Query 031613
Match_columns 156
No_of_seqs 315 out of 1379
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 02:57:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031613.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031613hhsearch_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 7.3E-49 1.6E-53 283.2 7.3 155 1-155 1-155 (156)
2 PF01599 Ribosomal_S27: Riboso 100.0 9.9E-31 2.1E-35 154.2 2.4 47 101-147 1-47 (47)
3 COG1998 RPS31 Ribosomal protei 99.9 8.1E-27 1.7E-31 137.2 3.3 49 99-150 1-49 (51)
4 cd01793 Fubi Fubi ubiquitin-li 99.9 3.4E-22 7.4E-27 130.4 9.0 74 1-76 1-74 (74)
5 PTZ00044 ubiquitin; Provisiona 99.9 9.5E-22 2.1E-26 128.6 9.5 76 1-76 1-76 (76)
6 cd01807 GDX_N ubiquitin-like d 99.9 1.7E-21 3.7E-26 127.1 9.0 73 1-73 1-73 (74)
7 cd01802 AN1_N ubiquitin-like d 99.9 2.5E-21 5.5E-26 133.9 9.2 76 1-76 28-103 (103)
8 cd01803 Ubiquitin Ubiquitin. U 99.9 4.1E-21 8.8E-26 125.2 9.3 76 1-76 1-76 (76)
9 cd01806 Nedd8 Nebb8-like ubiq 99.8 1E-20 2.2E-25 123.3 9.8 76 1-76 1-76 (76)
10 cd01810 ISG15_repeat2 ISG15 ub 99.8 8.3E-21 1.8E-25 123.8 8.5 74 3-76 1-74 (74)
11 cd01804 midnolin_N Ubiquitin-l 99.8 2.3E-20 4.9E-25 123.1 8.7 75 1-76 2-76 (78)
12 cd01797 NIRF_N amino-terminal 99.8 2.3E-20 4.9E-25 123.1 8.7 74 1-74 1-76 (78)
13 cd01791 Ubl5 UBL5 ubiquitin-li 99.8 8.7E-20 1.9E-24 118.9 7.8 71 1-71 2-72 (73)
14 cd01805 RAD23_N Ubiquitin-like 99.8 2.9E-19 6.3E-24 117.0 9.5 72 1-72 1-74 (77)
15 cd01800 SF3a120_C Ubiquitin-li 99.8 1.8E-19 4E-24 118.1 7.9 72 8-79 5-76 (76)
16 cd01809 Scythe_N Ubiquitin-lik 99.8 4.4E-19 9.6E-24 114.4 9.0 72 1-72 1-72 (72)
17 cd01794 DC_UbP_C dendritic cel 99.8 2.9E-19 6.2E-24 115.5 7.7 69 3-71 1-69 (70)
18 cd01798 parkin_N amino-termina 99.8 3.2E-19 7E-24 115.0 7.8 70 3-72 1-70 (70)
19 cd01792 ISG15_repeat1 ISG15 ub 99.8 9.6E-19 2.1E-23 115.8 8.1 72 1-72 3-76 (80)
20 cd01808 hPLIC_N Ubiquitin-like 99.8 2.4E-18 5.3E-23 111.2 8.4 71 1-72 1-71 (71)
21 KOG0003 Ubiquitin/60s ribosoma 99.8 6.6E-20 1.4E-24 125.1 0.6 78 1-78 1-78 (128)
22 PF00240 ubiquitin: Ubiquitin 99.8 3.3E-18 7.2E-23 109.6 8.2 68 6-73 1-68 (69)
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 3E-17 6.6E-22 110.3 9.6 76 1-76 12-87 (87)
25 cd01812 BAG1_N Ubiquitin-like 99.7 2.8E-17 6.2E-22 105.7 7.8 70 1-71 1-70 (71)
26 PRK00432 30S ribosomal protein 99.7 1E-17 2.2E-22 101.1 4.1 47 99-149 2-48 (50)
27 cd01790 Herp_N Homocysteine-re 99.7 5.1E-17 1.1E-21 106.9 7.3 71 1-71 2-78 (79)
28 cd01813 UBP_N UBP ubiquitin pr 99.7 1.3E-16 2.9E-21 104.1 7.9 69 1-70 1-72 (74)
29 KOG0005 Ubiquitin-like protein 99.7 5.1E-17 1.1E-21 99.8 4.8 70 1-70 1-70 (70)
30 smart00213 UBQ Ubiquitin homol 99.6 7.9E-16 1.7E-20 96.4 7.5 64 1-65 1-64 (64)
31 cd01814 NTGP5 Ubiquitin-like N 99.6 7.9E-16 1.7E-20 106.7 5.9 90 2-91 6-109 (113)
32 TIGR00601 rad23 UV excision re 99.6 5.9E-15 1.3E-19 122.6 9.0 72 1-72 1-75 (378)
33 cd01799 Hoil1_N Ubiquitin-like 99.6 1.3E-14 2.8E-19 94.9 7.3 64 7-71 9-74 (75)
34 cd01815 BMSC_UbP_N Ubiquitin-l 99.5 1.4E-14 3.1E-19 94.2 5.0 53 19-71 19-74 (75)
35 cd01769 UBL Ubiquitin-like dom 99.5 9.7E-14 2.1E-18 88.0 7.6 67 5-71 2-68 (69)
36 PF11976 Rad60-SLD: Ubiquitin- 99.5 3.8E-13 8.2E-18 86.8 7.5 71 1-71 1-72 (72)
37 cd01795 USP48_C USP ubiquitin- 99.4 3.1E-13 6.8E-18 91.5 6.6 61 12-72 16-77 (107)
38 KOG0010 Ubiquitin-like protein 99.4 3.3E-13 7.2E-18 113.5 6.4 73 1-74 16-88 (493)
39 KOG0011 Nucleotide excision re 99.3 4.4E-12 9.4E-17 102.2 7.3 74 1-74 1-76 (340)
40 cd01789 Alp11_N Ubiquitin-like 99.3 1.7E-11 3.7E-16 81.8 8.6 70 2-71 3-80 (84)
41 PF14560 Ubiquitin_2: Ubiquiti 99.2 6E-11 1.3E-15 79.4 7.6 70 2-71 3-82 (87)
42 PF13881 Rad60-SLD_2: Ubiquiti 99.2 3.8E-10 8.2E-15 79.0 9.6 77 2-78 4-94 (111)
43 KOG0001 Ubiquitin and ubiquiti 99.2 4.7E-10 1E-14 70.8 9.2 73 3-75 2-74 (75)
44 cd01788 ElonginB Ubiquitin-lik 99.2 2E-10 4.3E-15 79.7 7.7 76 1-76 1-84 (119)
45 PLN02560 enoyl-CoA reductase 99.1 2E-10 4.3E-15 93.5 8.0 74 1-76 1-85 (308)
46 cd01801 Tsc13_N Ubiquitin-like 98.9 4E-09 8.7E-14 69.0 6.9 68 2-69 2-74 (77)
47 PF11543 UN_NPL4: Nuclear pore 98.9 3.7E-09 8E-14 69.9 6.0 69 1-70 5-78 (80)
48 KOG4248 Ubiquitin-like protein 98.9 2.2E-09 4.8E-14 96.9 6.4 72 2-74 4-75 (1143)
49 cd00196 UBQ Ubiquitin-like pro 98.8 6.6E-08 1.4E-12 58.0 7.7 67 5-71 2-68 (69)
50 KOG1769 Ubiquitin-like protein 98.5 8.9E-07 1.9E-11 60.1 8.7 76 2-77 22-97 (99)
51 cd01811 OASL_repeat1 2'-5' oli 98.5 1E-06 2.2E-11 56.8 7.5 70 1-71 1-75 (80)
52 KOG0006 E3 ubiquitin-protein l 98.5 3.6E-07 7.9E-12 73.9 6.0 73 1-73 1-77 (446)
53 PF13019 Telomere_Sde2: Telome 98.3 4.9E-06 1.1E-10 61.6 9.0 78 1-78 1-90 (162)
54 KOG3493 Ubiquitin-like protein 98.3 4.2E-07 9E-12 57.0 1.9 69 2-70 3-71 (73)
55 KOG1872 Ubiquitin-specific pro 98.3 2.1E-06 4.6E-11 72.5 6.6 72 3-75 6-78 (473)
56 KOG4495 RNA polymerase II tran 98.2 1.7E-06 3.8E-11 58.3 4.1 62 1-62 1-65 (110)
57 PF08817 YukD: WXG100 protein 98.0 4E-05 8.8E-10 50.2 6.9 68 2-69 4-78 (79)
58 PF00789 UBX: UBX domain; Int 98.0 0.00012 2.7E-09 47.9 9.1 69 2-70 8-81 (82)
59 PF11470 TUG-UBL1: GLUT4 regul 97.9 6.4E-05 1.4E-09 47.7 6.6 63 7-69 3-65 (65)
60 smart00166 UBX Domain present 97.8 0.00019 4.1E-09 47.0 8.1 68 2-69 6-78 (80)
61 COG5227 SMT3 Ubiquitin-like pr 97.8 3.6E-05 7.9E-10 51.4 3.9 76 2-77 26-101 (103)
62 cd01772 SAKS1_UBX SAKS1-like U 97.7 0.00054 1.2E-08 44.9 8.3 68 2-70 6-78 (79)
63 PF10302 DUF2407: DUF2407 ubiq 97.6 0.00016 3.5E-09 49.4 5.6 58 2-59 2-64 (97)
64 cd01767 UBX UBX (ubiquitin reg 97.5 0.0011 2.4E-08 43.0 8.3 66 2-69 4-74 (77)
65 cd01770 p47_UBX p47-like ubiqu 97.5 0.0011 2.4E-08 43.5 7.9 65 2-67 6-74 (79)
66 cd01773 Faf1_like1_UBX Faf1 ik 97.4 0.0019 4E-08 42.8 8.6 69 2-71 7-80 (82)
67 cd01771 Faf1_UBX Faf1 UBX doma 97.3 0.0029 6.3E-08 41.6 8.3 68 2-70 6-78 (80)
68 cd01774 Faf1_like2_UBX Faf1 ik 97.3 0.0034 7.4E-08 41.8 8.4 68 2-70 6-83 (85)
69 KOG0013 Uncharacterized conser 97.3 0.00063 1.4E-08 52.3 5.3 65 9-73 155-219 (231)
70 KOG1639 Steroid reductase requ 97.0 0.0016 3.5E-08 51.4 5.5 75 1-77 1-82 (297)
71 COG5417 Uncharacterized small 97.0 0.0065 1.4E-07 39.3 7.3 64 6-69 12-80 (81)
72 KOG3206 Alpha-tubulin folding 96.9 0.0027 5.8E-08 48.8 6.1 71 2-72 3-81 (234)
73 PRK06437 hypothetical protein; 96.6 0.026 5.6E-07 35.8 8.0 59 9-76 9-67 (67)
74 PRK06488 sulfur carrier protei 96.5 0.023 4.9E-07 35.6 7.3 65 1-76 1-65 (65)
75 PLN02799 Molybdopterin synthas 96.4 0.018 3.8E-07 37.6 6.3 71 1-76 2-82 (82)
76 PRK08364 sulfur carrier protei 96.2 0.057 1.2E-06 34.4 7.7 56 12-76 15-70 (70)
77 PF12754 Blt1: Cell-cycle cont 96.1 0.0015 3.2E-08 53.1 0.0 77 2-78 80-183 (309)
78 cd00754 MoaD Ubiquitin domain 96.0 0.038 8.3E-07 35.5 6.6 60 12-76 17-80 (80)
79 KOG4583 Membrane-associated ER 96.0 0.0032 7E-08 51.6 1.5 60 2-61 11-74 (391)
80 PF15044 CLU_N: Mitochondrial 96.0 0.014 3E-07 38.0 4.1 56 17-72 1-58 (76)
81 cd06409 PB1_MUG70 The MUG70 pr 95.7 0.043 9.3E-07 36.6 5.8 44 2-45 2-48 (86)
82 PRK05863 sulfur carrier protei 95.6 0.076 1.6E-06 33.3 6.4 65 1-76 1-65 (65)
83 cd06406 PB1_P67 A PB1 domain i 95.6 0.062 1.3E-06 35.4 6.0 38 12-49 12-49 (80)
84 PF09379 FERM_N: FERM N-termin 95.6 0.14 3E-06 32.9 7.7 58 5-62 1-65 (80)
85 PRK08053 sulfur carrier protei 95.5 0.15 3.3E-06 31.9 7.6 66 1-76 1-66 (66)
86 PF11620 GABP-alpha: GA-bindin 95.5 0.062 1.3E-06 35.7 5.8 62 12-73 4-65 (88)
87 PRK05659 sulfur carrier protei 95.4 0.17 3.7E-06 31.5 7.5 66 1-76 1-66 (66)
88 PHA00626 hypothetical protein 95.4 0.011 2.3E-07 36.1 1.7 30 120-151 2-36 (59)
89 PF10790 DUF2604: Protein of U 95.1 0.15 3.2E-06 32.2 6.3 65 9-73 4-72 (76)
90 COG5100 NPL4 Nuclear pore prot 95.0 0.11 2.3E-06 44.0 7.0 71 1-72 1-79 (571)
91 TIGR01682 moaD molybdopterin c 95.0 0.21 4.5E-06 32.4 7.2 60 12-76 17-80 (80)
92 cd00565 ThiS ThiaminS ubiquiti 95.0 0.12 2.7E-06 32.2 5.9 58 14-76 8-65 (65)
93 PF14836 Ubiquitin_3: Ubiquiti 94.8 0.27 5.8E-06 33.0 7.4 65 11-76 14-84 (88)
94 TIGR01687 moaD_arch MoaD famil 94.8 0.32 7E-06 31.9 7.9 62 11-76 16-88 (88)
95 PRK06944 sulfur carrier protei 94.7 0.43 9.3E-06 29.5 7.8 65 1-76 1-65 (65)
96 PF02597 ThiS: ThiS family; I 94.7 0.19 4E-06 31.9 6.3 63 12-76 13-77 (77)
97 PRK07696 sulfur carrier protei 94.6 0.42 9.1E-06 30.1 7.6 66 1-76 1-67 (67)
98 cd06407 PB1_NLP A PB1 domain i 94.4 0.21 4.6E-06 32.9 6.1 46 1-47 1-47 (82)
99 TIGR01683 thiS thiamine biosyn 94.4 0.25 5.3E-06 30.7 6.1 61 9-76 4-64 (64)
100 PRK06083 sulfur carrier protei 94.3 0.31 6.7E-06 32.3 6.8 61 9-76 24-84 (84)
101 PF14453 ThiS-like: ThiS-like 94.3 0.2 4.3E-06 30.8 5.4 55 1-71 1-55 (57)
102 KOG0012 DNA damage inducible p 94.1 0.091 2E-06 43.7 4.7 70 1-70 1-74 (380)
103 PRK07440 hypothetical protein; 94.1 0.5 1.1E-05 30.1 7.2 61 9-76 10-70 (70)
104 PF09855 DUF2082: Nucleic-acid 93.8 0.06 1.3E-06 34.0 2.4 19 137-155 35-53 (64)
105 smart00666 PB1 PB1 domain. Pho 93.8 0.38 8.3E-06 30.9 6.4 45 2-47 3-47 (81)
106 smart00295 B41 Band 4.1 homolo 92.7 1.8 3.9E-05 32.2 9.6 71 2-72 5-83 (207)
107 KOG2086 Protein tyrosine phosp 92.0 0.37 8E-06 40.4 5.3 65 2-66 307-375 (380)
108 PF10571 UPF0547: Uncharacteri 91.9 0.06 1.3E-06 27.8 0.4 24 119-148 1-24 (26)
109 cd01760 RBD Ubiquitin-like dom 91.7 1.3 2.8E-05 28.5 6.6 44 3-46 2-45 (72)
110 KOG2689 Predicted ubiquitin re 91.7 0.65 1.4E-05 37.3 6.2 68 2-69 212-284 (290)
111 cd06408 PB1_NoxR The PB1 domai 91.7 1.1 2.3E-05 30.0 6.3 45 3-48 3-48 (86)
112 TIGR02958 sec_mycoba_snm4 secr 91.4 1.3 2.7E-05 38.3 8.2 70 2-72 4-80 (452)
113 COG2104 ThiS Sulfur transfer p 91.4 1.9 4.2E-05 27.4 7.1 58 14-76 11-68 (68)
114 smart00647 IBR In Between Ring 91.3 0.13 2.8E-06 31.4 1.6 34 118-151 18-53 (64)
115 KOG0009 Ubiquitin-like/40S rib 91.0 0.087 1.9E-06 32.4 0.5 28 75-102 6-33 (62)
116 smart00455 RBD Raf-like Ras-bi 90.7 1.4 3E-05 28.1 6.0 49 3-51 2-52 (70)
117 PRK11840 bifunctional sulfur c 90.6 1.5 3.3E-05 36.2 7.5 68 1-78 1-68 (326)
118 PF01485 IBR: IBR domain; Int 90.5 0.11 2.5E-06 31.6 0.8 33 119-151 19-53 (64)
119 PF00564 PB1: PB1 domain; Int 90.5 1.3 2.7E-05 28.5 5.8 44 3-47 4-48 (84)
120 COG2051 RPS27A Ribosomal prote 90.3 0.57 1.2E-05 29.6 3.7 38 111-150 12-50 (67)
121 COG1997 RPL43A Ribosomal prote 90.2 0.22 4.8E-06 33.2 1.9 32 115-148 32-63 (89)
122 PF01780 Ribosomal_L37ae: Ribo 89.8 0.3 6.5E-06 32.8 2.4 31 117-149 34-64 (90)
123 PRK05978 hypothetical protein; 89.6 0.18 3.8E-06 37.1 1.2 33 117-151 32-65 (148)
124 smart00661 RPOL9 RNA polymeras 89.5 0.2 4.3E-06 29.6 1.2 27 120-150 2-32 (52)
125 COG1645 Uncharacterized Zn-fin 89.5 0.15 3.3E-06 36.6 0.8 34 115-152 25-58 (131)
126 PRK11130 moaD molybdopterin sy 89.4 3 6.4E-05 27.0 6.9 57 15-76 19-81 (81)
127 cd05992 PB1 The PB1 domain is 88.6 2.5 5.5E-05 26.8 6.2 45 2-47 2-47 (81)
128 PRK00398 rpoP DNA-directed RNA 88.6 0.53 1.1E-05 27.3 2.6 34 118-153 3-36 (46)
129 PF02196 RBD: Raf-like Ras-bin 88.6 4.5 9.9E-05 25.7 8.2 56 3-58 3-60 (71)
130 cd06411 PB1_p51 The PB1 domain 87.8 1.3 2.8E-05 29.0 4.3 36 12-47 8-43 (78)
131 TIGR02098 MJ0042_CXXC MJ0042 f 87.7 0.47 1E-05 26.2 1.9 29 118-149 2-36 (38)
132 PF01907 Ribosomal_L37e: Ribos 87.1 0.42 9.1E-06 29.1 1.5 25 117-146 14-38 (55)
133 cd06398 PB1_Joka2 The PB1 doma 87.0 3.9 8.5E-05 27.4 6.4 70 3-73 3-88 (91)
134 cd06396 PB1_NBR1 The PB1 domai 86.7 3.6 7.9E-05 27.1 5.9 35 2-37 2-38 (81)
135 COG1096 Predicted RNA-binding 86.6 0.51 1.1E-05 35.9 2.1 31 119-153 150-180 (188)
136 TIGR00280 L37a ribosomal prote 86.3 0.52 1.1E-05 31.7 1.8 32 116-149 33-64 (91)
137 PRK01777 hypothetical protein; 85.8 5.2 0.00011 27.1 6.6 69 1-78 4-82 (95)
138 cd06410 PB1_UP2 Uncharacterize 85.4 4.1 8.9E-05 27.7 5.9 40 5-45 17-56 (97)
139 PTZ00380 microtubule-associate 85.3 1 2.3E-05 31.9 3.1 59 13-71 43-104 (121)
140 PF08825 E2_bind: E2 binding d 85.3 2 4.3E-05 28.4 4.3 56 15-71 1-70 (84)
141 PRK03976 rpl37ae 50S ribosomal 85.2 0.6 1.3E-05 31.4 1.7 32 116-149 34-65 (90)
142 KOG4250 TANK binding protein k 84.8 3.5 7.6E-05 37.4 6.7 41 9-49 323-363 (732)
143 PRK09710 lar restriction allev 84.5 0.86 1.9E-05 28.6 2.1 28 118-147 6-36 (64)
144 cd01766 Ufm1 Urm1-like ubiquit 84.0 7 0.00015 25.3 6.1 61 14-74 19-80 (82)
145 cd01787 GRB7_RA RA (RAS-associ 83.9 5 0.00011 26.7 5.6 65 3-67 5-80 (85)
146 PTZ00255 60S ribosomal protein 83.7 0.8 1.7E-05 30.8 1.8 32 116-149 34-65 (90)
147 PF04758 Ribosomal_S30: Riboso 83.5 0.22 4.7E-06 30.8 -0.9 26 74-99 3-28 (59)
148 PF13248 zf-ribbon_3: zinc-rib 83.2 0.47 1E-05 24.2 0.4 24 118-147 2-25 (26)
149 cd01764 Urm1 Urm1-like ubuitin 82.9 3.1 6.8E-05 28.0 4.5 59 16-76 24-94 (94)
150 PF02150 RNA_POL_M_15KD: RNA p 82.7 0.92 2E-05 24.9 1.5 28 119-150 2-32 (35)
151 COG1571 Predicted DNA-binding 82.5 1.3 2.7E-05 37.9 2.9 31 116-149 348-378 (421)
152 smart00154 ZnF_AN1 AN1-like Zi 82.3 0.74 1.6E-05 26.0 1.1 23 118-143 12-36 (39)
153 COG5349 Uncharacterized protei 82.1 0.44 9.5E-06 33.7 0.1 34 117-152 20-54 (126)
154 smart00144 PI3K_rbd PI3-kinase 82.0 14 0.0003 25.4 7.8 63 11-73 29-105 (108)
155 PF10209 DUF2340: Uncharacteri 81.9 3.2 6.9E-05 29.4 4.4 55 16-70 21-106 (122)
156 PF13719 zinc_ribbon_5: zinc-r 81.9 0.8 1.7E-05 25.4 1.1 30 118-149 2-36 (37)
157 PF08792 A2L_zn_ribbon: A2L zi 81.9 1.6 3.5E-05 23.7 2.3 29 119-149 4-32 (33)
158 PF09538 FYDLN_acid: Protein o 81.5 0.68 1.5E-05 32.2 0.8 32 117-151 8-39 (108)
159 PRK09336 30S ribosomal protein 81.3 0.62 1.3E-05 27.8 0.5 24 74-97 4-27 (50)
160 PF14803 Nudix_N_2: Nudix N-te 80.8 0.98 2.1E-05 24.8 1.1 27 120-148 2-32 (34)
161 PF00788 RA: Ras association ( 80.7 10 0.00022 24.4 6.4 41 3-43 5-51 (93)
162 KOG2507 Ubiquitin regulatory p 80.4 3.8 8.2E-05 35.1 5.0 72 2-73 316-392 (506)
163 PF02017 CIDE-N: CIDE-N domain 80.4 6.3 0.00014 25.7 5.1 48 21-71 21-70 (78)
164 PF14533 USP7_C2: Ubiquitin-sp 79.8 8.6 0.00019 29.7 6.6 48 12-59 35-90 (213)
165 cd01775 CYR1_RA Ubiquitin doma 79.8 11 0.00023 25.7 6.2 42 3-44 5-47 (97)
166 cd01768 RA RA (Ras-associating 79.6 11 0.00023 24.4 6.1 35 10-44 12-48 (87)
167 KOG2982 Uncharacterized conser 79.0 3.2 7E-05 34.4 4.1 57 14-70 351-415 (418)
168 PF08337 Plexin_cytopl: Plexin 78.4 8.1 0.00018 34.2 6.6 64 11-74 202-291 (539)
169 PTZ00467 40S ribosomal protein 78.2 0.81 1.8E-05 28.8 0.3 26 74-99 5-30 (66)
170 PF03671 Ufm1: Ubiquitin fold 77.8 16 0.00035 23.6 6.2 58 13-70 18-76 (76)
171 PF13717 zinc_ribbon_4: zinc-r 77.5 1.2 2.5E-05 24.6 0.8 29 118-148 2-35 (36)
172 COG3478 Predicted nucleic-acid 77.3 0.72 1.6E-05 29.0 -0.1 17 138-154 40-56 (68)
173 PF00276 Ribosomal_L23: Riboso 77.3 6.4 0.00014 26.3 4.5 38 11-48 21-59 (91)
174 cd01777 SNX27_RA Ubiquitin dom 77.1 7.1 0.00015 26.1 4.6 40 2-41 3-42 (87)
175 cd06397 PB1_UP1 Uncharacterize 76.2 14 0.00031 24.3 5.7 43 2-45 2-44 (82)
176 PF14451 Ub-Mut7C: Mut7-C ubiq 75.8 16 0.00034 23.9 6.0 53 10-71 22-75 (81)
177 PF08271 TF_Zn_Ribbon: TFIIB z 75.8 2.3 5E-05 24.2 1.8 28 120-149 2-30 (43)
178 KOG0007 Splicing factor 3a, su 75.3 1.4 3.1E-05 36.5 1.1 50 7-56 289-339 (341)
179 PF11069 DUF2870: Protein of u 75.2 4.7 0.0001 27.5 3.4 38 42-79 3-41 (98)
180 PF01428 zf-AN1: AN1-like Zinc 75.2 0.84 1.8E-05 26.1 -0.2 24 117-143 12-37 (43)
181 smart00314 RA Ras association 74.8 19 0.00042 23.3 6.4 35 10-44 15-51 (90)
182 TIGR02300 FYDLN_acid conserved 74.7 1.7 3.7E-05 31.1 1.2 31 117-150 8-38 (129)
183 PF02991 Atg8: Autophagy prote 74.6 7.9 0.00017 26.6 4.5 57 15-71 37-97 (104)
184 PLN00209 ribosomal protein S27 74.4 3.9 8.4E-05 27.2 2.8 33 115-149 33-66 (86)
185 PTZ00083 40S ribosomal protein 74.1 4.2 9E-05 27.0 2.9 33 115-149 32-65 (85)
186 PRK00420 hypothetical protein; 74.0 2.5 5.3E-05 29.6 1.9 32 117-151 22-53 (112)
187 COG5272 UBI4 Ubiquitin [Posttr 73.7 0.63 1.4E-05 28.3 -1.0 42 80-122 4-45 (57)
188 PF14732 UAE_UbL: Ubiquitin/SU 72.6 9.3 0.0002 25.3 4.4 56 15-70 2-67 (87)
189 KOG4572 Predicted DNA-binding 72.2 6.3 0.00014 36.7 4.4 62 9-70 3-68 (1424)
190 cd01818 TIAM1_RBD Ubiquitin do 71.9 16 0.00034 23.8 5.1 40 4-43 3-42 (77)
191 cd01817 RGS12_RBD Ubiquitin do 71.8 24 0.00052 22.8 7.6 47 5-51 4-52 (73)
192 PF05129 Elf1: Transcription e 71.6 3 6.6E-05 27.4 1.8 35 117-153 21-61 (81)
193 PRK05738 rplW 50S ribosomal pr 71.6 12 0.00026 25.0 4.8 33 10-42 20-52 (92)
194 PRK04179 rpl37e 50S ribosomal 71.1 2 4.3E-05 26.8 0.8 24 118-146 17-40 (62)
195 COG4888 Uncharacterized Zn rib 70.2 2.8 6E-05 28.8 1.4 37 117-155 21-63 (104)
196 PF07754 DUF1610: Domain of un 69.5 2.4 5.2E-05 21.4 0.7 22 125-146 3-24 (24)
197 PF14533 USP7_C2: Ubiquitin-sp 69.3 4.9 0.00011 31.0 2.8 30 10-39 132-161 (213)
198 PF03604 DNA_RNApol_7kD: DNA d 69.1 4.6 0.0001 21.8 1.9 30 120-152 2-31 (32)
199 PF12436 USP7_ICP0_bdg: ICP0-b 68.8 5.8 0.00013 31.3 3.2 73 2-74 70-154 (249)
200 TIGR03636 L23_arch archaeal ri 68.5 15 0.00034 23.8 4.6 33 11-43 15-47 (77)
201 cd01611 GABARAP Ubiquitin doma 68.4 11 0.00024 26.2 4.2 57 15-72 45-106 (112)
202 PRK00415 rps27e 30S ribosomal 68.3 5.2 0.00011 24.7 2.2 33 115-149 8-41 (59)
203 smart00266 CAD Domains present 68.2 17 0.00038 23.5 4.7 40 20-59 18-59 (74)
204 PF08783 DWNN: DWNN domain; I 67.8 18 0.0004 23.3 4.8 33 4-36 2-36 (74)
205 PF01783 Ribosomal_L32p: Ribos 67.4 5.5 0.00012 24.1 2.2 22 118-146 26-47 (56)
206 PF00794 PI3K_rbd: PI3-kinase 67.1 36 0.00078 22.9 7.1 71 2-72 18-102 (106)
207 PRK14892 putative transcriptio 66.5 3.3 7E-05 28.4 1.2 32 118-152 21-56 (99)
208 cd06539 CIDE_N_A CIDE_N domain 66.1 20 0.00043 23.5 4.7 47 21-69 21-69 (78)
209 PRK14548 50S ribosomal protein 65.4 20 0.00043 23.7 4.7 35 10-44 21-55 (84)
210 KOG2561 Adaptor protein NUB1, 65.2 2.2 4.7E-05 36.9 0.1 59 14-72 53-111 (568)
211 PF09297 zf-NADH-PPase: NADH p 65.0 4.7 0.0001 21.4 1.4 29 118-148 3-31 (32)
212 PF07282 OrfB_Zn_ribbon: Putat 64.8 3.7 8.1E-05 25.5 1.1 30 118-149 28-57 (69)
213 smart00659 RPOLCX RNA polymera 64.5 8.4 0.00018 22.2 2.5 32 118-152 2-33 (44)
214 PF05191 ADK_lid: Adenylate ki 64.0 2.4 5.2E-05 23.5 0.1 12 138-149 1-12 (36)
215 PF06677 Auto_anti-p27: Sjogre 63.9 6.4 0.00014 22.4 1.9 26 117-145 16-41 (41)
216 PF09788 Tmemb_55A: Transmembr 63.6 5.3 0.00011 31.9 2.0 62 89-154 98-173 (256)
217 COG0089 RplW Ribosomal protein 63.3 19 0.00042 24.3 4.4 34 10-43 21-54 (94)
218 cd01615 CIDE_N CIDE_N domain, 63.2 23 0.00049 23.2 4.6 39 21-59 21-61 (78)
219 PF08646 Rep_fac-A_C: Replicat 62.8 5 0.00011 28.8 1.6 29 118-148 18-47 (146)
220 PF12760 Zn_Tnp_IS1595: Transp 62.5 5.4 0.00012 23.0 1.4 26 119-146 19-45 (46)
221 PF02192 PI3K_p85B: PI3-kinase 61.5 13 0.00028 24.3 3.2 22 13-34 2-23 (78)
222 PF11834 DUF3354: Domain of un 60.1 22 0.00047 22.6 4.0 43 21-69 26-68 (69)
223 KOG3475 60S ribosomal protein 59.6 2 4.3E-05 28.5 -0.9 26 118-148 16-41 (92)
224 PTZ00073 60S ribosomal protein 59.1 4.6 0.0001 27.1 0.8 25 117-146 15-39 (91)
225 KOG3439 Protein conjugation fa 58.9 36 0.00077 23.8 5.2 38 13-50 47-84 (116)
226 cd06536 CIDE_N_ICAD CIDE_N dom 58.9 28 0.00061 22.8 4.5 39 21-59 21-63 (80)
227 PF09469 Cobl: Cordon-bleu ubi 58.9 8.6 0.00019 25.1 2.0 40 29-71 2-44 (79)
228 PF03658 Ub-RnfH: RnfH family 58.7 48 0.001 21.9 5.6 73 1-78 1-79 (84)
229 PF10407 Cytokin_check_N: Cdc1 58.7 46 0.001 21.4 5.5 61 11-72 3-70 (73)
230 cd01776 Rin1_RA Ubiquitin doma 58.2 29 0.00063 23.0 4.4 42 12-53 15-61 (87)
231 KOG4684 Uncharacterized conser 58.1 5.3 0.00012 31.2 1.1 37 116-152 136-184 (275)
232 KOG0006 E3 ubiquitin-protein l 57.7 2.4 5.2E-05 35.0 -0.9 34 119-152 316-350 (446)
233 COG3677 Transposase and inacti 57.5 11 0.00024 26.9 2.6 32 118-152 30-67 (129)
234 CHL00030 rpl23 ribosomal prote 57.5 28 0.0006 23.5 4.4 32 10-41 19-50 (93)
235 PRK01103 formamidopyrimidine/5 56.6 8.3 0.00018 30.9 2.1 28 118-147 245-274 (274)
236 cd00350 rubredoxin_like Rubred 56.4 5.6 0.00012 21.3 0.7 13 138-150 1-13 (33)
237 COG1977 MoaD Molybdopterin con 56.4 24 0.00051 23.0 3.9 55 18-76 25-84 (84)
238 KOG4598 Putative ubiquitin-spe 56.4 15 0.00033 33.7 3.8 58 12-71 878-941 (1203)
239 COG0675 Transposase and inacti 56.0 5.7 0.00012 31.7 1.0 24 119-149 310-333 (364)
240 smart00143 PI3K_p85B PI3-kinas 55.5 16 0.00035 23.8 2.9 22 13-34 2-23 (78)
241 PF11706 zf-CGNR: CGNR zinc fi 55.0 4 8.8E-05 23.6 0.0 26 119-145 3-32 (44)
242 cd01612 APG12_C Ubiquitin-like 54.9 26 0.00057 23.2 3.9 58 14-71 19-80 (87)
243 COG2888 Predicted Zn-ribbon RN 54.9 6.7 0.00015 24.3 1.0 11 135-145 47-57 (61)
244 PF12436 USP7_ICP0_bdg: ICP0-b 54.7 40 0.00088 26.6 5.7 35 10-44 189-223 (249)
245 PF01667 Ribosomal_S27e: Ribos 54.5 14 0.0003 22.5 2.3 34 115-150 4-38 (55)
246 PF14847 Ras_bdg_2: Ras-bindin 54.0 51 0.0011 22.7 5.4 36 3-38 3-38 (105)
247 COG2816 NPY1 NTP pyrophosphohy 53.8 5.1 0.00011 32.4 0.4 31 116-148 109-139 (279)
248 cd06537 CIDE_N_B CIDE_N domain 53.6 41 0.00089 22.1 4.6 47 21-69 21-68 (81)
249 PF13240 zinc_ribbon_2: zinc-r 52.8 5.4 0.00012 19.7 0.3 21 120-146 1-21 (23)
250 cd01782 AF6_RA_repeat1 Ubiquit 52.8 77 0.0017 22.1 6.1 37 1-37 24-62 (112)
251 PF09151 DUF1936: Domain of un 52.7 10 0.00022 20.4 1.3 14 120-135 3-16 (36)
252 PHA02942 putative transposase; 52.4 7.6 0.00016 32.8 1.2 27 118-148 325-352 (383)
253 cd06538 CIDE_N_FSP27 CIDE_N do 52.3 43 0.00093 21.9 4.5 40 20-59 20-60 (79)
254 PRK11827 hypothetical protein; 51.8 9.3 0.0002 23.7 1.3 30 120-151 10-39 (60)
255 PRK12286 rpmF 50S ribosomal pr 51.8 7.9 0.00017 23.7 0.9 22 118-146 27-48 (57)
256 TIGR00595 priA primosomal prot 50.8 7.9 0.00017 33.8 1.2 25 120-148 224-250 (505)
257 KOG1779 40s ribosomal protein 50.7 15 0.00033 24.0 2.2 54 87-150 11-65 (84)
258 PRK12280 rplW 50S ribosomal pr 50.6 37 0.00081 25.2 4.5 39 10-48 22-61 (158)
259 PF13453 zf-TFIIB: Transcripti 50.0 10 0.00022 21.2 1.2 25 120-148 1-29 (41)
260 COG3809 Uncharacterized protei 49.3 13 0.00029 24.4 1.7 26 120-147 3-30 (88)
261 COG1545 Predicted nucleic-acid 49.3 7.5 0.00016 28.1 0.7 35 105-147 18-52 (140)
262 PF06234 TmoB: Toluene-4-monoo 49.2 77 0.0017 21.1 6.7 60 12-71 16-83 (85)
263 PRK00241 nudC NADH pyrophospha 48.4 9.5 0.00021 30.3 1.2 30 117-148 98-127 (256)
264 KOG3483 Uncharacterized conser 47.2 79 0.0017 20.6 5.4 62 15-76 31-93 (94)
265 KOG1364 Predicted ubiquitin re 46.8 21 0.00046 29.8 3.0 65 2-66 279-349 (356)
266 PRK14714 DNA polymerase II lar 46.6 14 0.0003 36.0 2.1 18 92-109 618-635 (1337)
267 PRK12380 hydrogenase nickel in 46.3 18 0.00038 25.1 2.2 26 117-146 69-94 (113)
268 PRK03681 hypA hydrogenase nick 46.0 17 0.00036 25.3 2.0 27 116-146 68-95 (114)
269 KOG0466 Translation initiation 45.8 15 0.00033 30.6 2.0 46 93-147 71-118 (466)
270 PF01376 Enterotoxin_b: Heat-l 45.4 34 0.00075 22.6 3.2 31 3-33 38-68 (102)
271 PF15616 TerY-C: TerY-C metal 43.8 21 0.00045 25.7 2.2 13 119-133 78-90 (131)
272 PRK04023 DNA polymerase II lar 43.8 12 0.00026 35.6 1.2 37 91-129 583-635 (1121)
273 PF13878 zf-C2H2_3: zinc-finge 43.5 9.5 0.00021 21.6 0.4 15 137-151 12-26 (41)
274 TIGR00354 polC DNA polymerase, 43.1 18 0.00039 34.2 2.2 47 92-146 583-645 (1095)
275 PF04126 Cyclophil_like: Cyclo 42.4 19 0.00041 25.2 1.9 29 1-30 1-29 (120)
276 PRK14810 formamidopyrimidine-D 42.1 20 0.00044 28.7 2.2 27 118-146 244-272 (272)
277 PF11781 RRN7: RNA polymerase 42.0 14 0.0003 20.4 0.9 25 119-146 9-33 (36)
278 PLN03086 PRLI-interacting fact 41.7 15 0.00033 32.7 1.6 33 116-149 431-464 (567)
279 COG1594 RPB9 DNA-directed RNA 41.1 42 0.00092 23.3 3.4 31 118-150 72-112 (113)
280 PF09567 RE_MamI: MamI restric 40.9 8.5 0.00018 30.8 -0.1 36 102-150 73-108 (314)
281 PF03931 Skp1_POZ: Skp1 family 40.7 23 0.0005 21.5 1.9 32 1-32 1-32 (62)
282 PRK10445 endonuclease VIII; Pr 40.6 22 0.00047 28.3 2.1 26 118-145 235-262 (263)
283 KOG2906 RNA polymerase III sub 40.0 29 0.00063 23.7 2.3 30 120-151 3-34 (105)
284 PF00096 zf-C2H2: Zinc finger, 39.6 12 0.00026 17.6 0.4 9 140-148 2-10 (23)
285 PRK14811 formamidopyrimidine-D 39.6 23 0.0005 28.3 2.2 27 118-146 235-263 (269)
286 PHA00616 hypothetical protein 39.5 4.7 0.0001 23.4 -1.4 10 140-149 3-12 (44)
287 PTZ00191 60S ribosomal protein 39.4 72 0.0016 23.3 4.5 34 10-43 82-115 (145)
288 TIGR00100 hypA hydrogenase nic 39.3 27 0.00059 24.2 2.2 26 117-146 69-94 (115)
289 PRK13902 alaS alanyl-tRNA synt 39.1 18 0.00038 34.1 1.6 25 116-143 17-41 (900)
290 PF12172 DUF35_N: Rubredoxin-l 38.9 24 0.00052 19.1 1.5 24 118-147 11-34 (37)
291 COG3582 Predicted nucleic acid 38.7 62 0.0013 24.1 4.1 39 101-142 93-133 (162)
292 PHA02768 hypothetical protein; 38.1 17 0.00037 22.1 0.9 30 117-149 4-42 (55)
293 PF00301 Rubredoxin: Rubredoxi 37.5 11 0.00024 22.1 -0.0 11 138-148 1-11 (47)
294 KOG3183 Predicted Zn-finger pr 37.4 10 0.00022 30.1 -0.2 27 114-143 19-47 (250)
295 PF13913 zf-C2HC_2: zinc-finge 37.2 23 0.00049 17.7 1.2 10 139-148 3-12 (25)
296 PF13408 Zn_ribbon_recom: Reco 37.1 24 0.00052 20.6 1.5 13 139-151 6-18 (58)
297 KOG2660 Locus-specific chromos 37.0 30 0.00065 28.7 2.4 47 13-59 166-214 (331)
298 PRK13945 formamidopyrimidine-D 36.9 26 0.00057 28.1 2.1 27 118-146 254-282 (282)
299 PF10263 SprT-like: SprT-like 36.7 36 0.00079 24.3 2.7 32 115-150 120-155 (157)
300 TIGR01031 rpmF_bact ribosomal 36.6 19 0.00042 21.7 1.0 21 118-145 26-46 (55)
301 cd04482 RPA2_OBF_like RPA2_OBF 36.4 1.2E+02 0.0027 19.8 5.8 46 59-127 46-91 (91)
302 PF14354 Lar_restr_allev: Rest 36.3 38 0.00082 20.3 2.3 26 119-146 4-37 (61)
303 KOG3173 Predicted Zn-finger pr 36.1 18 0.00038 27.1 0.9 20 119-142 120-141 (167)
304 PF03833 PolC_DP2: DNA polymer 36.0 12 0.00026 34.8 0.0 55 91-147 611-689 (900)
305 COG3760 Uncharacterized conser 35.7 55 0.0012 24.2 3.4 55 2-66 47-101 (164)
306 PF13894 zf-C2H2_4: C2H2-type 35.5 16 0.00035 16.8 0.4 9 140-148 2-10 (24)
307 TIGR00577 fpg formamidopyrimid 35.5 30 0.00065 27.7 2.2 26 118-145 245-272 (272)
308 PF09138 Urm1: Urm1 (Ubiquitin 34.9 1.1E+02 0.0024 20.7 4.6 64 11-76 18-96 (96)
309 TIGR01206 lysW lysine biosynth 34.6 48 0.001 20.0 2.5 30 119-150 3-34 (54)
310 PF13465 zf-H2C2_2: Zinc-finge 34.1 19 0.00042 17.9 0.6 11 138-148 14-24 (26)
311 COG5131 URM1 Ubiquitin-like pr 33.8 1.5E+02 0.0033 20.0 6.4 67 10-76 17-96 (96)
312 PF02824 TGS: TGS domain; Int 33.7 1.1E+02 0.0024 18.4 6.5 59 3-70 1-59 (60)
313 PF14319 Zn_Tnp_IS91: Transpos 33.6 32 0.00069 23.8 1.8 29 117-148 41-70 (111)
314 PF13699 DUF4157: Domain of un 33.4 81 0.0018 20.3 3.6 46 24-69 4-49 (79)
315 PF12773 DZR: Double zinc ribb 33.3 19 0.00042 20.7 0.6 27 118-147 12-38 (50)
316 PF07191 zinc-ribbons_6: zinc- 32.8 40 0.00086 21.6 2.0 27 120-150 3-29 (70)
317 PRK14890 putative Zn-ribbon RN 32.8 28 0.0006 21.5 1.2 11 136-146 46-56 (59)
318 cd06404 PB1_aPKC PB1 domain is 32.6 1.5E+02 0.0032 19.6 5.6 43 2-45 2-45 (83)
319 cd00729 rubredoxin_SM Rubredox 32.5 24 0.00051 19.0 0.8 11 139-149 3-13 (34)
320 PF06827 zf-FPG_IleRS: Zinc fi 32.3 24 0.00051 18.2 0.8 25 119-145 2-28 (30)
321 PRK05580 primosome assembly pr 32.2 25 0.00053 32.0 1.3 25 120-148 392-418 (679)
322 PF08154 NLE: NLE (NUC135) dom 31.4 1.3E+02 0.0028 18.5 5.7 40 13-52 18-59 (65)
323 COG2260 Predicted Zn-ribbon RN 31.2 28 0.0006 21.5 1.0 20 117-139 16-35 (59)
324 PF14807 AP4E_app_platf: Adapt 31.1 1.4E+02 0.003 20.5 4.6 55 18-73 28-86 (104)
325 PRK14715 DNA polymerase II lar 30.6 37 0.00079 33.5 2.2 47 92-146 632-694 (1627)
326 KOG3391 Transcriptional co-rep 30.4 44 0.00095 24.3 2.1 26 49-74 113-138 (151)
327 PF11305 DUF3107: Protein of u 30.4 1.5E+02 0.0033 19.1 5.2 34 1-35 1-34 (74)
328 cd00730 rubredoxin Rubredoxin; 30.2 41 0.00089 19.9 1.6 12 138-149 1-12 (50)
329 PF11816 DUF3337: Domain of un 29.9 1.8E+02 0.0039 23.9 6.0 61 14-74 251-329 (331)
330 PF02505 MCR_D: Methyl-coenzym 29.7 1.5E+02 0.0032 21.9 4.8 44 12-59 76-120 (153)
331 PF08115 Toxin_28: SFI toxin f 29.6 46 0.001 18.0 1.6 17 129-145 7-23 (35)
332 PF13180 PDZ_2: PDZ domain; PD 29.5 99 0.0021 19.3 3.6 55 11-73 15-71 (82)
333 COG0375 HybF Zn finger protein 29.3 49 0.0011 23.2 2.2 32 116-151 68-100 (115)
334 PF10164 DUF2367: Uncharacteri 28.8 37 0.00079 23.2 1.4 13 117-131 48-60 (98)
335 KOG4146 Ubiquitin-like protein 28.6 1.9E+02 0.0042 19.6 5.3 57 19-76 34-101 (101)
336 COG0333 RpmF Ribosomal protein 28.6 33 0.00071 21.0 1.1 22 118-146 27-48 (57)
337 PF09358 UBA_e1_C: Ubiquitin-a 28.4 77 0.0017 22.3 3.1 25 15-39 37-61 (125)
338 TIGR03655 anti_R_Lar restricti 28.2 37 0.00081 20.0 1.3 28 119-148 2-36 (53)
339 TIGR03831 YgiT_finger YgiT-typ 27.6 71 0.0015 17.5 2.4 12 137-148 31-42 (46)
340 KOG0402 60S ribosomal protein 27.6 15 0.00033 24.3 -0.6 31 116-148 34-64 (92)
341 COG4919 Ribosomal protein S30 27.4 34 0.00073 20.3 0.9 26 74-99 4-29 (54)
342 TIGR03260 met_CoM_red_D methyl 27.4 1.5E+02 0.0033 21.7 4.5 44 12-59 75-118 (150)
343 PRK14873 primosome assembly pr 27.0 32 0.00069 31.3 1.1 26 119-148 393-420 (665)
344 PF13912 zf-C2H2_6: C2H2-type 26.8 26 0.00057 17.1 0.4 10 139-148 2-11 (27)
345 PF07295 DUF1451: Protein of u 26.8 81 0.0017 23.0 3.0 31 118-151 112-143 (146)
346 PF14599 zinc_ribbon_6: Zinc-r 26.2 48 0.001 20.5 1.5 25 119-145 31-55 (61)
347 cd04476 RPA1_DBD_C RPA1_DBD_C: 25.5 31 0.00068 25.1 0.7 29 116-148 32-61 (166)
348 PRK00564 hypA hydrogenase nick 25.2 58 0.0013 22.6 2.0 26 117-146 70-96 (117)
349 PF01396 zf-C4_Topoisom: Topoi 25.2 94 0.002 17.1 2.5 30 119-151 2-37 (39)
350 PF00684 DnaJ_CXXCXGXG: DnaJ c 25.1 63 0.0014 19.9 2.0 23 117-145 40-63 (66)
351 PRK03824 hypA hydrogenase nick 24.6 70 0.0015 22.8 2.4 10 117-128 69-78 (135)
352 TIGR00155 pqiA_fam integral me 24.6 42 0.00092 28.5 1.4 29 119-152 216-244 (403)
353 COG2080 CoxS Aerobic-type carb 24.6 1.1E+02 0.0024 22.7 3.4 64 1-67 2-72 (156)
354 smart00834 CxxC_CXXC_SSSS Puta 24.4 53 0.0011 17.7 1.4 9 118-128 5-13 (41)
355 PF10083 DUF2321: Uncharacteri 24.4 35 0.00075 25.3 0.7 31 119-151 40-81 (158)
356 PRK12366 replication factor A; 24.0 37 0.00081 30.6 1.0 26 118-147 532-557 (637)
357 COG4530 Uncharacterized protei 23.9 37 0.0008 23.8 0.7 29 117-148 8-36 (129)
358 PF08299 Bac_DnaA_C: Bacterial 23.8 32 0.0007 21.5 0.4 20 22-41 1-20 (70)
359 COG1996 RPC10 DNA-directed RNA 23.7 74 0.0016 18.9 1.9 32 118-151 6-37 (49)
360 COG0484 DnaJ DnaJ-class molecu 23.6 64 0.0014 27.3 2.3 16 15-30 10-25 (371)
361 cd06535 CIDE_N_CAD CIDE_N doma 23.5 2E+02 0.0044 18.7 4.1 31 21-51 21-53 (77)
362 KOG4842 Protein involved in si 23.4 38 0.00083 27.2 0.8 39 9-47 11-49 (278)
363 TIGR00244 transcriptional regu 23.1 57 0.0012 23.9 1.7 16 111-128 21-36 (147)
364 PF12143 PPO1_KFDV: Protein of 23.1 77 0.0017 22.7 2.3 25 53-77 94-118 (130)
365 PF01577 Peptidase_S30: Potyvi 23.0 2.6E+02 0.0057 21.5 5.6 73 2-75 151-226 (245)
366 KOG3456 NADH:ubiquinone oxidor 22.9 24 0.00051 24.6 -0.3 13 137-149 103-115 (120)
367 PF04060 FeS: Putative Fe-S cl 22.7 30 0.00065 18.8 0.1 10 138-147 4-13 (35)
368 PF01155 HypA: Hydrogenase exp 22.7 41 0.00088 23.2 0.8 30 115-148 67-96 (113)
369 PF06044 DRP: Dam-replacing fa 22.6 36 0.00079 27.1 0.6 31 118-151 31-66 (254)
370 COG3357 Predicted transcriptio 22.1 31 0.00068 23.3 0.1 10 141-150 61-70 (97)
371 PF09723 Zn-ribbon_8: Zinc rib 21.9 1E+02 0.0022 17.2 2.2 27 118-147 5-35 (42)
372 PRK13605 endoribonuclease SymE 21.9 1.1E+02 0.0024 21.4 2.8 41 1-41 56-96 (113)
373 PRK04351 hypothetical protein; 21.8 90 0.0019 22.8 2.5 33 117-152 111-146 (149)
374 PF13439 Glyco_transf_4: Glyco 21.8 1.1E+02 0.0023 21.1 2.9 27 24-51 148-174 (177)
375 PRK13552 frdB fumarate reducta 21.7 1.5E+02 0.0032 23.2 3.9 24 11-34 24-47 (239)
376 PHA02998 RNA polymerase subuni 21.6 60 0.0013 24.7 1.5 40 103-148 132-181 (195)
377 PF09332 Mcm10: Mcm10 replicat 21.4 48 0.001 27.7 1.1 29 118-148 285-313 (344)
378 cd01778 RASSF1_RA Ubiquitin-li 21.4 2.7E+02 0.0059 18.9 5.1 34 8-41 14-47 (96)
379 smart00760 Bac_DnaA_C Bacteria 21.3 53 0.0012 19.7 1.0 20 22-41 1-20 (60)
380 PF13511 DUF4124: Domain of un 20.8 1E+02 0.0022 18.2 2.3 20 104-123 14-34 (60)
381 COG2126 RPL37A Ribosomal prote 20.7 44 0.00096 20.6 0.6 26 117-147 15-40 (61)
382 KOG2834 Nuclear pore complex, 20.7 1.4E+02 0.0031 26.0 3.8 79 53-147 17-95 (510)
383 PF12647 RNHCP: RNHCP domain; 20.4 66 0.0014 21.7 1.4 35 119-155 5-41 (92)
384 KOG1973 Chromatin remodeling p 20.4 63 0.0014 25.9 1.6 24 119-145 233-266 (274)
385 KOG2378 cAMP-regulated guanine 20.3 4.6E+02 0.01 23.2 6.7 63 5-70 240-309 (573)
386 PF07929 PRiA4_ORF3: Plasmid p 20.2 3.6E+02 0.0077 19.7 6.1 40 2-41 6-48 (179)
387 cd02413 40S_S3_KH K homology R 20.2 2.6E+02 0.0055 18.0 4.9 25 19-43 48-72 (81)
388 KOG0956 PHD finger protein AF1 20.2 48 0.001 30.5 0.9 36 108-147 12-57 (900)
389 PRK05841 flgE flagellar hook p 20.2 1.3E+02 0.0028 27.2 3.5 38 2-39 250-296 (603)
390 KOG3896 Dynactin, subunit p62 20.0 47 0.001 27.9 0.7 25 118-145 27-52 (449)
No 1
>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.3e-49 Score=283.24 Aligned_cols=155 Identities=86% Similarity=1.310 Sum_probs=152.2
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCCcccc
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAKKR 80 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 ccccccCCcccccccceeeeeEeeeEEEcCCCeEEEeeccCCCCccCCceEEeEeCCCCccCCceeEEEeecCCC
Q 031613 81 KKKTYTKPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMANHFDRHYCGKCGLTYVYQKAGG 155 (156)
Q Consensus 81 ~kk~~~~pk~~k~~~kk~k~~~l~~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=9.9e-31 Score=154.20 Aligned_cols=47 Identities=74% Similarity=1.446 Sum_probs=39.3
Q ss_pred eEeeeEEEcCCCeEEEeeccCCCCccCCceEEeEeCCCCccCCceeE
Q 031613 101 AVLQFYKVDDSGKVQRLRKECPNAECGAGTFMANHFDRHYCGKCGLT 147 (156)
Q Consensus 101 ~~l~~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=8.1e-27 Score=137.22 Aligned_cols=49 Identities=55% Similarity=1.058 Sum_probs=45.2
Q ss_pred eeeEeeeEEEcCCCeEEEeeccCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031613 99 KLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMANHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 99 k~~~l~~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 46889999999 567999999999 99999999999999999999999954
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=3.4e-22 Score=130.41 Aligned_cols=74 Identities=41% Similarity=0.621 Sum_probs=71.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=9.5e-22 Score=128.60 Aligned_cols=76 Identities=50% Similarity=0.822 Sum_probs=74.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=1.7e-21 Score=127.07 Aligned_cols=73 Identities=36% Similarity=0.653 Sum_probs=71.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEee
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=133.94 Aligned_cols=76 Identities=51% Similarity=0.763 Sum_probs=74.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=4.1e-21 Score=125.18 Aligned_cols=76 Identities=96% Similarity=1.322 Sum_probs=74.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=1e-20 Score=123.33 Aligned_cols=76 Identities=55% Similarity=0.965 Sum_probs=74.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=8.3e-21 Score=123.83 Aligned_cols=74 Identities=32% Similarity=0.618 Sum_probs=72.2
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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
>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=123.09 Aligned_cols=75 Identities=25% Similarity=0.491 Sum_probs=73.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 12
>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=2.3e-20 Score=123.12 Aligned_cols=74 Identities=36% Similarity=0.634 Sum_probs=70.8
Q ss_pred CEEEEEeCCCCE-EEEE-ecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeec
Q 031613 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~~~stI~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 899999999996 6895 8999999999999999999999999999999999999999999999999999999875
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=8.7e-20 Score=118.85 Aligned_cols=71 Identities=24% Similarity=0.378 Sum_probs=68.5
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEE
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=2.9e-19 Score=116.98 Aligned_cols=72 Identities=39% Similarity=0.725 Sum_probs=70.1
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCC--CCCceEEecCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gi--p~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~ 72 (156)
|+|+|++.+|+++.+++++++||++||++|++.+|+ |+++|+|+|+|+.|+|+.+|++|||++|++|+++++
T Consensus 1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~ 74 (77)
T cd01805 1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVS 74 (77)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEe
Confidence 899999999999999999999999999999999999 999999999999999999999999999999999875
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=1.8e-19 Score=118.10 Aligned_cols=72 Identities=35% Similarity=0.676 Sum_probs=68.9
Q ss_pred CCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCCccc
Q 031613 8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAKK 79 (156)
Q Consensus 8 ~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 478999999999999999999999999999999999999999999999999999999999999999998763
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=99.80 E-value=4.4e-19 Score=114.37 Aligned_cols=72 Identities=44% Similarity=0.704 Sum_probs=69.8
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 899999999999999999999999999999999999999999999999999999999999999999999864
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=115.54 Aligned_cols=69 Identities=36% Similarity=0.587 Sum_probs=66.4
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEE
Q 031613 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 367889999999999999999999999999999999999999999999999999999999999999986
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=3.2e-19 Score=115.02 Aligned_cols=70 Identities=39% Similarity=0.733 Sum_probs=67.6
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=9.6e-19 Score=115.75 Aligned_cols=72 Identities=32% Similarity=0.451 Sum_probs=69.9
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEE--ecCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL--~~~G~~L~d~~tL~~~gi~~~stI~l~~~ 72 (156)
|+|+|+..+|+++.+++++++||++||++|++..|+|+++|+| +|+|+.|+|+.+|++|||++|++|+|+++
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~ 76 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQ 76 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEE
Confidence 7899999999999999999999999999999999999999999 89999999999999999999999999987
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=111.25 Aligned_cols=71 Identities=34% Similarity=0.489 Sum_probs=67.5
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 68999999997 589999999999999999999999999999999999999999999999999999999874
No 21
>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]
Probab=99.76 E-value=6.6e-20 Score=125.07 Aligned_cols=78 Identities=96% Similarity=1.290 Sum_probs=75.8
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCCcc
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAK 78 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 22
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=99.76 E-value=3.3e-18 Score=109.61 Aligned_cols=68 Identities=56% Similarity=0.962 Sum_probs=65.4
Q ss_pred EeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEee
Q 031613 6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 6 k~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 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=108.34 Aligned_cols=68 Identities=35% Similarity=0.543 Sum_probs=64.3
Q ss_pred EEEEeC-CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCC-CcccccccCCCCEEEEE
Q 031613 3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLV 70 (156)
Q Consensus 3 I~Vk~~-~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~-~tL~~~gi~~~stI~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=3e-17 Score=110.26 Aligned_cols=76 Identities=18% Similarity=0.467 Sum_probs=74.2
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=2.8e-17 Score=105.74 Aligned_cols=70 Identities=29% Similarity=0.469 Sum_probs=66.7
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEE
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 68999986 89999999999999999999999999999999999999999999999999999999999873
No 26
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=99.71 E-value=1e-17 Score=101.07 Aligned_cols=47 Identities=57% Similarity=1.128 Sum_probs=44.1
Q ss_pred eeeEeeeEEEcCCCeEEEeeccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 99 KLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMANHFDRHYCGKCGLTYV 149 (156)
Q Consensus 99 k~~~l~~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 27
>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=5.1e-17 Score=106.93 Aligned_cols=71 Identities=25% Similarity=0.279 Sum_probs=63.4
Q ss_pred CEEEEEeCCCCEE--EEEecCCCcHHHHHHHHHHHhC--CCCCceEEecCCeeccCCCcccccc--cCCCCEEEEEE
Q 031613 1 MQIFVKTLTGKTI--TLEVESSDTIDNVKAKIQDKEG--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~~~stI~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 5799999999984 4556899999999999999874 4579999999999999999999996 99999999985
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=1.3e-16 Score=104.11 Aligned_cols=69 Identities=23% Similarity=0.427 Sum_probs=65.2
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEec---CCeeccCCCcccccccCCCCEEEEE
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~---~G~~L~d~~tL~~~gi~~~stI~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=5.1e-17 Score=99.79 Aligned_cols=70 Identities=54% Similarity=0.911 Sum_probs=67.9
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEE
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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=7.9e-16 Score=96.45 Aligned_cols=64 Identities=61% Similarity=0.864 Sum_probs=61.3
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCC
Q 031613 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=99.62 E-value=7.9e-16 Score=106.68 Aligned_cols=90 Identities=27% Similarity=0.359 Sum_probs=76.8
Q ss_pred EEEEEeCCCCEE-EEEecCCCcHHHHHHHHHHHh-----CCC--CCceEEecCCeeccCCCcccccc------cCCCCEE
Q 031613 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~~~stI 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 577888889644 688999999999999999555 455 99999999999999999999999 6777999
Q ss_pred EEEEeecCCccccccccccCCccc
Q 031613 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 999999888887777777777654
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=99.58 E-value=5.9e-15 Score=122.62 Aligned_cols=72 Identities=31% Similarity=0.618 Sum_probs=69.8
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC---CCCCceEEecCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 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~~~stI~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 9999999999999999999999999999999998875
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=99.56 E-value=1.3e-14 Score=94.90 Aligned_cols=64 Identities=30% Similarity=0.372 Sum_probs=58.4
Q ss_pred eCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeecc-CCCcccccccC-CCCEEEEEE
Q 031613 7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQ-KESTLHLVL 71 (156)
Q Consensus 7 ~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~-d~~tL~~~gi~-~~stI~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 67899999998 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=99.53 E-value=1.4e-14 Score=94.24 Aligned_cols=53 Identities=32% Similarity=0.547 Sum_probs=49.0
Q ss_pred CCCcHHHHHHHHHHHh--CCC-CCceEEecCCeeccCCCcccccccCCCCEEEEEE
Q 031613 19 SSDTIDNVKAKIQDKE--GIP-PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 19 ~~~TV~~LK~~I~~~~--gip-~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~ 71 (156)
.++||.+||++|+++. |++ +++|+|+|.|++|+|+.+|++|||++|++|||+.
T Consensus 19 ~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~ 74 (75)
T cd01815 19 GGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR 74 (75)
T ss_pred ccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence 4789999999999995 575 8999999999999999999999999999999974
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=9.7e-14 Score=88.01 Aligned_cols=67 Identities=67% Similarity=0.992 Sum_probs=63.6
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEE
Q 031613 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 6777899999999999999999999999999999999999999999999999999999999999874
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=3.8e-13 Score=86.79 Aligned_cols=71 Identities=34% Similarity=0.633 Sum_probs=66.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC-CceEEecCCeeccCCCcccccccCCCCEEEEEE
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~-~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 999999999999999999999999999999874
No 37
>cd01795 USP48_C USP ubiquitin-specific protease. The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,
Probab=99.44 E-value=3.1e-13 Score=91.53 Aligned_cols=61 Identities=28% Similarity=0.335 Sum_probs=56.6
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccC-CCcccccccCCCCEEEEEEe
Q 031613 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED-GRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d-~~tL~~~gi~~~stI~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 46788999999999999999999999999999999999965 57999999999999999864
No 38
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=99.41 E-value=3.3e-13 Score=113.46 Aligned_cols=73 Identities=37% Similarity=0.592 Sum_probs=69.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeec
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 4689999877 899999999999999999999999999999999999999999999999999999999998754
No 39
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=99.32 E-value=4.4e-12 Score=102.17 Aligned_cols=74 Identities=38% Similarity=0.657 Sum_probs=70.4
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC--CCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeec
Q 031613 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~~~stI~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 999999999999999999999999999999988887643
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=99.31 E-value=1.7e-11 Score=81.75 Aligned_cols=70 Identities=21% Similarity=0.379 Sum_probs=58.8
Q ss_pred EEEEEeCC-CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe-cCCe-----ec-cCCCcccccccCCCCEEEEEE
Q 031613 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~~~stI~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 33455679999999999999999999999999995 7887 46 577899999999999999874
No 41
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=99.22 E-value=6e-11 Score=79.43 Aligned_cols=70 Identities=27% Similarity=0.538 Sum_probs=57.7
Q ss_pred EEEEEeCCC--CEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecC----Ce---ec-cCCCcccccccCCCCEEEEEE
Q 031613 2 QIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA----GK---QL-EDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 2 ~I~Vk~~~g--~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~----G~---~L-~d~~tL~~~gi~~~stI~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 577877655 488899999999999999999999999999999865 21 23 467899999999999999874
No 42
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=99.16 E-value=3.8e-10 Score=79.00 Aligned_cols=77 Identities=29% Similarity=0.466 Sum_probs=58.2
Q ss_pred EEEEEeCCCC-EEEEEecCCCcHHHHHHHHHHHhC-------CCCCceEEecCCeeccCCCcccccccCCCC------EE
Q 031613 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------tI 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 5667778999 889999999999999999987652 234689999999999999999999987665 68
Q ss_pred EEEEeecCCcc
Q 031613 68 HLVLRLRGGAK 78 (156)
Q Consensus 68 ~l~~~~~gg~~ 78 (156)
||++++.....
T Consensus 84 Hlvvrp~~~~~ 94 (111)
T PF13881_consen 84 HLVVRPNAPEP 94 (111)
T ss_dssp EEEE-SSSSSS
T ss_pred EEEecCCCCCc
Confidence 88887665544
No 43
>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=99.16 E-value=4.7e-10 Score=70.79 Aligned_cols=73 Identities=84% Similarity=1.145 Sum_probs=68.5
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecC
Q 031613 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG 75 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 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=2e-10 Score=79.70 Aligned_cols=76 Identities=30% Similarity=0.440 Sum_probs=65.3
Q ss_pred CEEEEEeCCCC-EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCccccccc-------CCCCEEEEEEe
Q 031613 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-------~~~stI~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 56777665554 77889999999999999999999999999999977889999999999999 66888888887
Q ss_pred ecCC
Q 031613 73 LRGG 76 (156)
Q Consensus 73 ~~gg 76 (156)
...|
T Consensus 81 ~~d~ 84 (119)
T cd01788 81 SSDD 84 (119)
T ss_pred cCCC
Confidence 5333
No 45
>PLN02560 enoyl-CoA reductase
Probab=99.13 E-value=2e-10 Score=93.47 Aligned_cols=74 Identities=31% Similarity=0.529 Sum_probs=63.7
Q ss_pred CEEEEEeCCCCEE---EEEecCCCcHHHHHHHHHHHhCC-CCCceEEecC---C----eeccCCCcccccccCCCCEEEE
Q 031613 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~~~stI~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 8999998888876 79999999999999999999986 8999999973 3 3789999999999999998765
Q ss_pred EEeecCC
Q 031613 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 44443
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=4e-09 Score=69.03 Aligned_cols=68 Identities=26% Similarity=0.318 Sum_probs=54.3
Q ss_pred EEEEEeCC-CCEEEEEe-cCCCcHHHHHHHHHHHhC-CCCCceEEe--cCCeeccCCCcccccccCCCCEEEE
Q 031613 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~~~stI~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 33323443 588999999999999876 578999885 8999999999999999999999876
No 47
>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=98.91 E-value=3.7e-09 Score=69.88 Aligned_cols=69 Identities=29% Similarity=0.434 Sum_probs=44.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCC---eec--cCCCcccccccCCCCEEEEE
Q 031613 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~~~stI~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 5688888776 778899999999999999999999999999886432 234 46789999999999999874
No 48
>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=2.2e-09 Score=96.94 Aligned_cols=72 Identities=35% Similarity=0.607 Sum_probs=68.8
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeec
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~ 74 (156)
.|.||+++.++.+|.|...+||.+||++|.+..+|+.+.|||+|.|+.|.|++++.+|+| +|-+|||+-|+.
T Consensus 4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlverpp 75 (1143)
T KOG4248|consen 4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVERPP 75 (1143)
T ss_pred ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC-CCeEEEeeccCC
Confidence 478999999999999999999999999999999999999999999999999999999999 999999997743
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=98.76 E-value=6.6e-08 Score=57.95 Aligned_cols=67 Identities=46% Similarity=0.666 Sum_probs=60.5
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEE
Q 031613 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 3444688889999999999999999999999999999999999999998888899999999998864
No 50
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=98.54 E-value=8.9e-07 Score=60.15 Aligned_cols=76 Identities=17% Similarity=0.427 Sum_probs=70.0
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCCc
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGA 77 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 4666665677889999999999999999999999999999999999999999999999999999999999988885
No 51
>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=98.49 E-value=1e-06 Score=56.82 Aligned_cols=70 Identities=29% Similarity=0.407 Sum_probs=60.3
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecC---C--eeccCCCcccccccCCCCEEEEEE
Q 031613 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~~~stI~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 58999998888999999999999999999999999986 8999872 3 357899999999997776666653
No 52
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=98.46 E-value=3.6e-07 Score=73.85 Aligned_cols=73 Identities=32% Similarity=0.604 Sum_probs=62.4
Q ss_pred CEEEEEeC---CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEE-Eee
Q 031613 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~~~stI~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 66777654 22367889999999999999999999999999999999999999999998888777777776 454
No 53
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=98.33 E-value=4.9e-06 Score=61.59 Aligned_cols=78 Identities=29% Similarity=0.503 Sum_probs=60.6
Q ss_pred CEEEEEeCCC----CEEEEEecCCCcHHHHHHHHHHHhCCCCCce-EEec-CCeec--cCCCcccccccCCC----CEEE
Q 031613 1 MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLIF-AGKQL--EDGRTLADYNIQKE----STLH 68 (156)
Q Consensus 1 M~I~Vk~~~g----~~~~l~V~~~~TV~~LK~~I~~~~gip~~~q-rL~~-~G~~L--~d~~tL~~~gi~~~----stI~ 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 7999999999 5888999999999999999999999998874 3443 34444 45556666554333 4788
Q ss_pred EEEeecCCcc
Q 031613 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 9999999865
No 54
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.27 E-value=4.2e-07 Score=56.97 Aligned_cols=69 Identities=26% Similarity=0.398 Sum_probs=61.0
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 456666678999999999999999999999999999998888777778899999999999999888764
No 55
>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.27 E-value=2.1e-06 Score=72.47 Aligned_cols=72 Identities=24% Similarity=0.410 Sum_probs=64.7
Q ss_pred EEEEeCCCCEEEEE-ecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecC
Q 031613 3 IFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG 75 (156)
Q Consensus 3 I~Vk~~~g~~~~l~-V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~g 75 (156)
|.|+. .|+.+.++ ++.++|+..||++|...+|++|++|+++..|..+.|+..+..+.|++|.+|+++-....
T Consensus 6 v~VKW-~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e~ 78 (473)
T KOG1872|consen 6 VIVKW-GGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAEA 78 (473)
T ss_pred Eeeee-cCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccccccccccCCCCEEEeeccccc
Confidence 56664 68889887 99999999999999999999999999999999999998899999999999998865443
No 56
>KOG4495 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription]
Probab=98.22 E-value=1.7e-06 Score=58.31 Aligned_cols=62 Identities=29% Similarity=0.435 Sum_probs=51.2
Q ss_pred CEEEEEeCCC-CEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEec-CC-eeccCCCcccccccC
Q 031613 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 4455555433 47788999999999999999999999999999985 44 578999999999763
No 57
>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=97.98 E-value=4e-05 Score=50.19 Aligned_cols=68 Identities=24% Similarity=0.405 Sum_probs=49.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCC------ceEEe-cCCeeccCCCcccccccCCCCEEEE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD------QQRLI-FAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~------~qrL~-~~G~~L~d~~tL~~~gi~~~stI~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 45666545689999999999999999999998876432 24666 7899999999999999999999986
No 58
>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=97.96 E-value=0.00012 Score=47.90 Aligned_cols=69 Identities=23% Similarity=0.347 Sum_probs=58.6
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCc-eEEe--cCCeeccCC--CcccccccCCCCEEEEE
Q 031613 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~~~stI~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 777788644 69999999999998763
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=97.90 E-value=6.4e-05 Score=47.66 Aligned_cols=63 Identities=19% Similarity=0.252 Sum_probs=47.1
Q ss_pred eCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEE
Q 031613 7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 7 ~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 457889999999999999999999999999999999999999999999999999999999875
No 60
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=97.82 E-value=0.00019 Score=47.02 Aligned_cols=68 Identities=22% Similarity=0.260 Sum_probs=56.6
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--cCCeeccC---CCcccccccCCCCEEEE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d---~~tL~~~gi~~~stI~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 66777753 47999999988888865
No 61
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=3.6e-05 Score=51.43 Aligned_cols=76 Identities=18% Similarity=0.385 Sum_probs=68.2
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCCc
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGA 77 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg~ 77 (156)
.+.|-.-+|.++.+.|..+++...|....+.+.|-..++.|++|+|+.++.+++-++++..+++.|.++....||.
T Consensus 26 nLkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~eQvGG~ 101 (103)
T COG5227 26 NLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVTEQVGGA 101 (103)
T ss_pred ceEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCCChhhcCCccchHHHHHHHHhcCc
Confidence 3455555778899999999999999999999999999999999999999999999999999999999888877775
No 62
>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=97.66 E-value=0.00054 Score=44.91 Aligned_cols=68 Identities=16% Similarity=0.320 Sum_probs=55.6
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--cCCeeccC---CCcccccccCCCCEEEEE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d---~~tL~~~gi~~~stI~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 588999999999999999999999999998765433 445665 77788853 479999999998888763
No 63
>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi. They contain a characteristic GFDRL sequence motif.
Probab=97.63 E-value=0.00016 Score=49.42 Aligned_cols=58 Identities=21% Similarity=0.352 Sum_probs=45.0
Q ss_pred EEEEEeCCC-CEEEEEec--CCCcHHHHHHHHHHHhC--CCCCceEEecCCeeccCCCccccc
Q 031613 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 467777663 34667777 78999999999999883 333578999999999999877654
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=97.52 E-value=0.0011 Score=42.98 Aligned_cols=66 Identities=17% Similarity=0.304 Sum_probs=51.9
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--cCCeeccC---CCcccccccCCCCEEEE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d---~~tL~~~gi~~~stI~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-AEPFTLMTSFPRRVLTDLDYELTLQEAGLV-NEVVFQ 74 (77)
T ss_pred EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEeCCCCccCCCCCccCcHHHcCCc-cceEEE
Confidence 58899999999999999999999999999876543 4456665 66677754 6899999998 455544
No 65
>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=97.48 E-value=0.0011 Score=43.49 Aligned_cols=65 Identities=23% Similarity=0.326 Sum_probs=51.9
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCC-CCceEEe--cCCeeccC-CCcccccccCCCCEE
Q 031613 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~~~stI 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 77787754 68999999985 444
No 66
>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=97.44 E-value=0.0019 Score=42.82 Aligned_cols=69 Identities=16% Similarity=0.316 Sum_probs=59.3
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--cCCeecc---CCCcccccccCCCCEEEEEE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~---d~~tL~~~gi~~~stI~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 6667663 34799999999999998754
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=97.30 E-value=0.0029 Score=41.63 Aligned_cols=68 Identities=21% Similarity=0.329 Sum_probs=57.7
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--cCCeecc---CCCcccccccCCCCEEEEE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~---d~~tL~~~gi~~~stI~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 68899999999999999999999999999874 7777788887 6667774 3579999999988888774
No 68
>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=97.26 E-value=0.0034 Score=41.78 Aligned_cols=68 Identities=13% Similarity=0.225 Sum_probs=55.1
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--cCCeecc--------CCCcccccccCCCCEEEEE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--------DGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~--------d~~tL~~~gi~~~stI~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 KIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLFVQ 83 (85)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEEEe
Confidence 6889999999999999999999999999965 34556778887 4446775 3579999999988877664
No 69
>KOG0013 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.26 E-value=0.00063 Score=52.30 Aligned_cols=65 Identities=28% Similarity=0.431 Sum_probs=57.7
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEee
Q 031613 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~ 73 (156)
.++.+.+.++..+|+.++|.++.+..|+.+-.|+++|+|..|.|...|.+++|+.|+...|.+..
T Consensus 155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqviV 219 (231)
T KOG0013|consen 155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQVIV 219 (231)
T ss_pred hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCCCEEEEEEEe
Confidence 35678888999999999999999999999999999999999999999999999999776655443
No 70
>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]
Probab=97.00 E-value=0.0016 Score=51.39 Aligned_cols=75 Identities=28% Similarity=0.369 Sum_probs=54.8
Q ss_pred CEEEEEeCCCC-EEE-EEecCCCcHHHHHHHHHHHh-CCCCCceEE----ecCCeeccCCCcccccccCCCCEEEEEEee
Q 031613 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~~~stI~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 78999877653 333 67778899999998776554 566644433 4678999999999999998887664 455
Q ss_pred cCCc
Q 031613 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=97.00 E-value=0.0065 Score=39.30 Aligned_cols=64 Identities=19% Similarity=0.264 Sum_probs=54.1
Q ss_pred EeCCCCEEEEEecCCCcHHHHHHHHHHHhCCC--C---CceEEecCCeeccCCCcccccccCCCCEEEE
Q 031613 6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIP--P---DQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 6 k~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip--~---~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 55679999999999999999998887766543 2 3568888999999999999999999999865
No 72
>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]
Probab=96.94 E-value=0.0027 Score=48.80 Aligned_cols=71 Identities=15% Similarity=0.297 Sum_probs=55.3
Q ss_pred EEEEEeCCCC-EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe-cCC-----eecc-CCCcccccccCCCCEEEEEEe
Q 031613 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~~~stI~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 4556443222 345678899999999999999999999999886 655 2454 567899999999999998844
No 73
>PRK06437 hypothetical protein; Provisional
Probab=96.62 E-value=0.026 Score=35.77 Aligned_cols=59 Identities=20% Similarity=0.388 Sum_probs=45.9
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
.++...++++...||++|-+. .+++++..-+..+|..+.. +.-|++|+.|.++-...||
T Consensus 9 g~~~~~~~i~~~~tv~dLL~~----Lgi~~~~vaV~vNg~iv~~-----~~~L~dgD~Veiv~~V~GG 67 (67)
T PRK06437 9 GHINKTIEIDHELTVNDIIKD----LGLDEEEYVVIVNGSPVLE-----DHNVKKEDDVLILEVFSGG 67 (67)
T ss_pred CCcceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCEECCC-----ceEcCCCCEEEEEecccCC
Confidence 456678888999999998766 4888888888899999974 4456689999877655554
No 74
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=96.53 E-value=0.023 Score=35.57 Aligned_cols=65 Identities=18% Similarity=0.398 Sum_probs=45.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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----DYEGNWLATAVNGELVHK-EARAQFVLHEGDRIEILSPMQGG 65 (65)
T ss_pred CEEEE---CCeEEEc--C-cCcHHHHHHHc----CCCCCeEEEEECCEEcCH-HHcCccccCCCCEEEEEEeccCC
Confidence 66776 5676666 3 46899988765 566665667789988863 22456667899999887666655
No 75
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=96.37 E-value=0.018 Score=37.64 Aligned_cols=71 Identities=18% Similarity=0.268 Sum_probs=48.7
Q ss_pred CEEEEEeCC------C-CEEEEEecCCCcHHHHHHHHHHHhC-CCC--CceEEecCCeeccCCCcccccccCCCCEEEEE
Q 031613 1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEG-IPP--DQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~~------g-~~~~l~V~~~~TV~~LK~~I~~~~g-ip~--~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYTTES-----AALKDGDELAII 76 (82)
T ss_pred eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEcCCC-----cCcCCCCEEEEe
Confidence 678887653 4 4677888889999999999976641 111 112456788876543 345689999888
Q ss_pred EeecCC
Q 031613 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 766665
No 76
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=96.18 E-value=0.057 Score=34.38 Aligned_cols=56 Identities=13% Similarity=0.238 Sum_probs=42.9
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 677777777799998854 4446789999887665554
No 77
>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=96.11 E-value=0.0015 Score=53.07 Aligned_cols=77 Identities=19% Similarity=0.434 Sum_probs=0.0
Q ss_pred EEEEEeCCCCEEEEEec---C--CCcHHHHHHHHHH----------HhCCCCCceE-----EecCCeeccCCCccccccc
Q 031613 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 45666665555544332 3 6899999999999 8899999888 9999999988888877754
Q ss_pred C-------CCCEEEEEEeecCCcc
Q 031613 62 Q-------KESTLHLVLRLRGGAK 78 (156)
Q Consensus 62 ~-------~~stI~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 4678888888888875
No 78
>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=96.04 E-value=0.038 Score=35.49 Aligned_cols=60 Identities=13% Similarity=0.228 Sum_probs=45.3
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCC----CCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 12 TITLEVESSDTIDNVKAKIQDKEGI----PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gi----p~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 4677888889999999999887542 2345567789988873 3456789999988777776
No 79
>KOG4583 consensus Membrane-associated ER protein involved in stress response (contains ubiquitin-like domain) [Posttranslational modification, protein turnover, chaperones]
Probab=96.01 E-value=0.0032 Score=51.60 Aligned_cols=60 Identities=22% Similarity=0.353 Sum_probs=47.3
Q ss_pred EEEEEeCCCC--EEEEEecCCCcHHHHHHHHHHHhCCC--CCceEEecCCeeccCCCccccccc
Q 031613 2 QIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEGIP--PDQQRLIFAGKQLEDGRTLADYNI 61 (156)
Q Consensus 2 ~I~Vk~~~g~--~~~l~V~~~~TV~~LK~~I~~~~gip--~~~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 4678887765 45566778899999999999876422 257999999999999988887754
No 80
>PF15044 CLU_N: Mitochondrial function, CLU-N-term
Probab=95.96 E-value=0.014 Score=38.00 Aligned_cols=56 Identities=23% Similarity=0.331 Sum_probs=45.1
Q ss_pred ecCCCcHHHHHHHHHHHhC-CCCCceEEecCCeeccCCCccccc-ccCCCCEEEEEEe
Q 031613 17 VESSDTIDNVKAKIQDKEG-IPPDQQRLIFAGKQLEDGRTLADY-NIQKESTLHLVLR 72 (156)
Q Consensus 17 V~~~~TV~~LK~~I~~~~g-ip~~~qrL~~~G~~L~d~~tL~~~-gi~~~stI~l~~~ 72 (156)
|+++++|.+|++.|..... ..-....|.++|..|++...|+++ |+.++++|.|+..
T Consensus 1 v~~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lve~ 58 (76)
T PF15044_consen 1 VSPTDTVQDVRQVLAESPETCYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELVEE 58 (76)
T ss_pred CChhhHHHHHHHHHHhCccccceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEEec
Confidence 5788999999999987654 333567888999999988888877 4888999988854
No 81
>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=95.74 E-value=0.043 Score=36.64 Aligned_cols=44 Identities=14% Similarity=0.241 Sum_probs=37.5
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCC---ceEEec
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD---QQRLIF 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 35678889999999999999999999999999998863 455555
No 82
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=95.60 E-value=0.076 Score=33.28 Aligned_cols=65 Identities=18% Similarity=0.310 Sum_probs=45.8
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
|+|+| +|+.+. +++..|+.+|-+. .++++...-+..++..+..+. .+.+ +++|+.|.++-...||
T Consensus 1 m~i~v---NG~~~~--~~~~~tl~~ll~~----l~~~~~~vav~~N~~iv~r~~-~~~~-L~~gD~ieIv~~VgGG 65 (65)
T PRK05863 1 MIVVV---NEEQVE--VDEQTTVAALLDS----LGFPEKGIAVAVDWSVLPRSD-WATK-LRDGARLEVVTAVQGG 65 (65)
T ss_pred CEEEE---CCEEEE--cCCCCcHHHHHHH----cCCCCCcEEEEECCcCcChhH-hhhh-cCCCCEEEEEeeccCC
Confidence 66766 465544 4567888887765 588888888889999876433 2344 8899999987655554
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=95.57 E-value=0.062 Score=35.36 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=35.3
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCee
Q 031613 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 89999999999999999999999999999999987654
No 84
>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=95.55 E-value=0.14 Score=32.88 Aligned_cols=58 Identities=26% Similarity=0.351 Sum_probs=45.3
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC-CceEEec----CCe--eccCCCcccccccC
Q 031613 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIF----AGK--QLEDGRTLADYNIQ 62 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~-~~qrL~~----~G~--~L~d~~tL~~~gi~ 62 (156)
|+.++|+..+++|++++|+.+|-++|.+..++.. +-.-|.+ +|. -|+.+.+|.+....
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~ 65 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKK 65 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBT
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCC
Confidence 5678999999999999999999999999999864 3345656 222 36777888888766
No 85
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=95.52 E-value=0.15 Score=31.90 Aligned_cols=66 Identities=15% Similarity=0.248 Sum_probs=44.9
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
|+|+| +|+.+. ++...||.+|-+.+ +++.....+-.++..+..+ ..++.-+++|+.|.++-...||
T Consensus 1 m~i~v---Ng~~~~--~~~~~tl~~ll~~l----~~~~~~vaVavN~~iv~r~-~w~~~~L~~gD~Ieii~~v~GG 66 (66)
T PRK08053 1 MQILF---NDQPMQ--CAAGQTVHELLEQL----NQLQPGAALAINQQIIPRE-QWAQHIVQDGDQILLFQVIAGG 66 (66)
T ss_pred CEEEE---CCeEEE--cCCCCCHHHHHHHc----CCCCCcEEEEECCEEeChH-HcCccccCCCCEEEEEEEccCC
Confidence 67777 465544 46678899888764 4555567777899988532 1344457889999987666665
No 86
>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=95.49 E-value=0.062 Score=35.69 Aligned_cols=62 Identities=19% Similarity=0.337 Sum_probs=45.3
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEee
Q 031613 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 44567788899999999999999999988888888888999999999999988888888764
No 87
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=95.41 E-value=0.17 Score=31.47 Aligned_cols=66 Identities=20% Similarity=0.387 Sum_probs=46.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
|+|+| +|+. ++++...||.+|-.. .++++...-+..+|..+.-+. ..+.-+++|+.|.++--..||
T Consensus 1 m~i~v---NG~~--~~~~~~~tl~~lL~~----l~~~~~~vav~vNg~iv~r~~-~~~~~l~~gD~vei~~~vgGG 66 (66)
T PRK05659 1 MNIQL---NGEP--RELPDGESVAALLAR----EGLAGRRVAVEVNGEIVPRSQ-HASTALREGDVVEIVHALGGG 66 (66)
T ss_pred CEEEE---CCeE--EEcCCCCCHHHHHHh----cCCCCCeEEEEECCeEeCHHH-cCcccCCCCCEEEEEEEecCC
Confidence 66666 4664 456677888888765 578888888889998876332 334456789999987665554
No 88
>PHA00626 hypothetical protein
Probab=95.35 E-value=0.011 Score=36.13 Aligned_cols=30 Identities=30% Similarity=0.758 Sum_probs=22.8
Q ss_pred cCCCCccCCceEEe-----EeCCCCccCCceeEEEee
Q 031613 120 ECPNAECGAGTFMA-----NHFDRHYCGKCGLTYVYQ 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 589 898753332 567999999999999654
No 89
>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function.
Probab=95.12 E-value=0.15 Score=32.18 Aligned_cols=65 Identities=23% Similarity=0.473 Sum_probs=53.4
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHh---CCCCCceEEe-cCCeeccCCCcccccccCCCCEEEEEEee
Q 031613 9 TGKTITLEVESSDTIDNVKAKIQDKE---GIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~---gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stI~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 68888999999998888877766555 4677777665 68889999999999999999999888764
No 90
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=94.99 E-value=0.11 Score=44.05 Aligned_cols=71 Identities=21% Similarity=0.255 Sum_probs=53.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHh--CCCCCceEEec--C--Cee--ccCCCcccccccCCCCEEEEEEe
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE--GIPPDQQRLIF--A--GKQ--LEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~--gip~~~qrL~~--~--G~~--L~d~~tL~~~gi~~~stI~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 6788888766 57899999999999998887665 34556665542 2 222 34678899999999999999874
No 91
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=94.99 E-value=0.21 Score=32.35 Aligned_cols=60 Identities=17% Similarity=0.294 Sum_probs=44.2
Q ss_pred EEEEEecCC-CcHHHHHHHHHHHhC-CC--CCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 12 TITLEVESS-DTIDNVKAKIQDKEG-IP--PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 12 ~~~l~V~~~-~TV~~LK~~I~~~~g-ip--~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
...++++.. .||.+|.+.+.++.. +- .....+..+++...+ +.-|++|++|.+.....||
T Consensus 17 ~~~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~PpvsGG 80 (80)
T TIGR01682 17 EETLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFIPPVSGG 80 (80)
T ss_pred eEEEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcCC-----CcCcCCCCEEEEeCCCCCC
Confidence 457888877 899999999988864 11 123466688888775 3456789999988777765
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=94.98 E-value=0.12 Score=32.17 Aligned_cols=58 Identities=21% Similarity=0.393 Sum_probs=42.3
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 34556778999998775 46777788889999886442 334457789999988766665
No 93
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=94.82 E-value=0.27 Score=32.95 Aligned_cols=65 Identities=20% Similarity=0.243 Sum_probs=45.8
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEec----CC-eecc-CCCcccccccCCCCEEEEEEeecCC
Q 031613 11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF----AG-KQLE-DGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~----~G-~~L~-d~~tL~~~gi~~~stI~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 36778899999999999999999999 66678862 22 2464 4579999999999999888876555
No 94
>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=94.79 E-value=0.32 Score=31.91 Aligned_cols=62 Identities=13% Similarity=0.286 Sum_probs=44.3
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCC------C-----CCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 11 KTITLEVESSDTIDNVKAKIQDKEGI------P-----PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gi------p-----~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 467899999988877776
No 95
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=94.67 E-value=0.43 Score=29.45 Aligned_cols=65 Identities=20% Similarity=0.252 Sum_probs=42.8
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
|+|+| +|+. +++++..||.+|-+.+. ++ ....+..+|..+..+. ..+.-+++|++|.++-...||
T Consensus 1 m~i~v---Ng~~--~~~~~~~tl~~ll~~l~----~~-~~~~v~vN~~~v~~~~-~~~~~L~~gD~vei~~~v~GG 65 (65)
T PRK06944 1 MDIQL---NQQT--LSLPDGATVADALAAYG----AR-PPFAVAVNGDFVARTQ-HAARALAAGDRLDLVQPVAGG 65 (65)
T ss_pred CEEEE---CCEE--EECCCCCcHHHHHHhhC----CC-CCeEEEECCEEcCchh-cccccCCCCCEEEEEeeccCC
Confidence 66666 3554 45667789999988763 33 2356678888875322 223346789999988766665
No 96
>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=94.66 E-value=0.19 Score=31.91 Aligned_cols=63 Identities=14% Similarity=0.249 Sum_probs=48.8
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCC--CCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 12 TITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gi--p~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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--DGLDTPLKDGDEVAILPPVSGG 77 (77)
T ss_dssp EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEEEGG--GTTTSBEETTEEEEEEESTSTS
T ss_pred CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEEcCC--ccCCcCcCCCCEEEEECCCCCC
Confidence 5678899999999999999877631 2256788899999888 2455666789999987776665
No 97
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=94.55 E-value=0.42 Score=30.10 Aligned_cols=66 Identities=18% Similarity=0.253 Sum_probs=45.5
Q ss_pred CEEEEEeCCCCEEEEEecCC-CcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 1 MQIFVKTLTGKTITLEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~-~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
|+|+| +|+.+ +++.. .||.+|-+. .++++...-+..++..+.-+. .++.-+++|+.|.++--..||
T Consensus 1 m~I~v---NG~~~--~~~~~~~tv~~lL~~----l~~~~~~vav~vN~~iv~r~~-w~~~~L~~gD~iEIv~~VgGG 67 (67)
T PRK07696 1 MNLKI---NGNQI--EVPESVKTVAELLTH----LELDNKIVVVERNKDILQKDD-HTDTSVFDGDQIEIVTFVGGG 67 (67)
T ss_pred CEEEE---CCEEE--EcCCCcccHHHHHHH----cCCCCCeEEEEECCEEeCHHH-cCceecCCCCEEEEEEEecCC
Confidence 66766 46655 44444 578877654 577777777789999886442 455667899999987655554
No 98
>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=94.39 E-value=0.21 Score=32.91 Aligned_cols=46 Identities=11% Similarity=0.154 Sum_probs=36.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC-CceEEecCC
Q 031613 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 VRVKAT-YGEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLD 47 (82)
T ss_pred CEEEEE-eCCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEEC
Confidence 455553 4677999999999999999999999999875 566666633
No 99
>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=94.36 E-value=0.25 Score=30.69 Aligned_cols=61 Identities=20% Similarity=0.394 Sum_probs=42.6
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
+|+. ++++...||.+|.+.+ +++++...+..+|..+..+. ..++-|++|+.|.++-...||
T Consensus 4 Ng~~--~~~~~~~tv~~ll~~l----~~~~~~v~v~vN~~iv~~~~-~~~~~L~~gD~veii~~V~GG 64 (64)
T TIGR01683 4 NGEP--VEVEDGLTLAALLESL----GLDPRRVAVAVNGEIVPRSE-WDDTILKEGDRIEIVTFVGGG 64 (64)
T ss_pred CCeE--EEcCCCCcHHHHHHHc----CCCCCeEEEEECCEEcCHHH-cCceecCCCCEEEEEEeccCC
Confidence 4544 4456778999988764 56677777789999885332 334567889999887666665
No 100
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=94.33 E-value=0.31 Score=32.30 Aligned_cols=61 Identities=11% Similarity=0.249 Sum_probs=43.0
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
+|+. .+++...||.+|-+. .++++...-+..+|..+.-+ ..++.-+++|+.|.++--..||
T Consensus 24 NG~~--~~~~~~~tl~~LL~~----l~~~~~~vAVevNg~iVpr~-~w~~t~L~egD~IEIv~~VgGG 84 (84)
T PRK06083 24 NDQS--IQVDISSSLAQIIAQ----LSLPELGCVFAINNQVVPRS-EWQSTVLSSGDAISLFQAIAGG 84 (84)
T ss_pred CCeE--EEcCCCCcHHHHHHH----cCCCCceEEEEECCEEeCHH-HcCcccCCCCCEEEEEEEecCC
Confidence 4543 344667788887765 47787777778999988533 3556668899999987666554
No 101
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=94.28 E-value=0.2 Score=30.83 Aligned_cols=55 Identities=18% Similarity=0.289 Sum_probs=40.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEE
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~ 71 (156)
|+|+|. | -.+++..+.|+.+||.++... .-.++++|-+..++..| ++|+.|.+.-
T Consensus 1 M~I~vN---~--k~~~~~~~~tl~~lr~~~k~~------~DI~I~NGF~~~~d~~L-----~e~D~v~~Ik 55 (57)
T PF14453_consen 1 MKIKVN---E--KEIETEENTTLFELRKESKPD------ADIVILNGFPTKEDIEL-----KEGDEVFLIK 55 (57)
T ss_pred CEEEEC---C--EEEEcCCCcCHHHHHHhhCCC------CCEEEEcCcccCCcccc-----CCCCEEEEEe
Confidence 677773 3 357788889999999887553 22678999998776655 4688887763
No 102
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=94.14 E-value=0.091 Score=43.66 Aligned_cols=70 Identities=21% Similarity=0.323 Sum_probs=58.8
Q ss_pred CEEEEEeC--CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCC--CcccccccCCCCEEEEE
Q 031613 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~~~stI~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 55666443 456788899999999999999999999999999999999999754 68999999999888654
No 103
>PRK07440 hypothetical protein; Provisional
Probab=94.09 E-value=0.5 Score=30.07 Aligned_cols=61 Identities=20% Similarity=0.329 Sum_probs=43.4
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 9 ~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 4654 556677899887754 467777778889999886332 445567889999987665554
No 104
>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=93.80 E-value=0.06 Score=33.96 Aligned_cols=19 Identities=26% Similarity=0.578 Sum_probs=15.3
Q ss_pred CCCccCCceeEEEeecCCC
Q 031613 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 105
>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=93.76 E-value=0.38 Score=30.91 Aligned_cols=45 Identities=16% Similarity=0.334 Sum_probs=37.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCC
Q 031613 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 355554 567889999999999999999999999987778887754
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=92.71 E-value=1.8 Score=32.25 Aligned_cols=71 Identities=28% Similarity=0.367 Sum_probs=49.0
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCC-ceEEec---CC---eeccCCCcccccccC-CCCEEEEEEe
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF---AG---KQLEDGRTLADYNIQ-KESTLHLVLR 72 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~-~qrL~~---~G---~~L~d~~tL~~~gi~-~~stI~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 57788899999999999999999999999999999642 223332 11 235555666665544 2345555444
No 107
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=91.96 E-value=0.37 Score=40.40 Aligned_cols=65 Identities=20% Similarity=0.314 Sum_probs=51.1
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC-CCCCceEEe--cCCeeccC-CCcccccccCCCCE
Q 031613 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 4788999999999999999999999999987654 333456665 77788865 57999999975443
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=91.89 E-value=0.06 Score=27.81 Aligned_cols=24 Identities=42% Similarity=1.096 Sum_probs=17.5
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 119 KECPNAECGAGTFMANHFDRHYCGKCGLTY 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 89865532 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=91.74 E-value=1.3 Score=28.46 Aligned_cols=44 Identities=20% Similarity=0.272 Sum_probs=38.8
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecC
Q 031613 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 46777899999999999999999999999999999987766644
No 110
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=91.74 E-value=0.65 Score=37.33 Aligned_cols=68 Identities=18% Similarity=0.283 Sum_probs=53.5
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--cCCeecc-C--CCcccccccCCCCEEEE
Q 031613 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~~~stI~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 4778999999999999999999999999998888766544443 4444453 2 36899999988888754
No 111
>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=91.68 E-value=1.1 Score=29.97 Aligned_cols=45 Identities=20% Similarity=0.271 Sum_probs=35.0
Q ss_pred EEEEe-CCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCe
Q 031613 3 IFVKT-LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK 48 (156)
Q Consensus 3 I~Vk~-~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~ 48 (156)
|.|+. ..|.+..+.|+++.+..+|.++|.+++++. ....|-|...
T Consensus 3 ikVKv~~~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE 48 (86)
T cd06408 3 IRVKVHAQDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD 48 (86)
T ss_pred EEEEEEecCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC
Confidence 34443 367899999999999999999999999985 4556656544
No 112
>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=91.44 E-value=1.3 Score=38.26 Aligned_cols=70 Identities=14% Similarity=0.172 Sum_probs=54.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCC----C--CCceEEe-cCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI----P--PDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gi----p--~~~qrL~-~~G~~L~d~~tL~~~gi~~~stI~l~~~ 72 (156)
+|+|... .+...+-++.+.+|.||--.|-+..+- + +..-.|. .+|.+|+.+.+|.+.||.||+.+++...
T Consensus 4 RVtV~~~-~~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L~p~ 80 (452)
T TIGR02958 4 RVTVLAG-RRAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVLVPA 80 (452)
T ss_pred EEEEeeC-CeeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEEeeC
Confidence 4666654 356788899999999999999887753 1 1223444 6888999999999999999999998753
No 113
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=91.43 E-value=1.9 Score=27.36 Aligned_cols=58 Identities=19% Similarity=0.389 Sum_probs=42.0
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
.++++...|+++|-+. .+++++..-+..+|..+..+. -.+.-+++++.|.++--..||
T Consensus 11 ~~e~~~~~tv~dLL~~----l~~~~~~vav~vNg~iVpr~~-~~~~~l~~gD~ievv~~v~GG 68 (68)
T COG2104 11 EVEIAEGTTVADLLAQ----LGLNPEGVAVAVNGEIVPRSQ-WADTILKEGDRIEVVRVVGGG 68 (68)
T ss_pred EEEcCCCCcHHHHHHH----hCCCCceEEEEECCEEccchh-hhhccccCCCEEEEEEeecCC
Confidence 4556666999998765 578888788889999887443 345567788999877555554
No 114
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=91.26 E-value=0.13 Score=31.39 Aligned_cols=34 Identities=29% Similarity=0.823 Sum_probs=27.1
Q ss_pred eccCCCCccCCceEEeE--eCCCCccCCceeEEEee
Q 031613 118 RKECPNAECGAGTFMAN--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 56899999987777643 45688899999999875
No 115
>KOG0009 consensus Ubiquitin-like/40S ribosomal S30 protein fusion [Translation, ribosomal structure and biogenesis; Posttranslational modification, protein turnover, chaperones]
Probab=90.97 E-value=0.087 Score=32.35 Aligned_cols=28 Identities=32% Similarity=0.278 Sum_probs=22.8
Q ss_pred CCccccccccccCCcccccccceeeeeE
Q 031613 75 GGAKKRKKKTYTKPKKIKHKKKKVKLAV 102 (156)
Q Consensus 75 gg~~k~~kk~~~~pk~~k~~~kk~k~~~ 102 (156)
|.-.+++|+..+|||.++++++|.|...
T Consensus 6 gslarAGKVr~QTPKv~kqeK~kkk~GR 33 (62)
T KOG0009|consen 6 GSLARAGKVRGQTPKVEKQEKKKKKRGR 33 (62)
T ss_pred eehhhcccccccCCcchhhhhcccccch
Confidence 3445778999999999999999988753
No 116
>smart00455 RBD Raf-like Ras-binding domain.
Probab=90.73 E-value=1.4 Score=28.07 Aligned_cols=49 Identities=22% Similarity=0.322 Sum_probs=41.9
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCC--eecc
Q 031613 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 356677999999999999999999999999999999988888755 3554
No 117
>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional
Probab=90.59 E-value=1.5 Score=36.19 Aligned_cols=68 Identities=19% Similarity=0.291 Sum_probs=50.2
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCCcc
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAK 78 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg~~ 78 (156)
|+|+| +|+. ++++...||.+|-+. .+++++..-+..||+.+.-+. ..+.-|++|+.|.++--..||.-
T Consensus 1 M~I~V---NGk~--~el~e~~TL~dLL~~----L~i~~~~VAVeVNgeIVpr~~-w~~t~LkeGD~IEII~~VgGGs~ 68 (326)
T PRK11840 1 MRIRL---NGEP--RQVPAGLTIAALLAE----LGLAPKKVAVERNLEIVPRSE-YGQVALEEGDELEIVHFVGGGSD 68 (326)
T ss_pred CEEEE---CCEE--EecCCCCcHHHHHHH----cCCCCCeEEEEECCEECCHHH-cCccccCCCCEEEEEEEecCCCC
Confidence 67776 4654 555677888888765 588888888889999986332 45666889999998877777754
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=90.50 E-value=0.11 Score=31.61 Aligned_cols=33 Identities=21% Similarity=0.592 Sum_probs=20.9
Q ss_pred ccCCCCccCCceEEeEeCCC--CccCCceeEEEee
Q 031613 119 KECPNAECGAGTFMANHFDR--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 59998899866655554444 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=90.49 E-value=1.3 Score=28.50 Aligned_cols=44 Identities=20% Similarity=0.397 Sum_probs=34.9
Q ss_pred EEEEeCCCCEEE-EEecCCCcHHHHHHHHHHHhCCCCCceEEecCC
Q 031613 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 899999999999999999999997888888743
No 120
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=90.26 E-value=0.57 Score=29.62 Aligned_cols=38 Identities=29% Similarity=0.570 Sum_probs=31.3
Q ss_pred CCeEEEeeccCCCCccCCceEEeEe-CCCCccCCceeEEEe
Q 031613 111 SGKVQRLRKECPNAECGAGTFMANH-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 89888777788 478999999998843
No 121
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=90.18 E-value=0.22 Score=33.20 Aligned_cols=32 Identities=34% Similarity=0.673 Sum_probs=22.0
Q ss_pred EEeeccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 115 QRLRKECPNAECGAGTFMANHFDRHYCGKCGLTY 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 897532211124789999999998
No 122
>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=89.84 E-value=0.3 Score=32.84 Aligned_cols=31 Identities=26% Similarity=0.594 Sum_probs=22.7
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGLTYV 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 9986654434456799999999984
No 123
>PRK05978 hypothetical protein; Provisional
Probab=89.58 E-value=0.18 Score=37.07 Aligned_cols=33 Identities=27% Similarity=0.764 Sum_probs=26.2
Q ss_pred eeccCCCCccCCceEEeEe-CCCCccCCceeEEEee
Q 031613 117 LRKECPNAECGAGTFMANH-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 3588999999988554
No 124
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.46 E-value=0.2 Score=29.61 Aligned_cols=27 Identities=33% Similarity=0.781 Sum_probs=18.8
Q ss_pred cCCCCccCCceEEeEeC----CCCccCCceeEEEe
Q 031613 120 ECPNAECGAGTFMANHF----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 589 8976 433321 37899999998744
No 125
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=89.46 E-value=0.15 Score=36.59 Aligned_cols=34 Identities=29% Similarity=0.666 Sum_probs=27.0
Q ss_pred EEeeccCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031613 115 QRLRKECPNAECGAGTFMANHFDRHYCGKCGLTYVYQK 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--KCGT--PLFRKDGEVFCPVCGYREVVVE 58 (131)
T ss_pred HHHHhhCc--ccCC--cceeeCCeEECCCCCceEEEee
Confidence 55789999 9966 4446889999999998886544
No 126
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=89.38 E-value=3 Score=26.99 Aligned_cols=57 Identities=12% Similarity=0.220 Sum_probs=35.8
Q ss_pred EEecC-CCcHHHHHHHHHHHhC-----CCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 15 LEVES-SDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 15 l~V~~-~~TV~~LK~~I~~~~g-----ip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 4799999999988752 11222344455544333 2346789999888777765
No 127
>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=88.64 E-value=2.5 Score=26.82 Aligned_cols=45 Identities=22% Similarity=0.335 Sum_probs=35.1
Q ss_pred EEEEEeCCCCEEEEEec-CCCcHHHHHHHHHHHhCCCCCceEEecCC
Q 031613 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 4678888888 89999999999999999886566666644
No 128
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.61 E-value=0.53 Score=27.30 Aligned_cols=34 Identities=18% Similarity=0.488 Sum_probs=22.8
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeEEEeecC
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLTYVYQKA 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 129
>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=88.61 E-value=4.5 Score=25.68 Aligned_cols=56 Identities=20% Similarity=0.242 Sum_probs=40.6
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecC--CeeccCCCcccc
Q 031613 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 56777899999999999999999999999999999987766543 345655544433
No 130
>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=87.85 E-value=1.3 Score=28.96 Aligned_cols=36 Identities=11% Similarity=0.250 Sum_probs=32.7
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCC
Q 031613 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 667889999999999999999999999999998854
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=87.72 E-value=0.47 Score=26.20 Aligned_cols=29 Identities=34% Similarity=0.858 Sum_probs=19.0
Q ss_pred eccCCCCccCCceEEeEe------CCCCccCCceeEEE
Q 031613 118 RKECPNAECGAGTFMANH------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 46799 8985 343331 22468999998874
No 132
>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=87.13 E-value=0.42 Score=29.11 Aligned_cols=25 Identities=28% Similarity=0.849 Sum_probs=19.5
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGL 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 999654 5999999999997
No 133
>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=86.95 E-value=3.9 Score=27.42 Aligned_cols=70 Identities=17% Similarity=0.299 Sum_probs=44.4
Q ss_pred EEEEeCCCCEEEEEecC-----CCcHHHHHHHHHHHhCCCC-CceEEecCCe-----eccCCCccccc-----ccCCCCE
Q 031613 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 VKVK-YGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYFCSGSRLNP 81 (91)
T ss_pred EEEE-eCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHHhccCCCce
Confidence 4443 356677788774 7999999999999999998 5566666443 23333323222 2234666
Q ss_pred EEEEEee
Q 031613 67 LHLVLRL 73 (156)
Q Consensus 67 I~l~~~~ 73 (156)
|.+.+++
T Consensus 82 lrl~v~~ 88 (91)
T cd06398 82 LRIDVTV 88 (91)
T ss_pred EEEEEEE
Confidence 6666553
No 134
>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=86.70 E-value=3.6 Score=27.09 Aligned_cols=35 Identities=23% Similarity=0.316 Sum_probs=29.4
Q ss_pred EEEEEeCCCCEEEEEecC--CCcHHHHHHHHHHHhCCC
Q 031613 2 QIFVKTLTGKTITLEVES--SDTIDNVKAKIQDKEGIP 37 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~--~~TV~~LK~~I~~~~gip 37 (156)
.|.+ +.+|.+..+.+++ +.+..+|++.|..+++++
T Consensus 2 ~vKa-ty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~ 38 (81)
T cd06396 2 NLKV-TYNGESQSFLVSDSENTTWASVEAMVKVSFGLN 38 (81)
T ss_pred EEEE-EECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC
Confidence 3444 3468899999998 779999999999999998
No 135
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=86.56 E-value=0.51 Score=35.86 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=24.0
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEEeecC
Q 031613 119 KECPNAECGAGTFMANHFDRHYCGKCGLTYVYQKA 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 136
>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=86.30 E-value=0.52 Score=31.73 Aligned_cols=32 Identities=28% Similarity=0.641 Sum_probs=22.6
Q ss_pred EeeccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 116 RLRKECPNAECGAGTFMANHFDRHYCGKCGLTYV 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 137
>PRK01777 hypothetical protein; Validated
Probab=85.82 E-value=5.2 Score=27.08 Aligned_cols=69 Identities=9% Similarity=0.108 Sum_probs=46.0
Q ss_pred CEEEEEeC-CCC--EEEEEecCCCcHHHHHHHHHHHhCCCCC--c-----eEEecCCeeccCCCcccccccCCCCEEEEE
Q 031613 1 MQIFVKTL-TGK--TITLEVESSDTIDNVKAKIQDKEGIPPD--Q-----QRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 1 M~I~Vk~~-~g~--~~~l~V~~~~TV~~LK~~I~~~~gip~~--~-----qrL~~~G~~L~d~~tL~~~gi~~~stI~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 222 4668899999999987765 55544 2 35556777765544 44679999998
Q ss_pred EeecCCcc
Q 031613 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 77766554
No 138
>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=85.44 E-value=4.1 Score=27.68 Aligned_cols=40 Identities=18% Similarity=0.249 Sum_probs=33.5
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEec
Q 031613 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 35567889999999999999999999999998876 55543
No 139
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=85.33 E-value=1 Score=31.90 Aligned_cols=59 Identities=15% Similarity=0.213 Sum_probs=41.1
Q ss_pred EEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCccccccc---CCCCEEEEEE
Q 031613 13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI---QKESTLHLVL 71 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi---~~~stI~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 3346999999999999999999999988555566655566666655411 1244555553
No 140
>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=85.32 E-value=2 Score=28.43 Aligned_cols=56 Identities=16% Similarity=0.248 Sum_probs=38.1
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCC-------CceEEecCCe-ecc------CCCcccccccCCCCEEEEEE
Q 031613 15 LEVESSDTIDNVKAKIQDKEGIPP-------DQQRLIFAGK-QLE------DGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~-------~~qrL~~~G~-~L~------d~~tL~~~gi~~~stI~l~~ 71 (156)
++|++++|+.+|-+.+.+.-.+.. ..-.|++.+- .|+ -+.+|.++ +.+|..|.|.-
T Consensus 1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL-~~~g~ei~VtD 70 (84)
T PF08825_consen 1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL-LSDGEEITVTD 70 (84)
T ss_dssp EEESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT-HHSSEEEEEEE
T ss_pred CCcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH-hcCCCEEEEEC
Confidence 579999999999999988743322 2334444332 132 24679999 89999998864
No 141
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=85.20 E-value=0.6 Score=31.38 Aligned_cols=32 Identities=28% Similarity=0.631 Sum_probs=22.8
Q ss_pred EeeccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 116 RLRKECPNAECGAGTFMANHFDRHYCGKCGLTYV 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 9975444333346799999999984
No 142
>KOG4250 consensus TANK binding protein kinase TBK1 [Signal transduction mechanisms]
Probab=84.78 E-value=3.5 Score=37.41 Aligned_cols=41 Identities=24% Similarity=0.488 Sum_probs=37.0
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCee
Q 031613 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 45578889999999999999999999999999999998764
No 143
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=84.51 E-value=0.86 Score=28.63 Aligned_cols=28 Identities=29% Similarity=0.706 Sum_probs=22.5
Q ss_pred eccCCCCccCCceEEeEeCCCCc---cCCceeE
Q 031613 118 RKECPNAECGAGTFMANHFDRHY---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 9998888888887666 9999854
No 144
>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=84.03 E-value=7 Score=25.32 Aligned_cols=61 Identities=21% Similarity=0.268 Sum_probs=48.9
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceEEe-cCCeeccCCCcccccccCCCCEEEEEEeec
Q 031613 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stI~l~~~~~ 74 (156)
.++|+.++....+-...++++.+|+..--++ -+|--+...++-+..=++.|+.+.|+.|.+
T Consensus 19 vlsVpE~aPftAvlkfaAEeFkv~~~TsAiiTndGvGINP~qtAGnvflkhgselrliPRDr 80 (82)
T cd01766 19 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRLIPRDR 80 (82)
T ss_pred EEeccccCchHHHHHHHHHhcCCCccceeEEecCccccChhhcccceeeecCCEeeeccccc
Confidence 4689999988888888899999998655554 667777778888888888999999887655
No 145
>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=83.86 E-value=5 Score=26.69 Aligned_cols=65 Identities=25% Similarity=0.307 Sum_probs=44.4
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCce-EEe-c-----CCeeccCCCc----ccccccCCCCEE
Q 031613 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLI-F-----AGKQLEDGRT----LADYNIQKESTL 67 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~q-rL~-~-----~G~~L~d~~t----L~~~gi~~~stI 67 (156)
|.|-+.+|.+-.+.|+..+|+.++-+.+..+.+...+.- .|+ . --+.++|... |+..+..++..+
T Consensus 5 vkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~LvE~~P~l~lER~~EDHE~vvdvl~~W~~~~~n~l 80 (85)
T cd01787 5 VKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLVEHLPHLQLERLFEDHELVVEVLSTWHSAGNSVL 80 (85)
T ss_pred EEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEEEecchhhhhhhccchHHHHHHHHhcccCCCcEE
Confidence 556667899999999999999999999999998766433 333 1 1234566644 344455344444
No 146
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=83.75 E-value=0.8 Score=30.78 Aligned_cols=32 Identities=22% Similarity=0.423 Sum_probs=22.3
Q ss_pred EeeccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 116 RLRKECPNAECGAGTFMANHFDRHYCGKCGLTYV 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 9974333222236799999999984
No 147
>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=83.49 E-value=0.22 Score=30.79 Aligned_cols=26 Identities=31% Similarity=0.305 Sum_probs=19.7
Q ss_pred cCCccccccccccCCcccccccceee
Q 031613 74 RGGAKKRKKKTYTKPKKIKHKKKKVK 99 (156)
Q Consensus 74 ~gg~~k~~kk~~~~pk~~k~~~kk~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 46667899999999999999987644
No 148
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=83.16 E-value=0.47 Score=24.22 Aligned_cols=24 Identities=38% Similarity=0.874 Sum_probs=17.3
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeE
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLT 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 149
>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=82.94 E-value=3.1 Score=27.97 Aligned_cols=59 Identities=19% Similarity=0.343 Sum_probs=35.9
Q ss_pred EecCCCcHHHHHHHHHHHhCCCCCceEEec-CCe------eccCCC---cc--cccccCCCCEEEEEEeecCC
Q 031613 16 EVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AGK------QLEDGR---TL--ADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 16 ~V~~~~TV~~LK~~I~~~~gip~~~qrL~~-~G~------~L~d~~---tL--~~~gi~~~stI~l~~~~~gg 76 (156)
+++...||.+|-+.|.+.. +....+|+. +|. .|-++. .| .++-+++|++|.+.....||
T Consensus 24 ~~~~~~tV~dll~~L~~~~--~~~~~~lf~~~g~lr~~i~VlvN~~di~~l~g~~t~L~dgD~v~i~P~v~GG 94 (94)
T cd01764 24 DGEKPVTVGDLLDYVASNL--LEERPDLFIEGGSVRPGIIVLINDTDWELLGEEDYILEDGDHVVFISTLHGG 94 (94)
T ss_pred cCCCCCcHHHHHHHHHHhC--chhhhhhEecCCcccCCEEEEECCccccccCCcccCCCCcCEEEEECCCCCC
Confidence 3435679999999998776 232333332 221 122222 23 35668899999988777765
No 150
>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=82.71 E-value=0.92 Score=24.94 Aligned_cols=28 Identities=32% Similarity=0.794 Sum_probs=16.4
Q ss_pred ccCCCCccCCceEEeEeCCCC---ccCCceeEEEe
Q 031613 119 KECPNAECGAGTFMANHFDRH---YCGKCGLTYVY 150 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~---~cg~c~~t~~~ 150 (156)
+-|| .|+. +|..-.++. .|-.|+|.+-.
T Consensus 2 ~FCp--~C~n--lL~p~~~~~~~~~C~~C~Y~~~~ 32 (35)
T PF02150_consen 2 RFCP--ECGN--LLYPKEDKEKRVACRTCGYEEPI 32 (35)
T ss_dssp -BET--TTTS--BEEEEEETTTTEEESSSS-EEE-
T ss_pred eeCC--CCCc--cceEcCCCccCcCCCCCCCccCC
Confidence 3589 8975 443333333 49999998744
No 151
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=82.54 E-value=1.3 Score=37.87 Aligned_cols=31 Identities=32% Similarity=0.753 Sum_probs=22.1
Q ss_pred EeeccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 116 RLRKECPNAECGAGTFMANHFDRHYCGKCGLTYV 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 444444334799999999873
No 152
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=82.33 E-value=0.74 Score=25.95 Aligned_cols=23 Identities=30% Similarity=0.713 Sum_probs=19.2
Q ss_pred eccCCCCccCCceEEeEe--CCCCccCC
Q 031613 118 RKECPNAECGAGTFMANH--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 153
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.13 E-value=0.44 Score=33.74 Aligned_cols=34 Identities=35% Similarity=0.844 Sum_probs=25.5
Q ss_pred eeccCCCCccCCceEEeEe-CCCCccCCceeEEEeec
Q 031613 117 LRKECPNAECGAGTFMANH-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 99988643222 46888999999886643
No 154
>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=81.95 E-value=14 Score=25.36 Aligned_cols=63 Identities=29% Similarity=0.307 Sum_probs=43.6
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHh------CCCCC-ceEEecCCe--eccCCCcccccc-----cCCCCEEEEEEee
Q 031613 11 KTITLEVESSDTIDNVKAKIQDKE------GIPPD-QQRLIFAGK--QLEDGRTLADYN-----IQKESTLHLVLRL 73 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~------gip~~-~qrL~~~G~--~L~d~~tL~~~g-----i~~~stI~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 478999999999999999886651 12222 455556665 356667777773 4668888888754
No 155
>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown.
Probab=81.93 E-value=3.2 Score=29.45 Aligned_cols=55 Identities=22% Similarity=0.522 Sum_probs=39.0
Q ss_pred EecC-CCcHHHHHHHHHHHh----CCCC------CceEEec----------------CC-eec---cCCCcccccccCCC
Q 031613 16 EVES-SDTIDNVKAKIQDKE----GIPP------DQQRLIF----------------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 899999999887664 4554 2334432 11 356 67788999999999
Q ss_pred CEEEEE
Q 031613 65 STLHLV 70 (156)
Q Consensus 65 stI~l~ 70 (156)
..|.+.
T Consensus 101 TEiSfF 106 (122)
T PF10209_consen 101 TEISFF 106 (122)
T ss_pred ceeeee
Confidence 888765
No 156
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=81.92 E-value=0.8 Score=25.43 Aligned_cols=30 Identities=23% Similarity=0.560 Sum_probs=19.8
Q ss_pred eccCCCCccCCceEEeEe-----CCCCccCCceeEEE
Q 031613 118 RKECPNAECGAGTFMANH-----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 35688 78754433332 34788999998874
No 157
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=81.90 E-value=1.6 Score=23.68 Aligned_cols=29 Identities=28% Similarity=0.702 Sum_probs=21.1
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 119 KECPNAECGAGTFMANHFDRHYCGKCGLTYV 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 6966555534457778999999884
No 158
>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=81.46 E-value=0.68 Score=32.17 Aligned_cols=32 Identities=34% Similarity=0.812 Sum_probs=22.2
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCceeEEEee
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGLTYVYQ 151 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~ 151 (156)
..+.|| .||+..+=... +--.|.+||.+|-..
T Consensus 8 tKR~Cp--~CG~kFYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCP--SCGAKFYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCC--CCcchhccCCC-CCccCCCCCCccCcc
Confidence 368999 89975443332 556799999887544
No 159
>PRK09336 30S ribosomal protein S30e; Provisional
Probab=81.33 E-value=0.62 Score=27.80 Aligned_cols=24 Identities=29% Similarity=0.282 Sum_probs=19.4
Q ss_pred cCCccccccccccCCcccccccce
Q 031613 74 RGGAKKRKKKTYTKPKKIKHKKKK 97 (156)
Q Consensus 74 ~gg~~k~~kk~~~~pk~~k~~~kk 97 (156)
.|.-.+++|+..+|||.+++++++
T Consensus 4 HGSLarAGKVr~qTPkv~k~ekkk 27 (50)
T PRK09336 4 HGSLTKAGKVRSQTPKIPPKPKKN 27 (50)
T ss_pred chhhhhcccccCCCCCcchhhhcc
Confidence 355568899999999999888755
No 160
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=80.79 E-value=0.98 Score=24.77 Aligned_cols=27 Identities=30% Similarity=0.704 Sum_probs=14.3
Q ss_pred cCCCCccCCceEEe----EeCCCCccCCceeEE
Q 031613 120 ECPNAECGAGTFMA----NHFDRHYCGKCGLTY 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 588 787554332 335699999998643
No 161
>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=80.73 E-value=10 Score=24.41 Aligned_cols=41 Identities=29% Similarity=0.280 Sum_probs=32.1
Q ss_pred EEEEeCCCC----EEEEEecCCCcHHHHHHHHHHHhCCC--CCceEE
Q 031613 3 IFVKTLTGK----TITLEVESSDTIDNVKAKIQDKEGIP--PDQQRL 43 (156)
Q Consensus 3 I~Vk~~~g~----~~~l~V~~~~TV~~LK~~I~~~~gip--~~~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 445455555 78899999999999999999999983 345566
No 162
>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]
Probab=80.43 E-value=3.8 Score=35.13 Aligned_cols=72 Identities=14% Similarity=0.284 Sum_probs=58.7
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--cCCeeccC---CCcccccccCCCCEEEEEEee
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d---~~tL~~~gi~~~stI~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 77777653 378999999888888766443
No 163
>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=80.37 E-value=6.3 Score=25.75 Aligned_cols=48 Identities=21% Similarity=0.428 Sum_probs=33.8
Q ss_pred CcHHHHHHHHHHHhCCCCCceEEe--cCCeeccCCCcccccccCCCCEEEEEE
Q 031613 21 DTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d~~tL~~~gi~~~stI~l~~ 71 (156)
.|+.+|+.+..+..+++....+|. -+|..++|+.-+..+. ..|+.+++
T Consensus 21 ~sL~eL~~K~~~~l~~~~~~~~lvL~eDGT~VddEeyF~tLp---~nT~lm~L 70 (78)
T PF02017_consen 21 SSLEELLEKACDKLQLPEEPVRLVLEEDGTEVDDEEYFQTLP---DNTVLMLL 70 (78)
T ss_dssp SSHHHHHHHHHHHHT-SSSTCEEEETTTTCBESSCHHHCCSS---SSEEEEEE
T ss_pred CCHHHHHHHHHHHhCCCCcCcEEEEeCCCcEEccHHHHhhCC---CCCEEEEE
Confidence 689999999999999997666665 4888888775444432 44554444
No 164
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=79.77 E-value=8.6 Score=29.65 Aligned_cols=48 Identities=21% Similarity=0.329 Sum_probs=29.2
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCC---ceEEe--cCCee---ccCCCccccc
Q 031613 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 56764 5566666554
No 165
>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=79.76 E-value=11 Score=25.71 Aligned_cols=42 Identities=21% Similarity=0.224 Sum_probs=32.4
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC-CceEEe
Q 031613 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLI 44 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~-~~qrL~ 44 (156)
|.|=-.++...++.++.++||+||-.++..++.++. ...+|+
T Consensus 5 IRIFr~D~Tf~Tls~~l~tTv~eli~~L~rK~~l~~~~ny~l~ 47 (97)
T cd01775 5 IRVFRSDGTFTTLSCPLNTTVSELIPQLAKKFYLPSGGNYQLS 47 (97)
T ss_pred EEEEecCCcEEEEEcCCcCcHHHHHHHHHHhhcCCCCCCeEEE
Confidence 444445677788999999999999999999998877 333443
No 166
>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=79.58 E-value=11 Score=24.38 Aligned_cols=35 Identities=29% Similarity=0.448 Sum_probs=29.3
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCC--CCceEEe
Q 031613 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 5678899999999999999999999987 4444554
No 167
>KOG2982 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.02 E-value=3.2 Score=34.43 Aligned_cols=57 Identities=12% Similarity=0.188 Sum_probs=45.1
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceEEec---CCeec-----cCCCcccccccCCCCEEEEE
Q 031613 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQL-----EDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~---~G~~L-----~d~~tL~~~gi~~~stI~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 44432 33467899999999998653
No 168
>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=78.40 E-value=8.1 Score=34.17 Aligned_cols=64 Identities=36% Similarity=0.514 Sum_probs=41.8
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHh--CCCC------CceEEec--C--Ce-eccCC-------------CcccccccCCC
Q 031613 11 KTITLEVESSDTIDNVKAKIQDKE--GIPP------DQQRLIF--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 468889999999999999997653 4442 3444432 2 23 45543 45999999999
Q ss_pred CEEEEEEeec
Q 031613 65 STLHLVLRLR 74 (156)
Q Consensus 65 stI~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 169
>PTZ00467 40S ribosomal protein S30; Provisional
Probab=78.20 E-value=0.81 Score=28.82 Aligned_cols=26 Identities=27% Similarity=0.321 Sum_probs=21.2
Q ss_pred cCCccccccccccCCcccccccceee
Q 031613 74 RGGAKKRKKKTYTKPKKIKHKKKKVK 99 (156)
Q Consensus 74 ~gg~~k~~kk~~~~pk~~k~~~kk~k 99 (156)
.|.-.+++|+..+||+++++++++.+
T Consensus 5 HGSLarAGKVr~QTPkv~k~eKkk~~ 30 (66)
T PTZ00467 5 HGSLARAGKVKNQTPKVAKQEKPKQP 30 (66)
T ss_pred hhhhhhcccccCCCCCchhhhcccCC
Confidence 45556889999999999999977655
No 170
>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=77.81 E-value=16 Score=23.56 Aligned_cols=58 Identities=17% Similarity=0.268 Sum_probs=43.4
Q ss_pred EEEEecCCCcHHHHHHHHHHHhCCCCCceEEe-cCCeeccCCCcccccccCCCCEEEEE
Q 031613 13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 13 ~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stI~l~ 70 (156)
..++|+.++....+-...++++.+|+..--++ -+|--+...++..+.-++.|+.|.|+
T Consensus 18 kv~sVPE~apftaVlkfaAeeF~vp~~tsaiItndG~GInP~QTag~vflKhGseLrli 76 (76)
T PF03671_consen 18 KVISVPEEAPFTAVLKFAAEEFKVPPATSAIITNDGVGINPQQTAGNVFLKHGSELRLI 76 (76)
T ss_dssp EEEEEETTSBHHHHHHHHHHHTTS-SSSEEEEESSS-EE-TTSBHHHHHHHT-SEEEEE
T ss_pred eEEecCCCCchHHHHHHHHHHcCCCCceEEEEecCCcccccchhhhhhHhhcCcEeeeC
Confidence 34689999988888888889999998766555 67777888888888888889988763
No 171
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=77.53 E-value=1.2 Score=24.64 Aligned_cols=29 Identities=28% Similarity=0.644 Sum_probs=17.9
Q ss_pred eccCCCCccCCceEEeEe-----CCCCccCCceeEE
Q 031613 118 RKECPNAECGAGTFMANH-----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 78753332222 2357899999887
No 172
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=77.26 E-value=0.72 Score=29.03 Aligned_cols=17 Identities=29% Similarity=0.507 Sum_probs=13.9
Q ss_pred CCccCCceeEEEeecCC
Q 031613 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 56899999999888653
No 173
>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=77.26 E-value=6.4 Score=26.27 Aligned_cols=38 Identities=24% Similarity=0.416 Sum_probs=31.7
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe-cCCe
Q 031613 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 5789999999999999999999999998766433 4444
No 174
>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=77.09 E-value=7.1 Score=26.06 Aligned_cols=40 Identities=23% Similarity=0.290 Sum_probs=36.0
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031613 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 5777778999999999999999999999999999998754
No 175
>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=76.25 E-value=14 Score=24.31 Aligned_cols=43 Identities=14% Similarity=0.220 Sum_probs=35.5
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEec
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 45 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~ 45 (156)
+..|+ .+|.+..+.++..-|-+.|.++|...+.+|+...-|.|
T Consensus 2 ~fKv~-~~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtY 44 (82)
T cd06397 2 QFKSS-FLGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTY 44 (82)
T ss_pred eEEEE-eCCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEE
Confidence 44564 46778888888889999999999999999998777766
No 176
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=75.80 E-value=16 Score=23.94 Aligned_cols=53 Identities=19% Similarity=0.386 Sum_probs=40.1
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe-cCCeeccCCCcccccccCCCCEEEEEE
Q 031613 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stI~l~~ 71 (156)
+..+.+.++..+||.++-+. .|||..+.-++ -||+..+-+ +-+++|+.|.+.-
T Consensus 22 ~~~~~~~~~~~~tvkd~IEs----LGVP~tEV~~i~vNG~~v~~~-----~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 22 GGPFTHPFDGGATVKDVIES----LGVPHTEVGLILVNGRPVDFD-----YRLKDGDRVAVYP 75 (81)
T ss_pred CCceEEecCCCCcHHHHHHH----cCCChHHeEEEEECCEECCCc-----ccCCCCCEEEEEe
Confidence 44677889999999988754 79999888665 688877554 4556899988763
No 177
>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=75.77 E-value=2.3 Score=24.17 Aligned_cols=28 Identities=29% Similarity=0.775 Sum_probs=19.2
Q ss_pred cCCCCccCCceEEeEeC-CCCccCCceeEEE
Q 031613 120 ECPNAECGAGTFMANHF-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 699 898876555543 4558999998653
No 178
>KOG0007 consensus Splicing factor 3a, subunit 1 [RNA processing and modification]
Probab=75.28 E-value=1.4 Score=36.48 Aligned_cols=50 Identities=34% Similarity=0.564 Sum_probs=43.4
Q ss_pred eCCCCEEEEEec-CCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcc
Q 031613 7 TLTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL 56 (156)
Q Consensus 7 ~~~g~~~~l~V~-~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL 56 (156)
..+|++..+.+. .+..+..||.++....+|+++.|.+.+.|..|.|..++
T Consensus 289 ~~dg~~~~~~~~~~~~~~~~~k~k~~~~~~i~~~~q~~~~~~~~l~d~~~~ 339 (341)
T KOG0007|consen 289 PADGQVIKITVQSLSENVASLKEKIADESQIPANKQKLRGEGAFLKDNRSL 339 (341)
T ss_pred CCCCceeeeccccccccccccccccccccccchhheeeccCCcccCccccc
Confidence 346788888777 78899999999999999999999999999999887544
No 179
>PF11069 DUF2870: Protein of unknown function (DUF2870); InterPro: IPR021298 This is a eukaryotic family of proteins with unknown function.
Probab=75.20 E-value=4.7 Score=27.50 Aligned_cols=38 Identities=32% Similarity=0.617 Sum_probs=28.1
Q ss_pred EEecCCeeccCCCccccc-ccCCCCEEEEEEeecCCccc
Q 031613 42 RLIFAGKQLEDGRTLADY-NIQKESTLHLVLRLRGGAKK 79 (156)
Q Consensus 42 rL~~~G~~L~d~~tL~~~-gi~~~stI~l~~~~~gg~~k 79 (156)
.|.|.|+.|..+.+|++| |-.+-+.|.|-+..+|.+..
T Consensus 3 ~LW~aGK~l~~~k~l~dy~GkNEKtKiivKl~~~g~g~P 41 (98)
T PF11069_consen 3 QLWWAGKELQRGKKLSDYIGKNEKTKIIVKLQKRGQGPP 41 (98)
T ss_pred eEEeccccccCCCcHHHhcCCCcceeEEEEeccCCCCCC
Confidence 578999999999999999 33344556666777776653
No 180
>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=75.18 E-value=0.84 Score=26.14 Aligned_cols=24 Identities=38% Similarity=0.844 Sum_probs=16.5
Q ss_pred eeccCCCCccCCceEEeEe--CCCCccCC
Q 031613 117 LRKECPNAECGAGTFMANH--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 667899 898 8999999 58888874
No 181
>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=74.83 E-value=19 Score=23.30 Aligned_cols=35 Identities=26% Similarity=0.318 Sum_probs=29.3
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCC--CceEEe
Q 031613 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 182
>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=74.65 E-value=1.7 Score=31.06 Aligned_cols=31 Identities=16% Similarity=0.255 Sum_probs=21.7
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~ 150 (156)
..+.|| .||+..+=.. .+--.|.+||.+|..
T Consensus 8 tKr~Cp--~cg~kFYDLn-k~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICP--NTGSKFYDLN-RRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCC--CcCccccccC-CCCccCCCcCCccCc
Confidence 368999 8986544332 366789999988743
No 183
>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=74.60 E-value=7.9 Score=26.64 Aligned_cols=57 Identities=14% Similarity=0.173 Sum_probs=38.4
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCc-eEEecCCeeccCCCccccccc---CCCCEEEEEE
Q 031613 15 LEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLADYNI---QKESTLHLVL 71 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~-qrL~~~G~~L~d~~tL~~~gi---~~~stI~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 35889999999999999999998764 455567766667777766421 2344555553
No 184
>PLN00209 ribosomal protein S27; Provisional
Probab=74.35 E-value=3.9 Score=27.19 Aligned_cols=33 Identities=21% Similarity=0.347 Sum_probs=27.1
Q ss_pred EEeeccCCCCccCCceEEeEeC-CCCccCCceeEEE
Q 031613 115 QRLRKECPNAECGAGTFMANHF-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 66779999 898777777884 6788999998874
No 185
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=74.10 E-value=4.2 Score=27.00 Aligned_cols=33 Identities=24% Similarity=0.499 Sum_probs=27.1
Q ss_pred EEeeccCCCCccCCceEEeEe-CCCCccCCceeEEE
Q 031613 115 QRLRKECPNAECGAGTFMANH-FDRHYCGKCGLTYV 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 66779999 89877777788 46889999998874
No 186
>PRK00420 hypothetical protein; Validated
Probab=74.02 E-value=2.5 Score=29.62 Aligned_cols=32 Identities=31% Similarity=0.611 Sum_probs=23.8
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCceeEEEee
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGLTYVYQ 151 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~ 151 (156)
+...|| .||+=.|.. .....+|..||..+...
T Consensus 22 l~~~CP--~Cg~pLf~l-k~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 22 LSKHCP--VCGLPLFEL-KDGEVVCPVHGKVYIVK 53 (112)
T ss_pred ccCCCC--CCCCcceec-CCCceECCCCCCeeeec
Confidence 568999 898644443 66789999999866543
No 187
>COG5272 UBI4 Ubiquitin [Posttranslational modification, protein turnover, chaperones]
Probab=73.71 E-value=0.63 Score=28.31 Aligned_cols=42 Identities=12% Similarity=-0.077 Sum_probs=33.3
Q ss_pred cccccccCCcccccccceeeeeEeeeEEEcCCCeEEEeeccCC
Q 031613 80 RKKKTYTKPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECP 122 (156)
Q Consensus 80 ~~kk~~~~pk~~k~~~kk~k~~~l~~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 88876555455455565
No 188
>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B.
Probab=72.55 E-value=9.3 Score=25.27 Aligned_cols=56 Identities=16% Similarity=0.289 Sum_probs=28.9
Q ss_pred EEec-CCCcHHHHHHHHH-HHhCCCCCc----eEEecCCee----ccCCCcccccccCCCCEEEEE
Q 031613 15 LEVE-SSDTIDNVKAKIQ-DKEGIPPDQ----QRLIFAGKQ----LEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 15 l~V~-~~~TV~~LK~~I~-~~~gip~~~----qrL~~~G~~----L~d~~tL~~~gi~~~stI~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 3679999998864 355544322 233333322 113478999999999988765
No 189
>KOG4572 consensus Predicted DNA-binding transcription factor, interacts with stathmin [Transcription; General function prediction only; Signal transduction mechanisms]
Probab=72.17 E-value=6.3 Score=36.65 Aligned_cols=62 Identities=18% Similarity=0.391 Sum_probs=46.3
Q ss_pred CCCEEEEEecC-CCcHHHHHHHHHHHhCCCCCceEEe-cCCeeccCCCccccccc--CCCCEEEEE
Q 031613 9 TGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNI--QKESTLHLV 70 (156)
Q Consensus 9 ~g~~~~l~V~~-~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi--~~~stI~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 47888888775 6799999999999999999999887 45667777777777652 233345444
No 190
>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=71.92 E-value=16 Score=23.81 Aligned_cols=40 Identities=8% Similarity=0.169 Sum_probs=34.5
Q ss_pred EEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEE
Q 031613 4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL 43 (156)
Q Consensus 4 ~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL 43 (156)
.|-..+|+...+.|.|++|+.++-+.+..+.++.|+.--|
T Consensus 3 ~V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh~L 42 (77)
T cd01818 3 WVCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEHYL 42 (77)
T ss_pred EEECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHhee
Confidence 3556789999999999999999999999999999876433
No 191
>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=71.81 E-value=24 Score=22.76 Aligned_cols=47 Identities=23% Similarity=0.345 Sum_probs=39.3
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCC--eecc
Q 031613 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 4457899999999999999999999999999999887777555 3554
No 192
>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=71.65 E-value=3 Score=27.35 Aligned_cols=35 Identities=17% Similarity=0.396 Sum_probs=15.7
Q ss_pred eeccCCCCccC-CceEEeEe-----CCCCccCCceeEEEeecC
Q 031613 117 LRKECPNAECG-AGTFMANH-----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 32222221 136789999999987654
No 193
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=71.64 E-value=12 Score=25.04 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=29.8
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceE
Q 031613 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 194
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=71.08 E-value=2 Score=26.81 Aligned_cols=24 Identities=29% Similarity=0.964 Sum_probs=20.0
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGL 146 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
+-.|. +||.- +.|.-..+|..|||
T Consensus 17 Ht~Cr--RCG~~---syh~qK~~CasCGy 40 (62)
T PRK04179 17 HIRCR--RCGRH---SYNVRKKYCAACGF 40 (62)
T ss_pred cchhc--ccCcc---cccccccchhhcCC
Confidence 56798 99864 45889999999998
No 195
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=70.16 E-value=2.8 Score=28.75 Aligned_cols=37 Identities=24% Similarity=0.630 Sum_probs=23.7
Q ss_pred eeccCCCCccCCceEE---eEe---CCCCccCCceeEEEeecCCC
Q 031613 117 LRKECPNAECGAGTFM---ANH---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 99753322 111 12457999999987765543
No 196
>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=69.47 E-value=2.4 Score=21.40 Aligned_cols=22 Identities=23% Similarity=0.513 Sum_probs=11.8
Q ss_pred ccCCceEEeEeCCCCccCCcee
Q 031613 125 ECGAGTFMANHFDRHYCGKCGL 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 197
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=69.33 E-value=4.9 Score=31.00 Aligned_cols=30 Identities=20% Similarity=0.450 Sum_probs=22.0
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCC
Q 031613 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 456788999999999999999999999863
No 198
>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=69.07 E-value=4.6 Score=21.75 Aligned_cols=30 Identities=37% Similarity=0.716 Sum_probs=20.2
Q ss_pred cCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031613 120 ECPNAECGAGTFMANHFDRHYCGKCGLTYVYQK 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--ECGAEVEL-KPGDPIRCPECGHRILYKK 31 (32)
T ss_dssp BES--SSSSSE-B-STSSTSSBSSSS-SEEBE-
T ss_pred CCC--cCCCeeEc-CCCCcEECCcCCCeEEEec
Confidence 577 78876663 3467888999998887764
No 199
>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=68.83 E-value=5.8 Score=31.35 Aligned_cols=73 Identities=18% Similarity=0.421 Sum_probs=47.2
Q ss_pred EEEEEeCC--CCEEE----EEecCCCcHHHHHHHHHHHhCCCCCceEEecC----C--eeccCCCcccccccCCCCEEEE
Q 031613 2 QIFVKTLT--GKTIT----LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA----G--KQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 2 ~I~Vk~~~--g~~~~----l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~----G--~~L~d~~tL~~~gi~~~stI~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 36777664 23333 46899999999999999999999976555542 2 3577889999999999999987
Q ss_pred EEeec
Q 031613 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 200
>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=68.48 E-value=15 Score=23.79 Aligned_cols=33 Identities=12% Similarity=0.214 Sum_probs=29.9
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceEE
Q 031613 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 589999999999999999999999999877654
No 201
>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=68.42 E-value=11 Score=26.24 Aligned_cols=57 Identities=14% Similarity=0.155 Sum_probs=38.6
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCce-EEecCCeeccCCCccccc----ccCCCCEEEEEEe
Q 031613 15 LEVESSDTIDNVKAKIQDKEGIPPDQQ-RLIFAGKQLEDGRTLADY----NIQKESTLHLVLR 72 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~q-rL~~~G~~L~d~~tL~~~----gi~~~stI~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 459999999999999999999888753 444555444555666544 32 2456666543
No 202
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=68.33 E-value=5.2 Score=24.74 Aligned_cols=33 Identities=30% Similarity=0.662 Sum_probs=27.4
Q ss_pred EEeeccCCCCccCCceEEeEeC-CCCccCCceeEEE
Q 031613 115 QRLRKECPNAECGAGTFMANHF-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 56788999 898888888894 6789999998873
No 203
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=68.17 E-value=17 Score=23.46 Aligned_cols=40 Identities=18% Similarity=0.372 Sum_probs=31.0
Q ss_pred CCcHHHHHHHHHHHhCCCCCceEEe--cCCeeccCCCccccc
Q 031613 20 SDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLEDGRTLADY 59 (156)
Q Consensus 20 ~~TV~~LK~~I~~~~gip~~~qrL~--~~G~~L~d~~tL~~~ 59 (156)
..|+.+|+.+..+..+++....+|. -+|..++|+.-+..+
T Consensus 18 A~sL~eL~~K~~~~l~l~~~~~~l~L~eDGT~VddEeyF~tL 59 (74)
T smart00266 18 ASSLEELLSKVCDKLALPDSPVTLVLEEDGTIVDDEEYFQTL 59 (74)
T ss_pred cCCHHHHHHHHHHHhCCCCCCcEEEEecCCcEEccHHHHhcC
Confidence 3589999999999999996555554 589999887655544
No 204
>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=67.83 E-value=18 Score=23.29 Aligned_cols=33 Identities=21% Similarity=0.217 Sum_probs=22.0
Q ss_pred EEEeCCCC-EEEEEecC-CCcHHHHHHHHHHHhCC
Q 031613 4 FVKTLTGK-TITLEVES-SDTIDNVKAKIQDKEGI 36 (156)
Q Consensus 4 ~Vk~~~g~-~~~l~V~~-~~TV~~LK~~I~~~~gi 36 (156)
+-|..+.+ ...+.++. ..+|.+||..|.+..++
T Consensus 2 ~YKFkS~k~~~~i~fdG~~Isv~dLKr~I~~~~~l 36 (74)
T PF08783_consen 2 HYKFKSQKDYDTITFDGTSISVFDLKREIIEKKKL 36 (74)
T ss_dssp EEEETT-SSEEEEEESSSEEEHHHHHHHHHHHHT-
T ss_pred eEEecccCCccEEEECCCeeEHHHHHHHHHHHhCC
Confidence 33444443 45677774 57999999999887765
No 205
>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=67.36 E-value=5.5 Score=24.13 Aligned_cols=22 Identities=32% Similarity=0.978 Sum_probs=16.1
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGL 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 4556678999983
No 206
>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=67.11 E-value=36 Score=22.94 Aligned_cols=71 Identities=23% Similarity=0.377 Sum_probs=43.2
Q ss_pred EEEEEeC-CCCEEEEEecCCCcHHHHHHHHHHH--hCCCCC----ceEEecCCe--eccCCCcccccc-----cCCCCEE
Q 031613 2 QIFVKTL-TGKTITLEVESSDTIDNVKAKIQDK--EGIPPD----QQRLIFAGK--QLEDGRTLADYN-----IQKESTL 67 (156)
Q Consensus 2 ~I~Vk~~-~g~~~~l~V~~~~TV~~LK~~I~~~--~gip~~----~qrL~~~G~--~L~d~~tL~~~g-----i~~~stI 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 3556555 3458899999999999999988666 222221 445555564 466777888884 3556677
Q ss_pred EEEEe
Q 031613 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 77653
No 207
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=66.46 E-value=3.3 Score=28.35 Aligned_cols=32 Identities=31% Similarity=0.755 Sum_probs=19.5
Q ss_pred eccCCCCccCCceEEe----EeCCCCccCCceeEEEeec
Q 031613 118 RKECPNAECGAGTFMA----NHFDRHYCGKCGLTYVYQK 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 2222 0113567999998765543
No 208
>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=66.09 E-value=20 Score=23.46 Aligned_cols=47 Identities=11% Similarity=0.130 Sum_probs=33.8
Q ss_pred CcHHHHHHHHHHHhCCCCCceEE--ecCCeeccCCCcccccccCCCCEEEE
Q 031613 21 DTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~qrL--~~~G~~L~d~~tL~~~gi~~~stI~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 57999999999999998654444 5789999887655544 24555543
No 209
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=65.39 E-value=20 Score=23.72 Aligned_cols=35 Identities=11% Similarity=0.231 Sum_probs=30.7
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe
Q 031613 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 44 (156)
Q Consensus 10 g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~ 44 (156)
...+.+.|++..+=.++|+.|+..+++.+...+.+
T Consensus 21 ~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~ 55 (84)
T PRK14548 21 ENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTL 55 (84)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeE
Confidence 35899999999999999999999999998776543
No 210
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=65.17 E-value=2.2 Score=36.88 Aligned_cols=59 Identities=24% Similarity=0.264 Sum_probs=50.8
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 34555667889999999999999999999999999999999999999988877766654
No 211
>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=64.98 E-value=4.7 Score=21.36 Aligned_cols=29 Identities=31% Similarity=0.429 Sum_probs=15.5
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLTY 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 56789 898765555444455688888764
No 212
>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=64.82 E-value=3.7 Score=25.52 Aligned_cols=30 Identities=23% Similarity=0.560 Sum_probs=20.7
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLTYV 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 213
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=64.51 E-value=8.4 Score=22.23 Aligned_cols=32 Identities=31% Similarity=0.628 Sum_probs=23.8
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~ 152 (156)
.+.|. +||.-+-+- -.+-..|..||+-..|++
T Consensus 2 ~Y~C~--~Cg~~~~~~-~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 2 IYICG--ECGRENEIK-SKDVVRCRECGYRILYKK 33 (44)
T ss_pred EEECC--CCCCEeecC-CCCceECCCCCceEEEEe
Confidence 35788 898655543 568888999999887775
No 214
>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=64.03 E-value=2.4 Score=23.47 Aligned_cols=12 Identities=50% Similarity=1.076 Sum_probs=8.8
Q ss_pred CCccCCceeEEE
Q 031613 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 567888887774
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=63.86 E-value=6.4 Score=22.44 Aligned_cols=26 Identities=38% Similarity=1.063 Sum_probs=19.6
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCce
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCG 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 45555577788998885
No 216
>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=63.55 E-value=5.3 Score=31.86 Aligned_cols=62 Identities=19% Similarity=0.359 Sum_probs=37.5
Q ss_pred cccccccceeeeeEeeeEEEcCCCeEEEeeccCCCCccCCceEEeEe--------------CCCCccCCceeEEEeecCC
Q 031613 89 KKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMANH--------------FDRHYCGKCGLTYVYQKAG 154 (156)
Q Consensus 89 k~~k~~~kk~k~~~l~~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 RNAPPGKKYVRCPCNCLLICKS----SSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLT 173 (256)
T ss_pred cCCCCCCeeEecCCceEEEeec----ccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCC
Confidence 3344456666665544433221 335889998889732222211 1388999999999998543
No 217
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=63.29 E-value=19 Score=24.33 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=29.7
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEE
Q 031613 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 218
>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=63.17 E-value=23 Score=23.16 Aligned_cols=39 Identities=15% Similarity=0.342 Sum_probs=30.1
Q ss_pred CcHHHHHHHHHHHhCCCCCceEEe--cCCeeccCCCccccc
Q 031613 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 589999999999999975555554 688999887655544
No 219
>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=62.83 E-value=5 Score=28.79 Aligned_cols=29 Identities=28% Similarity=0.590 Sum_probs=18.9
Q ss_pred eccCCCCccCCceEEeEe-CCCCccCCceeEE
Q 031613 118 RKECPNAECGAGTFMANH-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 3589999999764
No 220
>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=62.46 E-value=5.4 Score=22.99 Aligned_cols=26 Identities=27% Similarity=0.651 Sum_probs=16.8
Q ss_pred ccCCCCccCCc-eEEeEeCCCCccCCcee
Q 031613 119 KECPNAECGAG-TFMANHFDRHYCGKCGL 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 22222247889999975
No 221
>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=61.48 E-value=13 Score=24.27 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=18.0
Q ss_pred EEEEecCCCcHHHHHHHHHHHh
Q 031613 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 5788999999999999997654
No 222
>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=60.08 E-value=22 Score=22.62 Aligned_cols=43 Identities=19% Similarity=0.306 Sum_probs=30.0
Q ss_pred CcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEE
Q 031613 21 DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~l 69 (156)
.|+++|....++++|+++ ...+.-+|..++|=..+ .+|+.|++
T Consensus 26 ~SleeLl~ia~~kfg~~~-~~v~~~dgaeIdDI~~I-----RDgD~L~~ 68 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFSA-TKVLNEDGAEIDDIDVI-----RDGDHLYL 68 (69)
T ss_pred ccHHHHHHHHHHHhCCCc-eEEEcCCCCEEeEEEEE-----EcCCEEEE
Confidence 799999999999999973 33344556555554333 46777765
No 223
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=59.60 E-value=2 Score=28.47 Aligned_cols=26 Identities=27% Similarity=0.878 Sum_probs=20.7
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLTY 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 8986654 98999999999964
No 224
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=59.07 E-value=4.6 Score=27.07 Aligned_cols=25 Identities=28% Similarity=0.818 Sum_probs=20.3
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGL 146 (156)
Q Consensus 117 ~~~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
.+-.|. +||.-. .|.-..+|+.|||
T Consensus 15 tHtlCr--RCG~~s---yH~qK~~CasCGy 39 (91)
T PTZ00073 15 THTLCR--RCGKRS---FHVQKKRCASCGY 39 (91)
T ss_pred Ccchhc--ccCccc---cccccccchhcCC
Confidence 356798 999655 4888999999998
No 225
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=58.93 E-value=36 Score=23.82 Aligned_cols=38 Identities=5% Similarity=0.198 Sum_probs=32.0
Q ss_pred EEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeec
Q 031613 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 34689999999999999999999999988777755544
No 226
>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=58.89 E-value=28 Score=22.83 Aligned_cols=39 Identities=15% Similarity=0.228 Sum_probs=29.4
Q ss_pred CcHHHHHHHHHHHhCCCCCc--eE--EecCCeeccCCCccccc
Q 031613 21 DTIDNVKAKIQDKEGIPPDQ--QR--LIFAGKQLEDGRTLADY 59 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~~~--qr--L~~~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 57999999999999998432 44 44689999887655544
No 227
>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=58.89 E-value=8.6 Score=25.12 Aligned_cols=40 Identities=25% Similarity=0.363 Sum_probs=23.5
Q ss_pred HHHHHhCCCCCceEEe---cCCeeccCCCcccccccCCCCEEEEEE
Q 031613 29 KIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 29 ~I~~~~gip~~~qrL~---~~G~~L~d~~tL~~~gi~~~stI~l~~ 71 (156)
.|.++..+.|+...|+ .++.+|+-+.+|.++||. .|++.-
T Consensus 2 ~IC~KCEfdp~htvLLrD~~s~e~LdLsKSLndlGir---ELYA~D 44 (79)
T PF09469_consen 2 AICEKCEFDPEHTVLLRDYQSGEELDLSKSLNDLGIR---ELYAWD 44 (79)
T ss_dssp HHHHHTT--TTSEEEES-SS---B--TTS-HHHHT-S---EEEEEE
T ss_pred ccccccccCcceEEEeecCCCCCcccccccHHHhhHH---HHHhhc
Confidence 4677788888888887 456689999999999998 455543
No 228
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=58.68 E-value=48 Score=21.93 Aligned_cols=73 Identities=15% Similarity=0.217 Sum_probs=36.0
Q ss_pred CEEEEEeC--CCC-EEEEEecCCCcHHHHHHHH--HHH-hCCCCCceEEecCCeeccCCCcccccccCCCCEEEEEEeec
Q 031613 1 MQIFVKTL--TGK-TITLEVESSDTIDNVKAKI--QDK-EGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 1 M~I~Vk~~--~g~-~~~l~V~~~~TV~~LK~~I--~~~-~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 5678999999999876543 222 2456666777656665554443 45799999886665
Q ss_pred CCcc
Q 031613 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 5443
No 229
>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=58.66 E-value=46 Score=21.38 Aligned_cols=61 Identities=16% Similarity=0.317 Sum_probs=36.0
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhC-CCCCceEEe------cCCeeccCCCcccccccCCCCEEEEEEe
Q 031613 11 KTITLEVESSDTIDNVKAKIQDKEG-IPPDQQRLI------FAGKQLEDGRTLADYNIQKESTLHLVLR 72 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~g-ip~~~qrL~------~~G~~L~d~~tL~~~gi~~~stI~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 3455567899999999999999874 344333221 1222344444444332 35777776664
No 230
>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=58.22 E-value=29 Score=23.02 Aligned_cols=42 Identities=24% Similarity=0.220 Sum_probs=32.7
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCC-CCceEEe--cCCe--eccCC
Q 031613 12 TITLEVESSDTIDNVKAKIQDKEGIP-PDQQRLI--FAGK--QLEDG 53 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip-~~~qrL~--~~G~--~L~d~ 53 (156)
.-++.|.|.+|+.+|-+.+++++.|. |+...|+ -+|. +|.|+
T Consensus 15 ~KTL~V~P~~tt~~vc~lcA~Kf~V~qPe~y~LFl~vdg~~~qLadd 61 (87)
T cd01776 15 GKTLLVRPYITTEDVCQLCAEKFKVTQPEEYSLFLFVEETWQQLAPD 61 (87)
T ss_pred eeeeecCCCCcHHHHHHHHHHHhccCChhheeEEEEECCcEEEcCcc
Confidence 56799999999999999999999875 4666665 3453 56665
No 231
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=58.07 E-value=5.3 Score=31.22 Aligned_cols=37 Identities=24% Similarity=0.521 Sum_probs=26.1
Q ss_pred EeeccCCCCccCCceEEeE-e-----------CCCCccCCceeEEEeec
Q 031613 116 RLRKECPNAECGAGTFMAN-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 3678999999974222221 1 12899999999998863
No 232
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=57.69 E-value=2.4 Score=35.04 Aligned_cols=34 Identities=26% Similarity=0.664 Sum_probs=26.1
Q ss_pred ccCCCCccCCceEEeEeCCCCccCC-ceeEEEeec
Q 031613 119 KECPNAECGAGTFMANHFDRHYCGK-CGLTYVYQK 152 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~-c~~t~~~~~ 152 (156)
.-||++-||+|.+----.-+.+|.. ||+.|+.+=
T Consensus 316 VlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~C 350 (446)
T KOG0006|consen 316 VLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCREC 350 (446)
T ss_pred EecCCCCCCcccccCCCCCcccCCCCchhHhHHHH
Confidence 5699999999887655455788876 998887653
No 233
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=57.49 E-value=11 Score=26.90 Aligned_cols=32 Identities=25% Similarity=0.730 Sum_probs=22.7
Q ss_pred eccCCCCccCCceEEeEe------CCCCccCCceeEEEeec
Q 031613 118 RKECPNAECGAGTFMANH------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 234
>CHL00030 rpl23 ribosomal protein L23
Probab=57.45 E-value=28 Score=23.47 Aligned_cols=32 Identities=22% Similarity=0.158 Sum_probs=28.2
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031613 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 235
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=56.58 E-value=8.3 Score=30.88 Aligned_cols=28 Identities=18% Similarity=0.520 Sum_probs=20.7
Q ss_pred eccCCCCccCCceEEeEeCC--CCccCCceeE
Q 031613 118 RKECPNAECGAGTFMANHFD--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 8987776666654 5899999853
No 236
>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=56.45 E-value=5.6 Score=21.30 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=10.1
Q ss_pred CCccCCceeEEEe
Q 031613 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 237
>COG1977 MoaD Molybdopterin converting factor, small subunit [Coenzyme metabolism]
Probab=56.43 E-value=24 Score=23.01 Aligned_cols=55 Identities=9% Similarity=0.172 Sum_probs=32.7
Q ss_pred cCCCcHHHHHHHHHHHhC---CCCCceE-E-ecCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 18 ESSDTIDNVKAKIQDKEG---IPPDQQR-L-IFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 18 ~~~~TV~~LK~~I~~~~g---ip~~~qr-L-~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
..-+||++|.+.+.++.. .....+. + ..+...+.+. +..|++|++|.+..+..||
T Consensus 25 ~~~~tv~~L~~~l~~~~~~~~~~~~~~~~v~~~~~~~~~~~----~t~L~dGDeVa~~PPVsGG 84 (84)
T COG1977 25 TVGATVGELEELLPKEGERWLLALEDNIVVNAANNEFLVGL----DTPLKDGDEVAFFPPVSGG 84 (84)
T ss_pred cHHHHHHHHHHHHHhhhhhHHhccCccceEEeeeceeeccc----cccCCCCCEEEEeCCCCCC
Confidence 346799999999866654 1111112 1 1233334332 3346789999988877776
No 238
>KOG4598 consensus Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=56.36 E-value=15 Score=33.74 Aligned_cols=58 Identities=17% Similarity=0.271 Sum_probs=43.1
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe--c--CCeec--cCCCcccccccCCCCEEEEEE
Q 031613 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--F--AGKQL--EDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~--~--~G~~L--~d~~tL~~~gi~~~stI~l~~ 71 (156)
.+.+.|+..++++.+|+.|++..+++.+..+|+ + +|..+ .+..+|+.+ .++.+|.+-+
T Consensus 878 ~~kl~Vd~rmr~~AFKkHiE~~i~V~~~HFKi~R~~~~N~~~~S~~~NetLs~~--~~~~~iTI~L 941 (1203)
T KOG4598|consen 878 FHKLDVDSRMRVLAFKKHVEEQLEVDKDHFKIVRHASDNGSEASFMDNETLSGA--FQSCFITIKL 941 (1203)
T ss_pred heeeeccceeeHHHHHHHHHHHhCcChhHeEEEEEecCCcchhhhccchhhhhh--cccceEEEEe
Confidence 456789999999999999999999999988886 2 33333 356677654 3566765543
No 239
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.04 E-value=5.7 Score=31.67 Aligned_cols=24 Identities=33% Similarity=0.708 Sum_probs=18.3
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEE
Q 031613 119 KECPNAECGAGTFMANHFDRHYCGKCGLTYV 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 240
>smart00143 PI3K_p85B PI3-kinase family, p85-binding domain. Region of p110 PI3K that binds the p85 subunit.
Probab=55.49 E-value=16 Score=23.82 Aligned_cols=22 Identities=23% Similarity=0.388 Sum_probs=18.8
Q ss_pred EEEEecCCCcHHHHHHHHHHHh
Q 031613 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 4688999999999999997654
No 241
>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=54.98 E-value=4 Score=23.64 Aligned_cols=26 Identities=31% Similarity=0.989 Sum_probs=11.5
Q ss_pred ccCCCCccCCceEE--eEeCCCCccC--Cce
Q 031613 119 KECPNAECGAGTFM--ANHFDRHYCG--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 5556777787 665
No 242
>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=54.94 E-value=26 Score=23.17 Aligned_cols=58 Identities=5% Similarity=0.107 Sum_probs=37.4
Q ss_pred EEEecCCCcHHHHHHHHHHHhCCCCCc-eEEecCCeec-cCCCccccccc--CCCCEEEEEE
Q 031613 14 TLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFAGKQL-EDGRTLADYNI--QKESTLHLVL 71 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~gip~~~-qrL~~~G~~L-~d~~tL~~~gi--~~~stI~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 3444454323 33444443210 3456666654
No 243
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=54.91 E-value=6.7 Score=24.30 Aligned_cols=11 Identities=36% Similarity=0.649 Sum_probs=6.8
Q ss_pred eCCCCccCCce
Q 031613 135 HFDRHYCGKCG 145 (156)
Q Consensus 135 h~~r~~cg~c~ 145 (156)
|.+.+.|.+||
T Consensus 47 ~g~~Y~Cp~CG 57 (61)
T COG2888 47 LGNPYRCPKCG 57 (61)
T ss_pred cCCceECCCcC
Confidence 34566666666
No 244
>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=54.74 E-value=40 Score=26.55 Aligned_cols=35 Identities=20% Similarity=0.358 Sum_probs=27.8
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe
Q 031613 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 34899999999999999999999999999999886
No 245
>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=54.52 E-value=14 Score=22.51 Aligned_cols=34 Identities=21% Similarity=0.345 Sum_probs=23.3
Q ss_pred EEeeccCCCCccCCceEEeEe-CCCCccCCceeEEEe
Q 031613 115 QRLRKECPNAECGAGTFMANH-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 46778999 89887777888 468889999988743
No 246
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=53.99 E-value=51 Score=22.67 Aligned_cols=36 Identities=25% Similarity=0.319 Sum_probs=28.0
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC
Q 031613 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 566677899999999999999999999999999887
No 247
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=53.78 E-value=5.1 Score=32.44 Aligned_cols=31 Identities=29% Similarity=0.533 Sum_probs=27.7
Q ss_pred EeeccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 116 RLRKECPNAECGAGTFMANHFDRHYCGKCGLTY 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 4589999 999999999999999999999865
No 248
>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=53.64 E-value=41 Score=22.13 Aligned_cols=47 Identities=11% Similarity=0.087 Sum_probs=32.4
Q ss_pred CcHHHHHHHHHHHhCCCC-CceEEecCCeeccCCCcccccccCCCCEEEE
Q 031613 21 DTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 21 ~TV~~LK~~I~~~~gip~-~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 334445688899887655544 24555544
No 249
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=52.82 E-value=5.4 Score=19.70 Aligned_cols=21 Identities=43% Similarity=1.203 Sum_probs=13.2
Q ss_pred cCCCCccCCceEEeEeCCCCccCCcee
Q 031613 120 ECPNAECGAGTFMANHFDRHYCGKCGL 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 377 787633 22 5566888875
No 250
>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=52.75 E-value=77 Score=22.11 Aligned_cols=37 Identities=22% Similarity=0.237 Sum_probs=29.6
Q ss_pred CEEEEEeCCCC--EEEEEecCCCcHHHHHHHHHHHhCCC
Q 031613 1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEGIP 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 56777766665 34589999999999999999998754
No 251
>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=52.68 E-value=10 Score=20.37 Aligned_cols=14 Identities=36% Similarity=0.909 Sum_probs=10.4
Q ss_pred cCCCCccCCceEEeEe
Q 031613 120 ECPNAECGAGTFMANH 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 252
>PHA02942 putative transposase; Provisional
Probab=52.36 E-value=7.6 Score=32.77 Aligned_cols=27 Identities=33% Similarity=0.775 Sum_probs=18.2
Q ss_pred eccCCCCccCCceEEeEeCCC-CccCCceeEE
Q 031613 118 RKECPNAECGAGTFMANHFDR-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 253
>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=52.25 E-value=43 Score=21.92 Aligned_cols=40 Identities=13% Similarity=0.147 Sum_probs=29.7
Q ss_pred CCcHHHHHHHHHHHhCCCC-CceEEecCCeeccCCCccccc
Q 031613 20 SDTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADY 59 (156)
Q Consensus 20 ~~TV~~LK~~I~~~~gip~-~~qrL~~~G~~L~d~~tL~~~ 59 (156)
..|+.+|+.+..+..+++. ....|.-+|..++|+.-+..+
T Consensus 20 A~sL~eL~~K~~~~l~l~~~~~lvL~eDGT~Vd~EeyF~tL 60 (79)
T cd06538 20 ADSLEDLLNKVLDALLLDCISSLVLDEDGTGVDTEEFFQAL 60 (79)
T ss_pred cCCHHHHHHHHHHHcCCCCccEEEEecCCcEEccHHHHhhC
Confidence 3589999999999999963 234555789999887655544
No 254
>PRK11827 hypothetical protein; Provisional
Probab=51.83 E-value=9.3 Score=23.70 Aligned_cols=30 Identities=17% Similarity=0.464 Sum_probs=20.3
Q ss_pred cCCCCccCCceEEeEeCCCCccCCceeEEEee
Q 031613 120 ECPNAECGAGTFMANHFDRHYCGKCGLTYVYQ 151 (156)
Q Consensus 120 ~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~ 151 (156)
.|| .|+.-...-...+...|..|++.|-..
T Consensus 10 aCP--~ckg~L~~~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 10 ACP--VCNGKLWYNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred ECC--CCCCcCeEcCCCCeEECCccCeecccc
Confidence 499 897433333335678999999988543
No 255
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=51.82 E-value=7.9 Score=23.68 Aligned_cols=22 Identities=36% Similarity=0.892 Sum_probs=13.8
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGL 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 3356778873
No 256
>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=50.77 E-value=7.9 Score=33.82 Aligned_cols=25 Identities=28% Similarity=0.707 Sum_probs=18.2
Q ss_pred cCCCCccCCceEEeEeC--CCCccCCceeEE
Q 031613 120 ECPNAECGAGTFMANHF--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 4788884 667777777765
No 257
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=50.69 E-value=15 Score=24.02 Aligned_cols=54 Identities=26% Similarity=0.345 Sum_probs=32.9
Q ss_pred CCcccccccceeeeeEeeeEEEcCCCeEEEeeccCCCCccCCceEEeEe-CCCCccCCceeEEEe
Q 031613 87 KPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFMANH-FDRHYCGKCGLTYVY 150 (156)
Q Consensus 87 ~pk~~k~~~kk~k~~~l~~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h-~~r~~cg~c~~t~~~ 150 (156)
+|.+++.++|+..|.- .+.--++...|| .|-.=.....| .....|+.|+..++.
T Consensus 11 s~e~e~r~hK~krLvq--------~~nsyFm~VkC~--gc~~iT~vfSHaqtvVvc~~c~~il~~ 65 (84)
T KOG1779|consen 11 SPEKEKRKHKLKRLVQ--------SPNSYFMDVKCP--GCFKITTVFSHAQTVVVCEGCSTILCQ 65 (84)
T ss_pred CHHHHhhhhhhhhhee--------CCCceEEEEEcC--CceEEEEEeecCceEEEcCCCceEEEE
Confidence 4555666665444321 112244557899 78545566678 578899999876643
No 258
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=50.59 E-value=37 Score=25.18 Aligned_cols=39 Identities=10% Similarity=0.062 Sum_probs=32.6
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe-cCCe
Q 031613 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 46899999999999999999999999998776544 4443
No 259
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=50.04 E-value=10 Score=21.20 Aligned_cols=25 Identities=28% Similarity=0.830 Sum_probs=13.7
Q ss_pred cCCCCccCCceEEeEe----CCCCccCCceeEE
Q 031613 120 ECPNAECGAGTFMANH----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 2345677777554
No 260
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.32 E-value=13 Score=24.35 Aligned_cols=26 Identities=31% Similarity=0.744 Sum_probs=18.8
Q ss_pred cCCCCccCCceEEeEeC--CCCccCCceeE
Q 031613 120 ECPNAECGAGTFMANHF--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 46789998643
No 261
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=49.30 E-value=7.5 Score=28.07 Aligned_cols=35 Identities=37% Similarity=0.855 Sum_probs=23.4
Q ss_pred eEEEcCCCeEEEeeccCCCCccCCceEEeEeCCCCccCCceeE
Q 031613 105 FYKVDDSGKVQRLRKECPNAECGAGTFMANHFDRHYCGKCGLT 147 (156)
Q Consensus 105 ~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
+|+.-..|++. ...|+ .||. +| |..|.+|.+|+..
T Consensus 18 f~~~l~~~kl~--g~kC~--~CG~-v~---~PPr~~Cp~C~~~ 52 (140)
T COG1545 18 FFKGLKEGKLL--GTKCK--KCGR-VY---FPPRAYCPKCGSE 52 (140)
T ss_pred HhhhhhhCcEE--EEEcC--CCCe-EE---cCCcccCCCCCCC
Confidence 44332246666 48899 8984 43 5678888888765
No 262
>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=49.19 E-value=77 Score=21.06 Aligned_cols=60 Identities=23% Similarity=0.377 Sum_probs=42.4
Q ss_pred EEEEEecCCCcHHHHHHHHHHHh-C--CCC---CceEEecCC--eeccCCCcccccccCCCCEEEEEE
Q 031613 12 TITLEVESSDTIDNVKAKIQDKE-G--IPP---DQQRLIFAG--KQLEDGRTLADYNIQKESTLHLVL 71 (156)
Q Consensus 12 ~~~l~V~~~~TV~~LK~~I~~~~-g--ip~---~~qrL~~~G--~~L~d~~tL~~~gi~~~stI~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 45678999999999999987553 3 333 245777888 899999999999999999888764
No 263
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=48.36 E-value=9.5 Score=30.32 Aligned_cols=30 Identities=20% Similarity=0.373 Sum_probs=22.4
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGLTY 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 368999 998755554445678899999876
No 264
>KOG3483 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.19 E-value=79 Score=20.64 Aligned_cols=62 Identities=21% Similarity=0.275 Sum_probs=44.4
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCCceEEe-cCCeeccCCCcccccccCCCCEEEEEEeecCC
Q 031613 15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 15 l~V~~~~TV~~LK~~I~~~~gip~~~qrL~-~~G~~L~d~~tL~~~gi~~~stI~l~~~~~gg 76 (156)
++|+.++....+-...++++.+|+..--++ -+|--+...++-...=++.||.+.++.|.+-|
T Consensus 31 ~svpestpftavlkfaaeefkvpaatsaiitndgiginpaq~agnvflkhgselr~iprdrvg 93 (94)
T KOG3483|consen 31 LSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVG 93 (94)
T ss_pred ecCCCCCchHHHHHHHHHHccCCccceeEEecCccccCccccccceeeccCCEEEeccccccC
Confidence 467777776666666778888998765555 55555666677777778889999888775543
No 265
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=46.84 E-value=21 Score=29.78 Aligned_cols=65 Identities=17% Similarity=0.197 Sum_probs=49.8
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHH-hCCCCCceEEecCC---eecc--CCCcccccccCCCCE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDK-EGIPPDQQRLIFAG---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 37899999988777778899998888777654 46666778888655 4554 568999999987765
No 266
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=46.60 E-value=14 Score=35.98 Aligned_cols=18 Identities=28% Similarity=0.473 Sum_probs=11.8
Q ss_pred ccccceeeeeEeeeEEEc
Q 031613 92 KHKKKKVKLAVLQFYKVD 109 (156)
Q Consensus 92 k~~~kk~k~~~l~~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 344556778888877654
No 267
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.30 E-value=18 Score=25.13 Aligned_cols=26 Identities=19% Similarity=0.419 Sum_probs=16.9
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGL 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 3333334556999983
No 268
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=45.96 E-value=17 Score=25.28 Aligned_cols=27 Identities=19% Similarity=0.438 Sum_probs=17.4
Q ss_pred EeeccCCCCccCCceEEeEeCCC-CccCCcee
Q 031613 116 RLRKECPNAECGAGTFMANHFDR-HYCGKCGL 146 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~~r-~~cg~c~~ 146 (156)
+.+-.|+ .||. +.+..... ..|++||-
T Consensus 68 p~~~~C~--~Cg~--~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 68 EAECWCE--TCQQ--YVTLLTQRVRRCPQCHG 95 (114)
T ss_pred CcEEEcc--cCCC--eeecCCccCCcCcCcCC
Confidence 3578899 8975 33332223 56999993
No 269
>KOG0466 consensus Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=45.80 E-value=15 Score=30.60 Aligned_cols=46 Identities=28% Similarity=0.589 Sum_probs=31.4
Q ss_pred cccceeeeeE--eeeEEEcCCCeEEEeeccCCCCccCCceEEeEeCCCCccCCceeE
Q 031613 93 HKKKKVKLAV--LQFYKVDDSGKVQRLRKECPNAECGAGTFMANHFDRHYCGKCGLT 147 (156)
Q Consensus 93 ~~~kk~k~~~--l~~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t 147 (156)
.+.-.+||.. .+.|+-| ..+||.|-| +..|-..-.||..|-+||-+
T Consensus 71 ERNITIKLGYANAKIYkc~--------~~kCprP~c-y~s~gS~k~d~~~c~~~g~~ 118 (466)
T KOG0466|consen 71 ERNITIKLGYANAKIYKCD--------DPKCPRPGC-YRSFGSSKEDRPPCDRPGCE 118 (466)
T ss_pred hcceeEEeccccceEEecC--------CCCCCCcch-hhccCCCCCCCCCcccCCCC
Confidence 3344566644 3346666 368998888 45566666899999999865
No 270
>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=45.36 E-value=34 Score=22.62 Aligned_cols=31 Identities=29% Similarity=0.423 Sum_probs=21.1
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHH
Q 031613 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 3455668999999999998877777777644
No 271
>PF15616 TerY-C: TerY-C metal binding domain
Probab=43.82 E-value=21 Score=25.67 Aligned_cols=13 Identities=38% Similarity=0.889 Sum_probs=9.2
Q ss_pred ccCCCCccCCceEEe
Q 031613 119 KECPNAECGAGTFMA 133 (156)
Q Consensus 119 ~~cp~~~c~~g~fma 133 (156)
..|| .||+-..+|
T Consensus 78 PgCP--~CGn~~~fa 90 (131)
T PF15616_consen 78 PGCP--HCGNQYAFA 90 (131)
T ss_pred CCCC--CCcChhcEE
Confidence 7899 898764444
No 272
>PRK04023 DNA polymerase II large subunit; Validated
Probab=43.78 E-value=12 Score=35.58 Aligned_cols=37 Identities=32% Similarity=0.691 Sum_probs=24.4
Q ss_pred cccccceeeeeEeeeEEEcCC-C---------------eEEEeeccCCCCccCCc
Q 031613 91 IKHKKKKVKLAVLQFYKVDDS-G---------------KVQRLRKECPNAECGAG 129 (156)
Q Consensus 91 ~k~~~kk~k~~~l~~y~vd~~-g---------------~~~~~~~~cp~~~c~~g 129 (156)
+|.+.++.|.+++.+|-|.+- | .|.--.+.|| .||..
T Consensus 583 EKa~~RkMkP~~h~LFPiG~~GG~~R~i~~A~~~~g~~eVEVg~RfCp--sCG~~ 635 (1121)
T PRK04023 583 EKAKERKMKPPVHVLFPIGNAGGSTRDINKAAKYKGTIEVEIGRRKCP--SCGKE 635 (1121)
T ss_pred cccccccCCCCCcccccccccCcccccHHHHHhcCCceeecccCccCC--CCCCc
Confidence 334555688888888877542 2 2455578999 89864
No 273
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=43.47 E-value=9.5 Score=21.56 Aligned_cols=15 Identities=27% Similarity=0.658 Sum_probs=10.0
Q ss_pred CCCccCCceeEEEee
Q 031613 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 274
>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=43.06 E-value=18 Score=34.25 Aligned_cols=47 Identities=23% Similarity=0.469 Sum_probs=32.8
Q ss_pred ccccceeeeeEeeeEEEcCC-------------C---eEEEeeccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 92 KHKKKKVKLAVLQFYKVDDS-------------G---KVQRLRKECPNAECGAGTFMANHFDRHYCGKCGL 146 (156)
Q Consensus 92 k~~~kk~k~~~l~~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~y------Tlk~rCP~CG~ 645 (1095)
T TIGR00354 583 KAKERKMSPPPHILFPIGMAGGNTRDIKNAINYTKEIEVEIAIRKCP--QCGKE------SFWLKCPVCGE 645 (1095)
T ss_pred ccccccCCCCCcccccccccCcchhhHHHHhccCCeeEEEEEEEECC--CCCcc------cccccCCCCCC
Confidence 34455688888888866532 3 4666789999 89853 34567999984
No 275
>PF04126 Cyclophil_like: Cyclophilin-like; InterPro: IPR007256 Proteins of this family have no known function.; PDB: 2KA0_A 1ZX8_C 2NNZ_A.
Probab=42.43 E-value=19 Score=25.19 Aligned_cols=29 Identities=28% Similarity=0.398 Sum_probs=24.0
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHH
Q 031613 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 7888865 5889999999999998888765
No 276
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.09 E-value=20 Score=28.69 Aligned_cols=27 Identities=22% Similarity=0.498 Sum_probs=20.1
Q ss_pred eccCCCCccCCceEEeEeC--CCCccCCcee
Q 031613 118 RKECPNAECGAGTFMANHF--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 277
>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=41.99 E-value=14 Score=20.37 Aligned_cols=25 Identities=32% Similarity=0.918 Sum_probs=17.8
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 119 KECPNAECGAGTFMANHFDRHYCGKCGL 146 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~~ 146 (156)
-.|+ .|++- +...--.++||-.||.
T Consensus 9 ~~C~--~C~~~-~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCP--VCGSR-WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCC--CCCCe-EeEccCCEEEhhhCce
Confidence 3488 69865 5554456899999985
No 278
>PLN03086 PRLI-interacting factor K; Provisional
Probab=41.72 E-value=15 Score=32.66 Aligned_cols=33 Identities=27% Similarity=0.639 Sum_probs=22.2
Q ss_pred EeeccCCCCccCCceEEeEeCC-CCccCCceeEEE
Q 031613 116 RLRKECPNAECGAGTFMANHFD-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 455678866687 466665554 456999988763
No 279
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=41.07 E-value=42 Score=23.31 Aligned_cols=31 Identities=26% Similarity=0.679 Sum_probs=20.7
Q ss_pred eccCCCCccCCceEEeEe-CCC---------CccCCceeEEEe
Q 031613 118 RKECPNAECGAGTFMANH-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 280
>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=40.93 E-value=8.5 Score=30.83 Aligned_cols=36 Identities=31% Similarity=0.673 Sum_probs=25.5
Q ss_pred EeeeEEEcCCCeEEEeeccCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031613 102 VLQFYKVDDSGKVQRLRKECPNAECGAGTFMANHFDRHYCGKCGLTYVY 150 (156)
Q Consensus 102 ~l~~y~vd~~g~~~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~ 150 (156)
+..+|+||. -+.|. .||++|...+ ..|..|+-|-+.
T Consensus 73 iKsC~rvDQ-------l~~C~--~CGa~V~~~e----~~Cp~C~StnI~ 108 (314)
T PF09567_consen 73 IKSCYRVDQ-------LGKCN--NCGANVSRLE----ESCPNCGSTNIK 108 (314)
T ss_pred hhhhhhhhh-------hhhhc--cccceeeehh----hcCCCCCccccc
Confidence 345888984 57788 7988886554 568888877543
No 281
>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=40.73 E-value=23 Score=21.52 Aligned_cols=32 Identities=16% Similarity=0.315 Sum_probs=21.1
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHH
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD 32 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~ 32 (156)
|.|.+.+.+|+.|.++...-.--.-|+..++.
T Consensus 1 ~~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~~ 32 (62)
T PF03931_consen 1 MYVKLVSSDGQEFEVSREAAKQSKTIKNMLED 32 (62)
T ss_dssp -EEEEEETTSEEEEEEHHHHTTSHHHHHHHHC
T ss_pred CEEEEEcCCCCEEEeeHHHHHHhHHHHHHHhh
Confidence 77999999999999985543333444555543
No 282
>PRK10445 endonuclease VIII; Provisional
Probab=40.55 E-value=22 Score=28.34 Aligned_cols=26 Identities=19% Similarity=0.430 Sum_probs=19.4
Q ss_pred eccCCCCccCCceEEeEeC--CCCccCCce
Q 031613 118 RKECPNAECGAGTFMANHF--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 898776666654 458899997
No 283
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=39.99 E-value=29 Score=23.75 Aligned_cols=30 Identities=23% Similarity=0.640 Sum_probs=20.5
Q ss_pred cCCCCccCCceEEeEe--CCCCccCCceeEEEee
Q 031613 120 ECPNAECGAGTFMANH--FDRHYCGKCGLTYVYQ 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 489 89854333332 2689999999987554
No 284
>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=39.61 E-value=12 Score=17.63 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=7.0
Q ss_pred ccCCceeEE
Q 031613 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 285
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.61 E-value=23 Score=28.32 Aligned_cols=27 Identities=26% Similarity=0.631 Sum_probs=20.9
Q ss_pred eccCCCCccCCceEEeEeC--CCCccCCcee
Q 031613 118 RKECPNAECGAGTFMANHF--DRHYCGKCGL 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 999877766665 4589999985
No 286
>PHA00616 hypothetical protein
Probab=39.52 E-value=4.7 Score=23.44 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=6.8
Q ss_pred ccCCceeEEE
Q 031613 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 287
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=39.43 E-value=72 Score=23.35 Aligned_cols=34 Identities=9% Similarity=0.135 Sum_probs=29.8
Q ss_pred CCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEE
Q 031613 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 288
>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=39.27 E-value=27 Score=24.22 Aligned_cols=26 Identities=27% Similarity=0.580 Sum_probs=16.4
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGL 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--EVSPEIDLYRCPKCHG 94 (115)
T ss_pred cEEEcc--cCCC--EEecCCcCccCcCCcC
Confidence 578899 8974 2222223456999984
No 289
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=39.14 E-value=18 Score=34.11 Aligned_cols=25 Identities=40% Similarity=0.787 Sum_probs=20.7
Q ss_pred EeeccCCCCccCCceEEeEeCCCCccCC
Q 031613 116 RLRKECPNAECGAGTFMANHFDRHYCGK 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 467777789999997
No 290
>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=38.86 E-value=24 Score=19.10 Aligned_cols=24 Identities=29% Similarity=0.789 Sum_probs=13.3
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeE
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLT 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 47898 7974 3 46789999999744
No 291
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=38.66 E-value=62 Score=24.14 Aligned_cols=39 Identities=28% Similarity=0.467 Sum_probs=29.8
Q ss_pred eEeeeEEEcCCCeEEEeeccCCCCccCCceEEeEeC--CCCccC
Q 031613 101 AVLQFYKVDDSGKVQRLRKECPNAECGAGTFMANHF--DRHYCG 142 (156)
Q Consensus 101 ~~l~~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 4445666666788888999999 797 88999994 556564
No 292
>PHA02768 hypothetical protein; Provisional
Probab=38.12 E-value=17 Score=22.10 Aligned_cols=30 Identities=27% Similarity=0.578 Sum_probs=20.5
Q ss_pred eeccCCCCccCCceEEe---------EeCCCCccCCceeEEE
Q 031613 117 LRKECPNAECGAGTFMA---------NHFDRHYCGKCGLTYV 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 44532 2345778999998664
No 293
>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=37.54 E-value=11 Score=22.14 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=8.2
Q ss_pred CCccCCceeEE
Q 031613 138 RHYCGKCGLTY 148 (156)
Q Consensus 138 r~~cg~c~~t~ 148 (156)
|+.|..|||.|
T Consensus 1 ky~C~~CgyvY 11 (47)
T PF00301_consen 1 KYQCPVCGYVY 11 (47)
T ss_dssp EEEETTTSBEE
T ss_pred CcCCCCCCEEE
Confidence 46788898665
No 294
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=37.39 E-value=10 Score=30.08 Aligned_cols=27 Identities=33% Similarity=0.798 Sum_probs=22.1
Q ss_pred EEEeeccCCCCccCCceEEeEe--CCCCccCC
Q 031613 114 VQRLRKECPNAECGAGTFMANH--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 457788898 897 9999999 57888875
No 295
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=37.21 E-value=23 Score=17.67 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=7.4
Q ss_pred CccCCceeEE
Q 031613 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 4577888777
No 296
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=37.08 E-value=24 Score=20.62 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=7.0
Q ss_pred CccCCceeEEEee
Q 031613 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 3466666555443
No 297
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=36.99 E-value=30 Score=28.70 Aligned_cols=47 Identities=19% Similarity=0.262 Sum_probs=38.4
Q ss_pred EEEEecCCCcHHHHHHHHHHHhC-CC-CCceEEecCCeeccCCCccccc
Q 031613 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 35678889999999999999998 44 3566788999999999888754
No 298
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.86 E-value=26 Score=28.14 Aligned_cols=27 Identities=26% Similarity=0.614 Sum_probs=20.0
Q ss_pred eccCCCCccCCceEEeEeC--CCCccCCcee
Q 031613 118 RKECPNAECGAGTFMANHF--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 998776666555 4588999973
No 299
>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=36.73 E-value=36 Score=24.28 Aligned_cols=32 Identities=34% Similarity=0.779 Sum_probs=21.9
Q ss_pred EEeeccCCCCccCCceEEeEeC----CCCccCCceeEEEe
Q 031613 115 QRLRKECPNAECGAGTFMANHF----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 44578998 897432 3442 36789999987754
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=36.55 E-value=19 Score=21.72 Aligned_cols=21 Identities=43% Similarity=1.100 Sum_probs=13.0
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCce
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCG 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
>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=36.40 E-value=1.2e+02 Score=19.83 Aligned_cols=46 Identities=17% Similarity=0.251 Sum_probs=27.5
Q ss_pred cccCCCCEEEEEEeecCCccccccccccCCcccccccceeeeeEeeeEEEcCCCeEEEeeccCCCCccC
Q 031613 59 YNIQKESTLHLVLRLRGGAKKRKKKTYTKPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECG 127 (156)
Q Consensus 59 ~gi~~~stI~l~~~~~gg~~k~~kk~~~~pk~~k~~~kk~k~~~l~~y~vd~~g~~~~~~~~cp~~~c~ 127 (156)
..+.+|+.|.+.-.+.- |. .+.+-+..-...+..+.+.+..|| +||
T Consensus 46 ~~l~~Gd~V~v~G~v~~---------y~------------ql~ve~l~~~glg~~~~~~np~C~--~C~ 91 (91)
T cd04482 46 RLLIPGDEVTVYGSVRP---------GT------------TLNLEKLRVIRLARLYERENPVCP--KCG 91 (91)
T ss_pred CCCCCCCEEEEEEEEec---------CC------------EEEEEEEEECCCcceEEEcCCcCC--CCC
Confidence 34678888887754321 11 344444444443334777899999 885
No 302
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=36.27 E-value=38 Score=20.26 Aligned_cols=26 Identities=31% Similarity=0.788 Sum_probs=16.2
Q ss_pred ccCCCCccCCceEEeEeCCC--------CccCCcee
Q 031613 119 KECPNAECGAGTFMANHFDR--------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 99865555544221 34888875
No 303
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=36.05 E-value=18 Score=27.06 Aligned_cols=20 Identities=40% Similarity=0.989 Sum_probs=16.7
Q ss_pred ccCCCCccCCceEEeEe--CCCCccC
Q 031613 119 KECPNAECGAGTFMANH--FDRHYCG 142 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h--~~r~~cg 142 (156)
..| +|| .+|++.| .++|.|-
T Consensus 120 f~C---rCG-~~fC~~HRy~e~H~C~ 141 (167)
T KOG3173|consen 120 FKC---RCG-NTFCGTHRYPEQHDCS 141 (167)
T ss_pred ccc---ccC-CcccccccCCcccccc
Confidence 567 699 8999999 6999874
No 304
>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=35.95 E-value=12 Score=34.84 Aligned_cols=55 Identities=31% Similarity=0.664 Sum_probs=0.0
Q ss_pred cccccceeeeeEeeeEEEcCC-C----------------eEEEeeccCCCCccCCceE------EeEe-CCCCccCCcee
Q 031613 91 IKHKKKKVKLAVLQFYKVDDS-G----------------KVQRLRKECPNAECGAGTF------MANH-FDRHYCGKCGL 146 (156)
Q Consensus 91 ~k~~~kk~k~~~l~~y~vd~~-g----------------~~~~~~~~cp~~~c~~g~f------ma~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 445566788899999977543 2 2344467899 7976544 3333 23556666664
Q ss_pred E
Q 031613 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 305
>COG3760 Uncharacterized conserved protein [Function unknown]
Probab=35.65 E-value=55 Score=24.20 Aligned_cols=55 Identities=20% Similarity=0.358 Sum_probs=35.4
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCE
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKEST 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 47 nLfLkdkK~q~~lv~~~e~~-~vDLk-~ih~~IG~~----RlsFg~~----E~l~E~LGv~pG~V 101 (164)
T COG3760 47 NLFLKDKKDQFFLVTVDEDA-VVDLK-SIHETIGAA----RLSFGSP----ERLMEYLGVIPGSV 101 (164)
T ss_pred eeEeecCCCCEEEEEecccc-eecHH-HHHHHhcee----eeecCCH----HHHHHHhCCCcCce
Confidence 47888877888888887655 45777 466666643 7766543 23345557777764
No 306
>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=35.51 E-value=16 Score=16.85 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=5.1
Q ss_pred ccCCceeEE
Q 031613 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 577788776
No 307
>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=35.46 E-value=30 Score=27.68 Aligned_cols=26 Identities=23% Similarity=0.611 Sum_probs=19.6
Q ss_pred eccCCCCccCCceEEeEeCC--CCccCCce
Q 031613 118 RKECPNAECGAGTFMANHFD--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 8988777666654 57899996
No 308
>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=34.89 E-value=1.1e+02 Score=20.68 Aligned_cols=64 Identities=20% Similarity=0.367 Sum_probs=34.5
Q ss_pred CEEEEEec---CCCcHHHHHHHHHHHhCCCCCceEEecCCe-------eccCC--C-cc--cccccCCCCEEEEEEeecC
Q 031613 11 KTITLEVE---SSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLEDG--R-TL--ADYNIQKESTLHLVLRLRG 75 (156)
Q Consensus 11 ~~~~l~V~---~~~TV~~LK~~I~~~~gip~~~qrL~~~G~-------~L~d~--~-tL--~~~gi~~~stI~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 KKHKVSLPSDGEPATIKDLIDYLRDNLLK--ERPELFLEGGSVRPGILVLINDADWELLGEEDYVLKDGDNITFISTLHG 95 (96)
T ss_dssp SEEEEEE-SSCSC-BHHHHHHHHCCCT-S--SGHHHHBSSSSB-TTEEEEETTCEHHHHTCCCSB--TTEEEEEEETTT-
T ss_pred eeEEEEcCCCCCCcCHHHHHHHHHHhccC--CCHhHEecCCeEcCcEEEEEcCccceeecCcceEcCCCCEEEEEccCCC
Confidence 57788887 678999999888653211 1222222221 12122 1 12 3588999999999988887
Q ss_pred C
Q 031613 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 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=34.61 E-value=48 Score=20.00 Aligned_cols=30 Identities=33% Similarity=0.689 Sum_probs=18.1
Q ss_pred ccCCCCccCCceEEeEe--CCCCccCCceeEEEe
Q 031613 119 KECPNAECGAGTFMANH--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 245578888876643
No 310
>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=34.05 E-value=19 Score=17.92 Aligned_cols=11 Identities=27% Similarity=0.763 Sum_probs=8.5
Q ss_pred CCccCCceeEE
Q 031613 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 311
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=33.75 E-value=1.5e+02 Score=19.96 Aligned_cols=67 Identities=18% Similarity=0.301 Sum_probs=39.4
Q ss_pred CCEEEEEec--CCCcHHHHHHHHHHHhCCCCCceEEecCCee------ccCC---Ccccc--cccCCCCEEEEEEeecCC
Q 031613 10 GKTITLEVE--SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ------LEDG---RTLAD--YNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 10 g~~~~l~V~--~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~------L~d~---~tL~~--~gi~~~stI~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 444555555 4567888888877742223222223344432 2122 33444 889999999998888776
No 312
>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=33.68 E-value=1.1e+02 Score=18.38 Aligned_cols=59 Identities=14% Similarity=0.149 Sum_probs=37.7
Q ss_pred EEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEEE
Q 031613 3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 3 I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 456668888766 778899999999998665311 11223677666554444 467777654
No 313
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=33.59 E-value=32 Score=23.77 Aligned_cols=29 Identities=28% Similarity=0.621 Sum_probs=19.8
Q ss_pred eeccCCCCccCCceEEeEe-CCCCccCCceeEE
Q 031613 117 LRKECPNAECGAGTFMANH-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 467899 69865544432 578 799998643
No 314
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=33.44 E-value=81 Score=20.32 Aligned_cols=46 Identities=7% Similarity=0.138 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhCCCCCceEEecCCeeccCCCcccccccCCCCEEEE
Q 031613 24 DNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69 (156)
Q Consensus 24 ~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~gi~~~stI~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 3688999999999999999887743222222333444556888877
No 315
>PF12773 DZR: Double zinc ribbon
Probab=33.33 E-value=19 Score=20.69 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=17.1
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeE
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLT 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 7875333 233456778888865
No 316
>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=32.81 E-value=40 Score=21.57 Aligned_cols=27 Identities=22% Similarity=0.504 Sum_probs=16.3
Q ss_pred cCCCCccCCceEEeEeCCCCccCCceeEEEe
Q 031613 120 ECPNAECGAGTFMANHFDRHYCGKCGLTYVY 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 588 7865 36666678888888877643
No 317
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=32.78 E-value=28 Score=21.52 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=6.9
Q ss_pred CCCCccCCcee
Q 031613 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 45666777763
No 318
>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=32.57 E-value=1.5e+02 Score=19.59 Aligned_cols=43 Identities=12% Similarity=0.244 Sum_probs=33.1
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCC-ceEEec
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF 45 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~-~qrL~~ 45 (156)
+|.+. .+|..+...++++.|..+|.+++.+....+.+ ...+.|
T Consensus 2 ~~K~~-y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw 45 (83)
T cd06404 2 RVKAA-YNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKW 45 (83)
T ss_pred eEEEE-ecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEE
Confidence 34443 36888889999999999999999999988664 345544
No 319
>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=32.55 E-value=24 Score=19.04 Aligned_cols=11 Identities=27% Similarity=0.597 Sum_probs=7.2
Q ss_pred CccCCceeEEE
Q 031613 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 55777777664
No 320
>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=32.29 E-value=24 Score=18.18 Aligned_cols=25 Identities=20% Similarity=0.442 Sum_probs=12.5
Q ss_pred ccCCCCccCCceEEeEeC--CCCccCCce
Q 031613 119 KECPNAECGAGTFMANHF--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 887544444443 346788886
No 321
>PRK05580 primosome assembly protein PriA; Validated
Probab=32.16 E-value=25 Score=31.95 Aligned_cols=25 Identities=36% Similarity=0.833 Sum_probs=16.1
Q ss_pred cCCCCccCCceEEeEeC--CCCccCCceeEE
Q 031613 120 ECPNAECGAGTFMANHF--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 688 884 4778885 344466666654
No 322
>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=31.42 E-value=1.3e+02 Score=18.48 Aligned_cols=40 Identities=15% Similarity=0.192 Sum_probs=29.0
Q ss_pred EEEEecCCCcHHHHHHHHHHHh--CCCCCceEEecCCeeccC
Q 031613 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 4578999999999999998877 233334566677776654
No 323
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=31.18 E-value=28 Score=21.48 Aligned_cols=20 Identities=40% Similarity=0.878 Sum_probs=12.3
Q ss_pred eeccCCCCccCCceEEeEeCCCC
Q 031613 117 LRKECPNAECGAGTFMANHFDRH 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 44444575443
No 324
>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform
Probab=31.10 E-value=1.4e+02 Score=20.51 Aligned_cols=55 Identities=24% Similarity=0.244 Sum_probs=40.2
Q ss_pred cCCCcHHHHHHHHHHHhCCCC---CceEEecCCeeccCCC-cccccccCCCCEEEEEEee
Q 031613 18 ESSDTIDNVKAKIQDKEGIPP---DQQRLIFAGKQLEDGR-TLADYNIQKESTLHLVLRL 73 (156)
Q Consensus 18 ~~~~TV~~LK~~I~~~~gip~---~~qrL~~~G~~L~d~~-tL~~~gi~~~stI~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 356788888888888777433 2346778888888776 7888888666 88887764
No 325
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=30.59 E-value=37 Score=33.54 Aligned_cols=47 Identities=28% Similarity=0.571 Sum_probs=32.8
Q ss_pred ccccceeeeeEeeeEEEcC-CC---------------eEEEeeccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 92 KHKKKKVKLAVLQFYKVDD-SG---------------KVQRLRKECPNAECGAGTFMANHFDRHYCGKCGL 146 (156)
Q Consensus 92 k~~~kk~k~~~l~~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 3445568889998887754 23 3566678999 898533 4556999984
No 326
>KOG3391 consensus Transcriptional co-repressor component [Transcription]
Probab=30.44 E-value=44 Score=24.29 Aligned_cols=26 Identities=15% Similarity=0.290 Sum_probs=22.8
Q ss_pred eccCCCcccccccCCCCEEEEEEeec
Q 031613 49 QLEDGRTLADYNIQKESTLHLVLRLR 74 (156)
Q Consensus 49 ~L~d~~tL~~~gi~~~stI~l~~~~~ 74 (156)
..+|+.+|.+.+++-|+-|.|.+.+.
T Consensus 113 g~ddnktL~~~kf~iGD~lDVaI~~p 138 (151)
T KOG3391|consen 113 GIDDNKTLQQTKFEIGDYLDVAITPP 138 (151)
T ss_pred cCCccchhhhCCccccceEEEEecCc
Confidence 45788999999999999999998764
No 327
>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=30.40 E-value=1.5e+02 Score=19.06 Aligned_cols=34 Identities=26% Similarity=0.347 Sum_probs=25.9
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC
Q 031613 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 345667888888999999999988753
No 328
>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=30.17 E-value=41 Score=19.92 Aligned_cols=12 Identities=33% Similarity=0.794 Sum_probs=8.5
Q ss_pred CCccCCceeEEE
Q 031613 138 RHYCGKCGLTYV 149 (156)
Q Consensus 138 r~~cg~c~~t~~ 149 (156)
++-|.-|||.|.
T Consensus 1 ~y~C~~CgyiYd 12 (50)
T cd00730 1 KYECRICGYIYD 12 (50)
T ss_pred CcCCCCCCeEEC
Confidence 467888886653
No 329
>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=29.94 E-value=1.8e+02 Score=23.89 Aligned_cols=61 Identities=18% Similarity=0.230 Sum_probs=43.1
Q ss_pred EEEecCCCcHHHHHHHHHHHh--------------C-CCCCceEEecCCeeccCCCccccccc---CCCCEEEEEEeec
Q 031613 14 TLEVESSDTIDNVKAKIQDKE--------------G-IPPDQQRLIFAGKQLEDGRTLADYNI---QKESTLHLVLRLR 74 (156)
Q Consensus 14 ~l~V~~~~TV~~LK~~I~~~~--------------g-ip~~~qrL~~~G~~L~d~~tL~~~gi---~~~stI~l~~~~~ 74 (156)
.|..+.-.-|.-+...|.++. . .|.+...|+++|+.|+.+.+|+..-- +.+.-|.|..|..
T Consensus 251 rL~A~~mLrvkKI~~yV~ek~~~~~~~~~~~~~~~~~~p~e~lEl~C~gqvL~~~mtLaTVr~~~WK~~~di~L~YR~k 329 (331)
T PF11816_consen 251 RLNAPRMLRVKKILEYVAEKLEKTPESKTPEMKPKKLKPEEWLELLCNGQVLPPDMTLATVRTFIWKSSGDIVLHYRRK 329 (331)
T ss_pred eecccchhhhHHHHHHHHHHhccCccccCccccccCCCCCceEEEEeCCeEcCCcCCHHHHHHhhccCCCeEEEEEEec
Confidence 344555567888888888887 2 34456789999999999998876542 4566666766643
No 330
>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=29.70 E-value=1.5e+02 Score=21.94 Aligned_cols=44 Identities=30% Similarity=0.437 Sum_probs=30.9
Q ss_pred EEEEEecC-CCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCccccc
Q 031613 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 45667777 67778888777776543322 2468888999999887
No 331
>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=29.56 E-value=46 Score=17.96 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=13.2
Q ss_pred ceEEeEeCCCCccCCce
Q 031613 129 GTFMANHFDRHYCGKCG 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 332
>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=29.46 E-value=99 Score=19.35 Aligned_cols=55 Identities=18% Similarity=0.291 Sum_probs=37.3
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCccccc--ccCCCCEEEEEEee
Q 031613 11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY--NIQKESTLHLVLRL 73 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~L~d~~tL~~~--gi~~~stI~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 344456666653 44678999999999999999665444333 45679999888754
No 333
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=29.25 E-value=49 Score=23.23 Aligned_cols=32 Identities=22% Similarity=0.353 Sum_probs=18.4
Q ss_pred EeeccCCCCccCCceEEeEeCCCCccCCce-eEEEee
Q 031613 116 RLRKECPNAECGAGTFMANHFDRHYCGKCG-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 6752 333344566699998 444333
No 334
>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=28.82 E-value=37 Score=23.16 Aligned_cols=13 Identities=31% Similarity=0.928 Sum_probs=10.5
Q ss_pred eeccCCCCccCCceE
Q 031613 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 468899 8988876
No 335
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.62 E-value=1.9e+02 Score=19.60 Aligned_cols=57 Identities=25% Similarity=0.344 Sum_probs=36.3
Q ss_pred CCCcHHHHHHHHHHHhCCCCCceEEecCCee------ccCC---Ccc--cccccCCCCEEEEEEeecCC
Q 031613 19 SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ------LEDG---RTL--ADYNIQKESTLHLVLRLRGG 76 (156)
Q Consensus 19 ~~~TV~~LK~~I~~~~gip~~~qrL~~~G~~------L~d~---~tL--~~~gi~~~stI~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 4579999998888754322322 33344432 2122 222 57889999999998888876
No 336
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=28.61 E-value=33 Score=21.03 Aligned_cols=22 Identities=36% Similarity=0.948 Sum_probs=14.0
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCcee
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGL 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-Y----KLPHRVCLKCGY 48 (57)
T ss_pred ceecc--CCCC-c----ccCceEcCCCCC
Confidence 46788 7974 3 334456777874
No 337
>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=28.42 E-value=77 Score=22.32 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=18.8
Q ss_pred EEecCCCcHHHHHHHHHHHhCCCCC
Q 031613 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 5677789999999999999998664
No 338
>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=28.25 E-value=37 Score=20.01 Aligned_cols=28 Identities=29% Similarity=0.580 Sum_probs=14.6
Q ss_pred ccCCCCccCCceEEeE--eC---CC-C-ccCCceeEE
Q 031613 119 KECPNAECGAGTFMAN--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 339
>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=27.58 E-value=71 Score=17.53 Aligned_cols=12 Identities=33% Similarity=0.836 Sum_probs=5.6
Q ss_pred CCCccCCceeEE
Q 031613 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 340
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=27.55 E-value=15 Score=24.32 Aligned_cols=31 Identities=23% Similarity=0.489 Sum_probs=20.4
Q ss_pred EeeccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 116 RLRKECPNAECGAGTFMANHFDRHYCGKCGLTY 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 4478899 886432211123679999999876
No 341
>COG4919 Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]
Probab=27.41 E-value=34 Score=20.27 Aligned_cols=26 Identities=27% Similarity=0.266 Sum_probs=19.3
Q ss_pred cCCccccccccccCCcccccccceee
Q 031613 74 RGGAKKRKKKTYTKPKKIKHKKKKVK 99 (156)
Q Consensus 74 ~gg~~k~~kk~~~~pk~~k~~~kk~k 99 (156)
.|.-.+++|+.-+|||-..+.+++-.
T Consensus 4 HGSLTKAGKVR~QTPkipaK~kkn~~ 29 (54)
T COG4919 4 HGSLTKAGKVRKQTPKIPAKQKKNYP 29 (54)
T ss_pred ccccccccchhccCCCCCccccccCC
Confidence 35556888999999998877776533
No 342
>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=27.37 E-value=1.5e+02 Score=21.75 Aligned_cols=44 Identities=25% Similarity=0.404 Sum_probs=29.9
Q ss_pred EEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCCeeccCCCccccc
Q 031613 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 3556666777888888777776654322 3456778888888887
No 343
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.95 E-value=32 Score=31.29 Aligned_cols=26 Identities=19% Similarity=0.401 Sum_probs=18.0
Q ss_pred ccCCCCccCCceEEeEeC--CCCccCCceeEE
Q 031613 119 KECPNAECGAGTFMANHF--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 4788885 356788888754
No 344
>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=26.82 E-value=26 Score=17.13 Aligned_cols=10 Identities=40% Similarity=1.119 Sum_probs=7.8
Q ss_pred CccCCceeEE
Q 031613 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 345
>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=26.78 E-value=81 Score=23.01 Aligned_cols=31 Identities=29% Similarity=0.548 Sum_probs=21.7
Q ss_pred eccCCCCccCCceEEeEeCC-CCccCCceeEEEee
Q 031613 118 RKECPNAECGAGTFMANHFD-RHYCGKCGLTYVYQ 151 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~-r~~cg~c~~t~~~~ 151 (156)
...|- .||.-+-. .|.+ =-.|.+||.+++..
T Consensus 112 ~l~C~--~Cg~~~~~-~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 112 TLVCE--NCGHEVEL-THPERLPPCPKCGHTEFTR 143 (146)
T ss_pred eEecc--cCCCEEEe-cCCCcCCCCCCCCCCeeee
Confidence 57788 89865444 3544 45799999998443
No 346
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=26.21 E-value=48 Score=20.54 Aligned_cols=25 Identities=36% Similarity=0.806 Sum_probs=14.0
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCce
Q 031613 119 KECPNAECGAGTFMANHFDRHYCGKCG 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 4577 788888888999999999997
No 347
>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=25.53 E-value=31 Score=25.09 Aligned_cols=29 Identities=21% Similarity=0.463 Sum_probs=20.1
Q ss_pred EeeccCCCCccCCceEEeEeC-CCCccCCceeEE
Q 031613 116 RLRKECPNAECGAGTFMANHF-DRHYCGKCGLTY 148 (156)
Q Consensus 116 ~~~~~cp~~~c~~g~fma~h~-~r~~cg~c~~t~ 148 (156)
..=..|| .|...+ .... +.+.|.+|+.+.
T Consensus 32 ~~Y~aC~--~C~kkv--~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 32 WWYPACP--GCNKKV--VEEGNGTYRCEKCNKSV 61 (166)
T ss_pred eEEcccc--ccCccc--EeCCCCcEECCCCCCcC
Confidence 3457799 896533 3333 789999999763
No 348
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.22 E-value=58 Score=22.65 Aligned_cols=26 Identities=23% Similarity=0.502 Sum_probs=14.9
Q ss_pred eeccCCCCccCCceEEeEeCCCCc-cCCcee
Q 031613 117 LRKECPNAECGAGTFMANHFDRHY-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 7973 2222212333 999984
No 349
>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=25.15 E-value=94 Score=17.15 Aligned_cols=30 Identities=27% Similarity=0.713 Sum_probs=16.3
Q ss_pred ccCCCCccCCceEEeEeCCC---CccC---CceeEEEee
Q 031613 119 KECPNAECGAGTFMANHFDR---HYCG---KCGLTYVYQ 151 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r---~~cg---~c~~t~~~~ 151 (156)
..|| .|| +-+....... +.|- .|.+|+..+
T Consensus 2 ~~CP--~Cg-~~lv~r~~k~g~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 2 EKCP--KCG-GPLVLRRGKKGKFLGCSNYPECKYTEPLP 37 (39)
T ss_pred cCCC--CCC-ceeEEEECCCCCEEECCCCCCcCCeEeCC
Confidence 5799 898 4444443211 2343 477777443
No 350
>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=25.05 E-value=63 Score=19.85 Aligned_cols=23 Identities=30% Similarity=1.136 Sum_probs=12.8
Q ss_pred eeccCCCCcc-CCceEEeEeCCCCccCCce
Q 031613 117 LRKECPNAEC-GAGTFMANHFDRHYCGKCG 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 466777 77 556552 566777774
No 351
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.62 E-value=70 Score=22.84 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=7.9
Q ss_pred eeccCCCCccCC
Q 031613 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 352
>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=24.61 E-value=42 Score=28.54 Aligned_cols=29 Identities=17% Similarity=0.558 Sum_probs=20.3
Q ss_pred ccCCCCccCCceEEeEeCCCCccCCceeEEEeec
Q 031613 119 KECPNAECGAGTFMANHFDRHYCGKCGLTYVYQK 152 (156)
Q Consensus 119 ~~cp~~~c~~g~fma~h~~r~~cg~c~~t~~~~~ 152 (156)
..|| .|+. + + .+..+..|.+||.+....+
T Consensus 216 ~~C~--~Cd~-~-~-~~~~~a~CpRC~~~L~~~~ 244 (403)
T TIGR00155 216 RSCS--ACHT-T-I-LPAQEPVCPRCSTPLYVRR 244 (403)
T ss_pred CcCC--CCCC-c-c-CCCCCcCCcCCCCcccCCC
Confidence 4599 8986 2 2 3567888999998874433
No 353
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=24.61 E-value=1.1e+02 Score=22.66 Aligned_cols=64 Identities=19% Similarity=0.281 Sum_probs=35.9
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCC-------CceEEecCCeeccCCCcccccccCCCCEE
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-------DQQRLIFAGKQLEDGRTLADYNIQKESTL 67 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~-------~~qrL~~~G~~L~d~~tL~~~gi~~~stI 67 (156)
|.|.+ +.+|+.+.++++|.+++.++-..--..+|.-. ..-.++++|+....-.++... -+|..|
T Consensus 2 ~~i~l-tvNG~~~~~~~~p~~~Ll~~LRd~l~ltgtk~GC~~g~CGACtVlvDG~~v~SCl~~a~~--~~G~~I 72 (156)
T COG2080 2 MPITL-TVNGEPVELDVDPRTPLLDVLRDELGLTGTKKGCGHGQCGACTVLVDGEAVNSCLTLAVQ--AEGAEI 72 (156)
T ss_pred CcEEE-EECCeEEEEEeCCCChHHHHHHHhcCCCCcCCCCCCccCCceEEEECCeEehHHHHHHHH--hCCCeE
Confidence 34555 34899999999999998887653333333221 122555666655443333222 245555
No 354
>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=24.41 E-value=53 Score=17.72 Aligned_cols=9 Identities=33% Similarity=1.099 Sum_probs=5.8
Q ss_pred eccCCCCccCC
Q 031613 118 RKECPNAECGA 128 (156)
Q Consensus 118 ~~~cp~~~c~~ 128 (156)
...|| .||.
T Consensus 5 ~y~C~--~Cg~ 13 (41)
T smart00834 5 EYRCE--DCGH 13 (41)
T ss_pred EEEcC--CCCC
Confidence 35677 6874
No 355
>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=24.41 E-value=35 Score=25.31 Aligned_cols=31 Identities=35% Similarity=1.039 Sum_probs=20.5
Q ss_pred ccCCCCccCC---------ceEEe-EeC-CCCccCCceeEEEee
Q 031613 119 KECPNAECGA---------GTFMA-NHF-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 4688 6764 55544 343 367899999988653
No 356
>PRK12366 replication factor A; Reviewed
Probab=24.03 E-value=37 Score=30.63 Aligned_cols=26 Identities=23% Similarity=0.492 Sum_probs=19.4
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeE
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLT 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 79653 4456688999999864
No 357
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.85 E-value=37 Score=23.77 Aligned_cols=29 Identities=24% Similarity=0.303 Sum_probs=18.1
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGLTY 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 357899 787 34433223345688888776
No 358
>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=23.80 E-value=32 Score=21.54 Aligned_cols=20 Identities=15% Similarity=0.361 Sum_probs=14.4
Q ss_pred cHHHHHHHHHHHhCCCCCce
Q 031613 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 68899999999999987643
No 359
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=23.68 E-value=74 Score=18.86 Aligned_cols=32 Identities=19% Similarity=0.477 Sum_probs=17.2
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeEEEee
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLTYVYQ 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 666544222234555666666665544
No 360
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=23.62 E-value=64 Score=27.28 Aligned_cols=16 Identities=19% Similarity=0.299 Sum_probs=10.9
Q ss_pred EEecCCCcHHHHHHHH
Q 031613 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 4577777777777554
No 361
>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=23.45 E-value=2e+02 Score=18.69 Aligned_cols=31 Identities=13% Similarity=0.065 Sum_probs=24.2
Q ss_pred CcHHHHHHHHHHHhCCCCCc--eEEecCCeecc
Q 031613 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 44456788774
No 362
>KOG4842 consensus Protein involved in sister chromatid separation and/or segregation [Cell cycle control, cell division, chromosome partitioning]
Probab=23.36 E-value=38 Score=27.23 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=33.3
Q ss_pred CCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEecCC
Q 031613 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 578899999999999999999999999888777766544
No 363
>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=23.14 E-value=57 Score=23.91 Aligned_cols=16 Identities=44% Similarity=0.877 Sum_probs=12.6
Q ss_pred CCeEEEeeccCCCCccCC
Q 031613 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 576666699999 8984
No 364
>PF12143 PPO1_KFDV: Protein of unknown function (DUF_B2219); InterPro: IPR022740 This domain represents the C terminus of polyphenol oxidases. This region is primarily found in eukaryotes, although a few bacterial members also exist. It is typically between 138 and 152 amino acids in length and the family is found in association with PF00264 from PFAM and PF12142 from PFAM. Many members are plant or plastid polyphenol oxidases, and there is a highly conserved KFDV sequence motif. ; GO: 0004097 catechol oxidase activity, 0055114 oxidation-reduction process
Probab=23.08 E-value=77 Score=22.67 Aligned_cols=25 Identities=24% Similarity=0.444 Sum_probs=21.5
Q ss_pred CCcccccccCCCCEEEEEEeecCCc
Q 031613 53 GRTLADYNIQKESTLHLVLRLRGGA 77 (156)
Q Consensus 53 ~~tL~~~gi~~~stI~l~~~~~gg~ 77 (156)
...|.++|..+.+.|.|++-+++|.
T Consensus 94 tdlLedLga~~d~sIvVTLVPr~g~ 118 (130)
T PF12143_consen 94 TDLLEDLGAEDDDSIVVTLVPRGGG 118 (130)
T ss_pred hHHHHHhCCCCCCEEEEEEEEccCC
Confidence 3558999999999999999888886
No 365
>PF01577 Peptidase_S30: Potyvirus P1 protease; InterPro: IPR002540 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. The potyviridae are a family of positive strand RNA viruses, members of which include Zucchini yellow mosaic virus, and Turnip mosaic virus (strain Japanese) which cause considerable losses of crops worldwide. This entry represents a C-terminal region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine peptidase belonging to MEROPS peptidase family S30 (clan PA(S)). It is the protease responsible for autocatalytic cleavage between P1 and the helper component protease, which is a cysteine peptidase belonging to MEROPS peptidase family C6 IPR001456 from INTERPRO [, ]. The P1 protein may be involved in virus-host interactions [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=23.03 E-value=2.6e+02 Score=21.48 Aligned_cols=73 Identities=12% Similarity=0.139 Sum_probs=47.9
Q ss_pred EEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhC--CCCCceEE-ecCCeeccCCCcccccccCCCCEEEEEEeecC
Q 031613 2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--IPPDQQRL-IFAGKQLEDGRTLADYNIQKESTLHLVLRLRG 75 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~g--ip~~~qrL-~~~G~~L~d~~tL~~~gi~~~stI~l~~~~~g 75 (156)
+|.+++..|.....++..+.....|-..++.... ...+...+ =.+|-.|+....+. .+-..++.+.|--+..|
T Consensus 151 kv~~~He~G~~~r~Dl~~~~~~~~i~~~~a~~~~~~~~~~~~~~~G~SG~vl~~~~~~~-~~~~~~~~FIVRGr~~G 226 (245)
T PF01577_consen 151 KVETKHERGKRKRRDLNIDEFTESILRLLAKKTYRGRIVDDIKIKGDSGLVLPRRKLIG-FGRTRDDFFIVRGRHEG 226 (245)
T ss_pred EEECCccCCCcccEECCccHHHHHHHHHHHhhcCCCcccccceeccceEEEEeCCcccC-ccccCCCeEEEEeccCC
Confidence 3455567788778888888888888888877643 44455566 35566777666555 65555665555555443
No 366
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=22.90 E-value=24 Score=24.55 Aligned_cols=13 Identities=54% Similarity=1.303 Sum_probs=10.8
Q ss_pred CCCccCCceeEEE
Q 031613 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 367
>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=22.70 E-value=30 Score=18.79 Aligned_cols=10 Identities=40% Similarity=1.105 Sum_probs=4.3
Q ss_pred CCccCCceeE
Q 031613 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 4568999874
No 368
>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=22.66 E-value=41 Score=23.22 Aligned_cols=30 Identities=27% Similarity=0.651 Sum_probs=16.5
Q ss_pred EEeeccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 115 QRLRKECPNAECGAGTFMANHFDRHYCGKCGLTY 148 (156)
Q Consensus 115 ~~~~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
.+.+-.|+ .||. .|-... .+..|+.||-..
T Consensus 67 ~p~~~~C~--~Cg~-~~~~~~-~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 67 VPARARCR--DCGH-EFEPDE-FDFSCPRCGSPD 96 (113)
T ss_dssp E--EEEET--TTS--EEECHH-CCHH-SSSSSS-
T ss_pred cCCcEECC--CCCC-EEecCC-CCCCCcCCcCCC
Confidence 34578899 8973 443333 337799998653
No 369
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=22.60 E-value=36 Score=27.11 Aligned_cols=31 Identities=26% Similarity=0.772 Sum_probs=13.0
Q ss_pred eccCCCCccCCceEEeEeCC-----CCccCCceeEEEee
Q 031613 118 RKECPNAECGAGTFMANHFD-----RHYCGKCGLTYVYQ 151 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~-----r~~cg~c~~t~~~~ 151 (156)
+.-|| .||..- +..+.+ ..+|..|+.-|-.+
T Consensus 31 n~yCP--~Cg~~~-L~~f~NN~PVaDF~C~~C~eeyELK 66 (254)
T PF06044_consen 31 NMYCP--NCGSKP-LSKFENNRPVADFYCPNCNEEYELK 66 (254)
T ss_dssp H---T--TT--SS--EE--------EEE-TTT--EEEEE
T ss_pred CCcCC--CCCChh-HhhccCCCccceeECCCCchHHhhh
Confidence 67899 898642 333322 57999999877544
No 370
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.07 E-value=31 Score=23.26 Aligned_cols=10 Identities=40% Similarity=1.129 Sum_probs=7.2
Q ss_pred cCCceeEEEe
Q 031613 141 CGKCGLTYVY 150 (156)
Q Consensus 141 cg~c~~t~~~ 150 (156)
|-+|||+|.-
T Consensus 61 CkkCGfef~~ 70 (97)
T COG3357 61 CKKCGFEFRD 70 (97)
T ss_pred hcccCccccc
Confidence 7778888743
No 371
>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=21.94 E-value=1e+02 Score=17.24 Aligned_cols=27 Identities=37% Similarity=0.704 Sum_probs=16.1
Q ss_pred eccCCCCccCCceEEeEe----CCCCccCCceeE
Q 031613 118 RKECPNAECGAGTFMANH----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 372
>PRK13605 endoribonuclease SymE; Provisional
Probab=21.92 E-value=1.1e+02 Score=21.36 Aligned_cols=41 Identities=7% Similarity=0.126 Sum_probs=27.6
Q ss_pred CEEEEEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031613 1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ 41 (156)
Q Consensus 1 M~I~Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~q 41 (156)
+.|.|+...|..+...-++.-...+|.+.+.+...+.+..|
T Consensus 56 ~~V~V~V~~G~LVIt~~~~~~~~~el~~~l~~v~~~s~~kq 96 (113)
T PRK13605 56 TAVDVRVMEGCIVLTAQPPAAEESELMQSLRQVCKLSARKQ 96 (113)
T ss_pred CeEEEEEeCCEEEEEeCCCCcccHHHHHHHHHHHHhhhHHH
Confidence 35777777776544444455568899988888877666544
No 373
>PRK04351 hypothetical protein; Provisional
Probab=21.83 E-value=90 Score=22.78 Aligned_cols=33 Identities=27% Similarity=0.589 Sum_probs=22.4
Q ss_pred eeccCCCCccCCceEEeE--e-CCCCccCCceeEEEeec
Q 031613 117 LRKECPNAECGAGTFMAN--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 7974 33221 1 46899999998876653
No 374
>PF13439 Glyco_transf_4: Glycosyltransferase Family 4; PDB: 2JJM_E 3MBO_C 2GEJ_A 2GEK_A.
Probab=21.76 E-value=1.1e+02 Score=21.07 Aligned_cols=27 Identities=26% Similarity=0.634 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhCCCCCceEEecCCeecc
Q 031613 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 456777778 899999999999997654
No 375
>PRK13552 frdB fumarate reductase iron-sulfur subunit; Provisional
Probab=21.73 E-value=1.5e+02 Score=23.25 Aligned_cols=24 Identities=21% Similarity=0.182 Sum_probs=20.2
Q ss_pred CEEEEEecCCCcHHHHHHHHHHHh
Q 031613 11 KTITLEVESSDTIDNVKAKIQDKE 34 (156)
Q Consensus 11 ~~~~l~V~~~~TV~~LK~~I~~~~ 34 (156)
++|.+++++.+||.++-..|.+..
T Consensus 24 ~~y~v~~~~~~tvLdaL~~Ik~~~ 47 (239)
T PRK13552 24 VTYQLEETPGMTLFIALNRIREEQ 47 (239)
T ss_pred EEEEecCCCCCCHHHHHHHHHhcC
Confidence 457788889999999999998753
No 376
>PHA02998 RNA polymerase subunit; Provisional
Probab=21.64 E-value=60 Score=24.72 Aligned_cols=40 Identities=30% Similarity=0.687 Sum_probs=24.7
Q ss_pred eeeEEEcCCCeEEEeeccCCCCccCCc--eEEeEe---CC-----CCccCCceeEE
Q 031613 103 LQFYKVDDSGKVQRLRKECPNAECGAG--TFMANH---FD-----RHYCGKCGLTY 148 (156)
Q Consensus 103 l~~y~vd~~g~~~~~~~~cp~~~c~~g--~fma~h---~~-----r~~cg~c~~t~ 148 (156)
-.||+|-. +.....|| .|+.+ .||..+ .| .+.|-+||+++
T Consensus 132 ~~yfnvlp----kkt~v~CP--kCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~w 181 (195)
T PHA02998 132 DDYFNVLD----EKYNTPCP--NCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHF 181 (195)
T ss_pred hhheeccC----cccCCCCC--CCCCCceEEEEEeeccCCCCceEEEEcCCCCCcc
Confidence 45788752 11468999 89643 233333 12 56899999876
No 377
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=21.45 E-value=48 Score=27.75 Aligned_cols=29 Identities=24% Similarity=0.667 Sum_probs=14.6
Q ss_pred eccCCCCccCCceEEeEeCCCCccCCceeEE
Q 031613 118 RKECPNAECGAGTFMANHFDRHYCGKCGLTY 148 (156)
Q Consensus 118 ~~~cp~~~c~~g~fma~h~~r~~cg~c~~t~ 148 (156)
=..|+ .|+.......-+....|.+||..-
T Consensus 285 FFkC~--~C~~Rt~sl~r~P~~~C~~Cg~~~ 313 (344)
T PF09332_consen 285 FFKCK--DCGNRTISLERLPKKHCSNCGSSK 313 (344)
T ss_dssp EEE-T---TS-EEEESSSS--S--TTT-S--
T ss_pred eEECC--CCCCeeeecccCCCCCCCcCCcCc
Confidence 46899 799887766556778899999754
No 378
>cd01778 RASSF1_RA Ubiquitin-like domain of RASSF1 tumour supproessor protein. RASSF1 (also known as RASSF3 and NORE1) is a tumour suppressor protein with a C-terminal Ras-associating (RA) domain that binds Ras. RASSF1 also binds the proapoptotic protein kinase MST1 and is thus thought to regulate the proapoptotic signalling pathway. RASSF1 also associates with microtubule-associated proteins like MAP1B and regulates tubulin polymerization. RASSF1 also binds CDC20 and regulates mitosis by inhibiting the anaphase-promoting complex and preventing degradation of cyclin A and cyclin B until the spindle checkpoint becomes fully operational.
Probab=21.35 E-value=2.7e+02 Score=18.85 Aligned_cols=34 Identities=15% Similarity=0.139 Sum_probs=28.2
Q ss_pred CCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031613 8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ 41 (156)
Q Consensus 8 ~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~q 41 (156)
+.+.+-.|.|++++|+.++-+.+-.++.|.-+.+
T Consensus 14 p~~s~k~v~IsS~tTt~eVI~~LL~KF~v~~nP~ 47 (96)
T cd01778 14 PKDTAKHLHISSKTTVREVIEALLKKFLVVDNPR 47 (96)
T ss_pred cCCceeEEEEecCCcHHHHHHHHHHhheeccCCc
Confidence 3566778999999999999999999998765544
No 379
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=21.26 E-value=53 Score=19.69 Aligned_cols=20 Identities=20% Similarity=0.484 Sum_probs=16.6
Q ss_pred cHHHHHHHHHHHhCCCCCce
Q 031613 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 57889999999999987653
No 380
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=20.84 E-value=1e+02 Score=18.17 Aligned_cols=20 Identities=30% Similarity=0.502 Sum_probs=15.8
Q ss_pred eeEEE-cCCCeEEEeeccCCC
Q 031613 104 QFYKV-DDSGKVQRLRKECPN 123 (156)
Q Consensus 104 ~~y~v-d~~g~~~~~~~~cp~ 123 (156)
..|+. |++|.+.+...-|+.
T Consensus 14 ~vYk~~D~~G~v~ysd~P~~~ 34 (60)
T PF13511_consen 14 EVYKWVDENGVVHYSDTPPPD 34 (60)
T ss_pred cEEEEECCCCCEEECccCCCC
Confidence 56775 889999998887773
No 381
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=20.75 E-value=44 Score=20.61 Aligned_cols=26 Identities=31% Similarity=1.014 Sum_probs=19.8
Q ss_pred eeccCCCCccCCceEEeEeCCCCccCCceeE
Q 031613 117 LRKECPNAECGAGTFMANHFDRHYCGKCGLT 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 9986554 7788899999864
No 382
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.68 E-value=1.4e+02 Score=26.04 Aligned_cols=79 Identities=18% Similarity=0.228 Sum_probs=43.4
Q ss_pred CCcccccccCCCCEEEEEEeecCCccccccccccCCcccccccceeeeeEeeeEEEcCCCeEEEeeccCCCCccCCceEE
Q 031613 53 GRTLADYNIQKESTLHLVLRLRGGAKKRKKKTYTKPKKIKHKKKKVKLAVLQFYKVDDSGKVQRLRKECPNAECGAGTFM 132 (156)
Q Consensus 53 ~~tL~~~gi~~~stI~l~~~~~gg~~k~~kk~~~~pk~~k~~~kk~k~~~l~~y~vd~~g~~~~~~~~cp~~~c~~g~fm 132 (156)
+.+|.+.+++.|+.+.+... |.....+. .-.-++... ...-+...+..+-+. ++|.|.| ..-| .|
T Consensus 17 ~~~~~~~~~~hG~ml~l~~~--~~~e~~~s-v~~~~~~~~-~~~vr~~dvde~ls~-edg~I~r--sk~~--lc------ 81 (510)
T KOG2834|consen 17 DGTLLLAGLKHGQMLVLSAP--GNGELDKS-VAPGAKGLR-GQRVRSRDVDERLSK-EDGLITR--SKDK--LC------ 81 (510)
T ss_pred cchhHhhccccccEEEEecC--CCCCcCcc-cCCCccccC-CCceecccccchhhh-cCCceee--ccCc--cc------
Confidence 45678889999999888743 22221111 111122221 111223344444444 4788887 3344 56
Q ss_pred eEeCCCCccCCceeE
Q 031613 133 ANHFDRHYCGKCGLT 147 (156)
Q Consensus 133 a~h~~r~~cg~c~~t 147 (156)
.|..+..|-.|.--
T Consensus 82 -rh~~~~mc~~c~pL 95 (510)
T KOG2834|consen 82 -RHDPLQMCTHCSPL 95 (510)
T ss_pred -ccCccccCCcCCCC
Confidence 58899999999643
No 383
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=20.38 E-value=66 Score=21.68 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=20.1
Q ss_pred ccCCCCccCCceEEe--EeCCCCccCCceeEEEeecCCC
Q 031613 119 KECPNAECGAGTFMA--NHFDRHYCGKCGLTYVYQKAGG 155 (156)
Q Consensus 119 ~~cp~~~c~~g~fma--~h~~r~~cg~c~~t~~~~~~~~ 155 (156)
..|. .||.-|..+ -..-|.+|..|=+..-.+...|
T Consensus 5 F~C~--~CG~~V~p~~~g~~~RNHCP~CL~S~Hvd~~pG 41 (92)
T PF12647_consen 5 FTCV--HCGLTVSPLAAGSAHRNHCPSCLSSLHVDIVPG 41 (92)
T ss_pred cCcc--ccCCCcccCCCCCCccCcCcccccccccCCCCC
Confidence 4677 787655442 2235778888866554444333
No 384
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=20.36 E-value=63 Score=25.93 Aligned_cols=24 Identities=33% Similarity=0.812 Sum_probs=16.6
Q ss_pred ccCCCCccCCceEEeEe----------CCCCccCCce
Q 031613 119 KECPNAECGAGTFMANH----------FDRHYCGKCG 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 3455556765665 6 3689999995
No 385
>KOG2378 consensus cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms]
Probab=20.31 E-value=4.6e+02 Score=23.16 Aligned_cols=63 Identities=21% Similarity=0.362 Sum_probs=42.4
Q ss_pred EEeCCCCEEEEEecCCCcHHHHHHHHHHHhCCCCCceEEe---cCCee--cc--CCCcccccccCCCCEEEEE
Q 031613 5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQ--LE--DGRTLADYNIQKESTLHLV 70 (156)
Q Consensus 5 Vk~~~g~~~~l~V~~~~TV~~LK~~I~~~~gip~~~qrL~---~~G~~--L~--d~~tL~~~gi~~~stI~l~ 70 (156)
|-.++-.-+++.+.-+.||.++-..++++.|...+ +.|+ ++|.. |+ |..-..++|+ ++.+++.
T Consensus 240 vy~~Dhsy~tl~~~vs~svqEI~~~va~k~~~see-l~LV~v~s~GEkv~lqPnd~~v~tsL~l--n~rLfv~ 309 (573)
T KOG2378|consen 240 VYLPDHSYVTLRIRVSASVQEILEAVAEKLGYSEE-LILVKVSSSGEKVILQPNDRAVFTSLGL--NSRLFVV 309 (573)
T ss_pred EEecCceEEEEEeechhHHHHHHHHHHHHhccccc-eeEEEEccCCceeeecCCcceeeeeecc--cceEEEE
Confidence 33445566788899999999999999999998776 4443 67763 33 2233344454 5566655
No 386
>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=20.23 E-value=3.6e+02 Score=19.74 Aligned_cols=40 Identities=23% Similarity=0.166 Sum_probs=25.2
Q ss_pred EEEEEeCCC--C-EEEEEecCCCcHHHHHHHHHHHhCCCCCce
Q 031613 2 QIFVKTLTG--K-TITLEVESSDTIDNVKAKIQDKEGIPPDQQ 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 455654332 2 356899999999999999999999876543
No 387
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.18 E-value=2.6e+02 Score=18.05 Aligned_cols=25 Identities=16% Similarity=0.299 Sum_probs=21.1
Q ss_pred CCCcHHHHHHHHHHHhCCCCCceEE
Q 031613 19 SSDTIDNVKAKIQDKEGIPPDQQRL 43 (156)
Q Consensus 19 ~~~TV~~LK~~I~~~~gip~~~qrL 43 (156)
...++.+|++.|+..++++..+..+
T Consensus 48 ~G~~i~~L~~~L~k~~~~~~~~i~v 72 (81)
T cd02413 48 KGRRIRELTSLVQKRFNFPEGSVEL 72 (81)
T ss_pred CchhHHHHHHHHHHHhCCCCCeEEE
Confidence 3478999999999999998777665
No 388
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=20.17 E-value=48 Score=30.46 Aligned_cols=36 Identities=25% Similarity=0.438 Sum_probs=26.2
Q ss_pred EcCCCeEEEeeccCCCCccCCceEEeEeC----------CCCccCCceeE
Q 031613 108 VDDSGKVQRLRKECPNAECGAGTFMANHF----------DRHYCGKCGLT 147 (156)
Q Consensus 108 vd~~g~~~~~~~~cp~~~c~~g~fma~h~----------~r~~cg~c~~t 147 (156)
-||.||.+.=-.-|- |-+|-.|.|. .-|+|-||.--
T Consensus 12 SDErGWaeNPLVYCD----G~nCsVAVHQaCYGIvqVPtGpWfCrKCesq 57 (900)
T KOG0956|consen 12 SDERGWAENPLVYCD----GHNCSVAVHQACYGIVQVPTGPWFCRKCESQ 57 (900)
T ss_pred cCcCCCccCceeeec----CCCceeeeehhcceeEecCCCchhhhhhhhh
Confidence 478899887444443 6677888893 58999999743
No 389
>PRK05841 flgE flagellar hook protein FlgE; Validated
Probab=20.17 E-value=1.3e+02 Score=27.25 Aligned_cols=38 Identities=18% Similarity=0.348 Sum_probs=27.3
Q ss_pred EEEEEeCCCCEEEEEecCC---------CcHHHHHHHHHHHhCCCCC
Q 031613 2 QIFVKTLTGKTITLEVESS---------DTIDNVKAKIQDKEGIPPD 39 (156)
Q Consensus 2 ~I~Vk~~~g~~~~l~V~~~---------~TV~~LK~~I~~~~gip~~ 39 (156)
.|+|...+|++..+..... .|+.+||..|++++|+..+
T Consensus 250 ~i~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~l~~~~~~~~~~~~~ 296 (603)
T PRK05841 250 NITIQKEDGKKEDFVFTYGDAEKGENQFKTLGDLKKLLKEKTGLDLN 296 (603)
T ss_pred EEEEecCCCcEEEEEEeecCccccCCceeechhhhhhhhhccccccc
Confidence 5677777787655543333 4799999999999987643
No 390
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=20.02 E-value=47 Score=27.89 Aligned_cols=25 Identities=28% Similarity=0.669 Sum_probs=17.1
Q ss_pred eccCCCCccCCceEEeEe-CCCCccCCce
Q 031613 118 RKECPNAECGAGTFMANH-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 4567766776 56667 4778887773
Done!