Query 047298
Match_columns 192
No_of_seqs 209 out of 1614
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 09:42:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047298hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13639 zf-RING_2: Ring finge 99.5 3.7E-15 7.9E-20 90.9 1.8 42 133-175 1-44 (44)
2 KOG4628 Predicted E3 ubiquitin 99.5 1.3E-14 2.9E-19 123.2 4.6 74 109-184 208-283 (348)
3 KOG0823 Predicted E3 ubiquitin 99.4 1.2E-13 2.6E-18 110.4 3.2 61 129-190 44-106 (230)
4 PHA02929 N1R/p28-like protein; 99.4 3.5E-13 7.5E-18 109.8 4.5 71 109-180 151-228 (238)
5 KOG0804 Cytoplasmic Zn-finger 99.3 9.5E-14 2.1E-18 119.8 -0.6 136 19-180 74-223 (493)
6 PF12678 zf-rbx1: RING-H2 zinc 99.3 1.1E-12 2.3E-17 88.6 3.9 46 129-175 16-73 (73)
7 PLN03208 E3 ubiquitin-protein 99.3 2.7E-12 5.9E-17 100.9 4.1 60 129-189 15-89 (193)
8 COG5540 RING-finger-containing 99.3 1.9E-12 4.2E-17 107.0 3.3 52 129-180 320-373 (374)
9 KOG0317 Predicted E3 ubiquitin 99.3 2.3E-12 5E-17 106.0 3.0 55 128-184 235-289 (293)
10 COG5243 HRD1 HRD ubiquitin lig 99.2 3.5E-12 7.7E-17 108.0 2.8 53 127-180 282-346 (491)
11 PF13923 zf-C3HC4_2: Zinc fing 99.2 8.6E-12 1.9E-16 74.0 2.9 39 135-174 1-39 (39)
12 PF13920 zf-C3HC4_3: Zinc fing 99.2 1.1E-11 2.5E-16 77.5 3.1 47 131-179 1-48 (50)
13 KOG0320 Predicted E3 ubiquitin 99.1 2.3E-11 5E-16 93.7 2.8 59 128-187 127-186 (187)
14 cd00162 RING RING-finger (Real 99.1 5.9E-11 1.3E-15 71.3 3.5 45 134-178 1-45 (45)
15 PHA02926 zinc finger-like prot 99.1 5.6E-11 1.2E-15 94.8 3.0 60 129-188 167-239 (242)
16 PF15227 zf-C3HC4_4: zinc fing 99.1 9.8E-11 2.1E-15 70.6 3.2 39 135-174 1-42 (42)
17 PF00097 zf-C3HC4: Zinc finger 99.0 2.7E-10 5.9E-15 68.0 3.0 40 135-174 1-41 (41)
18 smart00504 Ubox Modified RING 99.0 4E-10 8.6E-15 73.4 3.9 49 133-183 2-50 (63)
19 KOG0802 E3 ubiquitin ligase [P 99.0 2.4E-10 5.1E-15 103.9 1.9 52 128-180 287-342 (543)
20 COG5574 PEX10 RING-finger-cont 98.9 3.5E-10 7.6E-15 92.2 2.5 52 130-183 213-266 (271)
21 smart00184 RING Ring finger. E 98.9 1.7E-09 3.6E-14 62.7 3.2 39 135-174 1-39 (39)
22 PF12861 zf-Apc11: Anaphase-pr 98.8 2.4E-09 5.3E-14 73.5 3.6 49 131-179 20-82 (85)
23 PF14634 zf-RING_5: zinc-RING 98.8 2.7E-09 5.9E-14 64.9 3.1 42 134-176 1-44 (44)
24 TIGR00599 rad18 DNA repair pro 98.8 2E-09 4.3E-14 93.8 3.2 51 129-181 23-73 (397)
25 KOG2164 Predicted E3 ubiquitin 98.7 4.6E-09 9.9E-14 92.6 2.4 56 132-188 186-245 (513)
26 PF04564 U-box: U-box domain; 98.6 3.5E-08 7.5E-13 66.5 3.0 54 131-185 3-56 (73)
27 COG5194 APC11 Component of SCF 98.6 5.1E-08 1.1E-12 65.6 2.9 32 150-182 53-84 (88)
28 PF13445 zf-RING_UBOX: RING-ty 98.5 3.3E-08 7.3E-13 59.7 1.8 37 135-172 1-43 (43)
29 KOG0828 Predicted E3 ubiquitin 98.5 3.4E-08 7.4E-13 86.7 1.3 51 130-180 569-635 (636)
30 TIGR00570 cdk7 CDK-activating 98.5 1.1E-07 2.3E-12 80.1 4.0 52 131-182 2-57 (309)
31 KOG0287 Postreplication repair 98.5 4.6E-08 9.9E-13 82.4 1.6 55 129-185 20-74 (442)
32 COG5219 Uncharacterized conser 98.5 4.5E-08 9.8E-13 91.5 1.7 51 129-179 1466-1523(1525)
33 KOG4265 Predicted E3 ubiquitin 98.3 3.4E-07 7.3E-12 77.8 3.6 55 130-186 288-343 (349)
34 KOG0824 Predicted E3 ubiquitin 98.3 1.8E-07 4E-12 77.7 1.9 51 131-182 6-56 (324)
35 KOG1734 Predicted RING-contain 98.3 1.8E-07 4E-12 76.6 1.1 55 128-182 220-284 (328)
36 KOG1493 Anaphase-promoting com 98.3 1.3E-07 2.9E-12 63.1 0.0 30 150-179 50-81 (84)
37 COG5432 RAD18 RING-finger-cont 98.3 3.7E-07 7.9E-12 75.7 2.3 50 129-180 22-71 (391)
38 smart00744 RINGv The RING-vari 98.3 6.7E-07 1.5E-11 55.6 2.9 42 134-175 1-49 (49)
39 KOG0311 Predicted E3 ubiquitin 98.3 7E-08 1.5E-12 81.7 -2.4 52 129-180 40-91 (381)
40 KOG4172 Predicted E3 ubiquitin 98.3 2.4E-07 5.2E-12 58.0 0.5 51 129-180 4-55 (62)
41 PF11793 FANCL_C: FANCL C-term 98.3 2.5E-07 5.5E-12 61.8 0.6 50 132-181 2-68 (70)
42 KOG0978 E3 ubiquitin ligase in 98.2 2.9E-07 6.2E-12 84.7 0.5 56 131-187 642-697 (698)
43 KOG2177 Predicted E3 ubiquitin 98.2 5.2E-07 1.1E-11 74.1 1.5 46 129-176 10-55 (386)
44 KOG2930 SCF ubiquitin ligase, 98.1 1.8E-06 3.9E-11 60.9 2.4 50 129-179 43-108 (114)
45 PF14835 zf-RING_6: zf-RING of 98.1 7.8E-07 1.7E-11 57.8 0.2 49 131-182 6-54 (65)
46 KOG1039 Predicted E3 ubiquitin 97.9 5.4E-06 1.2E-10 71.1 1.9 58 130-187 159-229 (344)
47 KOG0827 Predicted E3 ubiquitin 97.8 7E-06 1.5E-10 70.5 1.9 49 132-180 4-57 (465)
48 KOG4159 Predicted E3 ubiquitin 97.8 1.3E-05 2.8E-10 70.1 2.3 51 128-180 80-130 (398)
49 KOG0297 TNF receptor-associate 97.7 1.7E-05 3.8E-10 69.5 1.8 52 129-181 18-69 (391)
50 PF11789 zf-Nse: Zinc-finger o 97.7 2.9E-05 6.3E-10 49.7 2.2 45 129-173 8-53 (57)
51 KOG1645 RING-finger-containing 97.7 3E-05 6.4E-10 67.1 2.9 54 131-184 3-61 (463)
52 KOG1785 Tyrosine kinase negati 97.6 1.7E-05 3.7E-10 68.5 1.2 47 133-180 370-417 (563)
53 KOG0825 PHD Zn-finger protein 97.6 7.7E-06 1.7E-10 75.6 -1.1 57 130-187 121-179 (1134)
54 KOG4445 Uncharacterized conser 97.6 1.4E-05 3.1E-10 66.6 0.4 55 127-181 110-188 (368)
55 KOG2879 Predicted E3 ubiquitin 97.4 0.0002 4.4E-09 59.1 4.1 54 127-180 234-288 (298)
56 KOG3970 Predicted E3 ubiquitin 97.4 0.00015 3.3E-09 58.3 3.1 53 128-180 46-106 (299)
57 KOG2660 Locus-specific chromos 97.3 4.3E-05 9.2E-10 64.5 -0.6 50 131-181 14-63 (331)
58 KOG4275 Predicted E3 ubiquitin 97.3 3.6E-05 7.9E-10 64.0 -1.4 43 132-180 300-343 (350)
59 KOG1428 Inhibitor of type V ad 97.1 0.00025 5.3E-09 69.7 2.6 54 127-180 3481-3545(3738)
60 KOG1941 Acetylcholine receptor 97.1 0.00018 3.8E-09 62.2 0.8 47 129-175 362-412 (518)
61 PF14447 Prok-RING_4: Prokaryo 97.0 0.00034 7.5E-09 44.1 1.2 48 131-182 6-53 (55)
62 KOG1814 Predicted E3 ubiquitin 96.9 0.00078 1.7E-08 58.6 2.9 49 128-176 180-237 (445)
63 KOG1002 Nucleotide excision re 96.8 0.00041 8.9E-09 62.1 0.9 57 127-184 531-591 (791)
64 KOG4739 Uncharacterized protei 96.7 0.00077 1.7E-08 54.8 1.6 44 134-180 5-49 (233)
65 KOG4692 Predicted E3 ubiquitin 96.6 0.0011 2.3E-08 56.8 2.2 51 128-180 418-468 (489)
66 PF07800 DUF1644: Protein of u 96.6 0.002 4.4E-08 49.2 3.4 34 131-165 1-47 (162)
67 PHA02862 5L protein; Provision 96.6 0.0015 3.4E-08 49.1 2.6 47 132-180 2-54 (156)
68 PHA02825 LAP/PHD finger-like p 96.6 0.0021 4.5E-08 49.2 3.4 52 128-181 4-61 (162)
69 PF12906 RINGv: RING-variant d 96.6 0.0015 3.2E-08 40.1 2.1 40 135-174 1-47 (47)
70 COG5152 Uncharacterized conser 96.5 0.0011 2.5E-08 52.4 1.6 48 129-178 193-240 (259)
71 PF10367 Vps39_2: Vacuolar sor 96.5 0.001 2.3E-08 47.2 1.1 32 130-161 76-108 (109)
72 KOG1952 Transcription factor N 96.4 0.0014 3E-08 61.6 1.7 49 129-177 188-245 (950)
73 KOG1813 Predicted E3 ubiquitin 96.4 0.0011 2.4E-08 55.4 0.8 45 133-179 242-286 (313)
74 KOG3039 Uncharacterized conser 96.3 0.0034 7.5E-08 51.3 3.0 52 131-183 220-274 (303)
75 PF14570 zf-RING_4: RING/Ubox 96.3 0.0037 8E-08 38.5 2.4 44 135-178 1-47 (48)
76 PF10272 Tmpp129: Putative tra 96.3 0.0056 1.2E-07 53.1 4.4 32 151-182 311-354 (358)
77 KOG1571 Predicted E3 ubiquitin 96.3 0.0024 5.2E-08 54.8 2.0 47 129-180 302-348 (355)
78 COG5222 Uncharacterized conser 96.2 0.002 4.4E-08 54.0 1.5 48 133-180 275-323 (427)
79 KOG0826 Predicted E3 ubiquitin 96.2 0.0057 1.2E-07 51.9 3.8 60 128-188 296-355 (357)
80 PF05883 Baculo_RING: Baculovi 96.2 0.0029 6.3E-08 47.2 1.8 34 132-165 26-67 (134)
81 PHA03096 p28-like protein; Pro 96.0 0.0035 7.5E-08 52.8 1.9 44 133-176 179-231 (284)
82 PF03854 zf-P11: P-11 zinc fin 95.9 0.0035 7.5E-08 38.2 1.0 44 134-181 4-48 (50)
83 PF04641 Rtf2: Rtf2 RING-finge 95.9 0.0079 1.7E-07 50.0 3.4 57 128-186 109-168 (260)
84 KOG1001 Helicase-like transcri 95.6 0.0051 1.1E-07 57.6 1.3 51 133-185 455-506 (674)
85 KOG4185 Predicted E3 ubiquitin 95.5 0.01 2.3E-07 49.9 2.9 47 132-178 3-54 (296)
86 COG5175 MOT2 Transcriptional r 95.2 0.011 2.4E-07 50.5 1.9 53 129-181 11-66 (480)
87 COG5236 Uncharacterized conser 95.1 0.02 4.4E-07 49.1 3.2 51 127-179 56-108 (493)
88 KOG1940 Zn-finger protein [Gen 94.9 0.015 3.3E-07 48.6 1.8 45 131-176 157-204 (276)
89 PF08746 zf-RING-like: RING-li 94.7 0.035 7.5E-07 33.3 2.7 40 135-174 1-43 (43)
90 KOG2114 Vacuolar assembly/sort 94.6 0.018 3.9E-07 54.4 1.9 44 132-179 840-883 (933)
91 KOG0298 DEAD box-containing he 94.6 0.0074 1.6E-07 59.2 -0.7 45 131-176 1152-1196(1394)
92 COG5220 TFB3 Cdk activating ki 94.3 0.021 4.6E-07 46.6 1.4 48 129-176 7-61 (314)
93 KOG3800 Predicted E3 ubiquitin 94.2 0.04 8.6E-07 46.1 2.7 45 134-178 2-50 (300)
94 KOG3002 Zn finger protein [Gen 94.0 0.04 8.6E-07 46.8 2.5 48 128-179 44-91 (299)
95 KOG3268 Predicted E3 ubiquitin 93.8 0.043 9.3E-07 42.9 2.1 53 128-180 161-229 (234)
96 KOG2817 Predicted E3 ubiquitin 93.7 0.059 1.3E-06 46.9 3.0 47 131-177 333-383 (394)
97 KOG0801 Predicted E3 ubiquitin 93.5 0.027 5.8E-07 43.4 0.6 29 129-157 174-204 (205)
98 KOG0827 Predicted E3 ubiquitin 93.4 0.0043 9.4E-08 53.7 -4.3 53 129-182 193-248 (465)
99 KOG3899 Uncharacterized conser 93.0 0.038 8.2E-07 46.4 0.8 34 151-184 325-370 (381)
100 KOG2034 Vacuolar sorting prote 92.7 0.055 1.2E-06 51.5 1.5 37 129-165 814-851 (911)
101 KOG1100 Predicted E3 ubiquitin 92.2 0.085 1.9E-06 42.5 1.8 40 135-180 161-201 (207)
102 COG5183 SSM4 Protein involved 91.3 0.14 3E-06 48.5 2.3 53 128-180 8-67 (1175)
103 KOG2932 E3 ubiquitin ligase in 91.1 0.093 2E-06 44.5 0.9 43 133-178 91-133 (389)
104 KOG0309 Conserved WD40 repeat- 90.8 0.14 3E-06 48.2 1.8 40 133-173 1029-1069(1081)
105 KOG3053 Uncharacterized conser 90.6 0.1 2.2E-06 43.1 0.7 53 128-180 16-83 (293)
106 KOG4367 Predicted Zn-finger pr 89.1 0.18 3.8E-06 44.7 1.1 35 130-165 2-36 (699)
107 PF05290 Baculo_IE-1: Baculovi 88.3 0.55 1.2E-05 35.1 3.1 53 130-182 78-135 (140)
108 PF02891 zf-MIZ: MIZ/SP-RING z 88.3 0.45 9.7E-06 29.4 2.3 44 133-177 3-50 (50)
109 KOG3161 Predicted E3 ubiquitin 88.2 0.2 4.3E-06 46.4 0.9 41 131-176 10-54 (861)
110 KOG4362 Transcriptional regula 88.1 0.11 2.4E-06 48.4 -0.8 49 131-180 20-70 (684)
111 KOG4718 Non-SMC (structural ma 87.1 0.32 6.9E-06 39.1 1.3 45 130-175 179-223 (235)
112 KOG1609 Protein involved in mR 84.7 0.63 1.4E-05 39.1 2.1 48 132-179 78-134 (323)
113 KOG3113 Uncharacterized conser 82.4 1.2 2.6E-05 36.8 2.7 54 130-186 109-165 (293)
114 KOG0825 PHD Zn-finger protein 82.3 0.7 1.5E-05 43.9 1.5 52 129-180 93-155 (1134)
115 KOG0802 E3 ubiquitin ligase [P 81.9 0.55 1.2E-05 43.1 0.6 54 127-186 474-527 (543)
116 KOG1812 Predicted E3 ubiquitin 81.1 0.75 1.6E-05 40.5 1.2 36 130-165 144-182 (384)
117 KOG1829 Uncharacterized conser 80.9 0.62 1.3E-05 42.9 0.6 42 129-174 508-556 (580)
118 KOG0269 WD40 repeat-containing 76.6 1.9 4.2E-05 40.8 2.4 40 133-173 780-820 (839)
119 KOG1812 Predicted E3 ubiquitin 76.2 1.4 2.9E-05 38.9 1.3 43 131-174 305-351 (384)
120 PF06844 DUF1244: Protein of u 73.8 2 4.3E-05 28.1 1.2 12 154-165 11-22 (68)
121 KOG1815 Predicted E3 ubiquitin 73.6 2 4.2E-05 38.5 1.7 55 129-183 67-130 (444)
122 KOG2066 Vacuolar assembly/sort 70.2 1.8 4E-05 41.1 0.7 41 132-174 784-830 (846)
123 PF10571 UPF0547: Uncharacteri 68.4 2.5 5.3E-05 22.5 0.7 6 135-140 3-8 (26)
124 TIGR00622 ssl1 transcription f 67.9 5.9 0.00013 28.8 2.8 43 132-175 55-110 (112)
125 KOG2068 MOT2 transcription fac 67.3 4 8.8E-05 35.0 2.1 48 132-180 249-299 (327)
126 COG5109 Uncharacterized conser 66.5 4.5 9.7E-05 34.7 2.2 46 131-176 335-384 (396)
127 PF06906 DUF1272: Protein of u 62.7 8.5 0.00018 24.4 2.4 28 150-180 24-53 (57)
128 PF13901 DUF4206: Domain of un 62.5 5.5 0.00012 31.8 2.0 40 130-175 150-196 (202)
129 PF04423 Rad50_zn_hook: Rad50 62.1 3 6.5E-05 25.9 0.3 15 168-182 20-34 (54)
130 KOG3842 Adaptor protein Pellin 61.0 8.1 0.00018 33.2 2.8 52 129-180 338-415 (429)
131 PF00628 PHD: PHD-finger; Int 60.7 4.9 0.00011 24.2 1.1 42 134-175 1-49 (51)
132 PF10497 zf-4CXXC_R1: Zinc-fin 59.3 13 0.00028 26.5 3.3 45 132-176 7-69 (105)
133 KOG2807 RNA polymerase II tran 58.4 10 0.00022 32.6 3.0 60 116-176 314-375 (378)
134 PF04216 FdhE: Protein involve 57.4 1.3 2.8E-05 37.2 -2.5 45 131-176 171-219 (290)
135 smart00249 PHD PHD zinc finger 55.7 8.3 0.00018 22.0 1.5 29 134-162 1-31 (47)
136 PF01363 FYVE: FYVE zinc finge 55.7 4.9 0.00011 25.9 0.5 36 129-164 6-44 (69)
137 PF14569 zf-UDP: Zinc-binding 55.7 19 0.0004 24.4 3.3 51 129-179 6-62 (80)
138 KOG4218 Nuclear hormone recept 54.1 9.3 0.0002 33.2 2.1 50 128-177 11-76 (475)
139 smart00734 ZnF_Rad18 Rad18-lik 49.9 9 0.00019 20.2 0.9 13 170-182 3-15 (26)
140 PF14446 Prok-RING_1: Prokaryo 49.1 23 0.00051 22.2 2.8 31 131-161 4-37 (54)
141 PRK03564 formate dehydrogenase 47.9 6.7 0.00014 33.6 0.2 45 131-176 186-234 (309)
142 PF07975 C1_4: TFIIH C1-like d 47.8 11 0.00023 23.4 1.1 25 150-175 26-50 (51)
143 COG3492 Uncharacterized protei 47.6 8.8 0.00019 26.8 0.8 12 154-165 42-53 (104)
144 smart00132 LIM Zinc-binding do 46.8 24 0.00052 19.2 2.5 36 135-179 2-38 (39)
145 KOG3039 Uncharacterized conser 46.3 15 0.00033 30.5 2.0 34 131-165 42-75 (303)
146 smart00647 IBR In Between Ring 46.0 3.9 8.5E-05 25.6 -1.1 14 150-163 45-58 (64)
147 KOG0824 Predicted E3 ubiquitin 45.1 6.4 0.00014 33.5 -0.3 52 127-179 100-151 (324)
148 smart00064 FYVE Protein presen 44.3 17 0.00036 23.3 1.7 35 131-165 9-46 (68)
149 PF13832 zf-HC5HC2H_2: PHD-zin 43.6 21 0.00045 25.1 2.3 33 131-163 54-88 (110)
150 KOG4443 Putative transcription 43.1 13 0.00029 34.8 1.4 48 131-178 17-72 (694)
151 PF13240 zinc_ribbon_2: zinc-r 43.1 4.3 9.4E-05 20.8 -1.0 9 168-176 13-21 (23)
152 PF00412 LIM: LIM domain; Int 42.9 18 0.0004 22.0 1.7 38 135-181 1-39 (58)
153 cd00065 FYVE FYVE domain; Zinc 42.9 16 0.00035 22.3 1.4 34 132-165 2-38 (57)
154 COG3813 Uncharacterized protei 40.6 19 0.00041 24.1 1.4 27 152-181 28-54 (84)
155 TIGR01562 FdhE formate dehydro 38.3 9.1 0.0002 32.7 -0.4 45 131-176 183-232 (305)
156 KOG3005 GIY-YIG type nuclease 37.5 26 0.00056 29.4 2.1 50 133-182 183-246 (276)
157 PF04710 Pellino: Pellino; In 36.2 12 0.00026 33.1 0.0 50 131-180 327-402 (416)
158 PLN02189 cellulose synthase 36.1 41 0.0009 33.5 3.6 50 129-179 31-87 (1040)
159 PF07191 zinc-ribbons_6: zinc- 35.7 1.9 4.1E-05 28.7 -3.9 40 133-179 2-41 (70)
160 PF02318 FYVE_2: FYVE-type zin 35.7 21 0.00046 25.8 1.3 45 131-176 53-102 (118)
161 cd00350 rubredoxin_like Rubred 35.3 25 0.00053 19.4 1.2 20 150-176 6-25 (33)
162 KOG3799 Rab3 effector RIM1 and 32.5 16 0.00036 27.4 0.2 51 128-178 61-117 (169)
163 PF09723 Zn-ribbon_8: Zinc rib 32.1 11 0.00023 22.2 -0.7 26 149-176 9-34 (42)
164 PF09237 GAGA: GAGA factor; I 32.0 14 0.0003 23.1 -0.2 11 170-180 26-36 (54)
165 COG1545 Predicted nucleic-acid 31.4 25 0.00055 26.3 1.1 21 149-178 33-53 (140)
166 PLN02436 cellulose synthase A 30.8 56 0.0012 32.7 3.6 50 129-179 33-89 (1094)
167 PF12773 DZR: Double zinc ribb 30.4 33 0.00072 20.4 1.3 28 154-181 13-42 (50)
168 KOG3726 Uncharacterized conser 29.8 24 0.00053 33.3 0.9 39 132-174 654-695 (717)
169 PF14311 DUF4379: Domain of un 29.0 36 0.00078 20.9 1.3 23 150-174 33-55 (55)
170 KOG3579 Predicted E3 ubiquitin 28.8 38 0.00083 28.7 1.8 35 130-165 266-304 (352)
171 KOG4185 Predicted E3 ubiquitin 28.6 8.6 0.00019 32.2 -2.1 48 130-177 205-265 (296)
172 PF05715 zf-piccolo: Piccolo Z 27.7 31 0.00067 22.1 0.8 13 168-180 2-14 (61)
173 COG4647 AcxC Acetone carboxyla 27.4 38 0.00083 25.3 1.4 24 134-158 59-82 (165)
174 KOG2979 Protein involved in DN 27.3 30 0.00065 28.8 1.0 46 131-177 175-222 (262)
175 PF03119 DNA_ligase_ZBD: NAD-d 26.0 23 0.0005 18.9 0.0 12 170-181 1-12 (28)
176 PF13771 zf-HC5HC2H: PHD-like 25.4 65 0.0014 21.5 2.3 32 131-162 35-68 (90)
177 PF01485 IBR: IBR domain; Int 25.4 8.2 0.00018 24.0 -2.2 14 150-163 45-58 (64)
178 KOG1815 Predicted E3 ubiquitin 25.4 20 0.00043 32.1 -0.5 35 131-165 225-266 (444)
179 KOG4021 Mitochondrial ribosoma 25.2 33 0.00071 27.5 0.8 22 157-178 97-118 (239)
180 PRK00418 DNA gyrase inhibitor; 24.4 38 0.00082 21.9 0.8 13 168-180 6-18 (62)
181 PF10083 DUF2321: Uncharacteri 23.9 48 0.001 25.5 1.4 25 152-180 27-51 (158)
182 PF14169 YdjO: Cold-inducible 23.8 53 0.0012 21.0 1.4 20 130-149 37-56 (59)
183 PRK11827 hypothetical protein; 23.3 28 0.00061 22.3 0.1 19 162-181 3-21 (60)
184 PF07227 DUF1423: Protein of u 23.1 57 0.0012 29.3 2.0 31 133-163 129-164 (446)
185 PF13913 zf-C2HC_2: zinc-finge 22.7 42 0.00091 17.3 0.7 17 169-185 3-19 (25)
186 KOG2113 Predicted RNA binding 22.5 24 0.00051 30.4 -0.5 53 129-183 133-187 (394)
187 COG2835 Uncharacterized conser 22.4 40 0.00086 21.7 0.6 12 169-180 9-20 (60)
188 PF09889 DUF2116: Uncharacteri 22.3 53 0.0011 21.0 1.2 15 167-181 2-16 (59)
189 PRK01343 zinc-binding protein; 22.1 51 0.0011 20.9 1.1 13 167-179 8-20 (57)
190 TIGR01367 pyrE_Therm orotate p 22.1 32 0.00069 27.0 0.2 19 167-185 168-186 (187)
191 PF06750 DiS_P_DiS: Bacterial 21.7 80 0.0017 21.8 2.1 22 160-182 51-72 (92)
192 KOG4577 Transcription factor L 20.7 19 0.00042 30.5 -1.4 43 131-182 91-134 (383)
193 PLN02195 cellulose synthase A 20.3 1.3E+02 0.0029 29.9 3.9 49 131-179 5-59 (977)
No 1
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.52 E-value=3.7e-15 Score=90.94 Aligned_cols=42 Identities=45% Similarity=1.130 Sum_probs=35.9
Q ss_pred cccccccc--cCCCceEEecCCCccChHhHHHHHhCCCCCCcccC
Q 047298 133 ERCAICLG--SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCR 175 (192)
Q Consensus 133 ~~C~ICl~--~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR 175 (192)
++|+||++ ...+.++.++|+|+||.+||..|++ .+.+||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~-~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLK-RNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHH-HSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHH-hCCcCCccC
Confidence 47999999 3466778889999999999999999 788999997
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.50 E-value=1.3e-14 Score=123.16 Aligned_cols=74 Identities=28% Similarity=0.615 Sum_probs=55.5
Q ss_pred hHHHHHhhccceeeeccCcccccccccccccc--cCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhhhh
Q 047298 109 KKDVVKYLQSQPIVVDCEEEEEEEERCAICLG--SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIE 184 (192)
Q Consensus 109 ~~~~~~~l~~~~~~~~~~~~~~~~~~C~ICl~--~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~ 184 (192)
.+..+++++...+.... ......+|+||+| ..++.++.|||+|.||..||++||...+..||+||+++.+....
T Consensus 208 ~k~~l~~~p~~~f~~~~--~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~~ 283 (348)
T KOG4628|consen 208 IKRLLKKLPVRTFTKGD--DEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSGS 283 (348)
T ss_pred HHHHHhhCCcEEecccc--ccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCCC
Confidence 45666667777766222 1222259999999 66778899999999999999999994446699999998775543
No 3
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.40 E-value=1.2e-13 Score=110.44 Aligned_cols=61 Identities=21% Similarity=0.612 Sum_probs=53.1
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhC--CCCCCcccCcccchhhhhhccCCC
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDN--RNYSCPLCRFDMATAVIESMFSKP 190 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~--~~~~CP~CR~~l~~~~~~~~~~~~ 190 (192)
+....+|.||||.+.++|+ +.|||+||+.||.+||.. .+..||+||..|..+.+.++|.+.
T Consensus 44 ~~~~FdCNICLd~akdPVv-TlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGrG 106 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVV-TLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGRG 106 (230)
T ss_pred CCCceeeeeeccccCCCEE-eecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeeccC
Confidence 5678999999999999988 669999999999999984 345699999999999998888654
No 4
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.38 E-value=3.5e-13 Score=109.80 Aligned_cols=71 Identities=25% Similarity=0.514 Sum_probs=49.6
Q ss_pred hHHHHHhhccceeeeccCcccccccccccccccCCC-c------eEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 109 KKDVVKYLQSQPIVVDCEEEEEEEERCAICLGSGTG-S------VIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 109 ~~~~~~~l~~~~~~~~~~~~~~~~~~C~ICl~~~~~-~------~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
.+.++.++|..............+.+|+||++...+ + .+.++|+|.||..||..|++ .+.+||+||..+..
T Consensus 151 ~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-~~~tCPlCR~~~~~ 228 (238)
T PHA02929 151 YKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-EKNTCPVCRTPFIS 228 (238)
T ss_pred hHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-cCCCCCCCCCEeeE
Confidence 344555566554332111234457899999994332 2 13348999999999999999 89999999998874
No 5
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=99.35 E-value=9.5e-14 Score=119.78 Aligned_cols=136 Identities=22% Similarity=0.346 Sum_probs=82.8
Q ss_pred cccccccccCCeeeeccccccccCCCCC----------CchhhhhhhhhhccCCCcc-cHHHHHHHHHHhhhhhhhhccc
Q 047298 19 HKKMAIPIKGNRVNINDLFHFFEFPKAS----------SRYDDLRGLILNVKRLPAD-TYHELVDDILISMTDEIDTIIE 87 (192)
Q Consensus 19 ~~~~~~~~~~~~v~~~~l~~~~~~~~~s----------~~~~~~~~~~~~~~~l~~~-~f~~~~~~i~~~~~~~~~~~~~ 87 (192)
..|++|++.|+++.-.+|+++.. +... +.-++|..++..-...-.+ +|.++-.+-+..++..++
T Consensus 74 ~~mLcilaVP~~mt~~Dll~F~~-~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e~C---- 148 (493)
T KOG0804|consen 74 STMLCILAVPAYMTSHDLLRFCA-SFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPEVC---- 148 (493)
T ss_pred CcEEEEEeccccccHHHHHHHHH-HHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCccce----
Confidence 89999999999999999999987 2222 1112222222111111112 222444455544555555
Q ss_pred CceEEEEEEEEEeeecCCCCChHHHHHhhccceeeeccCcccccccccccccccCCCc---eEEecCCCccChHhHHHHH
Q 047298 88 HDVTVEFVVVVVIYRNNVNVTKKDVVKYLQSQPIVVDCEEEEEEEERCAICLGSGTGS---VIQMDCLHQFHEKCIACWF 164 (192)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~C~ICl~~~~~~---~~~l~C~H~Fh~~CI~~Wl 164 (192)
++..+..+.+.........+ .....+.++|||||+.++.. ++...|.|.||..|+.+|
T Consensus 149 -hll~V~~ve~~~s~d~as~~-----------------~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w- 209 (493)
T KOG0804|consen 149 -HLLYVDRVEVTESEDGASEP-----------------PTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW- 209 (493)
T ss_pred -eEEEEEEEEEEecccCCCCC-----------------CCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhc-
Confidence 44444444444222222111 12344688999999944443 365699999999999999
Q ss_pred hCCCCCCcccCcccch
Q 047298 165 DNRNYSCPLCRFDMAT 180 (192)
Q Consensus 165 ~~~~~~CP~CR~~l~~ 180 (192)
...+||+||.....
T Consensus 210 --~~~scpvcR~~q~p 223 (493)
T KOG0804|consen 210 --WDSSCPVCRYCQSP 223 (493)
T ss_pred --ccCcChhhhhhcCc
Confidence 77999999987664
No 6
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=99.33 E-value=1.1e-12 Score=88.60 Aligned_cols=46 Identities=37% Similarity=0.885 Sum_probs=35.2
Q ss_pred cccccccccccccC------------CCceEEecCCCccChHhHHHHHhCCCCCCcccC
Q 047298 129 EEEEERCAICLGSG------------TGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCR 175 (192)
Q Consensus 129 ~~~~~~C~ICl~~~------------~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR 175 (192)
+..++.|+||++.. .-.+...+|+|.||..||.+|++ .+.+||+||
T Consensus 16 ~~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~-~~~~CP~CR 73 (73)
T PF12678_consen 16 DIADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLK-QNNTCPLCR 73 (73)
T ss_dssp SSCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHT-TSSB-TTSS
T ss_pred cCcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHh-cCCcCCCCC
Confidence 33455699999943 12334459999999999999999 888999998
No 7
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.28 E-value=2.7e-12 Score=100.90 Aligned_cols=60 Identities=27% Similarity=0.615 Sum_probs=49.5
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhC---------------CCCCCcccCcccchhhhhhccCC
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDN---------------RNYSCPLCRFDMATAVIESMFSK 189 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~---------------~~~~CP~CR~~l~~~~~~~~~~~ 189 (192)
..++.+|+||++...++++ ++|||.||+.||..|+.. ....||+||..+......++|.+
T Consensus 15 ~~~~~~CpICld~~~dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygr 89 (193)
T PLN03208 15 SGGDFDCNICLDQVRDPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYGR 89 (193)
T ss_pred CCCccCCccCCCcCCCcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeecc
Confidence 4467899999998777766 799999999999999852 23579999999988877777754
No 8
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.28 E-value=1.9e-12 Score=106.99 Aligned_cols=52 Identities=27% Similarity=0.744 Sum_probs=44.3
Q ss_pred cccccccccccc--cCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 129 EEEEERCAICLG--SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 129 ~~~~~~C~ICl~--~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
....-+|+|||+ ...+.++.+||.|.||..|+.+|+...+..||+||.++|+
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 345589999999 4456678889999999999999998667889999999875
No 9
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.26 E-value=2.3e-12 Score=105.98 Aligned_cols=55 Identities=27% Similarity=0.648 Sum_probs=47.1
Q ss_pred ccccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhhhh
Q 047298 128 EEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIE 184 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~ 184 (192)
.......|.+||+...++.. +||||+||+.||..|.. .+..||+||.++.++.+.
T Consensus 235 i~~a~~kC~LCLe~~~~pSa-TpCGHiFCWsCI~~w~~-ek~eCPlCR~~~~pskvi 289 (293)
T KOG0317|consen 235 IPEATRKCSLCLENRSNPSA-TPCGHIFCWSCILEWCS-EKAECPLCREKFQPSKVI 289 (293)
T ss_pred CCCCCCceEEEecCCCCCCc-CcCcchHHHHHHHHHHc-cccCCCcccccCCCccee
Confidence 34566899999998777666 89999999999999999 888899999998876543
No 10
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.23 E-value=3.5e-12 Score=108.01 Aligned_cols=53 Identities=25% Similarity=0.715 Sum_probs=43.8
Q ss_pred cccccccccccccccCCC------------ceEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 127 EEEEEEERCAICLGSGTG------------SVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 127 ~~~~~~~~C~ICl~~~~~------------~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
....+|..|.||+++... ...+|||||+||..|++.|+. ++.+||+||.++.-
T Consensus 282 ql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-RqQTCPICr~p~if 346 (491)
T COG5243 282 QLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVIF 346 (491)
T ss_pred hhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-hccCCCcccCcccc
Confidence 446678999999994211 235699999999999999999 99999999999644
No 11
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=99.21 E-value=8.6e-12 Score=74.01 Aligned_cols=39 Identities=36% Similarity=0.939 Sum_probs=34.1
Q ss_pred cccccccCCCceEEecCCCccChHhHHHHHhCCCCCCccc
Q 047298 135 CAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLC 174 (192)
Q Consensus 135 C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~C 174 (192)
|+||++...++++.++|||+||.+|+.+|++ .+..||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~-~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLE-KNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHH-CTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHH-CcCCCcCC
Confidence 8999998888877789999999999999999 68899998
No 12
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=99.20 E-value=1.1e-11 Score=77.46 Aligned_cols=47 Identities=34% Similarity=0.837 Sum_probs=38.9
Q ss_pred cccccccccccCCCceEEecCCCc-cChHhHHHHHhCCCCCCcccCcccc
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQ-FHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~-Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
++..|.||++...+ +..+||||. ||..|+..|++ ....||+||+++.
T Consensus 1 ~~~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~-~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 1 EDEECPICFENPRD-VVLLPCGHLCFCEECAERLLK-RKKKCPICRQPIE 48 (50)
T ss_dssp -HSB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHH-TTSBBTTTTBB-S
T ss_pred CcCCCccCCccCCc-eEEeCCCChHHHHHHhHHhcc-cCCCCCcCChhhc
Confidence 36789999997655 455899999 99999999999 9999999999875
No 13
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.14 E-value=2.3e-11 Score=93.73 Aligned_cols=59 Identities=27% Similarity=0.634 Sum_probs=48.2
Q ss_pred ccccccccccccccCCCce-EEecCCCccChHhHHHHHhCCCCCCcccCcccchhhhhhcc
Q 047298 128 EEEEEERCAICLGSGTGSV-IQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIESMF 187 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~-~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~~~ 187 (192)
..++-+.|+|||+...+.+ ....|||+||..||...++ ....||+||+.|.....+.+|
T Consensus 127 ~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk-~~~~CP~C~kkIt~k~~~rI~ 186 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK-NTNKCPTCRKKITHKQFHRIY 186 (187)
T ss_pred ccccccCCCceecchhhccccccccchhHHHHHHHHHHH-hCCCCCCcccccchhhheecc
Confidence 4556699999999554444 4479999999999999999 899999999988776666555
No 14
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=99.12 E-value=5.9e-11 Score=71.32 Aligned_cols=45 Identities=36% Similarity=0.880 Sum_probs=37.3
Q ss_pred ccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCccc
Q 047298 134 RCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDM 178 (192)
Q Consensus 134 ~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l 178 (192)
.|+||++.....+...+|+|.||..|+..|+...+..||+||..+
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 599999966566665579999999999999983377899999764
No 15
>PHA02926 zinc finger-like protein; Provisional
Probab=99.08 E-value=5.6e-11 Score=94.77 Aligned_cols=60 Identities=25% Similarity=0.638 Sum_probs=42.9
Q ss_pred cccccccccccccCCCc--------eEEecCCCccChHhHHHHHhCC-----CCCCcccCcccchhhhhhccC
Q 047298 129 EEEEERCAICLGSGTGS--------VIQMDCLHQFHEKCIACWFDNR-----NYSCPLCRFDMATAVIESMFS 188 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~--------~~~l~C~H~Fh~~CI~~Wl~~~-----~~~CP~CR~~l~~~~~~~~~~ 188 (192)
...+.+|+||+|...++ ....+|+|.||..||..|.+.+ ..+||+||..+..-.+...|.
T Consensus 167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSrf~~ 239 (242)
T PHA02926 167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSKFYK 239 (242)
T ss_pred ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeecccccee
Confidence 44578999999942211 1223999999999999999732 345999999987655554444
No 16
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.08 E-value=9.8e-11 Score=70.60 Aligned_cols=39 Identities=33% Similarity=0.849 Sum_probs=30.3
Q ss_pred cccccccCCCceEEecCCCccChHhHHHHHhCCC---CCCccc
Q 047298 135 CAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRN---YSCPLC 174 (192)
Q Consensus 135 C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~---~~CP~C 174 (192)
|+||++.+.+++. |+|||.||..||..|.+... ..||.|
T Consensus 1 CpiC~~~~~~Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVS-LPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccc-cCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999999887 99999999999999998432 369988
No 17
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=99.00 E-value=2.7e-10 Score=68.04 Aligned_cols=40 Identities=38% Similarity=0.983 Sum_probs=35.5
Q ss_pred cccccccCCCceEEecCCCccChHhHHHHHh-CCCCCCccc
Q 047298 135 CAICLGSGTGSVIQMDCLHQFHEKCIACWFD-NRNYSCPLC 174 (192)
Q Consensus 135 C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~-~~~~~CP~C 174 (192)
|+||++....++..++|+|.||..|+.+|++ .....||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999998888776689999999999999998 566779998
No 18
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=99.00 E-value=4e-10 Score=73.36 Aligned_cols=49 Identities=16% Similarity=0.280 Sum_probs=42.8
Q ss_pred cccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhhh
Q 047298 133 ERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVI 183 (192)
Q Consensus 133 ~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~ 183 (192)
..|+||.+.+.+++. ++|||+|+.+||..|++ .+.+||+|+..+...+.
T Consensus 2 ~~Cpi~~~~~~~Pv~-~~~G~v~~~~~i~~~~~-~~~~cP~~~~~~~~~~l 50 (63)
T smart00504 2 FLCPISLEVMKDPVI-LPSGQTYERRAIEKWLL-SHGTDPVTGQPLTHEDL 50 (63)
T ss_pred cCCcCCCCcCCCCEE-CCCCCEEeHHHHHHHHH-HCCCCCCCcCCCChhhc
Confidence 479999998888876 89999999999999999 68899999999865443
No 19
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.95 E-value=2.4e-10 Score=103.91 Aligned_cols=52 Identities=33% Similarity=0.791 Sum_probs=43.1
Q ss_pred ccccccccccccccCCCc----eEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 128 EEEEEERCAICLGSGTGS----VIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~----~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
....+..|+||+|..... ..+|+|+|+||..|+..|++ ++.+||+||..+..
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~e-r~qtCP~CR~~~~~ 342 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFE-RQQTCPTCRTVLYD 342 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHH-HhCcCCcchhhhhc
Confidence 445689999999944442 56699999999999999999 99999999995543
No 20
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=3.5e-10 Score=92.17 Aligned_cols=52 Identities=27% Similarity=0.688 Sum_probs=45.0
Q ss_pred ccccccccccccCCCceEEecCCCccChHhHHH-HHhCCCCC-CcccCcccchhhh
Q 047298 130 EEEERCAICLGSGTGSVIQMDCLHQFHEKCIAC-WFDNRNYS-CPLCRFDMATAVI 183 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~-Wl~~~~~~-CP~CR~~l~~~~~ 183 (192)
..++.|+||++....+.. ++|||+||..||.. |-. ++.. ||+||+.+.+..+
T Consensus 213 ~~d~kC~lC~e~~~~ps~-t~CgHlFC~~Cl~~~~t~-~k~~~CplCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPEVPSC-TPCGHLFCLSCLLISWTK-KKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccCCccc-ccccchhhHHHHHHHHHh-hccccCchhhhhccchhh
Confidence 568999999998888776 89999999999999 988 5555 9999999877655
No 21
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.88 E-value=1.7e-09 Score=62.67 Aligned_cols=39 Identities=36% Similarity=0.974 Sum_probs=32.4
Q ss_pred cccccccCCCceEEecCCCccChHhHHHHHhCCCCCCccc
Q 047298 135 CAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLC 174 (192)
Q Consensus 135 C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~C 174 (192)
|+||++... ....++|+|.||..|+..|+...+..||+|
T Consensus 1 C~iC~~~~~-~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELK-DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCC-CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 789999744 455589999999999999998556679987
No 22
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.85 E-value=2.4e-09 Score=73.50 Aligned_cols=49 Identities=29% Similarity=0.725 Sum_probs=36.1
Q ss_pred cccccccccccC----------C-C-ceEEecCCCccChHhHHHHHhC--CCCCCcccCcccc
Q 047298 131 EEERCAICLGSG----------T-G-SVIQMDCLHQFHEKCIACWFDN--RNYSCPLCRFDMA 179 (192)
Q Consensus 131 ~~~~C~ICl~~~----------~-~-~~~~l~C~H~Fh~~CI~~Wl~~--~~~~CP~CR~~l~ 179 (192)
+++.|.||...+ + + +++.-.|+|.||..||.+|+.. .+..||+||++..
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 367777777621 1 1 3343489999999999999984 2568999998764
No 23
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.84 E-value=2.7e-09 Score=64.86 Aligned_cols=42 Identities=31% Similarity=0.680 Sum_probs=35.3
Q ss_pred ccccccccC--CCceEEecCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 134 RCAICLGSG--TGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 134 ~C~ICl~~~--~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
.|+||++.. ......++|||+||..|+..+.. ....||+||+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~-~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKG-KSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcC-CCCCCcCCCC
Confidence 489999944 44566679999999999999985 7889999985
No 24
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.83 E-value=2e-09 Score=93.75 Aligned_cols=51 Identities=29% Similarity=0.590 Sum_probs=44.3
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchh
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATA 181 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~ 181 (192)
.+....|+||++....++. ++|+|.||..||..|+. ....||+||..+...
T Consensus 23 Le~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~~~l~-~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 23 LDTSLRCHICKDFFDVPVL-TSCSHTFCSLCIRRCLS-NQPKCPLCRAEDQES 73 (397)
T ss_pred cccccCCCcCchhhhCccC-CCCCCchhHHHHHHHHh-CCCCCCCCCCccccc
Confidence 4567899999998777765 89999999999999999 777899999988654
No 25
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.73 E-value=4.6e-09 Score=92.57 Aligned_cols=56 Identities=29% Similarity=0.651 Sum_probs=45.5
Q ss_pred ccccccccccCCCceEEecCCCccChHhHHHHHhC----CCCCCcccCcccchhhhhhccC
Q 047298 132 EERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDN----RNYSCPLCRFDMATAVIESMFS 188 (192)
Q Consensus 132 ~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~----~~~~CP~CR~~l~~~~~~~~~~ 188 (192)
+..|||||+...-+++ +.|||+||..||..++.. +-..||+||..|...+..+++.
T Consensus 186 ~~~CPICL~~~~~p~~-t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~ 245 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVR-TNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFI 245 (513)
T ss_pred CCcCCcccCCCCcccc-cccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeee
Confidence 8899999997777776 569999999999988762 3457999999998876666554
No 26
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=98.59 E-value=3.5e-08 Score=66.50 Aligned_cols=54 Identities=19% Similarity=0.323 Sum_probs=42.2
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhhhhh
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIES 185 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~ 185 (192)
+...|+|+.+.+.++++ +++||.|...||..|+.....+||+|+..+......+
T Consensus 3 ~~f~CpIt~~lM~dPVi-~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~p 56 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVI-LPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIP 56 (73)
T ss_dssp GGGB-TTTSSB-SSEEE-ETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE
T ss_pred cccCCcCcCcHhhCcee-CCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceE
Confidence 46789999999999887 8999999999999999944889999999988765443
No 27
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.55 E-value=5.1e-08 Score=65.61 Aligned_cols=32 Identities=41% Similarity=0.777 Sum_probs=28.9
Q ss_pred cCCCccChHhHHHHHhCCCCCCcccCcccchhh
Q 047298 150 DCLHQFHEKCIACWFDNRNYSCPLCRFDMATAV 182 (192)
Q Consensus 150 ~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~ 182 (192)
.|.|.||..||.+||. .+..||++|++...+.
T Consensus 53 ~CnHaFH~HCI~rWL~-Tk~~CPld~q~w~~~~ 84 (88)
T COG5194 53 VCNHAFHDHCIYRWLD-TKGVCPLDRQTWVLAD 84 (88)
T ss_pred ecchHHHHHHHHHHHh-hCCCCCCCCceeEEec
Confidence 8999999999999999 8999999999876543
No 28
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.55 E-value=3.3e-08 Score=59.71 Aligned_cols=37 Identities=24% Similarity=0.665 Sum_probs=20.8
Q ss_pred cccccccCCC---ceEEecCCCccChHhHHHHHhCC---CCCCc
Q 047298 135 CAICLGSGTG---SVIQMDCLHQFHEKCIACWFDNR---NYSCP 172 (192)
Q Consensus 135 C~ICl~~~~~---~~~~l~C~H~Fh~~CI~~Wl~~~---~~~CP 172 (192)
|+||.+ +.+ +...|+|||+||.+||.+|++++ ...||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 333 34458999999999999999832 34576
No 29
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=3.4e-08 Score=86.67 Aligned_cols=51 Identities=27% Similarity=0.788 Sum_probs=38.4
Q ss_pred ccccccccccccC-----CCc-----------eEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 130 EEEERCAICLGSG-----TGS-----------VIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 130 ~~~~~C~ICl~~~-----~~~-----------~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
.....|+|||... ..+ -..+||.|+||..|+..|....+-.||+||.+++.
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 3457899999921 111 11249999999999999999555589999999875
No 30
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.49 E-value=1.1e-07 Score=80.11 Aligned_cols=52 Identities=25% Similarity=0.501 Sum_probs=38.8
Q ss_pred cccccccccc--cCCCceEEe--cCCCccChHhHHHHHhCCCCCCcccCcccchhh
Q 047298 131 EEERCAICLG--SGTGSVIQM--DCLHQFHEKCIACWFDNRNYSCPLCRFDMATAV 182 (192)
Q Consensus 131 ~~~~C~ICl~--~~~~~~~~l--~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~ 182 (192)
+++.||||.+ ........+ +|||.||..|+...+......||.|+..+....
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 4679999999 233332222 799999999999966546778999998876543
No 31
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.49 E-value=4.6e-08 Score=82.44 Aligned_cols=55 Identities=24% Similarity=0.541 Sum_probs=47.7
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhhhhh
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIES 185 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~ 185 (192)
.+....|-||.+++..+++ +||+|.||.-||...|. .+..||.|+.++.+....+
T Consensus 20 lD~lLRC~IC~eyf~ip~i-tpCsHtfCSlCIR~~L~-~~p~CP~C~~~~~Es~Lr~ 74 (442)
T KOG0287|consen 20 LDDLLRCGICFEYFNIPMI-TPCSHTFCSLCIRKFLS-YKPQCPTCCVTVTESDLRN 74 (442)
T ss_pred hHHHHHHhHHHHHhcCcee-ccccchHHHHHHHHHhc-cCCCCCceecccchhhhhh
Confidence 3456789999998888877 79999999999999999 9999999999987766544
No 32
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.48 E-value=4.5e-08 Score=91.45 Aligned_cols=51 Identities=31% Similarity=0.742 Sum_probs=38.6
Q ss_pred cccccccccccccCC-----Cce-EEecCCCccChHhHHHHHhC-CCCCCcccCcccc
Q 047298 129 EEEEERCAICLGSGT-----GSV-IQMDCLHQFHEKCIACWFDN-RNYSCPLCRFDMA 179 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~-----~~~-~~l~C~H~Fh~~CI~~Wl~~-~~~~CP~CR~~l~ 179 (192)
-.+-++|+||+.... -|- +.-.|.|.||.+|+.+|+++ .+++||+||.+++
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 456789999999211 121 22379999999999999984 6778999998775
No 33
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.35 E-value=3.4e-07 Score=77.83 Aligned_cols=55 Identities=24% Similarity=0.587 Sum_probs=45.3
Q ss_pred ccccccccccccCCCceEEecCCC-ccChHhHHHHHhCCCCCCcccCcccchhhhhhc
Q 047298 130 EEEERCAICLGSGTGSVIQMDCLH-QFHEKCIACWFDNRNYSCPLCRFDMATAVIESM 186 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~~~l~C~H-~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~~ 186 (192)
++..+|.||++...+.++ |||.| --|..|.+...- +.+.||+||+.+........
T Consensus 288 ~~gkeCVIClse~rdt~v-LPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ll~i~~ 343 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVV-LPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEELLEIYV 343 (349)
T ss_pred cCCCeeEEEecCCcceEE-ecchhhehhHhHHHHHHH-hhcCCCccccchHhhheecc
Confidence 457899999998777555 99999 789999998876 78999999999987654433
No 34
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.35 E-value=1.8e-07 Score=77.70 Aligned_cols=51 Identities=29% Similarity=0.799 Sum_probs=43.8
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhh
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAV 182 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~ 182 (192)
...+|+||+....-++. |+|+|.||.-||+--..+.+.+|++||.+++.+.
T Consensus 6 ~~~eC~IC~nt~n~Pv~-l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i 56 (324)
T KOG0824|consen 6 KKKECLICYNTGNCPVN-LYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI 56 (324)
T ss_pred cCCcceeeeccCCcCcc-ccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence 46799999997777755 9999999999999888767788999999998754
No 35
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.31 E-value=1.8e-07 Score=76.63 Aligned_cols=55 Identities=25% Similarity=0.624 Sum_probs=42.3
Q ss_pred ccccccccccccccCC---------CceEEecCCCccChHhHHHHHh-CCCCCCcccCcccchhh
Q 047298 128 EEEEEERCAICLGSGT---------GSVIQMDCLHQFHEKCIACWFD-NRNYSCPLCRFDMATAV 182 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~---------~~~~~l~C~H~Fh~~CI~~Wl~-~~~~~CP~CR~~l~~~~ 182 (192)
...++..|+||-.... +.+.+|.|+|+||..||.-|-. .++.+||.|+..+..+.
T Consensus 220 khl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r 284 (328)
T KOG1734|consen 220 KHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR 284 (328)
T ss_pred CCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence 3556889999988211 2456789999999999999964 26678999999886543
No 36
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.30 E-value=1.3e-07 Score=63.11 Aligned_cols=30 Identities=40% Similarity=1.038 Sum_probs=25.7
Q ss_pred cCCCccChHhHHHHHhC--CCCCCcccCcccc
Q 047298 150 DCLHQFHEKCIACWFDN--RNYSCPLCRFDMA 179 (192)
Q Consensus 150 ~C~H~Fh~~CI~~Wl~~--~~~~CP~CR~~l~ 179 (192)
-|.|.||..||.+|+.. .+..||+||++..
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 89999999999999974 4457999998753
No 37
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.28 E-value=3.7e-07 Score=75.68 Aligned_cols=50 Identities=28% Similarity=0.476 Sum_probs=43.4
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
.+.-..|-||-+....++. ++|||.||.-||...|. .+..||+||.+.-.
T Consensus 22 LDs~lrC~IC~~~i~ip~~-TtCgHtFCslCIR~hL~-~qp~CP~Cr~~~~e 71 (391)
T COG5432 22 LDSMLRCRICDCRISIPCE-TTCGHTFCSLCIRRHLG-TQPFCPVCREDPCE 71 (391)
T ss_pred chhHHHhhhhhheeeccee-cccccchhHHHHHHHhc-CCCCCccccccHHh
Confidence 4456789999997777666 79999999999999999 99999999997644
No 38
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=98.28 E-value=6.7e-07 Score=55.58 Aligned_cols=42 Identities=26% Similarity=0.832 Sum_probs=31.9
Q ss_pred ccccccc-cCCCceEEecCC-----CccChHhHHHHHhC-CCCCCcccC
Q 047298 134 RCAICLG-SGTGSVIQMDCL-----HQFHEKCIACWFDN-RNYSCPLCR 175 (192)
Q Consensus 134 ~C~ICl~-~~~~~~~~l~C~-----H~Fh~~CI~~Wl~~-~~~~CP~CR 175 (192)
.|.||++ ...+.....||. |.+|..|+.+|+.. ++.+||+|+
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4899998 333344557885 89999999999963 355899995
No 39
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.26 E-value=7e-08 Score=81.70 Aligned_cols=52 Identities=29% Similarity=0.591 Sum_probs=44.4
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
...+..|+|||+..........|.|.||.+||.+-+...++.||.||+.+..
T Consensus 40 ~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 40 FDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred hhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 3457899999996666666579999999999999999889999999998865
No 40
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.26 E-value=2.4e-07 Score=57.97 Aligned_cols=51 Identities=24% Similarity=0.479 Sum_probs=39.6
Q ss_pred cccccccccccccCCCceEEecCCC-ccChHhHHHHHhCCCCCCcccCcccch
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLH-QFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H-~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
++-+++|.||++-..+.+. ..||| -.|..|-.+..+..+..||+||+++..
T Consensus 4 ~~~~dECTICye~pvdsVl-YtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d 55 (62)
T KOG4172|consen 4 GQWSDECTICYEHPVDSVL-YTCGHMCMCYACGLRLKKALHGCCPICRAPIKD 55 (62)
T ss_pred cccccceeeeccCcchHHH-HHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence 3445899999997666554 58999 689999666555478899999998754
No 41
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.25 E-value=2.5e-07 Score=61.82 Aligned_cols=50 Identities=30% Similarity=0.735 Sum_probs=24.2
Q ss_pred ccccccccccC--CCceEEe-----cCCCccChHhHHHHHhC----C------CCCCcccCcccchh
Q 047298 132 EERCAICLGSG--TGSVIQM-----DCLHQFHEKCIACWFDN----R------NYSCPLCRFDMATA 181 (192)
Q Consensus 132 ~~~C~ICl~~~--~~~~~~l-----~C~H~Fh~~CI~~Wl~~----~------~~~CP~CR~~l~~~ 181 (192)
+..|.||++.. .+.+..+ .|+..||..|+..||.. + ...||.|+.+|...
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 46899999942 2222212 78899999999999973 1 13699999988653
No 42
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.22 E-value=2.9e-07 Score=84.72 Aligned_cols=56 Identities=21% Similarity=0.589 Sum_probs=48.0
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhhhhhcc
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIESMF 187 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~~~ 187 (192)
+-..|++|-+-..+ ++...|+|+||..|+.+-+..++..||.|-..++..+.+.+|
T Consensus 642 ~~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred hceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccC
Confidence 45689999964444 444799999999999999998889999999999999988876
No 43
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.20 E-value=5.2e-07 Score=74.10 Aligned_cols=46 Identities=33% Similarity=0.712 Sum_probs=40.0
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
..+...|+||++.+..+ ..++|+|.||..|+..+.. ....||.||.
T Consensus 10 ~~~~~~C~iC~~~~~~p-~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr~ 55 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREP-VLLPCGHNFCRACLTRSWE-GPLSCPVCRP 55 (386)
T ss_pred ccccccChhhHHHhhcC-ccccccchHhHHHHHHhcC-CCcCCcccCC
Confidence 45678999999977777 5589999999999999988 7789999993
No 44
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.10 E-value=1.8e-06 Score=60.95 Aligned_cols=50 Identities=28% Similarity=0.578 Sum_probs=37.2
Q ss_pred cccccccccccc-c-------------CCCceE--EecCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 129 EEEEERCAICLG-S-------------GTGSVI--QMDCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 129 ~~~~~~C~ICl~-~-------------~~~~~~--~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
+...+.|+||.. . ..+... -=.|.|.||..||.+|++ .++.||+|.++-.
T Consensus 43 Di~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlk-tr~vCPLdn~eW~ 108 (114)
T KOG2930|consen 43 DIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLK-TRNVCPLDNKEWV 108 (114)
T ss_pred eeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHh-hcCcCCCcCccee
Confidence 456778999875 1 111222 128999999999999999 9999999987643
No 45
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.08 E-value=7.8e-07 Score=57.77 Aligned_cols=49 Identities=29% Similarity=0.509 Sum_probs=26.4
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhh
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAV 182 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~ 182 (192)
+...|++|.+....++....|.|+||..||..-+. +.||+|+.+.-.++
T Consensus 6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQD 54 (65)
T ss_dssp HTTS-SSS-S--SS-B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS
T ss_pred HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHH
Confidence 45689999999888887569999999999988544 56999987765443
No 46
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.89 E-value=5.4e-06 Score=71.13 Aligned_cols=58 Identities=28% Similarity=0.646 Sum_probs=41.6
Q ss_pred ccccccccccccCCCce------EEe-cCCCccChHhHHHHHhC-C-----CCCCcccCcccchhhhhhcc
Q 047298 130 EEEERCAICLGSGTGSV------IQM-DCLHQFHEKCIACWFDN-R-----NYSCPLCRFDMATAVIESMF 187 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~------~~l-~C~H~Fh~~CI~~Wl~~-~-----~~~CP~CR~~l~~~~~~~~~ 187 (192)
..+..|.||++...+.. .++ +|.|.||..||.+|-.. + ...||.||....--.+...|
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~W 229 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFW 229 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccccccccee
Confidence 45889999999333322 223 79999999999999843 3 47899999876554444434
No 47
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.85 E-value=7e-06 Score=70.52 Aligned_cols=49 Identities=27% Similarity=0.846 Sum_probs=34.5
Q ss_pred ccccccccccC--CCceEEe-cCCCccChHhHHHHHhCC-C-CCCcccCcccch
Q 047298 132 EERCAICLGSG--TGSVIQM-DCLHQFHEKCIACWFDNR-N-YSCPLCRFDMAT 180 (192)
Q Consensus 132 ~~~C~ICl~~~--~~~~~~l-~C~H~Fh~~CI~~Wl~~~-~-~~CP~CR~~l~~ 180 (192)
-..|.||-+.. ...+.-+ .|||+||..|+..|+... . ..||.||-.++.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~ 57 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQE 57 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccc
Confidence 45899997622 2223223 599999999999999842 2 479999955543
No 48
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=1.3e-05 Score=70.15 Aligned_cols=51 Identities=29% Similarity=0.638 Sum_probs=45.6
Q ss_pred ccccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 128 EEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
....++.|.||+.....++. +||||.||..||.+-+. +...||.||.+++.
T Consensus 80 ~~~sef~c~vc~~~l~~pv~-tpcghs~c~~Cl~r~ld-~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 80 EIRSEFECCVCSRALYPPVV-TPCGHSFCLECLDRSLD-QETECPLCRDELVE 130 (398)
T ss_pred cccchhhhhhhHhhcCCCcc-ccccccccHHHHHHHhc-cCCCCccccccccc
Confidence 34678999999998888887 69999999999999888 89999999999985
No 49
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.68 E-value=1.7e-05 Score=69.53 Aligned_cols=52 Identities=27% Similarity=0.623 Sum_probs=45.1
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchh
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATA 181 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~ 181 (192)
.+++..|++|.....+++....|||.||..|+..|+. .+..||.|+..+...
T Consensus 18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~-~~~~cp~~~~~~~~~ 69 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLS-NHQKCPVCRQELTQA 69 (391)
T ss_pred CcccccCccccccccCCCCCCCCCCcccccccchhhc-cCcCCcccccccchh
Confidence 4578999999998888777569999999999999999 788999998877543
No 50
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.66 E-value=2.9e-05 Score=49.74 Aligned_cols=45 Identities=24% Similarity=0.468 Sum_probs=32.1
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHh-CCCCCCcc
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFD-NRNYSCPL 173 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~-~~~~~CP~ 173 (192)
..-...|||.+....++++...|+|+|-.+.|..|++ +....||+
T Consensus 8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 4457899999999999999889999999999999994 24567998
No 51
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=3e-05 Score=67.13 Aligned_cols=54 Identities=28% Similarity=0.718 Sum_probs=39.2
Q ss_pred cccccccccc--cC-C-CceEEecCCCccChHhHHHHHhC-CCCCCcccCcccchhhhh
Q 047298 131 EEERCAICLG--SG-T-GSVIQMDCLHQFHEKCIACWFDN-RNYSCPLCRFDMATAVIE 184 (192)
Q Consensus 131 ~~~~C~ICl~--~~-~-~~~~~l~C~H~Fh~~CI~~Wl~~-~~~~CP~CR~~l~~~~~~ 184 (192)
...+||||++ .. + ..+..+.|+|.|..+||.+|+.. ....||.|..+-......
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~ 61 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIR 61 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHH
Confidence 3568999999 22 2 24555699999999999999962 345799998765444433
No 52
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.65 E-value=1.7e-05 Score=68.53 Aligned_cols=47 Identities=32% Similarity=0.792 Sum_probs=38.1
Q ss_pred cccccccccCCCceEEecCCCccChHhHHHHHhC-CCCCCcccCcccch
Q 047298 133 ERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDN-RNYSCPLCRFDMAT 180 (192)
Q Consensus 133 ~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~-~~~~CP~CR~~l~~ 180 (192)
..|-||-+... ++.+-||||..|..|+..|... ...+||.||.++.-
T Consensus 370 eLCKICaendK-dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 370 ELCKICAENDK-DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred HHHHHhhccCC-CcccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 67999998443 3665699999999999999863 36789999998853
No 53
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.64 E-value=7.7e-06 Score=75.63 Aligned_cols=57 Identities=23% Similarity=0.484 Sum_probs=43.1
Q ss_pred ccccccccccccCCCceE--EecCCCccChHhHHHHHhCCCCCCcccCcccchhhhhhcc
Q 047298 130 EEEERCAICLGSGTGSVI--QMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIESMF 187 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~~--~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~~~ 187 (192)
.....|++|+....+..+ ..+|+|.||..||..|-+ .-.+||+||.++....+.-.+
T Consensus 121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR-~aqTCPiDR~EF~~v~V~eS~ 179 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSR-CAQTCPVDRGEFGEVKVLEST 179 (1134)
T ss_pred hhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhh-hcccCchhhhhhheeeeeccc
Confidence 445789999983322222 248999999999999999 899999999998776554433
No 54
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.62 E-value=1.4e-05 Score=66.56 Aligned_cols=55 Identities=25% Similarity=0.593 Sum_probs=42.3
Q ss_pred cccccccccccccc-cCCCc-eEEecCCCccChHhHHHHHhC----------------------CCCCCcccCcccchh
Q 047298 127 EEEEEEERCAICLG-SGTGS-VIQMDCLHQFHEKCIACWFDN----------------------RNYSCPLCRFDMATA 181 (192)
Q Consensus 127 ~~~~~~~~C~ICl~-~~~~~-~~~l~C~H~Fh~~CI~~Wl~~----------------------~~~~CP~CR~~l~~~ 181 (192)
+.+...-.|+|||- .+.++ ..+++|.|.||..|+...|.. ....||+||..|..+
T Consensus 110 ~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e 188 (368)
T KOG4445|consen 110 ENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE 188 (368)
T ss_pred cCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence 34556789999999 55555 677899999999999876642 345799999988643
No 55
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.38 E-value=0.0002 Score=59.12 Aligned_cols=54 Identities=22% Similarity=0.439 Sum_probs=44.1
Q ss_pred cccccccccccccccCCCceEEecCCCccChHhHHHHHhC-CCCCCcccCcccch
Q 047298 127 EEEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDN-RNYSCPLCRFDMAT 180 (192)
Q Consensus 127 ~~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~-~~~~CP~CR~~l~~ 180 (192)
.....+.+|++|-+....|-...+|+|+||.-||..-... ...+||.|-.+++.
T Consensus 234 s~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~ 288 (298)
T KOG2879|consen 234 STGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP 288 (298)
T ss_pred ccccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence 4456788999999988888776799999999999986551 34689999888773
No 56
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.36 E-value=0.00015 Score=58.34 Aligned_cols=53 Identities=26% Similarity=0.679 Sum_probs=42.5
Q ss_pred ccccccccccccc-cCCCceEEecCCCccChHhHHHHHhC-------CCCCCcccCcccch
Q 047298 128 EEEEEERCAICLG-SGTGSVIQMDCLHQFHEKCIACWFDN-------RNYSCPLCRFDMAT 180 (192)
Q Consensus 128 ~~~~~~~C~ICl~-~~~~~~~~l~C~H~Fh~~CI~~Wl~~-------~~~~CP~CR~~l~~ 180 (192)
+.+.+..|..|-. ...++.++|.|-|+||+.|+..|..+ ....||.|-.+|..
T Consensus 46 DsDY~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 46 DSDYNPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred hcCCCCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 3556778999988 55566677999999999999999863 35589999988754
No 57
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=97.30 E-value=4.3e-05 Score=64.54 Aligned_cols=50 Identities=24% Similarity=0.635 Sum_probs=43.6
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchh
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATA 181 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~ 181 (192)
...+|.+|-....+.+.+.-|-|.||..||.+.+. ....||+|...+...
T Consensus 14 ~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~-~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDATTITECLHTFCKSCIVKYLE-ESKYCPTCDIVIHKT 63 (331)
T ss_pred cceehhhccceeecchhHHHHHHHHHHHHHHHHHH-HhccCCccceeccCc
Confidence 46789999997777777789999999999999999 799999998877554
No 58
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.27 E-value=3.6e-05 Score=63.98 Aligned_cols=43 Identities=30% Similarity=0.689 Sum_probs=35.5
Q ss_pred ccccccccccCCCceEEecCCC-ccChHhHHHHHhCCCCCCcccCcccch
Q 047298 132 EERCAICLGSGTGSVIQMDCLH-QFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 132 ~~~C~ICl~~~~~~~~~l~C~H-~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
.+.|.||++...+-+. |+||| +-|.+|-..+ +.||+||+.+..
T Consensus 300 ~~LC~ICmDaP~DCvf-LeCGHmVtCt~CGkrm-----~eCPICRqyi~r 343 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVF-LECGHMVTCTKCGKRM-----NECPICRQYIVR 343 (350)
T ss_pred HHHHHHHhcCCcceEE-eecCcEEeehhhcccc-----ccCchHHHHHHH
Confidence 7899999997777555 99999 8899997654 489999997764
No 59
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.15 E-value=0.00025 Score=69.68 Aligned_cols=54 Identities=30% Similarity=0.753 Sum_probs=42.5
Q ss_pred cccccccccccccc--cCCCceEEecCCCccChHhHHHHHhC---------CCCCCcccCcccch
Q 047298 127 EEEEEEERCAICLG--SGTGSVIQMDCLHQFHEKCIACWFDN---------RNYSCPLCRFDMAT 180 (192)
Q Consensus 127 ~~~~~~~~C~ICl~--~~~~~~~~l~C~H~Fh~~CI~~Wl~~---------~~~~CP~CR~~l~~ 180 (192)
..++.++.|.||+. ....+.++|.|+|+||..|...-|.+ +--.||+|+.++..
T Consensus 3481 tkQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3481 TKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred hhcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 35778899999999 34457778999999999999876653 23479999998743
No 60
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.07 E-value=0.00018 Score=62.20 Aligned_cols=47 Identities=34% Similarity=0.721 Sum_probs=36.0
Q ss_pred cccccccccccc---cCCCceEEecCCCccChHhHHHHHhC-CCCCCcccC
Q 047298 129 EEEEERCAICLG---SGTGSVIQMDCLHQFHEKCIACWFDN-RNYSCPLCR 175 (192)
Q Consensus 129 ~~~~~~C~ICl~---~~~~~~~~l~C~H~Fh~~CI~~Wl~~-~~~~CP~CR 175 (192)
++.+.-|..|=+ ...+..--|||.|+||.+|+...|.+ ...+||.||
T Consensus 362 ~e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Cr 412 (518)
T KOG1941|consen 362 EETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCR 412 (518)
T ss_pred HHHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHH
Confidence 345678999999 33344455799999999999999872 345799999
No 61
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.97 E-value=0.00034 Score=44.06 Aligned_cols=48 Identities=25% Similarity=0.552 Sum_probs=37.2
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhh
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAV 182 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~ 182 (192)
....|..|.......++ +||+|+.+..|-.-+ +.+-||.|-..+....
T Consensus 6 ~~~~~~~~~~~~~~~~~-~pCgH~I~~~~f~~~---rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTV-LPCGHLICDNCFPGE---RYNGCPFCGTPFEFDD 53 (55)
T ss_pred cceeEEEcccccccccc-ccccceeeccccChh---hccCCCCCCCcccCCC
Confidence 45567777775555554 899999999998776 7789999988887654
No 62
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.85 E-value=0.00078 Score=58.60 Aligned_cols=49 Identities=20% Similarity=0.414 Sum_probs=37.1
Q ss_pred ccccccccccccc-cCC-CceEEecCCCccChHhHHHHHhC-------CCCCCcccCc
Q 047298 128 EEEEEERCAICLG-SGT-GSVIQMDCLHQFHEKCIACWFDN-------RNYSCPLCRF 176 (192)
Q Consensus 128 ~~~~~~~C~ICl~-~~~-~~~~~l~C~H~Fh~~CI~~Wl~~-------~~~~CP~CR~ 176 (192)
-......|.||++ ..+ .....+||+|+||..|+...+.. +.-.||-+..
T Consensus 180 F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C 237 (445)
T KOG1814|consen 180 FVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC 237 (445)
T ss_pred HHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence 3556789999999 333 55667899999999999998853 3446877654
No 63
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.82 E-value=0.00041 Score=62.13 Aligned_cols=57 Identities=25% Similarity=0.695 Sum_probs=44.7
Q ss_pred cccccccccccccccCCCceEEecCCCccChHhHHHHHhC----CCCCCcccCcccchhhhh
Q 047298 127 EEEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDN----RNYSCPLCRFDMATAVIE 184 (192)
Q Consensus 127 ~~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~----~~~~CP~CR~~l~~~~~~ 184 (192)
..+.+...|-+|-+...+.+. ..|.|.||.-||..+... .+-+||+|-..+.-++..
T Consensus 531 ~enk~~~~C~lc~d~aed~i~-s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse 591 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPAEDYIE-SSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSE 591 (791)
T ss_pred ccccCceeecccCChhhhhHh-hhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccc
Confidence 345667899999998777665 789999999999888753 456899998877655443
No 64
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=96.70 E-value=0.00077 Score=54.81 Aligned_cols=44 Identities=25% Similarity=0.637 Sum_probs=33.1
Q ss_pred ccccccc-cCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 134 RCAICLG-SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 134 ~C~ICl~-~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
.|.-|.- ....+...+.|+|+||..|...-. ...||+||..+..
T Consensus 5 hCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 5 HCNKCFRFPSQDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIRI 49 (233)
T ss_pred EeccccccCCCCceeeeechhhhhhhhcccCC---ccccccccceeee
Confidence 5888888 335566767999999999977632 2389999998643
No 65
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.65 E-value=0.0011 Score=56.83 Aligned_cols=51 Identities=22% Similarity=0.507 Sum_probs=43.0
Q ss_pred ccccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 128 EEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
...++..|+||+......+. .||+|.-|..||.+-+- +...|=.|+..+.+
T Consensus 418 p~sEd~lCpICyA~pi~Avf-~PC~H~SC~~CI~qHlm-N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 418 PDSEDNLCPICYAGPINAVF-APCSHRSCYGCITQHLM-NCKRCFFCKTTVID 468 (489)
T ss_pred CCcccccCcceecccchhhc-cCCCCchHHHHHHHHHh-cCCeeeEecceeee
Confidence 35688999999996555444 79999999999999999 88999999987763
No 66
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=96.63 E-value=0.002 Score=49.22 Aligned_cols=34 Identities=24% Similarity=0.586 Sum_probs=24.9
Q ss_pred cccccccccccCCCceEEecC------------C-CccChHhHHHHHh
Q 047298 131 EEERCAICLGSGTGSVIQMDC------------L-HQFHEKCIACWFD 165 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C------------~-H~Fh~~CI~~Wl~ 165 (192)
++..|+||||..-+.|. |-| + -.-|..|+++.-+
T Consensus 1 ed~~CpICme~PHNAVL-LlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 1 EDVTCPICMEHPHNAVL-LLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CCccCceeccCCCceEE-EEeccccCCccccccCCccchhHHHHHHHH
Confidence 46789999997777666 434 2 2568999998765
No 67
>PHA02862 5L protein; Provisional
Probab=96.62 E-value=0.0015 Score=49.12 Aligned_cols=47 Identities=23% Similarity=0.545 Sum_probs=36.2
Q ss_pred ccccccccccCCCceEEecCC-----CccChHhHHHHHhC-CCCCCcccCcccch
Q 047298 132 EERCAICLGSGTGSVIQMDCL-----HQFHEKCIACWFDN-RNYSCPLCRFDMAT 180 (192)
Q Consensus 132 ~~~C~ICl~~~~~~~~~l~C~-----H~Fh~~CI~~Wl~~-~~~~CP~CR~~l~~ 180 (192)
++.|-||.+...+.+ -||. -.-|.+|+.+|++. ++..||+|+.++..
T Consensus 2 ~diCWIC~~~~~e~~--~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 2 SDICWICNDVCDERN--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI 54 (156)
T ss_pred CCEEEEecCcCCCCc--ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence 568999999655443 4665 38899999999983 55679999998743
No 68
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=96.62 E-value=0.0021 Score=49.23 Aligned_cols=52 Identities=21% Similarity=0.457 Sum_probs=38.0
Q ss_pred ccccccccccccccCCCceEEecCCC-----ccChHhHHHHHhC-CCCCCcccCcccchh
Q 047298 128 EEEEEERCAICLGSGTGSVIQMDCLH-----QFHEKCIACWFDN-RNYSCPLCRFDMATA 181 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~~~l~C~H-----~Fh~~CI~~Wl~~-~~~~CP~CR~~l~~~ 181 (192)
....+..|-||.+..+... -||.. .-|.+|+..|+.. +...|+.|++++...
T Consensus 4 ~s~~~~~CRIC~~~~~~~~--~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 4 VSLMDKCCWICKDEYDVVT--NYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred cCCCCCeeEecCCCCCCcc--CCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 3456889999999644322 46654 6699999999984 455799999887543
No 69
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.61 E-value=0.0015 Score=40.10 Aligned_cols=40 Identities=28% Similarity=0.780 Sum_probs=25.8
Q ss_pred ccccccc-CCCceEEecCCC-----ccChHhHHHHHhC-CCCCCccc
Q 047298 135 CAICLGS-GTGSVIQMDCLH-----QFHEKCIACWFDN-RNYSCPLC 174 (192)
Q Consensus 135 C~ICl~~-~~~~~~~l~C~H-----~Fh~~CI~~Wl~~-~~~~CP~C 174 (192)
|-||++. ..+.....||.- ..|..|+..|+.. ++.+|++|
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 7799993 333334467753 7899999999973 45679987
No 70
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.55 E-value=0.0011 Score=52.40 Aligned_cols=48 Identities=23% Similarity=0.497 Sum_probs=39.8
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCccc
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDM 178 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l 178 (192)
+.-...|.||-.....+++ ..|||.||..|...-++ ....|-+|-+..
T Consensus 193 e~IPF~C~iCKkdy~spvv-t~CGH~FC~~Cai~~y~-kg~~C~~Cgk~t 240 (259)
T COG5152 193 EKIPFLCGICKKDYESPVV-TECGHSFCSLCAIRKYQ-KGDECGVCGKAT 240 (259)
T ss_pred CCCceeehhchhhccchhh-hhcchhHHHHHHHHHhc-cCCcceecchhh
Confidence 3344689999998778777 78999999999888888 788999996643
No 71
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=96.51 E-value=0.001 Score=47.21 Aligned_cols=32 Identities=28% Similarity=0.705 Sum_probs=25.2
Q ss_pred cccccccccccc-CCCceEEecCCCccChHhHH
Q 047298 130 EEEERCAICLGS-GTGSVIQMDCLHQFHEKCIA 161 (192)
Q Consensus 130 ~~~~~C~ICl~~-~~~~~~~l~C~H~Fh~~CI~ 161 (192)
.++..|++|-.. ........||||+||..|+.
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 357789999994 44555666999999999974
No 72
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=96.44 E-value=0.0014 Score=61.57 Aligned_cols=49 Identities=27% Similarity=0.672 Sum_probs=34.7
Q ss_pred cccccccccccccCC-CceEEe--cCCCccChHhHHHHHhCC------CCCCcccCcc
Q 047298 129 EEEEERCAICLGSGT-GSVIQM--DCLHQFHEKCIACWFDNR------NYSCPLCRFD 177 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~-~~~~~l--~C~H~Fh~~CI~~Wl~~~------~~~CP~CR~~ 177 (192)
....++|.||++... ...+.- .|-|+||..||.+|-.+. .-.||.|+..
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv 245 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV 245 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence 456799999999332 222211 678999999999998641 2269999843
No 73
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.40 E-value=0.0011 Score=55.35 Aligned_cols=45 Identities=24% Similarity=0.465 Sum_probs=39.3
Q ss_pred cccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 133 ERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 133 ~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
..|-||...+..+|+ ..|+|.||..|-..=++ ....|++|-+..-
T Consensus 242 f~c~icr~~f~~pVv-t~c~h~fc~~ca~~~~q-k~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVV-TKCGHYFCEVCALKPYQ-KGEKCYVCSQQTH 286 (313)
T ss_pred ccccccccccccchh-hcCCceeehhhhccccc-cCCcceecccccc
Confidence 459999998888887 89999999999888888 7889999977653
No 74
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.30 E-value=0.0034 Score=51.29 Aligned_cols=52 Identities=12% Similarity=0.202 Sum_probs=42.0
Q ss_pred cccccccccccCCC--ceEEe-cCCCccChHhHHHHHhCCCCCCcccCcccchhhh
Q 047298 131 EEERCAICLGSGTG--SVIQM-DCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVI 183 (192)
Q Consensus 131 ~~~~C~ICl~~~~~--~~~~l-~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~ 183 (192)
..+.||||.+.... +...| ||||+|+.+|+.+... ....||+|-.++...+.
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-~D~v~pv~d~plkdrdi 274 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-KDMVDPVTDKPLKDRDI 274 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-ccccccCCCCcCcccce
Confidence 56899999994433 33345 9999999999999998 89999999888866543
No 75
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.28 E-value=0.0037 Score=38.45 Aligned_cols=44 Identities=23% Similarity=0.409 Sum_probs=21.7
Q ss_pred cccccccCCC-ceEEe--cCCCccChHhHHHHHhCCCCCCcccCccc
Q 047298 135 CAICLGSGTG-SVIQM--DCLHQFHEKCIACWFDNRNYSCPLCRFDM 178 (192)
Q Consensus 135 C~ICl~~~~~-~~~~l--~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l 178 (192)
|++|.+.... ..... +|++..|..|...-+.+....||-||.+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7899994322 12223 77899999998888865688999999864
No 76
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=96.27 E-value=0.0056 Score=53.06 Aligned_cols=32 Identities=25% Similarity=0.736 Sum_probs=24.4
Q ss_pred CCCccChHhHHHHHhC------------CCCCCcccCcccchhh
Q 047298 151 CLHQFHEKCIACWFDN------------RNYSCPLCRFDMATAV 182 (192)
Q Consensus 151 C~H~Fh~~CI~~Wl~~------------~~~~CP~CR~~l~~~~ 182 (192)
|.-.+|.+|+-+|+-. ++..||+||+.+--.+
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD 354 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD 354 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence 3457899999999864 4668999999875433
No 77
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.0024 Score=54.75 Aligned_cols=47 Identities=23% Similarity=0.588 Sum_probs=34.9
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
....+.|.||++...+ ...+||||+=| |..--. ...+||+||+.+..
T Consensus 302 ~~~p~lcVVcl~e~~~-~~fvpcGh~cc--ct~cs~--~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKS-AVFVPCGHVCC--CTLCSK--HLPQCPVCRQRIRL 348 (355)
T ss_pred cCCCCceEEecCCccc-eeeecCCcEEE--chHHHh--hCCCCchhHHHHHH
Confidence 4456789999998777 55589999855 766543 34569999987754
No 78
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.24 E-value=0.002 Score=54.00 Aligned_cols=48 Identities=25% Similarity=0.590 Sum_probs=38.8
Q ss_pred cccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCccc-Ccccch
Q 047298 133 ERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLC-RFDMAT 180 (192)
Q Consensus 133 ~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~C-R~~l~~ 180 (192)
..|+.|-.....++..-.|+|.||.+||..-|......||.| |+++.-
T Consensus 275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvll 323 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLL 323 (427)
T ss_pred ccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCcccccchh
Confidence 789999997777777557899999999998887567789999 445543
No 79
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=96.17 E-value=0.0057 Score=51.91 Aligned_cols=60 Identities=17% Similarity=0.351 Sum_probs=47.2
Q ss_pred ccccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhhhhhccC
Q 047298 128 EEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIESMFS 188 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~~~~ 188 (192)
.......|+||+.....+.+...=|-+||..||...+. ....||+=-.+..-+.....+.
T Consensus 296 l~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p~~v~~l~rl~~ 355 (357)
T KOG0826|consen 296 LPPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVV-NYGHCPVTGYPASVDHLIRLFN 355 (357)
T ss_pred CCCccccChhHHhccCCCceEEecceEEeHHHHHHHHH-hcCCCCccCCcchHHHHHHHhc
Confidence 35567789999996666666345689999999999999 9999999877777666555543
No 80
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=96.16 E-value=0.0029 Score=47.22 Aligned_cols=34 Identities=21% Similarity=0.462 Sum_probs=27.1
Q ss_pred ccccccccc-cCC-CceEEecCC------CccChHhHHHHHh
Q 047298 132 EERCAICLG-SGT-GSVIQMDCL------HQFHEKCIACWFD 165 (192)
Q Consensus 132 ~~~C~ICl~-~~~-~~~~~l~C~------H~Fh~~CI~~Wl~ 165 (192)
.-+|.||++ ... +.++.++|+ |.||.+|+.+|-+
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 568999999 222 467767886 7999999999954
No 81
>PHA03096 p28-like protein; Provisional
Probab=96.04 E-value=0.0035 Score=52.77 Aligned_cols=44 Identities=25% Similarity=0.468 Sum_probs=29.8
Q ss_pred ccccccccc-CCC-----ceEEe-cCCCccChHhHHHHHhC--CCCCCcccCc
Q 047298 133 ERCAICLGS-GTG-----SVIQM-DCLHQFHEKCIACWFDN--RNYSCPLCRF 176 (192)
Q Consensus 133 ~~C~ICl~~-~~~-----~~~~l-~C~H~Fh~~CI~~Wl~~--~~~~CP~CR~ 176 (192)
..|.||++. ... ....| .|.|.||..||..|-.. ...+||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 789999992 111 12223 99999999999999863 2234555544
No 82
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=95.93 E-value=0.0035 Score=38.25 Aligned_cols=44 Identities=25% Similarity=0.702 Sum_probs=25.5
Q ss_pred ccccccccCCCceEEecCC-CccChHhHHHHHhCCCCCCcccCcccchh
Q 047298 134 RCAICLGSGTGSVIQMDCL-HQFHEKCIACWFDNRNYSCPLCRFDMATA 181 (192)
Q Consensus 134 ~C~ICl~~~~~~~~~l~C~-H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~ 181 (192)
.|--|+-...+ . ..|+ |..|-.|+..++. .+..||+|..++|+.
T Consensus 4 nCKsCWf~~k~--L-i~C~dHYLCl~CLt~ml~-~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 4 NCKSCWFANKG--L-IKCSDHYLCLNCLTLMLS-RSDRCPICGKPLPTK 48 (50)
T ss_dssp ---SS-S--SS--E-EE-SS-EEEHHHHHHT-S-SSSEETTTTEE----
T ss_pred cChhhhhcCCC--e-eeecchhHHHHHHHHHhc-cccCCCcccCcCccc
Confidence 45555544333 2 4685 9999999999999 999999999999874
No 83
>PF04641 Rtf2: Rtf2 RING-finger
Probab=95.89 E-value=0.0079 Score=50.00 Aligned_cols=57 Identities=19% Similarity=0.370 Sum_probs=43.3
Q ss_pred ccccccccccccccCCCc--eEEe-cCCCccChHhHHHHHhCCCCCCcccCcccchhhhhhc
Q 047298 128 EEEEEERCAICLGSGTGS--VIQM-DCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIESM 186 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~--~~~l-~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~~ 186 (192)
.....+.|||....+.+. .+.+ +|||+|...++... . ....||+|-.++...++..+
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k-~~~~Cp~c~~~f~~~DiI~L 168 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-K-KSKKCPVCGKPFTEEDIIPL 168 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-c-ccccccccCCccccCCEEEe
Confidence 356788999999966543 3334 99999999999997 2 36789999999877665443
No 84
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=95.61 E-value=0.0051 Score=57.57 Aligned_cols=51 Identities=27% Similarity=0.574 Sum_probs=40.5
Q ss_pred cccccccccCCCceEEecCCCccChHhHHHHHhCCCC-CCcccCcccchhhhhh
Q 047298 133 ERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNY-SCPLCRFDMATAVIES 185 (192)
Q Consensus 133 ~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~-~CP~CR~~l~~~~~~~ 185 (192)
..|.||++ .+.....+|+|.||..|+..-+...+. .||.||..+......+
T Consensus 455 ~~c~ic~~--~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s 506 (674)
T KOG1001|consen 455 HWCHICCD--LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS 506 (674)
T ss_pred cccccccc--cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence 89999999 444555799999999999988774333 5999999887766554
No 85
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.53 E-value=0.01 Score=49.90 Aligned_cols=47 Identities=23% Similarity=0.495 Sum_probs=36.8
Q ss_pred ccccccccccC-----CCceEEecCCCccChHhHHHHHhCCCCCCcccCccc
Q 047298 132 EERCAICLGSG-----TGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDM 178 (192)
Q Consensus 132 ~~~C~ICl~~~-----~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l 178 (192)
-+.|-||-+.. ..-.+.|.|||.||..|+.+.+.+....||.||...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 46899998822 112355799999999999999986677899999984
No 86
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=95.17 E-value=0.011 Score=50.48 Aligned_cols=53 Identities=26% Similarity=0.510 Sum_probs=34.3
Q ss_pred cccccccccccccCC---CceEEecCCCccChHhHHHHHhCCCCCCcccCcccchh
Q 047298 129 EEEEERCAICLGSGT---GSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATA 181 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~---~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~ 181 (192)
+++++-|+.|++.++ ....--+||-..|.-|...--++-+..||-||+....+
T Consensus 11 edeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de 66 (480)
T COG5175 11 EDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE 66 (480)
T ss_pred ccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence 444555999999332 22333378877777775555444668999999876543
No 87
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.10 E-value=0.02 Score=49.11 Aligned_cols=51 Identities=33% Similarity=0.663 Sum_probs=38.2
Q ss_pred cccccccccccccccCCCceEEecCCCccChHhHHHH--HhCCCCCCcccCcccc
Q 047298 127 EEEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACW--FDNRNYSCPLCRFDMA 179 (192)
Q Consensus 127 ~~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~W--l~~~~~~CP~CR~~l~ 179 (192)
+.+++...|.||-+...- +.++||+|..|--|.... |- ....||+||.+-.
T Consensus 56 dtDEen~~C~ICA~~~TY-s~~~PC~H~~CH~Ca~RlRALY-~~K~C~~CrTE~e 108 (493)
T COG5236 56 DTDEENMNCQICAGSTTY-SARYPCGHQICHACAVRLRALY-MQKGCPLCRTETE 108 (493)
T ss_pred ccccccceeEEecCCceE-EEeccCCchHHHHHHHHHHHHH-hccCCCccccccc
Confidence 456677889999984433 334899999999997654 34 6788999998653
No 88
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.85 E-value=0.015 Score=48.62 Aligned_cols=45 Identities=27% Similarity=0.637 Sum_probs=35.8
Q ss_pred cccccccccc---cCCCceEEecCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 131 EEERCAICLG---SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 131 ~~~~C~ICl~---~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
....||||.+ .....+..++|||.-|.+|...... ...+||+|.+
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~-~~y~CP~C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC-EGYTCPICSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhc-cCCCCCcccc
Confidence 3445999999 2333455589999999999999988 5599999988
No 89
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=94.70 E-value=0.035 Score=33.32 Aligned_cols=40 Identities=30% Similarity=0.713 Sum_probs=22.3
Q ss_pred cccccccCCCceEEe--cCCCccChHhHHHHHhCCCC-CCccc
Q 047298 135 CAICLGSGTGSVIQM--DCLHQFHEKCIACWFDNRNY-SCPLC 174 (192)
Q Consensus 135 C~ICl~~~~~~~~~l--~C~H~Fh~~CI~~Wl~~~~~-~CP~C 174 (192)
|.+|.+.....++-- .|+=.+|..|+..++..+.. .||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 678888544444423 58889999999999984333 69988
No 90
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.65 E-value=0.018 Score=54.43 Aligned_cols=44 Identities=25% Similarity=0.736 Sum_probs=37.0
Q ss_pred ccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 132 EERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 132 ~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
...|..|--...-|++.-.|+|.||.+|+. . +...||-|+.++.
T Consensus 840 ~skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~-~~~~CP~C~~e~~ 883 (933)
T KOG2114|consen 840 VSKCSACEGTLDLPFVHFLCGHSYHQHCLE---D-KEDKCPKCLPELR 883 (933)
T ss_pred eeeecccCCccccceeeeecccHHHHHhhc---c-CcccCCccchhhh
Confidence 358999988777788878999999999988 3 7789999998553
No 91
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=94.60 E-value=0.0074 Score=59.16 Aligned_cols=45 Identities=24% Similarity=0.513 Sum_probs=36.5
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
....|.||++.....-.+..|+|.+|.+|...|+. .+..||+|+.
T Consensus 1152 ~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~-~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLY-ASSRCPICKS 1196 (1394)
T ss_pred cccchHHHHHHHHhcCCeeeechhHhhhHHHHHHH-HhccCcchhh
Confidence 34589999995442223367999999999999999 9999999984
No 92
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=94.34 E-value=0.021 Score=46.64 Aligned_cols=48 Identities=27% Similarity=0.633 Sum_probs=37.5
Q ss_pred cccccccccccc--cCCCceEEe--c-CCCccChHhHHHHHhCCCCCCc--ccCc
Q 047298 129 EEEEERCAICLG--SGTGSVIQM--D-CLHQFHEKCIACWFDNRNYSCP--LCRF 176 (192)
Q Consensus 129 ~~~~~~C~ICl~--~~~~~~~~l--~-C~H~Fh~~CI~~Wl~~~~~~CP--~CR~ 176 (192)
...+..||||.. .....+..| | |-|..|.+|++.-+..+...|| -|-.
T Consensus 7 ~~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k 61 (314)
T COG5220 7 EMEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK 61 (314)
T ss_pred hhhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence 345779999999 344445544 5 9999999999999987888999 7754
No 93
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=94.16 E-value=0.04 Score=46.15 Aligned_cols=45 Identities=24% Similarity=0.524 Sum_probs=35.2
Q ss_pred ccccccc--cCCCceEEe--cCCCccChHhHHHHHhCCCCCCcccCccc
Q 047298 134 RCAICLG--SGTGSVIQM--DCLHQFHEKCIACWFDNRNYSCPLCRFDM 178 (192)
Q Consensus 134 ~C~ICl~--~~~~~~~~l--~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l 178 (192)
.||+|.. .....+..+ +|+|.-|.+|.+..+..+...||.|-..+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL 50 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence 5999999 333333333 99999999999999987888999996654
No 94
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=93.97 E-value=0.04 Score=46.78 Aligned_cols=48 Identities=21% Similarity=0.468 Sum_probs=37.4
Q ss_pred ccccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 128 EEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
...+-.+||||.+....++..-+=||+-|..|=.+ ..+.||.||.+++
T Consensus 44 ~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~----~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 44 LDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTK----VSNKCPTCRLPIG 91 (299)
T ss_pred cchhhccCchhhccCcccceecCCCcEehhhhhhh----hcccCCccccccc
Confidence 34567899999997777764323379999999764 6779999999987
No 95
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.76 E-value=0.043 Score=42.91 Aligned_cols=53 Identities=26% Similarity=0.686 Sum_probs=36.7
Q ss_pred ccccccccccccccCCCce------EEecCCCccChHhHHHHHhC----CC------CCCcccCcccch
Q 047298 128 EEEEEERCAICLGSGTGSV------IQMDCLHQFHEKCIACWFDN----RN------YSCPLCRFDMAT 180 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~------~~l~C~H~Fh~~CI~~Wl~~----~~------~~CP~CR~~l~~ 180 (192)
..++.-.|-||+...-+.+ -...|+.-||.-|+..||+. ++ ..||.|-.++..
T Consensus 161 kdd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial 229 (234)
T KOG3268|consen 161 KDDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL 229 (234)
T ss_pred cchhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence 3455567999998322111 12389999999999999973 11 379999887754
No 96
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.69 E-value=0.059 Score=46.93 Aligned_cols=47 Identities=17% Similarity=0.409 Sum_probs=37.7
Q ss_pred cccccccccc--cCCCceEEecCCCccChHhHHHHHhCCC--CCCcccCcc
Q 047298 131 EEERCAICLG--SGTGSVIQMDCLHQFHEKCIACWFDNRN--YSCPLCRFD 177 (192)
Q Consensus 131 ~~~~C~ICl~--~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~--~~CP~CR~~ 177 (192)
+.-.|||=.+ ...++...|.|||+...+-+.+..+++. ..||.|=.+
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 3467999988 4556667799999999999999998655 689999433
No 97
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.52 E-value=0.027 Score=43.37 Aligned_cols=29 Identities=24% Similarity=0.798 Sum_probs=24.8
Q ss_pred cccccccccccc--cCCCceEEecCCCccCh
Q 047298 129 EEEEERCAICLG--SGTGSVIQMDCLHQFHE 157 (192)
Q Consensus 129 ~~~~~~C~ICl~--~~~~~~~~l~C~H~Fh~ 157 (192)
.++.-+|.|||| ...+.+.+|||-.+||.
T Consensus 174 ~ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 455679999999 67888889999999996
No 98
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.36 E-value=0.0043 Score=53.72 Aligned_cols=53 Identities=17% Similarity=0.407 Sum_probs=42.3
Q ss_pred cccccccccccc---cCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhh
Q 047298 129 EEEEERCAICLG---SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAV 182 (192)
Q Consensus 129 ~~~~~~C~ICl~---~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~ 182 (192)
+.-...|+||.. ...+.+..+-|||.+|..||.+|+. ....||.||.+++...
T Consensus 193 ~slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~-~~~kl~~~~rel~~~~ 248 (465)
T KOG0827|consen 193 SSLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLA-TKRKLPSCRRELPKNG 248 (465)
T ss_pred HHHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHH-HHHHhHHHHhhhhhhh
Confidence 334578999998 3334455578999999999999999 7889999999987543
No 99
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.04 E-value=0.038 Score=46.40 Aligned_cols=34 Identities=24% Similarity=0.567 Sum_probs=26.4
Q ss_pred CCCccChHhHHHHHhC------------CCCCCcccCcccchhhhh
Q 047298 151 CLHQFHEKCIACWFDN------------RNYSCPLCRFDMATAVIE 184 (192)
Q Consensus 151 C~H~Fh~~CI~~Wl~~------------~~~~CP~CR~~l~~~~~~ 184 (192)
|.-.+|.+|+-+|+.. ++.+||+||+.+--.+++
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv~ 370 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDVH 370 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeeee
Confidence 5568999999998853 677899999987654443
No 100
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.70 E-value=0.055 Score=51.46 Aligned_cols=37 Identities=22% Similarity=0.378 Sum_probs=29.0
Q ss_pred cccccccccccc-cCCCceEEecCCCccChHhHHHHHh
Q 047298 129 EEEEERCAICLG-SGTGSVIQMDCLHQFHEKCIACWFD 165 (192)
Q Consensus 129 ~~~~~~C~ICl~-~~~~~~~~l~C~H~Fh~~CI~~Wl~ 165 (192)
.+.++.|.+|.- ....+...-||||.||.+||.+-..
T Consensus 814 ~ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred ecCccchHHhcchhhcCcceeeeccchHHHHHHHHHHH
Confidence 345889999999 4555666569999999999987653
No 101
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.22 E-value=0.085 Score=42.46 Aligned_cols=40 Identities=25% Similarity=0.563 Sum_probs=29.0
Q ss_pred cccccccCCCceEEecCCC-ccChHhHHHHHhCCCCCCcccCcccch
Q 047298 135 CAICLGSGTGSVIQMDCLH-QFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 135 C~ICl~~~~~~~~~l~C~H-~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
|-.|-+.... +..+||.| .+|..|-.. -..||+|+.....
T Consensus 161 Cr~C~~~~~~-VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~s 201 (207)
T KOG1100|consen 161 CRKCGEREAT-VLLLPCRHLCLCGICDES-----LRICPICRSPKTS 201 (207)
T ss_pred ceecCcCCce-EEeecccceEeccccccc-----CccCCCCcChhhc
Confidence 8888774433 66679998 889999543 3469999876544
No 102
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=91.25 E-value=0.14 Score=48.52 Aligned_cols=53 Identities=19% Similarity=0.629 Sum_probs=37.8
Q ss_pred ccccccccccccccC-CCceEEecCCC-----ccChHhHHHHHh-CCCCCCcccCcccch
Q 047298 128 EEEEEERCAICLGSG-TGSVIQMDCLH-----QFHEKCIACWFD-NRNYSCPLCRFDMAT 180 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~-~~~~~~l~C~H-----~Fh~~CI~~Wl~-~~~~~CP~CR~~l~~ 180 (192)
-++++..|-||..+. .+....=||.. ..|.+|+..|+. ++...|-+|..++.-
T Consensus 8 mN~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F 67 (1175)
T COG5183 8 MNEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF 67 (1175)
T ss_pred CCccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence 355679999999932 23232247764 789999999998 244569999987743
No 103
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=91.05 E-value=0.093 Score=44.46 Aligned_cols=43 Identities=23% Similarity=0.356 Sum_probs=27.0
Q ss_pred cccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCccc
Q 047298 133 ERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDM 178 (192)
Q Consensus 133 ~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l 178 (192)
-.|.-|=--....-+-+||.|+||.+|...- .-+.||.|-..|
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~---~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKHVFCLECARSD---SDKICPLCDDRV 133 (389)
T ss_pred EeecccCCcceeeecccccchhhhhhhhhcC---ccccCcCcccHH
Confidence 3455554311111233499999999997642 456899997655
No 104
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=90.80 E-value=0.14 Score=48.23 Aligned_cols=40 Identities=33% Similarity=0.585 Sum_probs=30.4
Q ss_pred cccccccc-cCCCceEEecCCCccChHhHHHHHhCCCCCCcc
Q 047298 133 ERCAICLG-SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPL 173 (192)
Q Consensus 133 ~~C~ICl~-~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~ 173 (192)
..|+||-- +.+.......|+|+-|..|...|+. ....||.
T Consensus 1029 ~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~-~gd~Cps 1069 (1081)
T KOG0309|consen 1029 FQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFR-TGDVCPS 1069 (1081)
T ss_pred eeeeeEeeEeeccchhhccccccccHHHHHHHHh-cCCcCCC
Confidence 34676655 4444455568999999999999999 7778984
No 105
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.58 E-value=0.1 Score=43.06 Aligned_cols=53 Identities=26% Similarity=0.716 Sum_probs=36.7
Q ss_pred ccccccccccccccCCCceEE---ecCC-----CccChHhHHHHHhC-------CCCCCcccCcccch
Q 047298 128 EEEEEERCAICLGSGTGSVIQ---MDCL-----HQFHEKCIACWFDN-------RNYSCPLCRFDMAT 180 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~~~~~---l~C~-----H~Fh~~CI~~Wl~~-------~~~~CP~CR~~l~~ 180 (192)
..+.+..|=||+.-..+.-+. -||. |-.|-.|+..|... +.-.||-|+.+...
T Consensus 16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYii 83 (293)
T KOG3053|consen 16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYII 83 (293)
T ss_pred ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhee
Confidence 456678899999933332221 2773 68999999999973 22369999987643
No 106
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=89.14 E-value=0.18 Score=44.74 Aligned_cols=35 Identities=26% Similarity=0.559 Sum_probs=30.4
Q ss_pred ccccccccccccCCCceEEecCCCccChHhHHHHHh
Q 047298 130 EEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFD 165 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~ 165 (192)
+++..|+||-.+..++++ |+|+|..|.-|...-+.
T Consensus 2 eeelkc~vc~~f~~epii-l~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 2 EEELKCPVCGSFYREPII-LPCSHNLCQACARNILV 36 (699)
T ss_pred cccccCceehhhccCceE-eecccHHHHHHHHhhcc
Confidence 467899999998888877 99999999999887664
No 107
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=88.32 E-value=0.55 Score=35.06 Aligned_cols=53 Identities=19% Similarity=0.458 Sum_probs=36.5
Q ss_pred ccccccccccccCCC-ceEEe--cCCCccChHhH-HHHHh-CCCCCCcccCcccchhh
Q 047298 130 EEEERCAICLGSGTG-SVIQM--DCLHQFHEKCI-ACWFD-NRNYSCPLCRFDMATAV 182 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~-~~~~l--~C~H~Fh~~CI-~~Wl~-~~~~~CP~CR~~l~~~~ 182 (192)
..-++|.||.|...+ ....- -||-..|.-|- .-|.. +....||+|+..+.+..
T Consensus 78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred CCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 378999999993332 22111 58988898884 55654 25678999999887643
No 108
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=88.30 E-value=0.45 Score=29.38 Aligned_cols=44 Identities=18% Similarity=0.466 Sum_probs=22.2
Q ss_pred cccccccccCCCceEEecCCCccChHhHHHHHh----CCCCCCcccCcc
Q 047298 133 ERCAICLGSGTGSVIQMDCLHQFHEKCIACWFD----NRNYSCPLCRFD 177 (192)
Q Consensus 133 ~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~----~~~~~CP~CR~~ 177 (192)
..|+|.......+++...|.|.-|.+ +..|+. +..-.||+|.++
T Consensus 3 L~CPls~~~i~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEeCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 47999999888899988999986533 333433 234479999763
No 109
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.22 E-value=0.2 Score=46.36 Aligned_cols=41 Identities=29% Similarity=0.571 Sum_probs=30.1
Q ss_pred cccccccccc----cCCCceEEecCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 131 EEERCAICLG----SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 131 ~~~~C~ICl~----~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
+-..|+||+. ....++ .+.|||..|..|+... .+.+|| |++
T Consensus 10 ~~l~c~ic~n~f~~~~~~Pv-sl~cghtic~~c~~~l---yn~scp-~~~ 54 (861)
T KOG3161|consen 10 LLLLCDICLNLFVVQRLEPV-SLQCGHTICGHCVQLL---YNASCP-TKR 54 (861)
T ss_pred HHhhchHHHHHHHHHhcCcc-cccccchHHHHHHHhH---hhccCC-CCc
Confidence 3467999987 222333 4899999999999987 457899 544
No 110
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=88.05 E-value=0.11 Score=48.39 Aligned_cols=49 Identities=27% Similarity=0.642 Sum_probs=37.0
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhC--CCCCCcccCcccch
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDN--RNYSCPLCRFDMAT 180 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~--~~~~CP~CR~~l~~ 180 (192)
-..+|+||++-...++. +.|.|.|+..|+..-+.. ....||+|+..+..
T Consensus 20 k~lEc~ic~~~~~~p~~-~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK 70 (684)
T KOG4362|consen 20 KILECPICLEHVKEPSL-LKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK 70 (684)
T ss_pred hhccCCceeEEeeccch-hhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence 36799999995555544 799999999998876652 34579999966543
No 111
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=87.05 E-value=0.32 Score=39.10 Aligned_cols=45 Identities=24% Similarity=0.607 Sum_probs=36.2
Q ss_pred ccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccC
Q 047298 130 EEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCR 175 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR 175 (192)
+.-..|.+|....-..++.=.|+=.+|..|+.+.++ ....||.|-
T Consensus 179 dnlk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q-~~~~cphc~ 223 (235)
T KOG4718|consen 179 DNLKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQ-RRDICPHCG 223 (235)
T ss_pred HHHHHHhHhHHHhheeeccCcccchhhhHHHHHHhc-ccCcCCchh
Confidence 346799999995444455447888999999999999 799999994
No 112
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=84.75 E-value=0.63 Score=39.07 Aligned_cols=48 Identities=25% Similarity=0.634 Sum_probs=34.8
Q ss_pred ccccccccccCCCc---eEEecCC-----CccChHhHHHHHhC-CCCCCcccCcccc
Q 047298 132 EERCAICLGSGTGS---VIQMDCL-----HQFHEKCIACWFDN-RNYSCPLCRFDMA 179 (192)
Q Consensus 132 ~~~C~ICl~~~~~~---~~~l~C~-----H~Fh~~CI~~Wl~~-~~~~CP~CR~~l~ 179 (192)
+..|-||.+..... ....||. +..|..|+..|+.. ++..|.+|.....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 57899999943321 2335775 47899999999973 4567999987553
No 113
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=82.39 E-value=1.2 Score=36.81 Aligned_cols=54 Identities=13% Similarity=0.194 Sum_probs=39.3
Q ss_pred ccccccccccccCCCceEE--e-cCCCccChHhHHHHHhCCCCCCcccCcccchhhhhhc
Q 047298 130 EEEERCAICLGSGTGSVIQ--M-DCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIESM 186 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~~~--l-~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~~ 186 (192)
.....|||=--.+.+.-+. + +|||+|-.+-+.+- ..++|++|.+.+...++.-+
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei---kas~C~~C~a~y~~~dvIvl 165 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI---KASVCHVCGAAYQEDDVIVL 165 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHh---hhccccccCCcccccCeEee
Confidence 4557788765555443332 2 99999999998886 67899999998877665543
No 114
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=82.30 E-value=0.7 Score=43.88 Aligned_cols=52 Identities=12% Similarity=0.220 Sum_probs=33.8
Q ss_pred cccccccccccccCCC---ceEEe---cCCCccChHhHHHHHhC-----CCCCCcccCcccch
Q 047298 129 EEEEERCAICLGSGTG---SVIQM---DCLHQFHEKCIACWFDN-----RNYSCPLCRFDMAT 180 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~---~~~~l---~C~H~Fh~~CI~~Wl~~-----~~~~CP~CR~~l~~ 180 (192)
..+..+|.||.-.... ..-.+ .|+|.||..||..|... ....|++|..-|..
T Consensus 93 ~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s 155 (1134)
T KOG0825|consen 93 TAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGS 155 (1134)
T ss_pred cccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhh
Confidence 3445566666653222 22223 49999999999999863 34568999776643
No 115
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.89 E-value=0.55 Score=43.10 Aligned_cols=54 Identities=30% Similarity=0.545 Sum_probs=42.7
Q ss_pred cccccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhhhhhc
Q 047298 127 EEEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAVIESM 186 (192)
Q Consensus 127 ~~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~~~~~ 186 (192)
...+....|.||+... ..+..+|. |..|+.+|+. .+..||+|+..+..++..+.
T Consensus 474 ~l~~~~~~~~~~~~~~--~~~~~~~~---~~~~l~~~~~-~~~~~pl~~~~~~~~~~~~~ 527 (543)
T KOG0802|consen 474 QLREPNDVCAICYQEM--SARITPCS---HALCLRKWLY-VQEVCPLCHTYMKEDDFLSK 527 (543)
T ss_pred hhhcccCcchHHHHHH--Hhcccccc---chhHHHhhhh-hccccCCCchhhhcccccCc
Confidence 4466778999999965 34446788 9999999999 89999999988876665443
No 116
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.12 E-value=0.75 Score=40.46 Aligned_cols=36 Identities=22% Similarity=0.592 Sum_probs=25.8
Q ss_pred ccccccccccc-c-CC-CceEEecCCCccChHhHHHHHh
Q 047298 130 EEEERCAICLG-S-GT-GSVIQMDCLHQFHEKCIACWFD 165 (192)
Q Consensus 130 ~~~~~C~ICl~-~-~~-~~~~~l~C~H~Fh~~CI~~Wl~ 165 (192)
....+|.||+. . .. .......|+|.||..|...-+.
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence 34679999994 2 11 2222358999999999998776
No 117
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=80.92 E-value=0.62 Score=42.94 Aligned_cols=42 Identities=29% Similarity=0.605 Sum_probs=27.4
Q ss_pred cccccccccccc----c-C-CCce-EEecCCCccChHhHHHHHhCCCCCCccc
Q 047298 129 EEEEERCAICLG----S-G-TGSV-IQMDCLHQFHEKCIACWFDNRNYSCPLC 174 (192)
Q Consensus 129 ~~~~~~C~ICl~----~-~-~~~~-~~l~C~H~Fh~~CI~~Wl~~~~~~CP~C 174 (192)
......|.+|.. + + .+.+ +...|+++||..|... .+..||-|
T Consensus 508 ~~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r----~s~~CPrC 556 (580)
T KOG1829|consen 508 TGKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR----KSPCCPRC 556 (580)
T ss_pred ccCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc----cCCCCCch
Confidence 444567778844 1 1 2222 2348999999999664 55569999
No 118
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=76.59 E-value=1.9 Score=40.77 Aligned_cols=40 Identities=23% Similarity=0.456 Sum_probs=29.2
Q ss_pred ccccccccc-CCCceEEecCCCccChHhHHHHHhCCCCCCcc
Q 047298 133 ERCAICLGS-GTGSVIQMDCLHQFHEKCIACWFDNRNYSCPL 173 (192)
Q Consensus 133 ~~C~ICl~~-~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~ 173 (192)
..|.+|-.. .+..+-.-.|+|.-|.+|+..|+. ..+.||.
T Consensus 780 ~~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~-~~s~ca~ 820 (839)
T KOG0269|consen 780 AKCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFF-KASPCAK 820 (839)
T ss_pred cCceeecceeeeeEeecccccccccHHHHHHHHh-cCCCCcc
Confidence 467777662 222222238999999999999999 8888877
No 119
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.23 E-value=1.4 Score=38.87 Aligned_cols=43 Identities=28% Similarity=0.470 Sum_probs=29.2
Q ss_pred cccccccccc---cCCCceEE-ecCCCccChHhHHHHHhCCCCCCccc
Q 047298 131 EEERCAICLG---SGTGSVIQ-MDCLHQFHEKCIACWFDNRNYSCPLC 174 (192)
Q Consensus 131 ~~~~C~ICl~---~~~~~~~~-l~C~H~Fh~~CI~~Wl~~~~~~CP~C 174 (192)
.-..|+.|.- ...+-... -.|+|.||+.|...|.. .+..|..|
T Consensus 305 ~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~-~~~~~~~~ 351 (384)
T KOG1812|consen 305 RWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKT-HNGECYEC 351 (384)
T ss_pred hcCcCcccceeeeecCCcceEEeeccccchhhcCcchhh-CCccccCc
Confidence 3567888877 22221111 15899999999999988 77767544
No 120
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=73.80 E-value=2 Score=28.14 Aligned_cols=12 Identities=25% Similarity=1.041 Sum_probs=8.8
Q ss_pred ccChHhHHHHHh
Q 047298 154 QFHEKCIACWFD 165 (192)
Q Consensus 154 ~Fh~~CI~~Wl~ 165 (192)
-||..|+.+|+.
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 399999999986
No 121
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.59 E-value=2 Score=38.51 Aligned_cols=55 Identities=22% Similarity=0.575 Sum_probs=38.2
Q ss_pred cccccccccccccCCCceEEecCCCccChHhHHHHHhC-----CC--CCC--cccCcccchhhh
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDN-----RN--YSC--PLCRFDMATAVI 183 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~-----~~--~~C--P~CR~~l~~~~~ 183 (192)
......|-||.+.....+..+.|+|.||..|....+.+ .. -+| +-|++.+..+..
T Consensus 67 ~~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i 130 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTV 130 (444)
T ss_pred CCccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCcee
Confidence 34578999999955445666799999999999988864 11 245 456666654443
No 122
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.18 E-value=1.8 Score=41.06 Aligned_cols=41 Identities=34% Similarity=0.718 Sum_probs=29.0
Q ss_pred cccccccccc---CC---CceEEecCCCccChHhHHHHHhCCCCCCccc
Q 047298 132 EERCAICLGS---GT---GSVIQMDCLHQFHEKCIACWFDNRNYSCPLC 174 (192)
Q Consensus 132 ~~~C~ICl~~---~~---~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~C 174 (192)
+..|.-|.+. .+ ..+..+.|+|.||..|+.--.. ++. |-.|
T Consensus 784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~-~~~-~~~~ 830 (846)
T KOG2066|consen 784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESL-RNA-CNIE 830 (846)
T ss_pred hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHH-hcc-cChh
Confidence 4489999992 12 5567789999999999876554 222 5555
No 123
>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=68.43 E-value=2.5 Score=22.46 Aligned_cols=6 Identities=33% Similarity=0.927 Sum_probs=2.9
Q ss_pred cccccc
Q 047298 135 CAICLG 140 (192)
Q Consensus 135 C~ICl~ 140 (192)
||-|-.
T Consensus 3 CP~C~~ 8 (26)
T PF10571_consen 3 CPECGA 8 (26)
T ss_pred CCCCcC
Confidence 444444
No 124
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=67.88 E-value=5.9 Score=28.78 Aligned_cols=43 Identities=21% Similarity=0.374 Sum_probs=30.4
Q ss_pred ccccccccccCCCc-------------eEEecCCCccChHhHHHHHhCCCCCCcccC
Q 047298 132 EERCAICLGSGTGS-------------VIQMDCLHQFHEKCIACWFDNRNYSCPLCR 175 (192)
Q Consensus 132 ~~~C~ICl~~~~~~-------------~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR 175 (192)
...|--|+..+.+. -.-..|.+.||.+|=.-+-. .=..||-|-
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe-~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE-SLHCCPGCI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh-hccCCcCCC
Confidence 45688888833321 11237899999999887766 667899995
No 125
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=67.32 E-value=4 Score=34.99 Aligned_cols=48 Identities=21% Similarity=0.351 Sum_probs=34.8
Q ss_pred ccccccccccC-CCceEEe--cCCCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 132 EERCAICLGSG-TGSVIQM--DCLHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 132 ~~~C~ICl~~~-~~~~~~l--~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
...|+||.+.. ......+ +|++.-|..|+..-.. ...+||.||.+...
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYER 299 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCcccc
Confidence 47899999932 2222224 6788888888888777 88999999976544
No 126
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=66.46 E-value=4.5 Score=34.66 Aligned_cols=46 Identities=15% Similarity=0.443 Sum_probs=34.0
Q ss_pred cccccccccc--cCCCceEEecCCCccChHhHHHHHhCC--CCCCcccCc
Q 047298 131 EEERCAICLG--SGTGSVIQMDCLHQFHEKCIACWFDNR--NYSCPLCRF 176 (192)
Q Consensus 131 ~~~~C~ICl~--~~~~~~~~l~C~H~Fh~~CI~~Wl~~~--~~~CP~CR~ 176 (192)
.-..||+=-+ ....+..-|.|||+.-.+-+...-+++ ...||.|=.
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~ 384 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE 384 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence 3467998877 334455658999999999999887743 456999943
No 127
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=62.68 E-value=8.5 Score=24.37 Aligned_cols=28 Identities=21% Similarity=0.559 Sum_probs=22.7
Q ss_pred cCCC--ccChHhHHHHHhCCCCCCcccCcccch
Q 047298 150 DCLH--QFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 150 ~C~H--~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
-|++ .||..|....|. ..||.|-.++..
T Consensus 24 ICSfECTFC~~C~e~~l~---~~CPNCgGelv~ 53 (57)
T PF06906_consen 24 ICSFECTFCADCAETMLN---GVCPNCGGELVR 53 (57)
T ss_pred EEeEeCcccHHHHHHHhc---CcCcCCCCcccc
Confidence 4653 799999999865 899999888765
No 128
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=62.48 E-value=5.5 Score=31.82 Aligned_cols=40 Identities=28% Similarity=0.574 Sum_probs=26.0
Q ss_pred ccccccccccc----cC-CC-ce-EEecCCCccChHhHHHHHhCCCCCCcccC
Q 047298 130 EEEERCAICLG----SG-TG-SV-IQMDCLHQFHEKCIACWFDNRNYSCPLCR 175 (192)
Q Consensus 130 ~~~~~C~ICl~----~~-~~-~~-~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR 175 (192)
.-+..|-+|-+ .+ .. .+ +--.|+-+||..|.. +..||-|-
T Consensus 150 ~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~------~~~CpkC~ 196 (202)
T PF13901_consen 150 QKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR------KKSCPKCA 196 (202)
T ss_pred hCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC------CCCCCCcH
Confidence 34567888876 11 11 22 222899999999955 25699993
No 129
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=62.13 E-value=3 Score=25.87 Aligned_cols=15 Identities=27% Similarity=0.600 Sum_probs=8.2
Q ss_pred CCCCcccCcccchhh
Q 047298 168 NYSCPLCRFDMATAV 182 (192)
Q Consensus 168 ~~~CP~CR~~l~~~~ 182 (192)
...||+|..++....
T Consensus 20 ~~~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 20 KGCCPLCGRPLDEEH 34 (54)
T ss_dssp SEE-TTT--EE-HHH
T ss_pred CCcCCCCCCCCCHHH
Confidence 348999999987654
No 130
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=61.04 E-value=8.1 Score=33.17 Aligned_cols=52 Identities=25% Similarity=0.533 Sum_probs=35.6
Q ss_pred cccccccccccccCC-----------------CceE-EecCCCccChHhHHHHHhC--------CCCCCcccCcccch
Q 047298 129 EEEEERCAICLGSGT-----------------GSVI-QMDCLHQFHEKCIACWFDN--------RNYSCPLCRFDMAT 180 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~-----------------~~~~-~l~C~H~Fh~~CI~~Wl~~--------~~~~CP~CR~~l~~ 180 (192)
...+.+||+|+.+.. .+.. .-||||+--..-..-|-+. -+..||.|-..+..
T Consensus 338 g~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~g 415 (429)
T KOG3842|consen 338 GQRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAG 415 (429)
T ss_pred CcccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhcc
Confidence 444789999998311 1111 1399999888888889763 24579999877754
No 131
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=60.72 E-value=4.9 Score=24.20 Aligned_cols=42 Identities=24% Similarity=0.624 Sum_probs=26.3
Q ss_pred ccccccccCCCceEEe--cCCCccChHhHHHHHhC-----CCCCCcccC
Q 047298 134 RCAICLGSGTGSVIQM--DCLHQFHEKCIACWFDN-----RNYSCPLCR 175 (192)
Q Consensus 134 ~C~ICl~~~~~~~~~l--~C~H~Fh~~CI~~Wl~~-----~~~~CP~CR 175 (192)
.|.||.....+..... .|+-.||..|+..=... ..-.||.|+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 3888988333322212 78889999998754321 245687775
No 132
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=59.28 E-value=13 Score=26.54 Aligned_cols=45 Identities=24% Similarity=0.598 Sum_probs=28.0
Q ss_pred ccccccccccCCC-ceEE------ecC---CCccChHhHHHHHhC--------CCCCCcccCc
Q 047298 132 EERCAICLGSGTG-SVIQ------MDC---LHQFHEKCIACWFDN--------RNYSCPLCRF 176 (192)
Q Consensus 132 ~~~C~ICl~~~~~-~~~~------l~C---~H~Fh~~CI~~Wl~~--------~~~~CP~CR~ 176 (192)
...|-.|.....+ .+.- -.| .=.||..||..++.. ..-.||.||.
T Consensus 7 g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 7 GKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 4566666663222 1221 245 557999999988752 3446999986
No 133
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=58.42 E-value=10 Score=32.63 Aligned_cols=60 Identities=22% Similarity=0.355 Sum_probs=35.5
Q ss_pred hccceeeeccCccccccccccccccc-CCC-ceEEecCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 116 LQSQPIVVDCEEEEEEEERCAICLGS-GTG-SVIQMDCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 116 l~~~~~~~~~~~~~~~~~~C~ICl~~-~~~-~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
.|-.++...+......+..|-.|.+. ... ..+.-.|.++||.+|=.--=. .-..||-|..
T Consensus 314 ~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHe-sLh~CpgCeh 375 (378)
T KOG2807|consen 314 FPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHE-SLHNCPGCEH 375 (378)
T ss_pred cCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHh-hhhcCCCcCC
Confidence 34444443333334455669999662 222 233338999999999554333 4557999964
No 134
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=57.42 E-value=1.3 Score=37.25 Aligned_cols=45 Identities=20% Similarity=0.342 Sum_probs=20.6
Q ss_pred cccccccccccCCCceEEec----CCCccChHhHHHHHhCCCCCCcccCc
Q 047298 131 EEERCAICLGSGTGSVIQMD----CLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~----C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
....||||=+...-.++.-. =.|.+|.-|-..|-- .+..||.|-.
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~-~R~~Cp~Cg~ 219 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF-VRIKCPYCGN 219 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE---TTS-TTT--
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee-cCCCCcCCCC
Confidence 34799999983211111111 145778889999977 8889999954
No 135
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=55.70 E-value=4.9 Score=25.93 Aligned_cols=36 Identities=17% Similarity=0.262 Sum_probs=18.1
Q ss_pred cccccccccccccCCCceEEe---cCCCccChHhHHHHH
Q 047298 129 EEEEERCAICLGSGTGSVIQM---DCLHQFHEKCIACWF 164 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l---~C~H~Fh~~CI~~Wl 164 (192)
+.+...|.+|...+.--.++- .||++||..|.....
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence 456789999999553322222 789999999976543
No 137
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=55.66 E-value=19 Score=24.43 Aligned_cols=51 Identities=22% Similarity=0.481 Sum_probs=22.0
Q ss_pred ccccccccccccc----CCCceEEe--cCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 129 EEEEERCAICLGS----GTGSVIQM--DCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 129 ~~~~~~C~ICl~~----~~~~~~~l--~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
......|.||=+. ..+.+... .|+--.|..|..-=.+..+..||-|+....
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred hcCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 4457799999992 22333322 666678899977666658889999987654
No 138
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=54.10 E-value=9.3 Score=33.20 Aligned_cols=50 Identities=26% Similarity=0.555 Sum_probs=27.5
Q ss_pred ccccccccccccccCCC-ceEEe---cCCCcc--------ChHhHHHHH----hCCCCCCcccCcc
Q 047298 128 EEEEEERCAICLGSGTG-SVIQM---DCLHQF--------HEKCIACWF----DNRNYSCPLCRFD 177 (192)
Q Consensus 128 ~~~~~~~C~ICl~~~~~-~~~~l---~C~H~F--------h~~CI~~Wl----~~~~~~CP~CR~~ 177 (192)
.+..++.||+|=+...+ .-..| .|.-.| |..|+..-- ++++..||.||..
T Consensus 11 dedl~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQ 76 (475)
T KOG4218|consen 11 DEDLGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQ 76 (475)
T ss_pred ccccccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHH
Confidence 35667899999994333 22223 444444 233332210 1156789999973
No 139
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=49.94 E-value=9 Score=20.17 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=9.1
Q ss_pred CCcccCcccchhh
Q 047298 170 SCPLCRFDMATAV 182 (192)
Q Consensus 170 ~CP~CR~~l~~~~ 182 (192)
.||+|-+.+....
T Consensus 3 ~CPiC~~~v~~~~ 15 (26)
T smart00734 3 QCPVCFREVPENL 15 (26)
T ss_pred cCCCCcCcccHHH
Confidence 5899987775443
No 140
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=49.13 E-value=23 Score=22.23 Aligned_cols=31 Identities=19% Similarity=0.561 Sum_probs=23.5
Q ss_pred cccccccccccC--CCceEEe-cCCCccChHhHH
Q 047298 131 EEERCAICLGSG--TGSVIQM-DCLHQFHEKCIA 161 (192)
Q Consensus 131 ~~~~C~ICl~~~--~~~~~~l-~C~H~Fh~~CI~ 161 (192)
....|++|-+.. .+++++- .|+-.+|..|..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~ 37 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE 37 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence 467899999944 5555533 899999999954
No 141
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=47.88 E-value=6.7 Score=33.57 Aligned_cols=45 Identities=20% Similarity=0.429 Sum_probs=31.0
Q ss_pred cccccccccccCCCceEEe--c--CCCccChHhHHHHHhCCCCCCcccCc
Q 047298 131 EEERCAICLGSGTGSVIQM--D--CLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l--~--C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
....||||=+...-.++.+ . =.+.+|.-|-..|-- .+..||.|-.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~-~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV-VRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccc-cCccCCCCCC
Confidence 4679999999432222212 1 135677889999977 8889999964
No 142
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=47.77 E-value=11 Score=23.44 Aligned_cols=25 Identities=24% Similarity=0.630 Sum_probs=13.7
Q ss_pred cCCCccChHhHHHHHhCCCCCCcccC
Q 047298 150 DCLHQFHEKCIACWFDNRNYSCPLCR 175 (192)
Q Consensus 150 ~C~H~Fh~~CI~~Wl~~~~~~CP~CR 175 (192)
.|++.||.+|=.- ....-..||-|-
T Consensus 26 ~C~~~FC~dCD~f-iHE~LH~CPGC~ 50 (51)
T PF07975_consen 26 KCKNHFCIDCDVF-IHETLHNCPGCE 50 (51)
T ss_dssp TTT--B-HHHHHT-TTTTS-SSSTT-
T ss_pred CCCCccccCcChh-hhccccCCcCCC
Confidence 7899999999443 222445799883
No 143
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.64 E-value=8.8 Score=26.79 Aligned_cols=12 Identities=25% Similarity=1.068 Sum_probs=10.8
Q ss_pred ccChHhHHHHHh
Q 047298 154 QFHEKCIACWFD 165 (192)
Q Consensus 154 ~Fh~~CI~~Wl~ 165 (192)
-||..|+..|..
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 499999999986
No 144
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=46.82 E-value=24 Score=19.19 Aligned_cols=36 Identities=22% Similarity=0.549 Sum_probs=21.0
Q ss_pred cccccccCCCc-eEEecCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 135 CAICLGSGTGS-VIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 135 C~ICl~~~~~~-~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
|..|-+..... .....=+..||..| ..|..|+..|.
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~~C---------f~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHPEC---------FKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEeCCccccccC---------CCCcccCCcCc
Confidence 66777733332 22223367888877 45777776653
No 145
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.31 E-value=15 Score=30.48 Aligned_cols=34 Identities=18% Similarity=0.176 Sum_probs=28.6
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHh
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFD 165 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~ 165 (192)
+-+.|+.||....++++ .+=||+|+.+||...+.
T Consensus 42 ~FdcCsLtLqPc~dPvi-t~~GylfdrEaILe~il 75 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRDPVI-TPDGYLFDREAILEYIL 75 (303)
T ss_pred CcceeeeecccccCCcc-CCCCeeeeHHHHHHHHH
Confidence 46789999997777776 77899999999998864
No 146
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=46.03 E-value=3.9 Score=25.61 Aligned_cols=14 Identities=29% Similarity=0.781 Sum_probs=12.8
Q ss_pred cCCCccChHhHHHH
Q 047298 150 DCLHQFHEKCIACW 163 (192)
Q Consensus 150 ~C~H~Fh~~CI~~W 163 (192)
.|+|.||..|...|
T Consensus 45 ~C~~~fC~~C~~~~ 58 (64)
T smart00647 45 KCGFSFCFRCKVPW 58 (64)
T ss_pred CCCCeECCCCCCcC
Confidence 68999999998888
No 147
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.12 E-value=6.4 Score=33.45 Aligned_cols=52 Identities=29% Similarity=0.540 Sum_probs=40.7
Q ss_pred cccccccccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 127 EEEEEEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 127 ~~~~~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
........|-||.....-+.+.-.|.|.|+..|...|.. ....||.||....
T Consensus 100 ~~~~~~~~~~~~~g~l~vpt~~qg~w~qf~~~~p~~~~~-~~~~~~d~~~~~~ 151 (324)
T KOG0824|consen 100 GFQQDHDICYICYGKLTVPTRIQGCWHQFCYVCPKSNFA-MGNDCPDCRGKIS 151 (324)
T ss_pred cccCCccceeeeeeeEEecccccCceeeeeecCCchhhh-hhhccchhhcCcC
Confidence 345567789999885444444457999999999999999 8889999987654
No 148
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=43.61 E-value=21 Score=25.15 Aligned_cols=33 Identities=27% Similarity=0.512 Sum_probs=23.8
Q ss_pred cccccccccccCCCceEEe--cCCCccChHhHHHH
Q 047298 131 EEERCAICLGSGTGSVIQM--DCLHQFHEKCIACW 163 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l--~C~H~Fh~~CI~~W 163 (192)
....|.||....+..+.-- .|...||..|....
T Consensus 54 ~~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 54 FKLKCSICGKSGGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred cCCcCcCCCCCCceeEEcCCCCCCcCCCHHHHHHC
Confidence 5679999999744433322 47779999998653
No 150
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=43.11 E-value=13 Score=34.75 Aligned_cols=48 Identities=29% Similarity=0.775 Sum_probs=32.9
Q ss_pred cccccccccccCCCceEEe----cCCCccChHhHHHHHhC----CCCCCcccCccc
Q 047298 131 EEERCAICLGSGTGSVIQM----DCLHQFHEKCIACWFDN----RNYSCPLCRFDM 178 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l----~C~H~Fh~~CI~~Wl~~----~~~~CP~CR~~l 178 (192)
....|++|-........+| .|+-.+|..|+..|+.. +.-.||-||.-.
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred hhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 3567778777444433323 77889999999999873 234599887644
No 151
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.09 E-value=4.3 Score=20.79 Aligned_cols=9 Identities=33% Similarity=0.711 Sum_probs=4.0
Q ss_pred CCCCcccCc
Q 047298 168 NYSCPLCRF 176 (192)
Q Consensus 168 ~~~CP~CR~ 176 (192)
...||.|-.
T Consensus 13 ~~fC~~CG~ 21 (23)
T PF13240_consen 13 AKFCPNCGT 21 (23)
T ss_pred CcchhhhCC
Confidence 334555543
No 152
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=42.88 E-value=18 Score=21.96 Aligned_cols=38 Identities=18% Similarity=0.451 Sum_probs=22.9
Q ss_pred cccccc-cCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchh
Q 047298 135 CAICLG-SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATA 181 (192)
Q Consensus 135 C~ICl~-~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~ 181 (192)
|.-|-. ..........-+..||..| ..|-.|+..|...
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~C---------f~C~~C~~~l~~~ 39 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPEC---------FKCSKCGKPLNDG 39 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTT---------SBETTTTCBTTTS
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccc---------cccCCCCCccCCC
Confidence 556666 2333333235677888877 5678887777654
No 153
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=42.87 E-value=16 Score=22.32 Aligned_cols=34 Identities=21% Similarity=0.231 Sum_probs=22.2
Q ss_pred ccccccccccCCCceE---EecCCCccChHhHHHHHh
Q 047298 132 EERCAICLGSGTGSVI---QMDCLHQFHEKCIACWFD 165 (192)
Q Consensus 132 ~~~C~ICl~~~~~~~~---~l~C~H~Fh~~CI~~Wl~ 165 (192)
...|.+|-..+..-.+ --.||++||..|......
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 3578888773332222 237999999999776543
No 154
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.61 E-value=19 Score=24.10 Aligned_cols=27 Identities=19% Similarity=0.405 Sum_probs=21.5
Q ss_pred CCccChHhHHHHHhCCCCCCcccCcccchh
Q 047298 152 LHQFHEKCIACWFDNRNYSCPLCRFDMATA 181 (192)
Q Consensus 152 ~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~ 181 (192)
.|.||..|...-|. ..||.|-.++...
T Consensus 28 EcTFCadCae~~l~---g~CPnCGGelv~R 54 (84)
T COG3813 28 ECTFCADCAENRLH---GLCPNCGGELVAR 54 (84)
T ss_pred eeehhHhHHHHhhc---CcCCCCCchhhcC
Confidence 47899999998755 7899998776543
No 155
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=38.30 E-value=9.1 Score=32.68 Aligned_cols=45 Identities=16% Similarity=0.335 Sum_probs=29.3
Q ss_pred cccccccccccCCCceEEe-----cCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 131 EEERCAICLGSGTGSVIQM-----DCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l-----~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
....||||=+...-.+++. .=.+.+|.-|-..|-- .+..||.|-.
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~-~R~~C~~Cg~ 232 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY-VRVKCSHCEE 232 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc-cCccCCCCCC
Confidence 3458999999332111111 1124677788889977 8889999965
No 156
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=37.50 E-value=26 Score=29.38 Aligned_cols=50 Identities=22% Similarity=0.329 Sum_probs=34.2
Q ss_pred ccccccccc--CCCceEEe----cCCCccChHhHHHHHhC--------CCCCCcccCcccchhh
Q 047298 133 ERCAICLGS--GTGSVIQM----DCLHQFHEKCIACWFDN--------RNYSCPLCRFDMATAV 182 (192)
Q Consensus 133 ~~C~ICl~~--~~~~~~~l----~C~H~Fh~~CI~~Wl~~--------~~~~CP~CR~~l~~~~ 182 (192)
..|-+|.+. ..+..+.. .|.-++|..|+..-+.. ....||.|++-+....
T Consensus 183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~w~~ 246 (276)
T KOG3005|consen 183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLSWTT 246 (276)
T ss_pred hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceeeHHH
Confidence 589999983 23333311 57779999999984432 3568999998765544
No 157
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=36.25 E-value=12 Score=33.08 Aligned_cols=50 Identities=22% Similarity=0.486 Sum_probs=0.0
Q ss_pred cccccccccccC-----------------CCce-EEecCCCccChHhHHHHHhC--------CCCCCcccCcccch
Q 047298 131 EEERCAICLGSG-----------------TGSV-IQMDCLHQFHEKCIACWFDN--------RNYSCPLCRFDMAT 180 (192)
Q Consensus 131 ~~~~C~ICl~~~-----------------~~~~-~~l~C~H~Fh~~CI~~Wl~~--------~~~~CP~CR~~l~~ 180 (192)
...+||+|+... ..+. ..-||||+-=.+...-|-+. -+..||.|-..|..
T Consensus 327 ~~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g 402 (416)
T PF04710_consen 327 RSRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDG 402 (416)
T ss_dssp ----------------------------------------------------------------------------
T ss_pred ccccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccC
Confidence 378999999821 0011 12399999988999999752 13579999887754
No 158
>PLN02189 cellulose synthase
Probab=36.09 E-value=41 Score=33.46 Aligned_cols=50 Identities=18% Similarity=0.465 Sum_probs=34.4
Q ss_pred ccccccccccccc----CCCceEEe---cCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 129 EEEEERCAICLGS----GTGSVIQM---DCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 129 ~~~~~~C~ICl~~----~~~~~~~l---~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
......|.||-+. ..+... . .|+--.|..|..-=-+.++..||-|+....
T Consensus 31 ~~~~~~C~iCgd~vg~~~~g~~f-vaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 31 NLDGQVCEICGDEIGLTVDGDLF-VACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccCccccccccccCcCCCCCEE-EeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 3456699999993 223333 3 466668899986544557889999998775
No 159
>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=35.74 E-value=1.9 Score=28.65 Aligned_cols=40 Identities=20% Similarity=0.375 Sum_probs=18.9
Q ss_pred cccccccccCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 133 ERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 133 ~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
..||.|.... .... +|.+|..|-... . ....||-|..+|.
T Consensus 2 ~~CP~C~~~L----~~~~-~~~~C~~C~~~~-~-~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQEL----EWQG-GHYHCEACQKDY-K-KEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBE----EEET-TEEEETTT--EE-E-EEEE-TTT-SB-E
T ss_pred CcCCCCCCcc----EEeC-CEEECccccccc-e-ecccCCCcccHHH
Confidence 4688888731 1112 566667775543 3 4667888887763
No 160
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=35.74 E-value=21 Score=25.79 Aligned_cols=45 Identities=24% Similarity=0.506 Sum_probs=27.5
Q ss_pred ccccccccccc---C-CCceEEecCCCccChHhHHHHHh-CCCCCCcccCc
Q 047298 131 EEERCAICLGS---G-TGSVIQMDCLHQFHEKCIACWFD-NRNYSCPLCRF 176 (192)
Q Consensus 131 ~~~~C~ICl~~---~-~~~~~~l~C~H~Fh~~CI~~Wl~-~~~~~CP~CR~ 176 (192)
++..|.+|... . .....-..|+|.+|..|-.. .. ...-.|-+|..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-SKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-TSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-CCCCCCEEChhhHH
Confidence 57799999882 2 23444459999999999665 11 01124888854
No 161
>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=35.27 E-value=25 Score=19.42 Aligned_cols=20 Identities=20% Similarity=0.562 Sum_probs=11.8
Q ss_pred cCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 150 DCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 150 ~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
.|||++-..- ....||+|..
T Consensus 6 ~CGy~y~~~~-------~~~~CP~Cg~ 25 (33)
T cd00350 6 VCGYIYDGEE-------APWVCPVCGA 25 (33)
T ss_pred CCCCEECCCc-------CCCcCcCCCC
Confidence 4666554322 3457999965
No 162
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.53 E-value=16 Score=27.41 Aligned_cols=51 Identities=22% Similarity=0.423 Sum_probs=29.1
Q ss_pred ccccccccccccc-cCCCceEE--ecCCCccChHhHHHHHhCCC---CCCcccCccc
Q 047298 128 EEEEEERCAICLG-SGTGSVIQ--MDCLHQFHEKCIACWFDNRN---YSCPLCRFDM 178 (192)
Q Consensus 128 ~~~~~~~C~ICl~-~~~~~~~~--l~C~H~Fh~~CI~~Wl~~~~---~~CP~CR~~l 178 (192)
....+.+|-||+. .+.+.+.. -=|.-.||.+|--+-....+ -.|-+||...
T Consensus 61 Gv~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~q 117 (169)
T KOG3799|consen 61 GVGDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQQ 117 (169)
T ss_pred ccCcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHHH
Confidence 4567899999999 44332221 12344677777554433112 2588887643
No 163
>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=32.09 E-value=11 Score=22.16 Aligned_cols=26 Identities=27% Similarity=0.469 Sum_probs=15.8
Q ss_pred ecCCCccChHhHHHHHhCCCCCCcccCc
Q 047298 149 MDCLHQFHEKCIACWFDNRNYSCPLCRF 176 (192)
Q Consensus 149 l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~ 176 (192)
..|||.|-..--..= . ....||.|..
T Consensus 9 ~~Cg~~fe~~~~~~~-~-~~~~CP~Cg~ 34 (42)
T PF09723_consen 9 EECGHEFEVLQSISE-D-DPVPCPECGS 34 (42)
T ss_pred CCCCCEEEEEEEcCC-C-CCCcCCCCCC
Confidence 368887765431111 1 4567999987
No 164
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=32.01 E-value=14 Score=23.09 Aligned_cols=11 Identities=27% Similarity=0.926 Sum_probs=5.0
Q ss_pred CCcccCcccch
Q 047298 170 SCPLCRFDMAT 180 (192)
Q Consensus 170 ~CP~CR~~l~~ 180 (192)
+||+|.+.+..
T Consensus 26 tCP~C~a~~~~ 36 (54)
T PF09237_consen 26 TCPICGAVIRQ 36 (54)
T ss_dssp E-TTT--EESS
T ss_pred CCCcchhhccc
Confidence 57777666544
No 165
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=31.41 E-value=25 Score=26.33 Aligned_cols=21 Identities=19% Similarity=0.507 Sum_probs=17.6
Q ss_pred ecCCCccChHhHHHHHhCCCCCCcccCccc
Q 047298 149 MDCLHQFHEKCIACWFDNRNYSCPLCRFDM 178 (192)
Q Consensus 149 l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l 178 (192)
-.|||+|+. -+..||.|....
T Consensus 33 ~~CG~v~~P---------Pr~~Cp~C~~~~ 53 (140)
T COG1545 33 KKCGRVYFP---------PRAYCPKCGSET 53 (140)
T ss_pred CCCCeEEcC---------CcccCCCCCCCC
Confidence 378999987 788999998774
No 166
>PLN02436 cellulose synthase A
Probab=30.79 E-value=56 Score=32.68 Aligned_cols=50 Identities=22% Similarity=0.496 Sum_probs=34.1
Q ss_pred ccccccccccccc----CCCceEEe---cCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 129 EEEEERCAICLGS----GTGSVIQM---DCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 129 ~~~~~~C~ICl~~----~~~~~~~l---~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
......|.||=+. ..+... . .|+--.|..|..-=-+..+..||-|+....
T Consensus 33 ~~~~~iCqICGD~Vg~t~dGe~F-VACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 33 ELSGQTCQICGDEIELTVDGEPF-VACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccCCccccccccccCcCCCCCEE-EeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 3346699999992 222233 3 455568899986555557889999998775
No 167
>PF12773 DZR: Double zinc ribbon
Probab=30.43 E-value=33 Score=20.44 Aligned_cols=28 Identities=21% Similarity=0.409 Sum_probs=15.8
Q ss_pred ccChHhHHHHH--hCCCCCCcccCcccchh
Q 047298 154 QFHEKCIACWF--DNRNYSCPLCRFDMATA 181 (192)
Q Consensus 154 ~Fh~~CI~~Wl--~~~~~~CP~CR~~l~~~ 181 (192)
.||..|-.+.. ......||.|...+...
T Consensus 13 ~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLPPPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChhhccCCCCCCcCCcCCCcCC
Confidence 35555555444 21345688887776543
No 168
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.85 E-value=24 Score=33.29 Aligned_cols=39 Identities=15% Similarity=0.353 Sum_probs=27.2
Q ss_pred ccccccccccCC---CceEEecCCCccChHhHHHHHhCCCCCCccc
Q 047298 132 EERCAICLGSGT---GSVIQMDCLHQFHEKCIACWFDNRNYSCPLC 174 (192)
Q Consensus 132 ~~~C~ICl~~~~---~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~C 174 (192)
...|-+|..... +-.+.+.|+-.||..|-. . -.+.||+|
T Consensus 654 ~r~C~vcq~pedse~~v~rt~~C~~~~C~~c~~---~-~~~~~~vC 695 (717)
T KOG3726|consen 654 IRTCKVCQLPEDSETDVCRTTFCYTPYCVACSL---D-YASISEVC 695 (717)
T ss_pred HHHHHHhcCCcCccccccCccccCCcchHhhhh---h-hhccCccc
Confidence 468999988222 223345899999888744 4 56789999
No 169
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=28.97 E-value=36 Score=20.93 Aligned_cols=23 Identities=26% Similarity=0.712 Sum_probs=12.3
Q ss_pred cCCCccChHhHHHHHhCCCCCCccc
Q 047298 150 DCLHQFHEKCIACWFDNRNYSCPLC 174 (192)
Q Consensus 150 ~C~H~Fh~~CI~~Wl~~~~~~CP~C 174 (192)
.|+|.|-.. |..-.. ....||.|
T Consensus 33 ~Cgh~w~~~-v~~R~~-~~~~CP~C 55 (55)
T PF14311_consen 33 KCGHEWKAS-VNDRTR-RGKGCPYC 55 (55)
T ss_pred CCCCeeEcc-Hhhhcc-CCCCCCCC
Confidence 456655332 222223 67789988
No 170
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.78 E-value=38 Score=28.72 Aligned_cols=35 Identities=17% Similarity=0.338 Sum_probs=25.7
Q ss_pred ccccccccccccCCCceEEecC----CCccChHhHHHHHh
Q 047298 130 EEEERCAICLGSGTGSVIQMDC----LHQFHEKCIACWFD 165 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~~~l~C----~H~Fh~~CI~~Wl~ 165 (192)
.....|.+|.|...+. ....| .|.||.-|-..-.+
T Consensus 266 ~apLcCTLC~ERLEDT-HFVQCPSVp~HKFCFPCSResIK 304 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDT-HFVQCPSVPSHKFCFPCSRESIK 304 (352)
T ss_pred CCceeehhhhhhhccC-ceeecCCCcccceecccCHHHHH
Confidence 3447899999944442 23557 69999999888877
No 171
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.62 E-value=8.6 Score=32.17 Aligned_cols=48 Identities=21% Similarity=0.474 Sum_probs=34.6
Q ss_pred ccccccccccccCC---C--ceEEec--------CCCccChHhHHHHHhCCCCCCcccCcc
Q 047298 130 EEEERCAICLGSGT---G--SVIQMD--------CLHQFHEKCIACWFDNRNYSCPLCRFD 177 (192)
Q Consensus 130 ~~~~~C~ICl~~~~---~--~~~~l~--------C~H~Fh~~CI~~Wl~~~~~~CP~CR~~ 177 (192)
.....|.||..... . ..+.+. |+|..|..|+..-+....-.||.||..
T Consensus 205 ~~~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 205 IIEKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 34578999998322 1 122345 999999999999987344689999864
No 172
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=27.74 E-value=31 Score=22.13 Aligned_cols=13 Identities=31% Similarity=0.881 Sum_probs=10.0
Q ss_pred CCCCcccCcccch
Q 047298 168 NYSCPLCRFDMAT 180 (192)
Q Consensus 168 ~~~CP~CR~~l~~ 180 (192)
+..||+|+..+..
T Consensus 2 k~~CPlCkt~~n~ 14 (61)
T PF05715_consen 2 KSLCPLCKTTLNV 14 (61)
T ss_pred CccCCcccchhhc
Confidence 4679999988743
No 173
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.37 E-value=38 Score=25.30 Aligned_cols=24 Identities=29% Similarity=0.574 Sum_probs=15.9
Q ss_pred ccccccccCCCceEEecCCCccChH
Q 047298 134 RCAICLGSGTGSVIQMDCLHQFHEK 158 (192)
Q Consensus 134 ~C~ICl~~~~~~~~~l~C~H~Fh~~ 158 (192)
.=-||.+-.. .+.+-.|||.|+..
T Consensus 59 hlfi~qs~~~-rv~rcecghsf~d~ 82 (165)
T COG4647 59 HLFICQSAQK-RVIRCECGHSFGDY 82 (165)
T ss_pred cEEEEecccc-cEEEEeccccccCh
Confidence 3446766333 36667999999853
No 174
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=27.34 E-value=30 Score=28.79 Aligned_cols=46 Identities=20% Similarity=0.283 Sum_probs=34.3
Q ss_pred cccccccccccCCCceEEecCCCccChHhHHHHHhCC--CCCCcccCcc
Q 047298 131 EEERCAICLGSGTGSVIQMDCLHQFHEKCIACWFDNR--NYSCPLCRFD 177 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~l~C~H~Fh~~CI~~Wl~~~--~~~CP~CR~~ 177 (192)
-+..|||=......+++.-.|+|+|-..=|...+. . .-.||+=-.+
T Consensus 175 fs~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~-~~~~i~CPv~gC~ 222 (262)
T KOG2979|consen 175 FSNRDPISKKPIVNPVISKKCGHVYDRDSIMQILC-DEITIRCPVLGCE 222 (262)
T ss_pred hcccCchhhhhhhchhhhcCcCcchhhhhHHHHhc-cCceeecccccCC
Confidence 35678887766666777679999999999999987 5 3458874333
No 175
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=25.98 E-value=23 Score=18.95 Aligned_cols=12 Identities=25% Similarity=0.924 Sum_probs=5.9
Q ss_pred CCcccCcccchh
Q 047298 170 SCPLCRFDMATA 181 (192)
Q Consensus 170 ~CP~CR~~l~~~ 181 (192)
.||.|-.++...
T Consensus 1 ~CP~C~s~l~~~ 12 (28)
T PF03119_consen 1 TCPVCGSKLVRE 12 (28)
T ss_dssp B-TTT--BEEE-
T ss_pred CcCCCCCEeEcC
Confidence 488998887743
No 176
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=25.44 E-value=65 Score=21.53 Aligned_cols=32 Identities=25% Similarity=0.568 Sum_probs=22.3
Q ss_pred cccccccccccCCCceEE--ecCCCccChHhHHH
Q 047298 131 EEERCAICLGSGTGSVIQ--MDCLHQFHEKCIAC 162 (192)
Q Consensus 131 ~~~~C~ICl~~~~~~~~~--l~C~H~Fh~~CI~~ 162 (192)
....|.+|-...+..+.- -.|.-.||..|...
T Consensus 35 ~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 35 RKLKCSICKKKGGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred hCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence 456999999863433321 16888999999764
No 177
>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=25.43 E-value=8.2 Score=24.03 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=12.0
Q ss_pred cCCCccChHhHHHH
Q 047298 150 DCLHQFHEKCIACW 163 (192)
Q Consensus 150 ~C~H~Fh~~CI~~W 163 (192)
.|++.||..|-..|
T Consensus 45 ~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 45 SCGTEFCFKCGEPW 58 (64)
T ss_dssp SCCSEECSSSTSES
T ss_pred CCCCcCccccCccc
Confidence 49999999998777
No 178
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.36 E-value=20 Score=32.12 Aligned_cols=35 Identities=26% Similarity=0.506 Sum_probs=24.0
Q ss_pred ccccccccccc---CCCce--EEe--cCCCccChHhHHHHHh
Q 047298 131 EEERCAICLGS---GTGSV--IQM--DCLHQFHEKCIACWFD 165 (192)
Q Consensus 131 ~~~~C~ICl~~---~~~~~--~~l--~C~H~Fh~~CI~~Wl~ 165 (192)
....||.|... ..+.. ... +|.|.||+.|+..|..
T Consensus 225 ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~ 266 (444)
T KOG1815|consen 225 NTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSD 266 (444)
T ss_pred cCccCCCcccchhccCCccccccccCCcCCeeceeeeccccc
Confidence 44559999982 11111 112 5999999999999987
No 179
>KOG4021 consensus Mitochondrial ribosomal protein S18b [Translation, ribosomal structure and biogenesis]
Probab=25.20 E-value=33 Score=27.45 Aligned_cols=22 Identities=27% Similarity=0.523 Sum_probs=14.3
Q ss_pred hHhHHHHHhCCCCCCcccCccc
Q 047298 157 EKCIACWFDNRNYSCPLCRFDM 178 (192)
Q Consensus 157 ~~CI~~Wl~~~~~~CP~CR~~l 178 (192)
..||.+--....+-||+||.+.
T Consensus 97 ktCIrkn~~~~gnpCPICRDey 118 (239)
T KOG4021|consen 97 KTCIRKNGRFLGNPCPICRDEY 118 (239)
T ss_pred hHHHhhcCeecCCCCCccccce
Confidence 3566654332456799999865
No 180
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=24.43 E-value=38 Score=21.92 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=10.1
Q ss_pred CCCCcccCcccch
Q 047298 168 NYSCPLCRFDMAT 180 (192)
Q Consensus 168 ~~~CP~CR~~l~~ 180 (192)
...||.|++.+..
T Consensus 6 ~v~CP~C~k~~~w 18 (62)
T PRK00418 6 TVNCPTCGKPVEW 18 (62)
T ss_pred cccCCCCCCcccc
Confidence 3579999998764
No 181
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.86 E-value=48 Score=25.48 Aligned_cols=25 Identities=32% Similarity=0.539 Sum_probs=20.2
Q ss_pred CCccChHhHHHHHhCCCCCCcccCcccch
Q 047298 152 LHQFHEKCIACWFDNRNYSCPLCRFDMAT 180 (192)
Q Consensus 152 ~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~ 180 (192)
.+-||..|-.+-.. .||.|..++.-
T Consensus 27 ~~~fC~kCG~~tI~----~Cp~C~~~IrG 51 (158)
T PF10083_consen 27 REKFCSKCGAKTIT----SCPNCSTPIRG 51 (158)
T ss_pred HHHHHHHhhHHHHH----HCcCCCCCCCC
Confidence 35799999888655 79999988854
No 182
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=23.85 E-value=53 Score=21.01 Aligned_cols=20 Identities=25% Similarity=0.498 Sum_probs=11.7
Q ss_pred ccccccccccccCCCceEEe
Q 047298 130 EEEERCAICLGSGTGSVIQM 149 (192)
Q Consensus 130 ~~~~~C~ICl~~~~~~~~~l 149 (192)
.+...||+|-..+....+.|
T Consensus 37 ~~~p~CPlC~s~M~~~~r~L 56 (59)
T PF14169_consen 37 EEEPVCPLCKSPMVSGTRML 56 (59)
T ss_pred CCCccCCCcCCccccceeec
Confidence 34567777777554444433
No 183
>PRK11827 hypothetical protein; Provisional
Probab=23.26 E-value=28 Score=22.34 Aligned_cols=19 Identities=16% Similarity=0.319 Sum_probs=13.2
Q ss_pred HHHhCCCCCCcccCcccchh
Q 047298 162 CWFDNRNYSCPLCRFDMATA 181 (192)
Q Consensus 162 ~Wl~~~~~~CP~CR~~l~~~ 181 (192)
+||. .--.||+|+.++...
T Consensus 3 ~~LL-eILaCP~ckg~L~~~ 21 (60)
T PRK11827 3 HRLL-EIIACPVCNGKLWYN 21 (60)
T ss_pred hHHH-hheECCCCCCcCeEc
Confidence 4554 456799999888654
No 184
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=23.10 E-value=57 Score=29.33 Aligned_cols=31 Identities=23% Similarity=0.403 Sum_probs=21.2
Q ss_pred cccccccc--cCCCceEEe---cCCCccChHhHHHH
Q 047298 133 ERCAICLG--SGTGSVIQM---DCLHQFHEKCIACW 163 (192)
Q Consensus 133 ~~C~ICl~--~~~~~~~~l---~C~H~Fh~~CI~~W 163 (192)
=.|.||.. ...++...+ .|+|.=|.+|..+-
T Consensus 129 C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~ 164 (446)
T PF07227_consen 129 CMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRH 164 (446)
T ss_pred CCccccCCcccCCCCeeEEeccCCCceehhhhhccc
Confidence 35677766 234455555 78999999997653
No 185
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=22.69 E-value=42 Score=17.29 Aligned_cols=17 Identities=24% Similarity=0.679 Sum_probs=11.4
Q ss_pred CCCcccCcccchhhhhh
Q 047298 169 YSCPLCRFDMATAVIES 185 (192)
Q Consensus 169 ~~CP~CR~~l~~~~~~~ 185 (192)
..||.|...+..+....
T Consensus 3 ~~C~~CgR~F~~~~l~~ 19 (25)
T PF13913_consen 3 VPCPICGRKFNPDRLEK 19 (25)
T ss_pred CcCCCCCCEECHHHHHH
Confidence 35899988776655443
No 186
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=22.54 E-value=24 Score=30.37 Aligned_cols=53 Identities=11% Similarity=0.033 Sum_probs=34.9
Q ss_pred cccccccccccccCCCceEEecCCC-ccChHhHHHH-HhCCCCCCcccCcccchhhh
Q 047298 129 EEEEERCAICLGSGTGSVIQMDCLH-QFHEKCIACW-FDNRNYSCPLCRFDMATAVI 183 (192)
Q Consensus 129 ~~~~~~C~ICl~~~~~~~~~l~C~H-~Fh~~CI~~W-l~~~~~~CP~CR~~l~~~~~ 183 (192)
....-.|.+|++-..-.. ..+|+| +||..|.-+- .+ +...||+|-..+....+
T Consensus 133 ~~~ti~~iqq~tnt~I~T-~v~~~~~Vf~Vtg~~~nC~k-ra~s~eie~ta~~ra~~ 187 (394)
T KOG2113|consen 133 KGATIKRIQQFTNTYIAT-PVRCGEPVFCVTGAPKNCVK-RARSCEIEQTAVTRAGQ 187 (394)
T ss_pred ccCccchheecccceEee-eccCCCceEEEecCCcchhh-hccccchhhhhhhhhhc
Confidence 445667999988322211 148998 9999996554 44 56679999776654443
No 187
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=22.41 E-value=40 Score=21.66 Aligned_cols=12 Identities=25% Similarity=0.869 Sum_probs=9.2
Q ss_pred CCCcccCcccch
Q 047298 169 YSCPLCRFDMAT 180 (192)
Q Consensus 169 ~~CP~CR~~l~~ 180 (192)
-.||+||..+..
T Consensus 9 LaCP~~kg~L~~ 20 (60)
T COG2835 9 LACPVCKGPLVY 20 (60)
T ss_pred eeccCcCCcceE
Confidence 369999998654
No 188
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.31 E-value=53 Score=20.98 Aligned_cols=15 Identities=20% Similarity=0.623 Sum_probs=11.8
Q ss_pred CCCCCcccCcccchh
Q 047298 167 RNYSCPLCRFDMATA 181 (192)
Q Consensus 167 ~~~~CP~CR~~l~~~ 181 (192)
.+..||+|-.+++.+
T Consensus 2 ~HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPD 16 (59)
T ss_pred CCCcCCcCCCcCCcc
Confidence 467899998888764
No 189
>PRK01343 zinc-binding protein; Provisional
Probab=22.12 E-value=51 Score=20.95 Aligned_cols=13 Identities=23% Similarity=0.519 Sum_probs=9.7
Q ss_pred CCCCCcccCcccc
Q 047298 167 RNYSCPLCRFDMA 179 (192)
Q Consensus 167 ~~~~CP~CR~~l~ 179 (192)
....||+|++.+.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3467999998764
No 190
>TIGR01367 pyrE_Therm orotate phosphoribosyltransferase, Thermus family. This model represents a distinct clade of orotate phosphoribosyltransferases. Members include the experimentally determined example from Thermus aquaticus and additional examples from Caulobacter crescentus, Helicobacter pylori, Mesorhizobium loti, and related species.
Probab=22.12 E-value=32 Score=26.99 Aligned_cols=19 Identities=26% Similarity=0.515 Sum_probs=14.6
Q ss_pred CCCCCcccCcccchhhhhh
Q 047298 167 RNYSCPLCRFDMATAVIES 185 (192)
Q Consensus 167 ~~~~CP~CR~~l~~~~~~~ 185 (192)
-...||+|+..++-+.+.+
T Consensus 168 ~~~~c~~~~~~~~~~~~~~ 186 (187)
T TIGR01367 168 DSHECPLCLAGIPAEKPGS 186 (187)
T ss_pred CcccCChhhcCCCCcCCCC
Confidence 3468999999998776553
No 191
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=21.74 E-value=80 Score=21.85 Aligned_cols=22 Identities=14% Similarity=0.277 Sum_probs=18.4
Q ss_pred HHHHHhCCCCCCcccCcccchhh
Q 047298 160 IACWFDNRNYSCPLCRFDMATAV 182 (192)
Q Consensus 160 I~~Wl~~~~~~CP~CR~~l~~~~ 182 (192)
|..|+. .+..|..|+++++...
T Consensus 51 i~S~l~-lrGrCr~C~~~I~~~y 72 (92)
T PF06750_consen 51 ILSYLL-LRGRCRYCGAPIPPRY 72 (92)
T ss_pred HHHHHH-hCCCCcccCCCCChHH
Confidence 567888 8999999999987654
No 192
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=20.67 E-value=19 Score=30.51 Aligned_cols=43 Identities=21% Similarity=0.490 Sum_probs=30.6
Q ss_pred cccccccccc-cCCCceEEecCCCccChHhHHHHHhCCCCCCcccCcccchhh
Q 047298 131 EEERCAICLG-SGTGSVIQMDCLHQFHEKCIACWFDNRNYSCPLCRFDMATAV 182 (192)
Q Consensus 131 ~~~~C~ICl~-~~~~~~~~l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~~~~ 182 (192)
-...|+-|.+ .....|++-.=.|+||..|. .|-+|+..+.+.+
T Consensus 91 fGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF---------~C~iC~R~L~TGd 134 (383)
T KOG4577|consen 91 FGTKCSACQEGIPPTQVVRKAQDFVYHLHCF---------ACFICKRQLATGD 134 (383)
T ss_pred hCCcchhhcCCCChHHHHHHhhcceeehhhh---------hhHhhhcccccCC
Confidence 3568999998 66666665667899999883 4677776665543
No 193
>PLN02195 cellulose synthase A
Probab=20.34 E-value=1.3e+02 Score=29.89 Aligned_cols=49 Identities=16% Similarity=0.367 Sum_probs=33.5
Q ss_pred ccccccccccc----CCCceE-E-ecCCCccChHhHHHHHhCCCCCCcccCcccc
Q 047298 131 EEERCAICLGS----GTGSVI-Q-MDCLHQFHEKCIACWFDNRNYSCPLCRFDMA 179 (192)
Q Consensus 131 ~~~~C~ICl~~----~~~~~~-~-l~C~H~Fh~~CI~~Wl~~~~~~CP~CR~~l~ 179 (192)
....|.||=+. ..+.+. . -.|+---|..|..-=-+.++..||-|+....
T Consensus 5 ~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 5 GAPICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CCccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 45689999992 222222 1 1667778999985444447888999988776
Done!