 557 (637)
T ss_pred Eeccc--ccCeE--eEcCCCcEECCCCCCC
Confidence 46799 69653 4455688999999864
No 371
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 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 family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=21.02 E-value=1.7e+02 Score=19.05 Aligned_cols=25 Identities=12% Similarity=0.271 Sum_probs=19.4
Q ss_pred CCCcHHHHHHHHHHHhCCCCCceeE
Q 031604 19 SSDTIDNVKAKIQDKEGIPPDQQRL 43 (156)
Q Consensus 19 ~~~TV~~LK~~I~~~~gip~~~qrL 43 (156)
++-+-.+|+++|++..+++++.+.+
T Consensus 11 ~Tpsr~ei~~klA~~~~~~~~~ivv 35 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNVDPDLIVV 35 (84)
T ss_dssp SS--HHHHHHHHHHHHTSTGCCEEE
T ss_pred CCCCHHHHHHHHHHHhCCCCCeEEE
Confidence 5678899999999999998776544
No 372
>KOG4842 consensus Protein involved in sister chromatid separation and/or segregation [Cell cycle control, cell division, chromosome partitioning]
Probab=20.96 E-value=32 Score=27.63 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=33.3
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceeEeeCC
Q 031604 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG 47 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G 47 (156)
.|..+.++++..++|.|.+..++...++.+...++++.+
T Consensus 11 ~gn~i~ls~~~~~ri~D~~~~l~K~~~vss~~~kll~~~ 49 (278)
T KOG4842|consen 11 SGNAIYLSMAGSQRIPDKNPHLQKVAVVSSKPNKLLALN 49 (278)
T ss_pred cCcEEEEEeccccccCCCCcccceeeeeccchHHHHhhh
Confidence 578899999999999999999999988888777766544
No 373
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.88 E-value=1.1e+02 Score=20.71 Aligned_cols=57 Identities=25% Similarity=0.344 Sum_probs=36.1
Q ss_pred CCCcHHHHHHHHHHHhCCCCCceeEeeCCee------cCC--C-Ccc--cccCcCCCCEEEEEEEecCC
Q 031604 19 SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ------LED--G-RTL--ADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 19 ~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~------L~d--~-~tL--~~~gi~~~stv~l~~~~~gg 76 (156)
..+||.+|-..|....--.+++ -.+.+|.. |-+ + ..| .+|.+++|+.|.++-.+.||
T Consensus 34 ~~~tvgdll~yi~~~~ie~r~~-lFi~~gsvrpGii~lINd~DWEllekedy~ledgD~ivfiSTlHGg 101 (101)
T KOG4146|consen 34 SPATVGDLLDYIFGKYIETRDS-LFIHHGSVRPGIIVLINDMDWELLEKEDYPLEDGDHIVFISTLHGG 101 (101)
T ss_pred CcccHHHHHHHHHHHHhcCCcc-eEeeCCcCcCcEEEEEeccchhhhcccccCcccCCEEEEEEeccCC
Confidence 4679999998888754222222 23344432 211 1 122 57899999999998888876
No 374
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=20.73 E-value=75 Score=26.88 Aligned_cols=16 Identities=19% Similarity=0.299 Sum_probs=11.3
Q ss_pred EEecCCCcHHHHHHHH
Q 031604 15 LEVESSDTIDNVKAKI 30 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I 30 (156)
|.|+.++|.++||.+-
T Consensus 10 LGV~k~As~~EIKkAY 25 (371)
T COG0484 10 LGVSKDASEEEIKKAY 25 (371)
T ss_pred cCCCCCCCHHHHHHHH
Confidence 5677777777777654
No 375
>PF08154 NLE: NLE (NUC135) domain; InterPro: IPR012972 This domain is located N-terminal to WD40 repeats(IPR001680 from INTERPRO). It is found in the microtubule-associated protein Q12024 from SWISSPROT [].
Probab=20.73 E-value=2.2e+02 Score=17.44 Aligned_cols=40 Identities=15% Similarity=0.192 Sum_probs=28.4
Q ss_pred EEEEecCCCcHHHHHHHHHHHh--CCCCCceeEeeCCeecCC
Q 031604 13 ITLEVESSDTIDNVKAKIQDKE--GIPPDQQRLIFAGKQLED 52 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~--gip~~~qrL~~~G~~L~d 52 (156)
-.+.|+.+.|..+|-+.+.+.. .-.+-....+.+|..|.+
T Consensus 18 ~~~~VP~~~t~~~Ls~LvN~LL~~~~~~vpfdF~i~~~~lr~ 59 (65)
T PF08154_consen 18 TPISVPSNITRKELSELVNQLLDDEEEPVPFDFLINGEELRT 59 (65)
T ss_pred CCEEEeCCCCHHHHHHHHHHHhccCCCCCcEEEEECCEEeec
Confidence 4578999999999999998876 233334556667776654
No 376
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.64 E-value=35 Score=23.04 Aligned_cols=9 Identities=44% Similarity=1.357 Sum_probs=6.9
Q ss_pred cCCceeEEE
Q 031604 141 CGKCGLTYV 149 (156)
Q Consensus 141 cg~c~~t~~ 149 (156)
|-+|||+|.
T Consensus 61 CkkCGfef~ 69 (97)
T COG3357 61 CKKCGFEFR 69 (97)
T ss_pred hcccCcccc
Confidence 778888874
No 377
>PF11305 DUF3107: Protein of unknown function (DUF3107); InterPro: IPR021456 Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=20.48 E-value=2.5e+02 Score=18.07 Aligned_cols=34 Identities=26% Similarity=0.347 Sum_probs=25.3
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC
Q 031604 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG 35 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~g 35 (156)
|+|.|=. ......|.++.+.|-.++.+.|.+...
T Consensus 1 MeIkIGi-~~~~REl~ies~~s~dev~~~v~~Al~ 34 (74)
T PF11305_consen 1 MEIKIGI-QNVARELVIESDQSADEVEAAVTDALA 34 (74)
T ss_pred CeEEEee-ecCCceEEEecCCCHHHHHHHHHHHHh
Confidence 7777743 235567778888899999999988753
No 378
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.42 E-value=81 Score=25.53 Aligned_cols=28 Identities=21% Similarity=0.447 Sum_probs=18.0
Q ss_pred ecccCCCCccCCceEEeEeC--CCCccCCcee
Q 031604 117 LRKECPNAECGAGTFMASHF--DRHYCGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~--~r~~cg~c~~ 146 (156)
...-|+ +||.=+-=..+. ..|+|..|+.
T Consensus 244 ~GepC~--~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCR--RCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCC--ccCCEeEEEEEcCCcCEeCCCCCC
Confidence 357899 998422222232 5789999973
No 379
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=20.40 E-value=1.1e+02 Score=17.23 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=6.2
Q ss_pred CccCCceeEE
Q 031604 139 HYCGKCGLTY 148 (156)
Q Consensus 139 ~~cg~c~~t~ 148 (156)
..|+-|+..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 4566666665
No 380
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.33 E-value=1e+02 Score=17.16 Aligned_cols=27 Identities=37% Similarity=0.715 Sum_probs=16.0
Q ss_pred cccCCCCccCCceEEeEe----CCCCccCCceeE
Q 031604 118 RKECPNAECGAGTFMASH----FDRHYCGKCGLT 147 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h----~~r~~cg~c~~t 147 (156)
...|+ .|| ..|=..+ .+...|..||-+
T Consensus 5 ey~C~--~Cg-~~fe~~~~~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 5 EYRCE--ECG-HEFEVLQSISEDDPVPCPECGST 35 (42)
T ss_pred EEEeC--CCC-CEEEEEEEcCCCCCCcCCCCCCC
Confidence 35677 786 2332222 357888888863
No 381
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=20.14 E-value=46 Score=20.53 Aligned_cols=26 Identities=31% Similarity=1.014 Sum_probs=19.6
Q ss_pred ecccCCCCccCCceEEeEeCCCCccCCceeE
Q 031604 117 LRKECPNAECGAGTFMASHFDRHYCGKCGLT 147 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
..-.|- +||.-.| |--..+|--||+-
T Consensus 15 tH~~CR--RCGr~sy---hv~k~~CaaCGfg 40 (61)
T COG2126 15 THIRCR--RCGRRSY---HVRKKYCAACGFG 40 (61)
T ss_pred ceehhh--hccchhe---eeccceecccCCC
Confidence 456788 8986554 7778899999864
No 382
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=20.11 E-value=2.7e+02 Score=18.22 Aligned_cols=26 Identities=23% Similarity=0.491 Sum_probs=16.1
Q ss_pred eeeeeeEEEcCCCeEEEecccCCCCccC
Q 031604 100 LAVLQFYKVDDSGKVQRLRKECPNAECG 127 (156)
Q Consensus 100 ~~v~k~y~vd~~g~~~~~~~~cp~~~c~ 127 (156)
+.+.+..-...+-.+.+.+-.|| +||
T Consensus 66 l~ve~l~~~glg~~~~~~np~C~--~C~ 91 (91)
T cd04482 66 LNLEKLRVIRLARLYERENPVCP--KCG 91 (91)
T ss_pred EEEEEEEECCCcceEEEcCCcCC--CCC
Confidence 44544444443334777789999 885
Done!