Query 023376
Match_columns 283
No_of_seqs 241 out of 1749
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 03:33:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023376hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4628 Predicted E3 ubiquitin 99.6 1.2E-15 2.6E-20 143.8 5.0 80 196-281 203-283 (348)
2 PF13639 zf-RING_2: Ring finge 99.5 5.4E-15 1.2E-19 99.9 2.1 44 229-272 1-44 (44)
3 PHA02929 N1R/p28-like protein; 99.2 6.6E-12 1.4E-16 113.6 5.1 75 198-276 148-227 (238)
4 PF12678 zf-rbx1: RING-H2 zinc 99.2 7.4E-12 1.6E-16 93.8 3.8 46 227-272 18-73 (73)
5 COG5243 HRD1 HRD ubiquitin lig 99.2 1.4E-11 2.9E-16 116.1 3.4 56 226-281 285-350 (491)
6 COG5540 RING-finger-containing 99.2 1.4E-11 3.1E-16 113.3 2.8 51 227-277 322-373 (374)
7 KOG0317 Predicted E3 ubiquitin 99.1 6.2E-11 1.4E-15 108.6 3.4 53 225-280 236-288 (293)
8 KOG0823 Predicted E3 ubiquitin 99.0 9.5E-11 2.1E-15 104.5 2.4 52 226-280 45-99 (230)
9 PLN03208 E3 ubiquitin-protein 99.0 2.2E-10 4.7E-15 100.3 4.1 51 226-279 16-82 (193)
10 PF13923 zf-C3HC4_2: Zinc fing 99.0 4.2E-10 9.1E-15 74.0 3.0 39 231-271 1-39 (39)
11 PF13920 zf-C3HC4_3: Zinc fing 99.0 4.4E-10 9.5E-15 77.8 3.1 46 228-276 2-48 (50)
12 cd00162 RING RING-finger (Real 98.9 6.1E-10 1.3E-14 73.3 3.4 44 230-275 1-45 (45)
13 KOG0320 Predicted E3 ubiquitin 98.9 5.1E-10 1.1E-14 96.2 2.4 53 226-279 129-181 (187)
14 PHA02926 zinc finger-like prot 98.8 3.3E-09 7.1E-14 94.4 3.6 53 226-278 168-232 (242)
15 PF15227 zf-C3HC4_4: zinc fing 98.8 3.3E-09 7.2E-14 71.2 1.9 38 231-271 1-42 (42)
16 PF00097 zf-C3HC4: Zinc finger 98.8 4.2E-09 9.1E-14 69.6 2.4 39 231-271 1-41 (41)
17 PF14634 zf-RING_5: zinc-RING 98.8 6.2E-09 1.3E-13 70.3 3.0 44 230-273 1-44 (44)
18 PF12861 zf-Apc11: Anaphase-pr 98.7 7.2E-09 1.6E-13 79.5 3.6 52 227-278 20-84 (85)
19 smart00504 Ubox Modified RING 98.7 7.5E-09 1.6E-13 74.2 3.5 47 229-278 2-48 (63)
20 KOG0802 E3 ubiquitin ligase [P 98.7 3.6E-09 7.9E-14 106.5 1.6 50 226-275 289-340 (543)
21 smart00184 RING Ring finger. E 98.7 1.2E-08 2.6E-13 64.8 3.2 38 231-271 1-39 (39)
22 TIGR00599 rad18 DNA repair pro 98.6 3.2E-08 6.9E-13 95.8 3.8 50 226-278 24-73 (397)
23 COG5574 PEX10 RING-finger-cont 98.5 4.9E-08 1.1E-12 88.7 2.2 52 226-280 213-266 (271)
24 KOG2164 Predicted E3 ubiquitin 98.5 7.3E-08 1.6E-12 94.5 2.8 51 228-281 186-241 (513)
25 COG5194 APC11 Component of SCF 98.5 1.4E-07 3.1E-12 71.1 3.6 33 248-280 53-85 (88)
26 PF11793 FANCL_C: FANCL C-term 98.3 2.7E-07 6E-12 68.5 1.0 51 228-278 2-68 (70)
27 PF13445 zf-RING_UBOX: RING-ty 98.2 7.3E-07 1.6E-11 60.1 2.8 38 231-269 1-43 (43)
28 KOG0828 Predicted E3 ubiquitin 98.2 3.2E-07 6.9E-12 89.5 1.2 52 226-277 569-635 (636)
29 KOG1734 Predicted RING-contain 98.2 2.2E-07 4.8E-12 84.7 0.1 53 226-278 222-283 (328)
30 KOG2177 Predicted E3 ubiquitin 98.2 4.4E-07 9.6E-12 80.9 1.4 44 226-272 11-54 (386)
31 smart00744 RINGv The RING-vari 98.2 1.1E-06 2.4E-11 60.9 3.0 42 230-272 1-49 (49)
32 PF04564 U-box: U-box domain; 98.2 5.4E-07 1.2E-11 67.3 1.5 49 227-278 3-52 (73)
33 KOG0287 Postreplication repair 98.2 4.3E-07 9.3E-12 85.2 0.6 50 226-278 21-70 (442)
34 COG5432 RAD18 RING-finger-cont 98.2 7.4E-07 1.6E-11 82.1 1.8 48 226-276 23-70 (391)
35 KOG1493 Anaphase-promoting com 98.1 1.2E-06 2.6E-11 65.6 1.1 53 226-278 18-83 (84)
36 COG5219 Uncharacterized conser 97.9 1.4E-06 3E-11 90.5 -0.8 52 226-277 1467-1524(1525)
37 KOG1785 Tyrosine kinase negati 97.8 5.1E-06 1.1E-10 79.6 1.1 52 227-281 368-421 (563)
38 PF14835 zf-RING_6: zf-RING of 97.8 1E-05 2.2E-10 58.9 1.4 49 228-280 7-55 (65)
39 KOG4265 Predicted E3 ubiquitin 97.8 1.5E-05 3.3E-10 75.5 2.9 48 226-276 288-336 (349)
40 KOG2930 SCF ubiquitin ligase, 97.7 1.9E-05 4.2E-10 62.4 2.8 31 248-278 80-110 (114)
41 KOG0311 Predicted E3 ubiquitin 97.7 4E-06 8.7E-11 79.1 -1.9 51 226-278 41-92 (381)
42 KOG0804 Cytoplasmic Zn-finger 97.7 1.6E-05 3.4E-10 77.2 1.6 50 225-276 172-222 (493)
43 KOG0825 PHD Zn-finger protein 97.6 7.7E-06 1.7E-10 83.7 -1.2 53 226-278 121-173 (1134)
44 KOG4172 Predicted E3 ubiquitin 97.6 1.6E-05 3.4E-10 56.0 0.3 47 227-276 6-54 (62)
45 KOG1039 Predicted E3 ubiquitin 97.6 2.9E-05 6.3E-10 74.1 2.1 51 226-276 159-221 (344)
46 KOG4445 Uncharacterized conser 97.5 2.1E-05 4.6E-10 72.9 0.3 54 227-280 114-190 (368)
47 KOG0978 E3 ubiquitin ligase in 97.4 5.5E-05 1.2E-09 77.6 0.9 53 226-281 641-694 (698)
48 KOG4159 Predicted E3 ubiquitin 97.3 0.00013 2.8E-09 70.9 2.0 49 226-277 82-130 (398)
49 KOG1941 Acetylcholine receptor 97.0 0.0002 4.3E-09 68.7 0.6 47 227-273 364-413 (518)
50 KOG4692 Predicted E3 ubiquitin 97.0 0.00046 9.9E-09 65.6 2.9 48 226-276 420-467 (489)
51 KOG0297 TNF receptor-associate 96.9 0.00043 9.4E-09 67.4 2.3 52 226-279 19-70 (391)
52 KOG2660 Locus-specific chromos 96.9 0.0002 4.3E-09 67.3 -0.1 51 226-278 13-63 (331)
53 KOG2879 Predicted E3 ubiquitin 96.9 0.00088 1.9E-08 61.7 3.8 49 226-276 237-287 (298)
54 TIGR00570 cdk7 CDK-activating 96.8 0.00061 1.3E-08 64.1 2.4 36 244-279 21-57 (309)
55 KOG1952 Transcription factor N 96.8 0.0063 1.4E-07 63.5 9.5 48 226-273 189-244 (950)
56 KOG0827 Predicted E3 ubiquitin 96.7 0.00067 1.5E-08 65.1 1.3 26 248-273 25-53 (465)
57 PF11789 zf-Nse: Zinc-finger o 96.7 0.0006 1.3E-08 48.7 0.6 43 226-270 9-53 (57)
58 KOG3970 Predicted E3 ubiquitin 96.6 0.0014 3E-08 58.9 3.0 52 226-278 48-107 (299)
59 PF05883 Baculo_RING: Baculovi 96.6 0.0011 2.4E-08 55.1 1.8 40 227-266 25-70 (134)
60 KOG1428 Inhibitor of type V ad 96.6 0.0013 2.8E-08 71.5 2.6 50 226-275 3484-3543(3738)
61 COG5152 Uncharacterized conser 96.5 0.00084 1.8E-08 59.2 0.8 44 228-274 196-239 (259)
62 KOG1814 Predicted E3 ubiquitin 96.3 0.002 4.3E-08 62.3 1.8 49 226-274 182-238 (445)
63 KOG1002 Nucleotide excision re 96.2 0.0018 3.8E-08 64.5 1.1 50 226-278 534-588 (791)
64 PF12906 RINGv: RING-variant d 96.2 0.0029 6.2E-08 43.4 1.9 40 231-271 1-47 (47)
65 PF14570 zf-RING_4: RING/Ubox 96.2 0.0026 5.7E-08 43.8 1.5 44 231-275 1-47 (48)
66 PF10367 Vps39_2: Vacuolar sor 96.0 0.0039 8.4E-08 48.8 1.8 33 226-259 76-108 (109)
67 KOG1571 Predicted E3 ubiquitin 95.9 0.0045 9.6E-08 59.0 2.2 45 226-276 303-347 (355)
68 KOG3268 Predicted E3 ubiquitin 95.9 0.0054 1.2E-07 53.4 2.5 54 228-281 165-233 (234)
69 KOG1813 Predicted E3 ubiquitin 95.8 0.0034 7.4E-08 58.4 1.0 45 228-275 241-285 (313)
70 KOG0801 Predicted E3 ubiquitin 95.7 0.0036 7.8E-08 53.6 0.7 30 226-255 175-204 (205)
71 KOG4275 Predicted E3 ubiquitin 95.3 0.004 8.7E-08 57.9 -0.4 42 228-276 300-342 (350)
72 PHA02862 5L protein; Provision 95.3 0.011 2.3E-07 49.9 2.1 47 228-278 2-55 (156)
73 PHA03096 p28-like protein; Pro 95.3 0.0078 1.7E-07 56.3 1.3 47 229-275 179-236 (284)
74 COG5222 Uncharacterized conser 95.1 0.011 2.3E-07 55.4 1.7 48 228-278 274-324 (427)
75 KOG3039 Uncharacterized conser 94.9 0.024 5.3E-07 51.7 3.5 53 226-278 219-272 (303)
76 PHA02825 LAP/PHD finger-like p 94.9 0.023 5E-07 48.6 3.0 49 226-278 6-61 (162)
77 PF04641 Rtf2: Rtf2 RING-finge 94.7 0.029 6.2E-07 51.7 3.3 53 225-278 110-163 (260)
78 COG5236 Uncharacterized conser 94.6 0.024 5.2E-07 54.0 2.7 47 225-274 58-106 (493)
79 KOG0826 Predicted E3 ubiquitin 94.3 0.054 1.2E-06 51.3 4.2 49 226-276 298-346 (357)
80 KOG1001 Helicase-like transcri 93.7 0.027 5.8E-07 58.6 1.2 45 229-277 455-501 (674)
81 KOG0827 Predicted E3 ubiquitin 93.7 0.0038 8.3E-08 60.0 -4.6 53 227-279 195-248 (465)
82 KOG2034 Vacuolar sorting prote 93.6 0.034 7.4E-07 58.5 1.8 37 226-263 815-851 (911)
83 PF08746 zf-RING-like: RING-li 93.6 0.036 7.7E-07 37.2 1.3 41 231-271 1-43 (43)
84 PF05290 Baculo_IE-1: Baculovi 93.6 0.046 9.9E-07 45.5 2.1 52 227-280 79-136 (140)
85 PF14447 Prok-RING_4: Prokaryo 93.5 0.041 8.8E-07 39.0 1.5 47 228-279 7-53 (55)
86 KOG1645 RING-finger-containing 92.7 0.076 1.7E-06 51.6 2.5 33 243-275 21-55 (463)
87 KOG1940 Zn-finger protein [Gen 92.6 0.054 1.2E-06 50.4 1.3 46 228-273 158-204 (276)
88 COG5175 MOT2 Transcriptional r 91.9 0.098 2.1E-06 49.9 2.1 52 226-277 12-65 (480)
89 KOG2114 Vacuolar assembly/sort 91.6 0.089 1.9E-06 55.3 1.6 41 229-274 841-881 (933)
90 PF03854 zf-P11: P-11 zinc fin 91.3 0.094 2E-06 36.1 1.0 31 248-278 17-48 (50)
91 KOG2932 E3 ubiquitin ligase in 91.1 0.091 2E-06 49.5 1.0 44 228-275 90-133 (389)
92 PF10272 Tmpp129: Putative tra 91.0 0.24 5.3E-06 47.8 3.8 32 249-280 311-355 (358)
93 KOG2817 Predicted E3 ubiquitin 89.9 0.23 4.9E-06 48.2 2.6 51 226-276 332-385 (394)
94 KOG0298 DEAD box-containing he 89.3 0.1 2.2E-06 57.0 -0.2 46 226-273 1151-1196(1394)
95 COG5183 SSM4 Protein involved 88.3 0.28 6.2E-06 51.5 2.2 53 226-279 10-69 (1175)
96 PF07800 DUF1644: Protein of u 87.7 0.69 1.5E-05 39.7 3.8 36 228-263 2-47 (162)
97 KOG3002 Zn finger protein [Gen 87.5 0.39 8.5E-06 45.3 2.4 46 226-276 46-91 (299)
98 KOG4362 Transcriptional regula 86.3 0.19 4.1E-06 52.0 -0.4 50 227-279 20-72 (684)
99 KOG0309 Conserved WD40 repeat- 86.2 0.36 7.7E-06 50.4 1.5 26 245-270 1044-1069(1081)
100 KOG0825 PHD Zn-finger protein 86.2 0.37 8.1E-06 50.5 1.6 49 227-275 95-153 (1134)
101 KOG1812 Predicted E3 ubiquitin 85.4 0.33 7.2E-06 47.3 0.8 38 227-264 145-183 (384)
102 KOG1609 Protein involved in mR 84.5 0.55 1.2E-05 43.4 1.8 48 228-275 78-133 (323)
103 KOG0802 E3 ubiquitin ligase [P 84.1 0.53 1.1E-05 47.8 1.6 49 225-280 476-524 (543)
104 COG5220 TFB3 Cdk activating ki 83.2 0.64 1.4E-05 42.5 1.5 49 227-275 9-63 (314)
105 PF14446 Prok-RING_1: Prokaryo 83.1 1.4 2.9E-05 31.2 2.8 44 227-274 4-50 (54)
106 KOG3899 Uncharacterized conser 82.7 0.49 1.1E-05 44.4 0.6 31 249-279 325-368 (381)
107 KOG3053 Uncharacterized conser 82.6 0.49 1.1E-05 43.6 0.6 50 226-275 18-81 (293)
108 KOG4185 Predicted E3 ubiquitin 80.7 0.8 1.7E-05 42.4 1.3 31 245-275 23-54 (296)
109 KOG1829 Uncharacterized conser 80.1 0.68 1.5E-05 47.4 0.6 43 226-271 509-556 (580)
110 KOG1100 Predicted E3 ubiquitin 78.1 1.2 2.6E-05 39.8 1.6 38 231-275 161-199 (207)
111 KOG1812 Predicted E3 ubiquitin 77.6 1.1 2.3E-05 43.8 1.2 44 228-271 306-351 (384)
112 KOG1815 Predicted E3 ubiquitin 76.6 1.4 3.1E-05 43.5 1.8 37 226-264 68-104 (444)
113 KOG0269 WD40 repeat-containing 76.3 1.7 3.8E-05 45.4 2.3 42 228-270 779-820 (839)
114 KOG3161 Predicted E3 ubiquitin 73.9 0.91 2E-05 46.7 -0.4 43 228-273 11-54 (861)
115 COG5109 Uncharacterized conser 73.7 2 4.4E-05 40.8 1.8 49 226-274 334-385 (396)
116 KOG2066 Vacuolar assembly/sort 70.9 1.9 4.2E-05 45.3 1.1 45 226-271 782-830 (846)
117 PF02891 zf-MIZ: MIZ/SP-RING z 70.4 3.2 6.8E-05 28.6 1.8 43 229-274 3-50 (50)
118 KOG2068 MOT2 transcription fac 69.9 3.9 8.4E-05 39.0 2.8 51 228-278 249-300 (327)
119 KOG3842 Adaptor protein Pellin 68.9 4.2 9.1E-05 38.7 2.8 51 227-277 340-415 (429)
120 KOG3579 Predicted E3 ubiquitin 68.2 2.9 6.2E-05 39.2 1.5 40 226-266 266-307 (352)
121 PF13901 DUF4206: Domain of un 64.2 5.8 0.00013 35.2 2.7 41 227-272 151-196 (202)
122 KOG3005 GIY-YIG type nuclease 63.9 3.7 8E-05 38.1 1.4 49 228-276 182-243 (276)
123 smart00249 PHD PHD zinc finger 63.6 5.6 0.00012 25.3 1.9 32 230-261 1-32 (47)
124 KOG3113 Uncharacterized conser 61.6 6.1 0.00013 36.5 2.3 52 226-279 109-161 (293)
125 PF10571 UPF0547: Uncharacteri 60.4 4.8 0.0001 24.1 1.0 22 230-253 2-24 (26)
126 PF00628 PHD: PHD-finger; Int 58.8 7.3 0.00016 26.1 1.8 43 230-272 1-49 (51)
127 KOG2807 RNA polymerase II tran 57.1 10 0.00022 36.3 3.0 46 227-272 329-374 (378)
128 PF06844 DUF1244: Protein of u 55.3 6.6 0.00014 28.9 1.2 13 252-264 11-23 (68)
129 KOG4718 Non-SMC (structural ma 54.9 5.2 0.00011 36.0 0.7 44 227-272 180-223 (235)
130 PF04216 FdhE: Protein involve 53.2 2.4 5.2E-05 39.5 -1.8 48 226-273 170-219 (290)
131 KOG0824 Predicted E3 ubiquitin 51.6 9 0.0002 36.2 1.7 15 227-241 6-20 (324)
132 smart00132 LIM Zinc-binding do 51.0 17 0.00036 22.2 2.5 36 231-275 2-37 (39)
133 KOG3039 Uncharacterized conser 49.5 12 0.00027 34.5 2.2 36 226-264 41-76 (303)
134 PF04710 Pellino: Pellino; In 49.4 5.6 0.00012 38.9 0.0 50 228-277 328-402 (416)
135 PF01363 FYVE: FYVE zinc finge 48.0 9.8 0.00021 27.3 1.1 37 227-263 8-45 (69)
136 KOG0824 Predicted E3 ubiquitin 47.6 6.4 0.00014 37.2 0.1 48 226-275 103-150 (324)
137 PF06906 DUF1272: Protein of u 45.1 37 0.00081 24.2 3.6 49 229-279 6-55 (57)
138 cd00065 FYVE FYVE domain; Zinc 43.0 18 0.00038 24.8 1.8 35 229-263 3-38 (57)
139 KOG0956 PHD finger protein AF1 42.6 8.5 0.00018 40.2 0.1 49 228-276 117-182 (900)
140 PF06750 DiS_P_DiS: Bacterial 42.2 23 0.0005 27.5 2.5 38 228-277 33-70 (92)
141 COG4847 Uncharacterized protei 38.4 26 0.00056 27.7 2.2 36 228-264 6-41 (103)
142 smart00064 FYVE Protein presen 38.3 26 0.00056 24.9 2.1 37 228-264 10-47 (68)
143 PF05605 zf-Di19: Drought indu 37.2 13 0.00029 25.5 0.4 38 228-275 2-41 (54)
144 PF04710 Pellino: Pellino; In 37.1 11 0.00024 36.9 0.0 30 244-276 304-339 (416)
145 PRK03564 formate dehydrogenase 36.9 16 0.00036 34.6 1.1 45 227-273 186-234 (309)
146 TIGR00622 ssl1 transcription f 35.1 57 0.0012 26.5 3.7 45 228-272 55-110 (112)
147 KOG1729 FYVE finger containing 33.7 7.5 0.00016 36.6 -1.8 39 227-265 213-251 (288)
148 KOG4185 Predicted E3 ubiquitin 33.1 7.4 0.00016 36.0 -1.9 47 228-274 207-265 (296)
149 KOG1815 Predicted E3 ubiquitin 32.6 16 0.00034 36.2 0.2 37 228-264 226-267 (444)
150 PF00412 LIM: LIM domain; Int 32.1 27 0.00058 23.7 1.3 14 228-241 26-39 (58)
151 PF07975 C1_4: TFIIH C1-like d 32.0 30 0.00066 24.1 1.5 42 231-272 2-50 (51)
152 PF07191 zinc-ribbons_6: zinc- 31.7 5.6 0.00012 29.6 -2.4 39 229-275 2-40 (70)
153 COG3492 Uncharacterized protei 31.4 21 0.00046 27.9 0.7 13 252-264 42-54 (104)
154 TIGR01562 FdhE formate dehydro 30.1 18 0.00039 34.3 0.2 42 227-273 183-232 (305)
155 PF13717 zinc_ribbon_4: zinc-r 29.0 34 0.00074 21.8 1.3 13 230-242 4-16 (36)
156 PLN02189 cellulose synthase 29.0 50 0.0011 36.4 3.2 49 227-276 33-87 (1040)
157 PF14311 DUF4379: Domain of un 27.5 35 0.00077 23.5 1.2 9 263-271 47-55 (55)
158 smart00647 IBR In Between Ring 26.9 25 0.00053 24.3 0.4 18 244-261 40-58 (64)
159 KOG3726 Uncharacterized conser 26.7 32 0.00069 36.0 1.2 42 228-272 654-696 (717)
160 PF10146 zf-C4H2: Zinc finger- 26.6 37 0.0008 30.9 1.5 23 253-275 196-218 (230)
161 PF04423 Rad50_zn_hook: Rad50 25.7 28 0.0006 24.0 0.4 11 267-277 22-32 (54)
162 KOG2169 Zn-finger transcriptio 25.6 68 0.0015 33.5 3.4 49 226-279 304-359 (636)
163 PF09943 DUF2175: Uncharacteri 25.5 50 0.0011 26.3 1.8 35 229-264 3-37 (101)
164 PF14169 YdjO: Cold-inducible 25.3 34 0.00074 24.6 0.8 14 265-278 39-52 (59)
165 PF07649 C1_3: C1-like domain; 25.2 55 0.0012 19.7 1.6 29 230-258 2-30 (30)
166 KOG1245 Chromatin remodeling c 25.1 25 0.00054 40.0 0.1 49 227-275 1107-1159(1404)
167 PF14569 zf-UDP: Zinc-binding 25.0 62 0.0014 24.6 2.2 50 227-276 8-62 (80)
168 PF10497 zf-4CXXC_R1: Zinc-fin 24.7 89 0.0019 24.8 3.2 24 250-273 37-69 (105)
169 PF06937 EURL: EURL protein; 24.2 62 0.0013 30.2 2.5 45 226-270 28-75 (285)
170 PLN02436 cellulose synthase A 24.0 69 0.0015 35.5 3.2 49 227-276 35-89 (1094)
171 PF13832 zf-HC5HC2H_2: PHD-zin 23.7 51 0.0011 25.7 1.7 33 227-261 54-88 (110)
172 KOG2071 mRNA cleavage and poly 22.6 44 0.00095 34.4 1.3 37 226-262 511-557 (579)
173 KOG1819 FYVE finger-containing 22.3 1.6E+02 0.0034 30.2 5.1 33 227-259 900-933 (990)
174 KOG4451 Uncharacterized conser 22.2 45 0.00098 30.5 1.2 24 252-275 250-273 (286)
175 PF02318 FYVE_2: FYVE-type zin 22.1 68 0.0015 25.7 2.1 46 227-273 53-102 (118)
176 KOG2979 Protein involved in DN 21.2 53 0.0012 30.4 1.5 44 228-273 176-221 (262)
177 cd00350 rubredoxin_like Rubred 20.9 55 0.0012 20.3 1.1 9 265-273 17-25 (33)
178 PF09889 DUF2116: Uncharacteri 20.8 45 0.00098 23.9 0.7 16 264-279 2-17 (59)
No 1
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.58 E-value=1.2e-15 Score=143.81 Aligned_cols=80 Identities=36% Similarity=0.818 Sum_probs=67.5
Q ss_pred CCCCCCHHHHhhccceeeccccccccccCCCCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCC-CCCcccc
Q 023376 196 KPPGLTQEALDCLHVEIFNSFAISSEGEASKTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGD-CPYCRRN 274 (283)
Q Consensus 196 ~~~~ls~~~i~~L~~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~t-CPlCR~~ 274 (283)
....+.+..++++|..+|....... ....|+||||+|..|+++++|||+|.||..||++||..+.+ ||+||.+
T Consensus 203 ~~~r~~k~~l~~~p~~~f~~~~~~~------~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~d 276 (348)
T KOG4628|consen 203 RRNRLIKRLLKKLPVRTFTKGDDED------ATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRD 276 (348)
T ss_pred hhhhhHHHHHhhCCcEEeccccccC------CCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCc
Confidence 4456788899999999998765442 12799999999999999999999999999999999998755 9999998
Q ss_pred eecCCCC
Q 023376 275 IVVNSDK 281 (283)
Q Consensus 275 l~~~~~~ 281 (283)
+......
T Consensus 277 i~~~~~~ 283 (348)
T KOG4628|consen 277 IRTDSGS 283 (348)
T ss_pred CCCCCCC
Confidence 8766543
No 2
>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=99.51 E-value=5.4e-15 Score=99.86 Aligned_cols=44 Identities=45% Similarity=1.237 Sum_probs=40.4
Q ss_pred CcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 229 LDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 229 ~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
++|+||++.|..++.++.|+|+|.||..||..|++.+++||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 36999999999889999999999999999999999999999997
No 3
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.24 E-value=6.6e-12 Score=113.64 Aligned_cols=75 Identities=23% Similarity=0.503 Sum_probs=55.2
Q ss_pred CCCCHHHHhhccceeeccccccccccCCCCCCcCccccCccCCCCe-----eEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 198 PGLTQEALDCLHVEIFNSFAISSEGEASKTSLDCSICLESFTDGDE-----LICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 198 ~~ls~~~i~~L~~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~-----l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
.+..+..++.+|.......... ......+|+||++.+..+.. ...++|+|.||..||.+|+..+.+||+||
T Consensus 148 ~~~~~~~i~~lp~vl~~~e~~~----~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR 223 (238)
T PHA02929 148 GKNYKKFLKTIPSVLSEYEKLY----NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223 (238)
T ss_pred cchhHHHHHhcchhhhhhhhhh----cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCC
Confidence 3447777888877654433221 12446899999999876531 23346999999999999999999999999
Q ss_pred ccee
Q 023376 273 RNIV 276 (283)
Q Consensus 273 ~~l~ 276 (283)
..+.
T Consensus 224 ~~~~ 227 (238)
T PHA02929 224 TPFI 227 (238)
T ss_pred CEee
Confidence 9875
No 4
>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=99.22 E-value=7.4e-12 Score=93.77 Aligned_cols=46 Identities=35% Similarity=0.946 Sum_probs=36.8
Q ss_pred CCCcCccccCccCCC----------CeeEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 227 TSLDCSICLESFTDG----------DELICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 227 ~~~~C~ICle~~~~~----------~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
.+..|+||++.|... ..+...+|||.||..||.+||..+.+||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 355699999999332 2445568999999999999999999999997
No 5
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.17 E-value=1.4e-11 Score=116.07 Aligned_cols=56 Identities=29% Similarity=0.813 Sum_probs=46.3
Q ss_pred CCCCcCccccCcc-CCCC---------eeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCCCC
Q 023376 226 KTSLDCSICLESF-TDGD---------ELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNSDK 281 (283)
Q Consensus 226 ~~~~~C~ICle~~-~~~~---------~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~~~ 281 (283)
..+..|.|||+++ ..+. ....|||||+||.+|++.|++.+.+||+||.++..+..+
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~~~ 350 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQSS 350 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccccccCC
Confidence 5678999999995 3331 336789999999999999999999999999997666544
No 6
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.15 E-value=1.4e-11 Score=113.31 Aligned_cols=51 Identities=41% Similarity=1.056 Sum_probs=47.1
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHh-cCCCCCCcccceec
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVR-SCGDCPYCRRNIVV 277 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~-~~~tCPlCR~~l~~ 277 (283)
...+|+|||+.|..++.++.|||.|.||..||..|+. -+..||+||.++++
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 4579999999999999999999999999999999998 57789999999875
No 7
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.08 E-value=6.2e-11 Score=108.56 Aligned_cols=53 Identities=28% Similarity=0.741 Sum_probs=46.6
Q ss_pred CCCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCCC
Q 023376 225 SKTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNSD 280 (283)
Q Consensus 225 ~~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~~ 280 (283)
......|.|||+....+... ||||+||+.||..|...+..||+||..+.+.+.
T Consensus 236 ~~a~~kC~LCLe~~~~pSaT---pCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv 288 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSNPSAT---PCGHIFCWSCILEWCSEKAECPLCREKFQPSKV 288 (293)
T ss_pred CCCCCceEEEecCCCCCCcC---cCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence 35568999999998887666 999999999999999999999999998877653
No 8
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.03 E-value=9.5e-11 Score=104.49 Aligned_cols=52 Identities=29% Similarity=0.718 Sum_probs=43.4
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC---CCCCCcccceecCCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC---GDCPYCRRNIVVNSD 280 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~---~tCPlCR~~l~~~~~ 280 (283)
...++|.|||+.-+++... .|||+||+.||.+||..+ +.||+||..|..++.
T Consensus 45 ~~~FdCNICLd~akdPVvT---lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v 99 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVT---LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV 99 (230)
T ss_pred CCceeeeeeccccCCCEEe---ecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence 5679999999998876433 799999999999999873 459999999876654
No 9
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.01 E-value=2.2e-10 Score=100.33 Aligned_cols=51 Identities=27% Similarity=0.766 Sum_probs=41.5
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc----------------CCCCCCcccceecCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS----------------CGDCPYCRRNIVVNS 279 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~----------------~~tCPlCR~~l~~~~ 279 (283)
.+..+|+||++.+..+ ++++|||+||+.||..|+.. ...||+||..|...+
T Consensus 16 ~~~~~CpICld~~~dP---VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 16 GGDFDCNICLDQVRDP---VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CCccCCccCCCcCCCc---EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 4678999999998766 34589999999999999853 246999999886543
No 10
>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=98.97 E-value=4.2e-10 Score=74.02 Aligned_cols=39 Identities=33% Similarity=1.072 Sum_probs=33.2
Q ss_pred CccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCc
Q 023376 231 CSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYC 271 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlC 271 (283)
|+||++.+.. .++.++|||.||..||..|++.+..||+|
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 8999999887 44567999999999999999998899998
No 11
>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=98.96 E-value=4.4e-10 Score=77.81 Aligned_cols=46 Identities=35% Similarity=0.886 Sum_probs=38.7
Q ss_pred CCcCccccCccCCCCeeEEcCCCCc-cChhhHHHHHhcCCCCCCccccee
Q 023376 228 SLDCSICLESFTDGDELICLPCKHR-FHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~-FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
+..|.||++.... +..+||||. ||..|+..|+.....||+||++|.
T Consensus 2 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD---VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCc---eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4679999998654 566799999 999999999999999999999874
No 12
>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=98.95 E-value=6.1e-10 Score=73.35 Aligned_cols=44 Identities=45% Similarity=1.191 Sum_probs=36.2
Q ss_pred cCccccCccCCCCeeEEcCCCCccChhhHHHHHhc-CCCCCCcccce
Q 023376 230 DCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS-CGDCPYCRRNI 275 (283)
Q Consensus 230 ~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~-~~tCPlCR~~l 275 (283)
.|+||++.+. ..+..++|||.||..|+..|+.. ...||+|+..+
T Consensus 1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 4999999983 33444569999999999999998 77899998764
No 13
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.91 E-value=5.1e-10 Score=96.20 Aligned_cols=53 Identities=28% Similarity=0.740 Sum_probs=44.5
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNS 279 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~ 279 (283)
+....|+|||+.+.+...+ -..|||+||..||+..+.....||+|++.|..+.
T Consensus 129 ~~~~~CPiCl~~~sek~~v-sTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPV-STKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred ccccCCCceecchhhcccc-ccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence 4568899999999876543 3579999999999999999999999998776543
No 14
>PHA02926 zinc finger-like protein; Provisional
Probab=98.79 E-value=3.3e-09 Score=94.37 Aligned_cols=53 Identities=28% Similarity=0.673 Sum_probs=40.1
Q ss_pred CCCCcCccccCccCCCC-----eeEEc-CCCCccChhhHHHHHhcC------CCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGD-----ELICL-PCKHRFHSDCLDPWVRSC------GDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~-----~l~~L-PCgH~FH~~CI~~WL~~~------~tCPlCR~~l~~~ 278 (283)
..+.+|+|||+.+..+. .-.+| +|+|.||..||..|...+ ..||+||..+..-
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I 232 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI 232 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence 45789999999874321 22344 599999999999999753 3599999987543
No 15
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.76 E-value=3.3e-09 Score=71.16 Aligned_cols=38 Identities=42% Similarity=0.967 Sum_probs=30.0
Q ss_pred CccccCccCCCCeeEEcCCCCccChhhHHHHHhcC----CCCCCc
Q 023376 231 CSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC----GDCPYC 271 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~----~tCPlC 271 (283)
|+||++.|.++..+ +|||.||..||..|++.. ..||.|
T Consensus 1 CpiC~~~~~~Pv~l---~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSL---PCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE----SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCcccc---CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999999988555 999999999999999874 359987
No 16
>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=98.76 E-value=4.2e-09 Score=69.57 Aligned_cols=39 Identities=51% Similarity=1.215 Sum_probs=33.8
Q ss_pred CccccCccCCCCeeEEcCCCCccChhhHHHHHh--cCCCCCCc
Q 023376 231 CSICLESFTDGDELICLPCKHRFHSDCLDPWVR--SCGDCPYC 271 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~--~~~tCPlC 271 (283)
|+||++.+..+. ..++|||.||..||..|+. ....||+|
T Consensus 1 C~iC~~~~~~~~--~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPV--ILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEE--EETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCC--EEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 899999988765 4679999999999999999 45679998
No 17
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.75 E-value=6.2e-09 Score=70.30 Aligned_cols=44 Identities=30% Similarity=0.777 Sum_probs=38.0
Q ss_pred cCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCccc
Q 023376 230 DCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRR 273 (283)
Q Consensus 230 ~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~ 273 (283)
.|.||++.|........++|||+||..||..+......||+|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 49999999955556778899999999999999866778999984
No 18
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.74 E-value=7.2e-09 Score=79.45 Aligned_cols=52 Identities=35% Similarity=0.842 Sum_probs=40.1
Q ss_pred CCCcCccccCccCC--------CC--eeEEcCCCCccChhhHHHHHhc---CCCCCCcccceecC
Q 023376 227 TSLDCSICLESFTD--------GD--ELICLPCKHRFHSDCLDPWVRS---CGDCPYCRRNIVVN 278 (283)
Q Consensus 227 ~~~~C~ICle~~~~--------~~--~l~~LPCgH~FH~~CI~~WL~~---~~tCPlCR~~l~~~ 278 (283)
.++.|.||...|.. ++ .+..-.|+|.||..||.+||.. ++.||+||.+...+
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK 84 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence 47789999888862 11 2333459999999999999986 46799999987654
No 19
>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=98.74 E-value=7.5e-09 Score=74.22 Aligned_cols=47 Identities=23% Similarity=0.531 Sum_probs=41.2
Q ss_pred CcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 229 LDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 229 ~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
..|+||++.+..+ ..++|||+|+..||..|+..+++||+|+..+..+
T Consensus 2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence 4699999999986 3459999999999999999999999999887543
No 20
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.72 E-value=3.6e-09 Score=106.46 Aligned_cols=50 Identities=38% Similarity=0.864 Sum_probs=43.9
Q ss_pred CCCCcCccccCccCCCCe--eEEcCCCCccChhhHHHHHhcCCCCCCcccce
Q 023376 226 KTSLDCSICLESFTDGDE--LICLPCKHRFHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~--l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
.....|+||++.+..+.. ...|||+|+||..||+.|++..++||+||..+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 347889999999998644 56779999999999999999999999999944
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=98.70 E-value=1.2e-08 Score=64.79 Aligned_cols=38 Identities=39% Similarity=1.188 Sum_probs=31.9
Q ss_pred CccccCccCCCCeeEEcCCCCccChhhHHHHHh-cCCCCCCc
Q 023376 231 CSICLESFTDGDELICLPCKHRFHSDCLDPWVR-SCGDCPYC 271 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~-~~~tCPlC 271 (283)
|+||++... ....++|+|.||..|+..|+. ....||+|
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 889998833 455679999999999999998 56779987
No 22
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.59 E-value=3.2e-08 Score=95.76 Aligned_cols=50 Identities=32% Similarity=0.616 Sum_probs=43.3
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
.....|+||++.|..+. +++|||.||..||..|+.....||+|+..+...
T Consensus 24 e~~l~C~IC~d~~~~Pv---itpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFFDVPV---LTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73 (397)
T ss_pred ccccCCCcCchhhhCcc---CCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence 45678999999998764 459999999999999999988999999987643
No 23
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=4.9e-08 Score=88.74 Aligned_cols=52 Identities=29% Similarity=0.638 Sum_probs=43.0
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHH-HHhcCCC-CCCcccceecCCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDP-WVRSCGD-CPYCRRNIVVNSD 280 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~-WL~~~~t-CPlCR~~l~~~~~ 280 (283)
..+..|+||++....+... +|||+||..||.. |-.++.. ||+||+.+..++.
T Consensus 213 ~~d~kC~lC~e~~~~ps~t---~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPEVPSCT---PCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccCCcccc---cccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence 4578999999997776544 9999999999999 8777665 9999998876653
No 24
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.47 E-value=7.3e-08 Score=94.48 Aligned_cols=51 Identities=27% Similarity=0.602 Sum_probs=41.4
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC-----CCCCCcccceecCCCC
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC-----GDCPYCRRNIVVNSDK 281 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~-----~tCPlCR~~l~~~~~~ 281 (283)
...|+|||+....+... .|||+||..||.++|... ..||+|+..|...+..
T Consensus 186 ~~~CPICL~~~~~p~~t---~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~ 241 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRT---NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLL 241 (513)
T ss_pred CCcCCcccCCCCccccc---ccCceeeHHHHHHHHhhhcccCCccCCchhhhcccccee
Confidence 67899999987765444 699999999999998763 4699999998775543
No 25
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.47 E-value=1.4e-07 Score=71.09 Aligned_cols=33 Identities=33% Similarity=0.856 Sum_probs=29.7
Q ss_pred CCCCccChhhHHHHHhcCCCCCCcccceecCCC
Q 023376 248 PCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNSD 280 (283)
Q Consensus 248 PCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~~ 280 (283)
-|.|.||..||.+||..++.||+||++....+.
T Consensus 53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~~ 85 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWVLADG 85 (88)
T ss_pred ecchHHHHHHHHHHHhhCCCCCCCCceeEEecc
Confidence 499999999999999999999999998876543
No 26
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.26 E-value=2.7e-07 Score=68.53 Aligned_cols=51 Identities=39% Similarity=0.976 Sum_probs=25.1
Q ss_pred CCcCccccCccCCCCee---EE--cCCCCccChhhHHHHHhc-----------CCCCCCcccceecC
Q 023376 228 SLDCSICLESFTDGDEL---IC--LPCKHRFHSDCLDPWVRS-----------CGDCPYCRRNIVVN 278 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l---~~--LPCgH~FH~~CI~~WL~~-----------~~tCPlCR~~l~~~ 278 (283)
+.+|.||+..+.....+ .- -.|+..||..||..||.. .+.||+|+.+|..+
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 45799999987633222 11 149999999999999974 12499999998754
No 27
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.25 E-value=7.3e-07 Score=60.14 Aligned_cols=38 Identities=39% Similarity=0.937 Sum_probs=22.3
Q ss_pred CccccCccCCCC-eeEEcCCCCccChhhHHHHHhcC----CCCC
Q 023376 231 CSICLESFTDGD-ELICLPCKHRFHSDCLDPWVRSC----GDCP 269 (283)
Q Consensus 231 C~ICle~~~~~~-~l~~LPCgH~FH~~CI~~WL~~~----~tCP 269 (283)
|+||.+ |...+ .-..|+|||+|+.+||..|+... ..||
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 75533 44678999999999999999854 2476
No 28
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.24 E-value=3.2e-07 Score=89.54 Aligned_cols=52 Identities=31% Similarity=0.794 Sum_probs=40.6
Q ss_pred CCCCcCccccCccCCCC---e-----------eEEcCCCCccChhhHHHHHhcCC-CCCCcccceec
Q 023376 226 KTSLDCSICLESFTDGD---E-----------LICLPCKHRFHSDCLDPWVRSCG-DCPYCRRNIVV 277 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~---~-----------l~~LPCgH~FH~~CI~~WL~~~~-tCPlCR~~l~~ 277 (283)
....+|+|||..+..-. . -...||.|+||..||.+|...-+ .||+||++++.
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 45678999998874321 1 12459999999999999999654 89999999874
No 29
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.24 E-value=2.2e-07 Score=84.71 Aligned_cols=53 Identities=25% Similarity=0.678 Sum_probs=42.4
Q ss_pred CCCCcCccccCccCCCC-------eeEEcCCCCccChhhHHHHH--hcCCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGD-------ELICLPCKHRFHSDCLDPWV--RSCGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~-------~l~~LPCgH~FH~~CI~~WL--~~~~tCPlCR~~l~~~ 278 (283)
.++..|+||-..+.... .+-+|.|+|+||..||+-|- .++.+||+|+..+..+
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~ 283 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK 283 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence 45778999977765443 55678999999999999995 5678999999887654
No 30
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.21 E-value=4.4e-07 Score=80.87 Aligned_cols=44 Identities=41% Similarity=0.896 Sum_probs=39.1
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
.+...|+||++.|..+ ..|||+|.||..||..|+.....||.||
T Consensus 11 ~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred cccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccC
Confidence 4678999999999998 5679999999999999998556799999
No 31
>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=98.21 E-value=1.1e-06 Score=60.88 Aligned_cols=42 Identities=29% Similarity=0.922 Sum_probs=32.6
Q ss_pred cCccccCccCCCCeeEEcCCC-----CccChhhHHHHHhcC--CCCCCcc
Q 023376 230 DCSICLESFTDGDELICLPCK-----HRFHSDCLDPWVRSC--GDCPYCR 272 (283)
Q Consensus 230 ~C~ICle~~~~~~~l~~LPCg-----H~FH~~CI~~WL~~~--~tCPlCR 272 (283)
.|.||++. ..++...++||. |.||..||.+|+... .+||+|+
T Consensus 1 ~CrIC~~~-~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDE-GDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCC-CCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 48999993 334444578985 899999999999764 4799995
No 32
>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=98.20 E-value=5.4e-07 Score=67.27 Aligned_cols=49 Identities=22% Similarity=0.499 Sum_probs=38.3
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc-CCCCCCcccceecC
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS-CGDCPYCRRNIVVN 278 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~-~~tCPlCR~~l~~~ 278 (283)
+.+.|+||.+.|.++..+ ||||.|...||..|+.. ..+||+|+..+...
T Consensus 3 ~~f~CpIt~~lM~dPVi~---~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~ 52 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVIL---PSGHTYERSAIERWLEQNGGTDPFTRQPLSES 52 (73)
T ss_dssp GGGB-TTTSSB-SSEEEE---TTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred cccCCcCcCcHhhCceeC---CcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence 357899999999988544 99999999999999999 88999999887654
No 33
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.17 E-value=4.3e-07 Score=85.19 Aligned_cols=50 Identities=30% Similarity=0.650 Sum_probs=43.4
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
.....|.||.+.|..+.. +||+|.||.-||..+|..+..||.|+.++...
T Consensus 21 D~lLRC~IC~eyf~ip~i---tpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es 70 (442)
T KOG0287|consen 21 DDLLRCGICFEYFNIPMI---TPCSHTFCSLCIRKFLSYKPQCPTCCVTVTES 70 (442)
T ss_pred HHHHHHhHHHHHhcCcee---ccccchHHHHHHHHHhccCCCCCceecccchh
Confidence 345789999999998744 49999999999999999999999999887544
No 34
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.16 E-value=7.4e-07 Score=82.14 Aligned_cols=48 Identities=29% Similarity=0.560 Sum_probs=42.2
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
.....|-||-+.|..+... +|||.||.-||...|..+..||+||.+..
T Consensus 23 Ds~lrC~IC~~~i~ip~~T---tCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 23 DSMLRCRICDCRISIPCET---TCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred hhHHHhhhhhheeecceec---ccccchhHHHHHHHhcCCCCCccccccHH
Confidence 3467899999999987555 99999999999999999999999998754
No 35
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=1.2e-06 Score=65.60 Aligned_cols=53 Identities=34% Similarity=0.863 Sum_probs=38.3
Q ss_pred CCCCcCccccCccCC--------CCe--eEEcCCCCccChhhHHHHHhc---CCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTD--------GDE--LICLPCKHRFHSDCLDPWVRS---CGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~--------~~~--l~~LPCgH~FH~~CI~~WL~~---~~tCPlCR~~l~~~ 278 (283)
...+.|.||...|.. ++. ++.-.|.|.||..||..|+.. +..||+||.+....
T Consensus 18 ~~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~ 83 (84)
T KOG1493|consen 18 APDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFK 83 (84)
T ss_pred CCCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEec
Confidence 345689999888743 221 211139999999999999976 45699999987653
No 36
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.95 E-value=1.4e-06 Score=90.47 Aligned_cols=52 Identities=35% Similarity=0.886 Sum_probs=38.5
Q ss_pred CCCCcCccccCccCC-CCee---EEcCCCCccChhhHHHHHhc--CCCCCCcccceec
Q 023376 226 KTSLDCSICLESFTD-GDEL---ICLPCKHRFHSDCLDPWVRS--CGDCPYCRRNIVV 277 (283)
Q Consensus 226 ~~~~~C~ICle~~~~-~~~l---~~LPCgH~FH~~CI~~WL~~--~~tCPlCR~~l~~ 277 (283)
....+|+||...+.. ...+ +.-.|.|.||..||..|++. +++||+||.+++.
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence 457899999876651 1111 11239999999999999987 5679999988763
No 37
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.84 E-value=5.1e-06 Score=79.56 Aligned_cols=52 Identities=33% Similarity=0.678 Sum_probs=41.3
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc--CCCCCCcccceecCCCC
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS--CGDCPYCRRNIVVNSDK 281 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~--~~tCPlCR~~l~~~~~~ 281 (283)
....|.||-|.- ..+.+-||||+.|..||..|-.. ..+||+||++|.-.+..
T Consensus 368 TFeLCKICaend---KdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v 421 (563)
T KOG1785|consen 368 TFELCKICAEND---KDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV 421 (563)
T ss_pred hHHHHHHhhccC---CCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence 457899998863 34556699999999999999855 56899999998765543
No 38
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.77 E-value=1e-05 Score=58.90 Aligned_cols=49 Identities=31% Similarity=0.674 Sum_probs=25.6
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCCC
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNSD 280 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~~ 280 (283)
...|++|.+.+.++..+. .|.|+||..||..-+.. .||+|..+....+.
T Consensus 7 lLrCs~C~~~l~~pv~l~--~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~ 55 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLG--GCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDI 55 (65)
T ss_dssp TTS-SSS-S--SS-B-----SSS--B-TTTGGGGTTT--B-SSS--B-S-SS-
T ss_pred hcCCcHHHHHhcCCceec--cCccHHHHHHhHHhcCC--CCCCcCChHHHHHH
Confidence 467999999999876542 79999999999886553 49999998766543
No 39
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.76 E-value=1.5e-05 Score=75.46 Aligned_cols=48 Identities=33% Similarity=0.809 Sum_probs=39.8
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCc-cChhhHHHHHhcCCCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHR-FHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~-FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
+...+|.|||.+-.+ +.+|||.|. .|..|.+..--..+.||+||.+|.
T Consensus 288 ~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred cCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 446899999998553 567899997 699999988777899999999874
No 40
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=97.75 E-value=1.9e-05 Score=62.43 Aligned_cols=31 Identities=29% Similarity=0.839 Sum_probs=27.6
Q ss_pred CCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 248 PCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 248 PCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
-|.|.||..||.+||+.++.||+|.++-...
T Consensus 80 ~CNHaFH~hCisrWlktr~vCPLdn~eW~~q 110 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTRNVCPLDNKEWVFQ 110 (114)
T ss_pred ecchHHHHHHHHHHHhhcCcCCCcCcceeEe
Confidence 3999999999999999999999998875543
No 41
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=4e-06 Score=79.15 Aligned_cols=51 Identities=33% Similarity=0.703 Sum_probs=40.2
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc-CCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS-CGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~-~~tCPlCR~~l~~~ 278 (283)
..+..|+|||+.++..-.+ .-|.|.||..||..-++. ++.||.||+.+...
T Consensus 41 ~~~v~c~icl~llk~tmtt--keClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 41 DIQVICPICLSLLKKTMTT--KECLHRFCFDCIWKALRSGNNECPTCRKKLVSK 92 (381)
T ss_pred hhhhccHHHHHHHHhhccc--HHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence 4478899999998754333 249999999999888876 67899999987543
No 42
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.67 E-value=1.6e-05 Score=77.18 Aligned_cols=50 Identities=30% Similarity=0.788 Sum_probs=39.5
Q ss_pred CCCCCcCccccCccCCCC-eeEEcCCCCccChhhHHHHHhcCCCCCCccccee
Q 023376 225 SKTSLDCSICLESFTDGD-ELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 225 ~~~~~~C~ICle~~~~~~-~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
..+...|+||||.+.... .+....|.|.||..|+..|.. .+||+||....
T Consensus 172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~--~scpvcR~~q~ 222 (493)
T KOG0804|consen 172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD--SSCPVCRYCQS 222 (493)
T ss_pred cccCCCcchhHhhcCccccceeeeecccccchHHHhhccc--CcChhhhhhcC
Confidence 355789999999998654 334446999999999999964 56999997654
No 43
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.64 E-value=7.7e-06 Score=83.69 Aligned_cols=53 Identities=26% Similarity=0.473 Sum_probs=45.2
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
.....|+||+..+.+.......+|+|+||..||..|-+.-.+||+||..+...
T Consensus 121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v 173 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEV 173 (1134)
T ss_pred hhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhee
Confidence 44678999999988776666668999999999999999999999999976543
No 44
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=1.6e-05 Score=55.99 Aligned_cols=47 Identities=32% Similarity=0.589 Sum_probs=35.1
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCc-cChhhHHHHHh-cCCCCCCccccee
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHR-FHSDCLDPWVR-SCGDCPYCRRNIV 276 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~-FH~~CI~~WL~-~~~tCPlCR~~l~ 276 (283)
...+|.||+|.-.+. +.-.|||. .|.+|-.+.++ .+..||+||++|.
T Consensus 6 ~~dECTICye~pvds---VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 6 WSDECTICYEHPVDS---VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cccceeeeccCcchH---HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 348999999874432 22359986 68889777666 6889999999873
No 45
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.59 E-value=2.9e-05 Score=74.06 Aligned_cols=51 Identities=29% Similarity=0.866 Sum_probs=39.8
Q ss_pred CCCCcCccccCccCCCC----eeEEcC-CCCccChhhHHHHH--hc-----CCCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGD----ELICLP-CKHRFHSDCLDPWV--RS-----CGDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~----~l~~LP-CgH~FH~~CI~~WL--~~-----~~tCPlCR~~l~ 276 (283)
..+.+|.|||+.+.+.. ...+|| |.|.||..||..|- .. .+.||.||....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 45788999999987654 134556 99999999999997 33 467999998653
No 46
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=97.53 E-value=2.1e-05 Score=72.91 Aligned_cols=54 Identities=28% Similarity=0.695 Sum_probs=45.0
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc-----------------------CCCCCCcccceecCCC
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS-----------------------CGDCPYCRRNIVVNSD 280 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~-----------------------~~tCPlCR~~l~~~~~ 280 (283)
....|.|||--|..++..++++|-|.||..|+.++|.. ...||+||..|..+..
T Consensus 114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~ 190 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEEN 190 (368)
T ss_pred CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccccc
Confidence 35679999999999998889999999999999988652 2249999999876644
No 47
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=5.5e-05 Score=77.61 Aligned_cols=53 Identities=26% Similarity=0.634 Sum_probs=42.7
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc-CCCCCCcccceecCCCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS-CGDCPYCRRNIVVNSDK 281 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~-~~tCPlCR~~l~~~~~~ 281 (283)
.....|++|-..+++. ++..|+|+||..||..-+.. ...||.|.+.+...+..
T Consensus 641 K~~LkCs~Cn~R~Kd~---vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 641 KELLKCSVCNTRWKDA---VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH 694 (698)
T ss_pred HhceeCCCccCchhhH---HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence 4567899999776653 34479999999999999976 67899999988777654
No 48
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=0.00013 Score=70.93 Aligned_cols=49 Identities=29% Similarity=0.769 Sum_probs=43.0
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceec
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVV 277 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~ 277 (283)
..+++|.||+..+..+... ||||.||..||.+-+.....||.||..++.
T Consensus 82 ~sef~c~vc~~~l~~pv~t---pcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVVT---PCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCCCccc---cccccccHHHHHHHhccCCCCccccccccc
Confidence 4579999999998887555 999999999999988888889999998864
No 49
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.01 E-value=0.0002 Score=68.73 Aligned_cols=47 Identities=43% Similarity=0.921 Sum_probs=39.9
Q ss_pred CCCcCccccCccCC-CCeeEEcCCCCccChhhHHHHHhcCC--CCCCccc
Q 023376 227 TSLDCSICLESFTD-GDELICLPCKHRFHSDCLDPWVRSCG--DCPYCRR 273 (283)
Q Consensus 227 ~~~~C~ICle~~~~-~~~l~~LPCgH~FH~~CI~~WL~~~~--tCPlCR~ 273 (283)
.+..|..|-+.+.. ++.+.-|||.|+||..|+...|.++. +||-||+
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 36789999999874 45677889999999999999998765 6999994
No 50
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.00 E-value=0.00046 Score=65.56 Aligned_cols=48 Identities=23% Similarity=0.692 Sum_probs=40.8
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
.++..|+||...-. ..+..||+|.-|+.||.+.+.+++.|=+|++++-
T Consensus 420 sEd~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence 56788999987633 3445699999999999999999999999999875
No 51
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.95 E-value=0.00043 Score=67.36 Aligned_cols=52 Identities=29% Similarity=0.680 Sum_probs=44.7
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNS 279 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~ 279 (283)
.....|+||+..+.++... ..|||.||..|+..|+..+..||.|+..+....
T Consensus 19 ~~~l~C~~C~~vl~~p~~~--~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~ 70 (391)
T KOG0297|consen 19 DENLLCPICMSVLRDPVQT--TTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE 70 (391)
T ss_pred cccccCccccccccCCCCC--CCCCCcccccccchhhccCcCCcccccccchhh
Confidence 5568899999999988663 379999999999999999999999988776543
No 52
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.94 E-value=0.0002 Score=67.31 Aligned_cols=51 Identities=22% Similarity=0.583 Sum_probs=42.9
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
.....|.+|-..|.+...+ .-|-|.||..||...|..++.||.|...|-..
T Consensus 13 n~~itC~LC~GYliDATTI--~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDATTI--TECLHTFCKSCIVKYLEESKYCPTCDIVIHKT 63 (331)
T ss_pred ccceehhhccceeecchhH--HHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence 4567899999988876555 25999999999999999999999998876544
No 53
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.90 E-value=0.00088 Score=61.67 Aligned_cols=49 Identities=22% Similarity=0.446 Sum_probs=39.6
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc--CCCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS--CGDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~--~~tCPlCR~~l~ 276 (283)
....+|++|-+.-..+-.. .+|+|+||..||..-+.. ..+||.|-.++.
T Consensus 237 t~~~~C~~Cg~~PtiP~~~--~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVI--GKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCCeee--ccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 5578999999886666443 479999999999987664 468999988876
No 54
>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=96.85 E-value=0.00061 Score=64.05 Aligned_cols=36 Identities=28% Similarity=0.646 Sum_probs=28.6
Q ss_pred eEEcCCCCccChhhHHHHHhc-CCCCCCcccceecCC
Q 023376 244 LICLPCKHRFHSDCLDPWVRS-CGDCPYCRRNIVVNS 279 (283)
Q Consensus 244 l~~LPCgH~FH~~CI~~WL~~-~~tCPlCR~~l~~~~ 279 (283)
+.+.+|||.||..||...+.. ...||.|+.++....
T Consensus 21 l~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 21 LMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred cccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 334499999999999996644 567999999887654
No 55
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=96.82 E-value=0.0063 Score=63.49 Aligned_cols=48 Identities=33% Similarity=0.905 Sum_probs=35.8
Q ss_pred CCCCcCccccCccCCCCee-EEcCCCCccChhhHHHHHhcCC-------CCCCccc
Q 023376 226 KTSLDCSICLESFTDGDEL-ICLPCKHRFHSDCLDPWVRSCG-------DCPYCRR 273 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l-~~LPCgH~FH~~CI~~WL~~~~-------tCPlCR~ 273 (283)
....+|.||.+.+..-..+ .--.|-|+||..||..|-.... .||.|..
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 3467899999999865533 2223889999999999987521 3999984
No 56
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.68 E-value=0.00067 Score=65.07 Aligned_cols=26 Identities=38% Similarity=1.074 Sum_probs=23.2
Q ss_pred CCCCccChhhHHHHHhcC---CCCCCccc
Q 023376 248 PCKHRFHSDCLDPWVRSC---GDCPYCRR 273 (283)
Q Consensus 248 PCgH~FH~~CI~~WL~~~---~tCPlCR~ 273 (283)
.|||+||..|+.+|+... ..||+|+-
T Consensus 25 ~cGhifh~~cl~qwfe~~Ps~R~cpic~i 53 (465)
T KOG0827|consen 25 TCGHIFHTTCLTQWFEGDPSNRGCPICQI 53 (465)
T ss_pred chhhHHHHHHHHHHHccCCccCCCCceee
Confidence 799999999999999974 46999993
No 57
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.66 E-value=0.0006 Score=48.70 Aligned_cols=43 Identities=28% Similarity=0.627 Sum_probs=28.3
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc--CCCCCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS--CGDCPY 270 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~--~~tCPl 270 (283)
.....|+|.+..|.++. +...|+|+|-.+.|.+||.. ...||+
T Consensus 9 ~~~~~CPiT~~~~~~PV--~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFEDPV--KSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-SSEE--EESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChhhCCc--CcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 34678999999998764 33479999999999999944 345998
No 58
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.65 E-value=0.0014 Score=58.87 Aligned_cols=52 Identities=29% Similarity=0.666 Sum_probs=42.5
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC--------CCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC--------GDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~--------~tCPlCR~~l~~~ 278 (283)
+-...|..|-..+..++.+ .|-|-|+||++|+.+|-..- -.||.|-.+|+..
T Consensus 48 DY~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 48 DYNPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred CCCCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 3456799999999988876 57799999999999998752 2499999988654
No 59
>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=96.57 E-value=0.0011 Score=55.08 Aligned_cols=40 Identities=23% Similarity=0.663 Sum_probs=32.8
Q ss_pred CCCcCccccCccCCCCeeEEcCCC------CccChhhHHHHHhcCC
Q 023376 227 TSLDCSICLESFTDGDELICLPCK------HRFHSDCLDPWVRSCG 266 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCg------H~FH~~CI~~WL~~~~ 266 (283)
...+|.||++.+.....++.++|| |.||..|+++|-..++
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~ 70 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERN 70 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhcc
Confidence 367899999999986667777887 9999999999954433
No 60
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=96.56 E-value=0.0013 Score=71.51 Aligned_cols=50 Identities=28% Similarity=0.603 Sum_probs=41.9
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC----------CCCCCcccce
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC----------GDCPYCRRNI 275 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~----------~tCPlCR~~l 275 (283)
..++.|.||+.+-......++|-|+|+||..|....|++. -.||+|+.+|
T Consensus 3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence 5678999999988777778899999999999998877652 2599998875
No 61
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.53 E-value=0.00084 Score=59.23 Aligned_cols=44 Identities=23% Similarity=0.515 Sum_probs=38.8
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccc
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRN 274 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~ 274 (283)
.+.|.||-.+|..+... .|||.||..|...-++....|-+|-+.
T Consensus 196 PF~C~iCKkdy~spvvt---~CGH~FC~~Cai~~y~kg~~C~~Cgk~ 239 (259)
T COG5152 196 PFLCGICKKDYESPVVT---ECGHSFCSLCAIRKYQKGDECGVCGKA 239 (259)
T ss_pred ceeehhchhhccchhhh---hcchhHHHHHHHHHhccCCcceecchh
Confidence 57899999999987555 899999999999999989999999654
No 62
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.002 Score=62.33 Aligned_cols=49 Identities=29% Similarity=0.619 Sum_probs=39.3
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC--------CCCCCcccc
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC--------GDCPYCRRN 274 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~--------~tCPlCR~~ 274 (283)
...+.|.||+++..-..-...|||+|+||..|++.++... -.||-|...
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~ 238 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG 238 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence 4568999999997766788899999999999999998752 248766543
No 63
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=96.21 E-value=0.0018 Score=64.48 Aligned_cols=50 Identities=28% Similarity=0.716 Sum_probs=39.8
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc-----CCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS-----CGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~-----~~tCPlCR~~l~~~ 278 (283)
....+|.+|-+.-++.... .|.|.||..||++++.. +.+||.|-..+..+
T Consensus 534 k~~~~C~lc~d~aed~i~s---~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 534 KGEVECGLCHDPAEDYIES---SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID 588 (791)
T ss_pred cCceeecccCChhhhhHhh---hhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence 5578899998886655444 89999999999999865 45799998877654
No 64
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=96.21 E-value=0.0029 Score=43.35 Aligned_cols=40 Identities=38% Similarity=1.021 Sum_probs=27.5
Q ss_pred CccccCccCCCCeeEEcCCC-----CccChhhHHHHHhc--CCCCCCc
Q 023376 231 CSICLESFTDGDELICLPCK-----HRFHSDCLDPWVRS--CGDCPYC 271 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LPCg-----H~FH~~CI~~WL~~--~~tCPlC 271 (283)
|-||++...+...+ +.||. -..|..||..|+.. +..|++|
T Consensus 1 CrIC~~~~~~~~~l-i~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPL-ISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-E-E-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCCce-ecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 67999987766533 56865 37899999999985 4569887
No 65
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=96.17 E-value=0.0026 Score=43.85 Aligned_cols=44 Identities=27% Similarity=0.693 Sum_probs=22.3
Q ss_pred CccccCccCCCCeeEEcC--CCCccChhhHHHHHh-cCCCCCCcccce
Q 023376 231 CSICLESFTDGDELICLP--CKHRFHSDCLDPWVR-SCGDCPYCRRNI 275 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LP--CgH~FH~~CI~~WL~-~~~tCPlCR~~l 275 (283)
|++|.+++...+. ..+| ||..+|..|....+. ..+.||-||.+.
T Consensus 1 cp~C~e~~d~~d~-~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDK-DFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCT-T--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCC-ccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7899999843332 2335 999999999988886 478899999863
No 66
>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=95.97 E-value=0.0039 Score=48.77 Aligned_cols=33 Identities=27% Similarity=0.779 Sum_probs=27.4
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHH
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLD 259 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~ 259 (283)
.....|+||-..+... .....||||+||..|+.
T Consensus 76 ~~~~~C~vC~k~l~~~-~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNS-VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCc-eEEEeCCCeEEeccccc
Confidence 4567799999999874 45577999999999985
No 67
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.90 E-value=0.0045 Score=59.03 Aligned_cols=45 Identities=27% Similarity=0.549 Sum_probs=32.9
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
.....|.||+++......+ ||||+-| |..-- +....||+||..|.
T Consensus 303 ~~p~lcVVcl~e~~~~~fv---pcGh~cc--ct~cs-~~l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPKSAVFV---PCGHVCC--CTLCS-KHLPQCPVCRQRIR 347 (355)
T ss_pred CCCCceEEecCCccceeee---cCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence 4468899999998775444 9999976 65443 23445999998764
No 68
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.90 E-value=0.0054 Score=53.37 Aligned_cols=54 Identities=33% Similarity=0.784 Sum_probs=36.9
Q ss_pred CCcCccccCccCCCC----eeEEcCCCCccChhhHHHHHhc-----------CCCCCCcccceecCCCC
Q 023376 228 SLDCSICLESFTDGD----ELICLPCKHRFHSDCLDPWVRS-----------CGDCPYCRRNIVVNSDK 281 (283)
Q Consensus 228 ~~~C~ICle~~~~~~----~l~~LPCgH~FH~~CI~~WL~~-----------~~tCPlCR~~l~~~~~~ 281 (283)
...|.||+..-..|. ..-...||--||.-||..||+. -+.||+|-.+|..+-++
T Consensus 165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmSg 233 (234)
T KOG3268|consen 165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMSG 233 (234)
T ss_pred hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeeccC
Confidence 345777765433332 1123369999999999999975 23499999998776543
No 69
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.82 E-value=0.0034 Score=58.41 Aligned_cols=45 Identities=22% Similarity=0.426 Sum_probs=39.6
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccce
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
.+.|-||...|..+... .|+|.||..|...-++....|++|-..+
T Consensus 241 Pf~c~icr~~f~~pVvt---~c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYFYRPVVT---KCGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred Cccccccccccccchhh---cCCceeehhhhccccccCCcceeccccc
Confidence 47799999999988555 8999999999999999999999997654
No 70
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.70 E-value=0.0036 Score=53.64 Aligned_cols=30 Identities=37% Similarity=0.823 Sum_probs=27.4
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccCh
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHS 255 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~ 255 (283)
+..-+|.||||++..++.+..|||-.+||+
T Consensus 175 ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 456799999999999999999999999986
No 71
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.32 E-value=0.004 Score=57.91 Aligned_cols=42 Identities=31% Similarity=0.757 Sum_probs=31.8
Q ss_pred CCcCccccCccCCCCeeEEcCCCCc-cChhhHHHHHhcCCCCCCccccee
Q 023376 228 SLDCSICLESFTDGDELICLPCKHR-FHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~-FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
...|+|||+... ....|+|||. -|..|-+.. +.||+||.-|.
T Consensus 300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKRM----NECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCCc---ceEEeecCcEEeehhhcccc----ccCchHHHHHH
Confidence 678999998744 4567799995 477786553 48999998764
No 72
>PHA02862 5L protein; Provisional
Probab=95.30 E-value=0.011 Score=49.89 Aligned_cols=47 Identities=21% Similarity=0.536 Sum_probs=35.2
Q ss_pred CCcCccccCccCCCCeeEEcCCC-----CccChhhHHHHHhc--CCCCCCcccceecC
Q 023376 228 SLDCSICLESFTDGDELICLPCK-----HRFHSDCLDPWVRS--CGDCPYCRRNIVVN 278 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCg-----H~FH~~CI~~WL~~--~~tCPlCR~~l~~~ 278 (283)
...|=||.+.-.+. + -||. -..|.+||.+|+.. +..|++|+.+...+
T Consensus 2 ~diCWIC~~~~~e~--~--~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik 55 (156)
T PHA02862 2 SDICWICNDVCDER--N--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK 55 (156)
T ss_pred CCEEEEecCcCCCC--c--ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence 35799999985433 2 3765 57899999999976 45699999876543
No 73
>PHA03096 p28-like protein; Provisional
Probab=95.25 E-value=0.0078 Score=56.28 Aligned_cols=47 Identities=26% Similarity=0.416 Sum_probs=33.9
Q ss_pred CcCccccCccCCCC----eeEEcC-CCCccChhhHHHHHhcC------CCCCCcccce
Q 023376 229 LDCSICLESFTDGD----ELICLP-CKHRFHSDCLDPWVRSC------GDCPYCRRNI 275 (283)
Q Consensus 229 ~~C~ICle~~~~~~----~l~~LP-CgH~FH~~CI~~WL~~~------~tCPlCR~~l 275 (283)
..|.||++...... .-..|+ |.|.||..||..|-... ..||.|+..+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence 67999999887542 234566 99999999999997652 2355555443
No 74
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.10 E-value=0.011 Score=55.36 Aligned_cols=48 Identities=29% Similarity=0.766 Sum_probs=36.5
Q ss_pred CCcCccccCccCCCCeeEEcC-CCCccChhhHHHHHh-cCCCCCCc-ccceecC
Q 023376 228 SLDCSICLESFTDGDELICLP-CKHRFHSDCLDPWVR-SCGDCPYC-RRNIVVN 278 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LP-CgH~FH~~CI~~WL~-~~~tCPlC-R~~l~~~ 278 (283)
...|+.|-.....+... | |+|.||.+||..-|. .-..||.| |..|..+
T Consensus 274 ~LkCplc~~Llrnp~kT---~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld 324 (427)
T COG5222 274 SLKCPLCHCLLRNPMKT---PCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLD 324 (427)
T ss_pred cccCcchhhhhhCcccC---ccccchHHHHHHhhhhhhccccCCCcccccchhh
Confidence 36799998887776544 5 999999999997765 46789999 4455443
No 75
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.94 E-value=0.024 Score=51.67 Aligned_cols=53 Identities=15% Similarity=0.306 Sum_probs=45.3
Q ss_pred CCCCcCccccCccCCCCeeEEc-CCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICL-PCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~L-PCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
..-+.|+||.+.+.....+..| ||||+|+.+|+...+..-..||+|-.++...
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR 272 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence 4578999999999887766666 6999999999999999999999998776544
No 76
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=94.90 E-value=0.023 Score=48.60 Aligned_cols=49 Identities=20% Similarity=0.583 Sum_probs=36.0
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCC-----ccChhhHHHHHhcC--CCCCCcccceecC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKH-----RFHSDCLDPWVRSC--GDCPYCRRNIVVN 278 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH-----~FH~~CI~~WL~~~--~tCPlCR~~l~~~ 278 (283)
.....|=||.++... . .-||.- ..|.+|+..|+... ..|++|..+....
T Consensus 6 ~~~~~CRIC~~~~~~--~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYDV--V--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCCC--c--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 457789999988532 2 237654 56999999999874 4699999876443
No 77
>PF04641 Rtf2: Rtf2 RING-finger
Probab=94.66 E-value=0.029 Score=51.68 Aligned_cols=53 Identities=19% Similarity=0.419 Sum_probs=40.9
Q ss_pred CCCCCcCccccCccCCCC-eeEEcCCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 225 SKTSLDCSICLESFTDGD-ELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 225 ~~~~~~C~ICle~~~~~~-~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
....+.|||+..+|.... .+...||||+|...+|.+.- ....||+|-.++...
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEE 163 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccC
Confidence 356789999999995444 44455899999999999973 356799998876643
No 78
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.60 E-value=0.024 Score=54.01 Aligned_cols=47 Identities=28% Similarity=0.632 Sum_probs=37.6
Q ss_pred CCCCCcCccccCccCCCCeeEEcCCCCccChhhHHHH--HhcCCCCCCcccc
Q 023376 225 SKTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPW--VRSCGDCPYCRRN 274 (283)
Q Consensus 225 ~~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~W--L~~~~tCPlCR~~ 274 (283)
.++...|.||.+.+.- +..+||+|..|-.|..+. |...+.||+||.+
T Consensus 58 DEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE 106 (493)
T COG5236 58 DEENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQKGCPLCRTE 106 (493)
T ss_pred ccccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhccCCCccccc
Confidence 3567889999987553 456799999999998664 5668899999985
No 79
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=94.25 E-value=0.054 Score=51.26 Aligned_cols=49 Identities=20% Similarity=0.364 Sum_probs=39.5
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
.....|+||+.....+..+. --|-+||..||-..+.+.+.||+--.++.
T Consensus 298 ~~~~~CpvClk~r~Nptvl~--vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVLE--VSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred CccccChhHHhccCCCceEE--ecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 45678999999988775542 36999999999999999999998655543
No 80
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=93.74 E-value=0.027 Score=58.58 Aligned_cols=45 Identities=29% Similarity=0.696 Sum_probs=35.4
Q ss_pred CcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC--CCCCCcccceec
Q 023376 229 LDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC--GDCPYCRRNIVV 277 (283)
Q Consensus 229 ~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~--~tCPlCR~~l~~ 277 (283)
..|.||++ .+.....+|+|.||..|+..-+... ..||+||..+..
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKE 501 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence 78999999 3334455899999999999988763 359999987644
No 81
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.68 E-value=0.0038 Score=60.02 Aligned_cols=53 Identities=30% Similarity=0.622 Sum_probs=45.4
Q ss_pred CCCcCccccCccCCC-CeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCC
Q 023376 227 TSLDCSICLESFTDG-DELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNS 279 (283)
Q Consensus 227 ~~~~C~ICle~~~~~-~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~ 279 (283)
-...|+||.+.++.. +.+..+-|||.+|..||..||.....||.|+.+++...
T Consensus 195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~ 248 (465)
T KOG0827|consen 195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKNG 248 (465)
T ss_pred HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence 357899999999876 55666679999999999999999999999999987653
No 82
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.64 E-value=0.034 Score=58.52 Aligned_cols=37 Identities=30% Similarity=0.536 Sum_probs=29.2
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHh
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVR 263 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~ 263 (283)
+....|.||.-.+...... +.||||.||..||..-..
T Consensus 815 ep~d~C~~C~~~ll~~pF~-vf~CgH~FH~~Cl~~~v~ 851 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIKPFY-VFPCGHCFHRDCLIRHVL 851 (911)
T ss_pred cCccchHHhcchhhcCcce-eeeccchHHHHHHHHHHH
Confidence 4578899998887755433 569999999999988754
No 83
>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=93.64 E-value=0.036 Score=37.24 Aligned_cols=41 Identities=34% Similarity=0.843 Sum_probs=24.7
Q ss_pred CccccCccCCCCeeEEcCCCCccChhhHHHHHhcCC--CCCCc
Q 023376 231 CSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCG--DCPYC 271 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~--tCPlC 271 (283)
|.+|.+.+..|..-..-.|+=.+|..|+..+++... .||.|
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 778888888876552223888999999999998865 69987
No 84
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=93.55 E-value=0.046 Score=45.48 Aligned_cols=52 Identities=23% Similarity=0.524 Sum_probs=41.2
Q ss_pred CCCcCccccCccCCCCeeEEcC---CCCccChhhHHHHHhc---CCCCCCcccceecCCC
Q 023376 227 TSLDCSICLESFTDGDELICLP---CKHRFHSDCLDPWVRS---CGDCPYCRRNIVVNSD 280 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LP---CgH~FH~~CI~~WL~~---~~tCPlCR~~l~~~~~ 280 (283)
...+|.||.|...+...+. | ||-..|..|-...|+. ...||+|+..+.....
T Consensus 79 ~lYeCnIC~etS~ee~FLK--PneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLK--PNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS 136 (140)
T ss_pred CceeccCcccccchhhcCC--cccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence 5789999999877655443 3 9999999999888876 5679999998876543
No 85
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.54 E-value=0.041 Score=38.97 Aligned_cols=47 Identities=23% Similarity=0.564 Sum_probs=32.6
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCC
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNS 279 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~ 279 (283)
...|..|...-.. -..+||||+.+..|..- ..-+.||+|-.++...+
T Consensus 7 ~~~~~~~~~~~~~---~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 7 EQPCVFCGFVGTK---GTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFDD 53 (55)
T ss_pred ceeEEEccccccc---cccccccceeeccccCh--hhccCCCCCCCcccCCC
Confidence 4456666554333 34669999999999654 34567999988876554
No 86
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.74 E-value=0.076 Score=51.62 Aligned_cols=33 Identities=30% Similarity=0.894 Sum_probs=26.1
Q ss_pred eeEEcCCCCccChhhHHHHHhc--CCCCCCcccce
Q 023376 243 ELICLPCKHRFHSDCLDPWVRS--CGDCPYCRRNI 275 (283)
Q Consensus 243 ~l~~LPCgH~FH~~CI~~WL~~--~~tCPlCR~~l 275 (283)
.+..|.|||.|-..||..||.+ ...||.|....
T Consensus 21 r~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 21 RIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred EEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 4556679999999999999964 23599997653
No 87
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=92.61 E-value=0.054 Score=50.41 Aligned_cols=46 Identities=28% Similarity=0.651 Sum_probs=38.1
Q ss_pred CCcCccccCccCCCC-eeEEcCCCCccChhhHHHHHhcCCCCCCccc
Q 023376 228 SLDCSICLESFTDGD-ELICLPCKHRFHSDCLDPWVRSCGDCPYCRR 273 (283)
Q Consensus 228 ~~~C~ICle~~~~~~-~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~ 273 (283)
...|+||.+.+.... .+..++|||.-|..|+......+-.||+|.+
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence 455999999887654 4456799999999999998888888999977
No 88
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=91.93 E-value=0.098 Score=49.86 Aligned_cols=52 Identities=25% Similarity=0.536 Sum_probs=35.5
Q ss_pred CCCCcCccccCccCCCCee-EEcCCCCccChhhHHHHHhc-CCCCCCcccceec
Q 023376 226 KTSLDCSICLESFTDGDEL-ICLPCKHRFHSDCLDPWVRS-CGDCPYCRRNIVV 277 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l-~~LPCgH~FH~~CI~~WL~~-~~tCPlCR~~l~~ 277 (283)
.+++.|+.|+|.+...++- .-.|||-..|.-|....-+. ++-||-||.....
T Consensus 12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~d 65 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDD 65 (480)
T ss_pred cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence 3456699999999866643 22369987777775544332 6779999986543
No 89
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.57 E-value=0.089 Score=55.26 Aligned_cols=41 Identities=27% Similarity=0.735 Sum_probs=32.3
Q ss_pred CcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccc
Q 023376 229 LDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRN 274 (283)
Q Consensus 229 ~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~ 274 (283)
..|.+|--.+..| .+...|||.||..|+. .+...||-|+.+
T Consensus 841 skCs~C~~~LdlP--~VhF~CgHsyHqhC~e---~~~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTLDLP--FVHFLCGHSYHQHCLE---DKEDKCPKCLPE 881 (933)
T ss_pred eeecccCCccccc--eeeeecccHHHHHhhc---cCcccCCccchh
Confidence 5899998776665 3455799999999998 455679999874
No 90
>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=91.33 E-value=0.094 Score=36.06 Aligned_cols=31 Identities=23% Similarity=0.667 Sum_probs=22.7
Q ss_pred CCC-CccChhhHHHHHhcCCCCCCcccceecC
Q 023376 248 PCK-HRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 248 PCg-H~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
.|. |..|..||.-.|.....||+|..+++..
T Consensus 17 ~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 17 KCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK 48 (50)
T ss_dssp E-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred eecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence 687 9999999999999999999999998864
No 91
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=91.10 E-value=0.091 Score=49.50 Aligned_cols=44 Identities=27% Similarity=0.505 Sum_probs=29.1
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccce
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
.-.|.-|=-.+.. .-+.+||.|+||.+|... ..-+.||.|-..|
T Consensus 90 VHfCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 90 VHFCDRCDFPIAI--YGRMIPCKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred eEeecccCCccee--eecccccchhhhhhhhhc--CccccCcCcccHH
Confidence 4456667444332 224459999999999643 4466899996654
No 92
>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=90.96 E-value=0.24 Score=47.77 Aligned_cols=32 Identities=25% Similarity=0.738 Sum_probs=25.3
Q ss_pred CCCccChhhHHHHHhc-------------CCCCCCcccceecCCC
Q 023376 249 CKHRFHSDCLDPWVRS-------------CGDCPYCRRNIVVNSD 280 (283)
Q Consensus 249 CgH~FH~~CI~~WL~~-------------~~tCPlCR~~l~~~~~ 280 (283)
|.-.+|.+|+-+|+.. +..||+||+.+..-+.
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilDV 355 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILDV 355 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeeee
Confidence 6678899999999865 3359999999876543
No 93
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.87 E-value=0.23 Score=48.18 Aligned_cols=51 Identities=24% Similarity=0.507 Sum_probs=40.4
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC---CCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC---GDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~---~tCPlCR~~l~ 276 (283)
-..+.|||=.+.-.+......|.|||+....-|.+..++. ..||+|-.+..
T Consensus 332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~ 385 (394)
T KOG2817|consen 332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQL 385 (394)
T ss_pred cceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcccC
Confidence 4578999988777766667788999999999999987764 36999965443
No 94
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=89.31 E-value=0.1 Score=57.00 Aligned_cols=46 Identities=24% Similarity=0.694 Sum_probs=37.8
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCccc
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRR 273 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~ 273 (283)
.....|.||++.+..-.. +..|||.||..|+..|+..+..||+|+.
T Consensus 1151 ~~~~~c~ic~dil~~~~~--I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGG--IAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred hcccchHHHHHHHHhcCC--eeeechhHhhhHHHHHHHHhccCcchhh
Confidence 345689999999873222 2369999999999999999999999974
No 95
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=88.34 E-value=0.28 Score=51.47 Aligned_cols=53 Identities=26% Similarity=0.649 Sum_probs=40.5
Q ss_pred CCCCcCccccCccCCCCeeEEcCCC-----CccChhhHHHHHhcC--CCCCCcccceecCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCK-----HRFHSDCLDPWVRSC--GDCPYCRRNIVVNS 279 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCg-----H~FH~~CI~~WL~~~--~tCPlCR~~l~~~~ 279 (283)
.+...|-||..+-..++.+ .-||. -..|.+|+.+|+.-. ..|-+|..++..++
T Consensus 10 ~d~~~CRICr~e~~~d~pL-fhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~ 69 (1175)
T COG5183 10 EDKRSCRICRTEDIRDDPL-FHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD 69 (1175)
T ss_pred ccchhceeecCCCCCCCcC-cccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence 3457899999887777665 34776 468999999999864 45999998876543
No 96
>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=87.68 E-value=0.69 Score=39.65 Aligned_cols=36 Identities=36% Similarity=0.874 Sum_probs=23.0
Q ss_pred CCcCccccCccCCCCeeEEc-------C--CC-CccChhhHHHHHh
Q 023376 228 SLDCSICLESFTDGDELICL-------P--CK-HRFHSDCLDPWVR 263 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~L-------P--Cg-H~FH~~CI~~WL~ 263 (283)
+..|+|||+--.....+..- | |+ -.-|..||+++-+
T Consensus 2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk 47 (162)
T PF07800_consen 2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK 47 (162)
T ss_pred CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence 45799999986655433211 1 54 2347899998844
No 97
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=87.50 E-value=0.39 Score=45.31 Aligned_cols=46 Identities=26% Similarity=0.486 Sum_probs=34.9
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCccccee
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIV 276 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~ 276 (283)
....+|+||.+.+..+..- -+=||+-|..|-. +..+.||.||.++.
T Consensus 46 ~~lleCPvC~~~l~~Pi~Q--C~nGHlaCssC~~---~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLSPPIFQ--CDNGHLACSSCRT---KVSNKCPTCRLPIG 91 (299)
T ss_pred hhhccCchhhccCccccee--cCCCcEehhhhhh---hhcccCCccccccc
Confidence 4578999999999886432 1236888888854 45778999998876
No 98
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=86.32 E-value=0.19 Score=52.03 Aligned_cols=50 Identities=34% Similarity=0.712 Sum_probs=39.3
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCC---CCCCcccceecCC
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCG---DCPYCRRNIVVNS 279 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~---tCPlCR~~l~~~~ 279 (283)
...+|+||+..+..+. .+.|-|.|+..|+..-|...+ .||+|+..+.+..
T Consensus 20 k~lEc~ic~~~~~~p~---~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s 72 (684)
T KOG4362|consen 20 KILECPICLEHVKEPS---LLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRS 72 (684)
T ss_pred hhccCCceeEEeeccc---hhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhh
Confidence 3678999999999883 448999999999877665544 5999997766543
No 99
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=86.22 E-value=0.36 Score=50.43 Aligned_cols=26 Identities=35% Similarity=0.885 Sum_probs=22.9
Q ss_pred EEcCCCCccChhhHHHHHhcCCCCCC
Q 023376 245 ICLPCKHRFHSDCLDPWVRSCGDCPY 270 (283)
Q Consensus 245 ~~LPCgH~FH~~CI~~WL~~~~tCPl 270 (283)
....|+|+.|..|...|+.....||.
T Consensus 1044 ~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1044 FCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred hhccccccccHHHHHHHHhcCCcCCC
Confidence 34569999999999999999999984
No 100
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=86.17 E-value=0.37 Score=50.49 Aligned_cols=49 Identities=12% Similarity=0.213 Sum_probs=35.3
Q ss_pred CCCcCccccCccCCCC-eeEEcC---CCCccChhhHHHHHhc------CCCCCCcccce
Q 023376 227 TSLDCSICLESFTDGD-ELICLP---CKHRFHSDCLDPWVRS------CGDCPYCRRNI 275 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~-~l~~LP---CgH~FH~~CI~~WL~~------~~tCPlCR~~l 275 (283)
....|.||.-++..++ ...++| |+|.||..||..|+.. +-.|++|...|
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci 153 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV 153 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence 3566777777776532 344456 9999999999999865 33589997654
No 101
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.44 E-value=0.33 Score=47.28 Aligned_cols=38 Identities=29% Similarity=0.700 Sum_probs=28.4
Q ss_pred CCCcCccccCccCCC-CeeEEcCCCCccChhhHHHHHhc
Q 023376 227 TSLDCSICLESFTDG-DELICLPCKHRFHSDCLDPWVRS 264 (283)
Q Consensus 227 ~~~~C~ICle~~~~~-~~l~~LPCgH~FH~~CI~~WL~~ 264 (283)
...+|.||+.+.... .....+.|+|.||..|+++.+..
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev 183 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEV 183 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhh
Confidence 467899999444433 33335579999999999998875
No 102
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=84.51 E-value=0.55 Score=43.43 Aligned_cols=48 Identities=27% Similarity=0.662 Sum_probs=35.8
Q ss_pred CCcCccccCccCCCCe-eEEcCCC-----CccChhhHHHHHhc--CCCCCCcccce
Q 023376 228 SLDCSICLESFTDGDE-LICLPCK-----HRFHSDCLDPWVRS--CGDCPYCRRNI 275 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~-l~~LPCg-----H~FH~~CI~~WL~~--~~tCPlCR~~l 275 (283)
...|-||.++...... ....||. ...|..|+..|+.. ...|.+|....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~ 133 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF 133 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence 5789999998765432 3455765 67899999999984 55699998754
No 103
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.08 E-value=0.53 Score=47.81 Aligned_cols=49 Identities=24% Similarity=0.623 Sum_probs=39.9
Q ss_pred CCCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCCC
Q 023376 225 SKTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNSD 280 (283)
Q Consensus 225 ~~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~~ 280 (283)
.+....|.||+..+ ..+..+|. |..|+..|+..+..||+|...+..++.
T Consensus 476 ~~~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~ 524 (543)
T KOG0802|consen 476 REPNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDF 524 (543)
T ss_pred hcccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhcccc
Confidence 35578899999998 34455788 899999999999999999988766554
No 104
>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=83.16 E-value=0.64 Score=42.50 Aligned_cols=49 Identities=24% Similarity=0.648 Sum_probs=35.5
Q ss_pred CCCcCccccCccC-CCC-eeEEcC-CCCccChhhHHHHHhcCC-CCC--Ccccce
Q 023376 227 TSLDCSICLESFT-DGD-ELICLP-CKHRFHSDCLDPWVRSCG-DCP--YCRRNI 275 (283)
Q Consensus 227 ~~~~C~ICle~~~-~~~-~l~~LP-CgH~FH~~CI~~WL~~~~-tCP--lCR~~l 275 (283)
.+..|+||..+.. .++ .+.+-| |-|..|..|+.+.+.... .|| -|-+-+
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 4568999987654 343 333446 999999999999998754 599 675443
No 105
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=83.09 E-value=1.4 Score=31.21 Aligned_cols=44 Identities=32% Similarity=0.932 Sum_probs=32.4
Q ss_pred CCCcCccccCccCCCCeeEEcC-CCCccChhhHHHHHhcCCCCCC--cccc
Q 023376 227 TSLDCSICLESFTDGDELICLP-CKHRFHSDCLDPWVRSCGDCPY--CRRN 274 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LP-CgH~FH~~CI~~WL~~~~tCPl--CR~~ 274 (283)
....|.+|-+.|..++.+++-| ||-.+|..|... ...|-+ |...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~~~c~~~ 50 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCINYSCGTG 50 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEeccCCCC
Confidence 3457999999998666666667 999999999543 556655 5443
No 106
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=82.65 E-value=0.49 Score=44.37 Aligned_cols=31 Identities=26% Similarity=0.764 Sum_probs=24.8
Q ss_pred CCCccChhhHHHHHhc-------------CCCCCCcccceecCC
Q 023376 249 CKHRFHSDCLDPWVRS-------------CGDCPYCRRNIVVNS 279 (283)
Q Consensus 249 CgH~FH~~CI~~WL~~-------------~~tCPlCR~~l~~~~ 279 (283)
|.-.+|.+||-+|+.. +-+||+||+.+...+
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d 368 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD 368 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence 6788999999999754 346999999876544
No 107
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=82.62 E-value=0.49 Score=43.59 Aligned_cols=50 Identities=26% Similarity=0.676 Sum_probs=35.3
Q ss_pred CCCCcCccccCccCCCCee-EEcCCC-----CccChhhHHHHHhcCC--------CCCCcccce
Q 023376 226 KTSLDCSICLESFTDGDEL-ICLPCK-----HRFHSDCLDPWVRSCG--------DCPYCRRNI 275 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l-~~LPCg-----H~FH~~CI~~WL~~~~--------tCPlCR~~l 275 (283)
+.+..|-||+..-++.... -+-||. |..|..||..|+..+. .||-|+++.
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY 81 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence 4567899999875544311 122664 8999999999996522 499998864
No 108
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.73 E-value=0.8 Score=42.45 Aligned_cols=31 Identities=26% Similarity=0.675 Sum_probs=25.1
Q ss_pred EEcCCCCccChhhHHHHHhcC-CCCCCcccce
Q 023376 245 ICLPCKHRFHSDCLDPWVRSC-GDCPYCRRNI 275 (283)
Q Consensus 245 ~~LPCgH~FH~~CI~~WL~~~-~tCPlCR~~l 275 (283)
+.|.|||.||..|+...+... ..||+||...
T Consensus 23 ~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 23 RVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred cccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 455799999999998877653 4699999984
No 109
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=80.12 E-value=0.68 Score=47.36 Aligned_cols=43 Identities=28% Similarity=0.736 Sum_probs=27.7
Q ss_pred CCCCcCccccCc-----cCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCc
Q 023376 226 KTSLDCSICLES-----FTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYC 271 (283)
Q Consensus 226 ~~~~~C~ICle~-----~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlC 271 (283)
...+.|.||... |.........-|+++||..|+.. ...-||.|
T Consensus 509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC 556 (580)
T KOG1829|consen 509 GKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRC 556 (580)
T ss_pred cCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCch
Confidence 346788888432 22222344556999999999654 34449999
No 110
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.12 E-value=1.2 Score=39.80 Aligned_cols=38 Identities=32% Similarity=0.739 Sum_probs=27.1
Q ss_pred CccccCccCCCCeeEEcCCCC-ccChhhHHHHHhcCCCCCCcccce
Q 023376 231 CSICLESFTDGDELICLPCKH-RFHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LPCgH-~FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
|-+|-+. ...+..|||.| .+|..|-.. -..||+|+...
T Consensus 161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~ 199 (207)
T KOG1100|consen 161 CRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPK 199 (207)
T ss_pred ceecCcC---CceEEeecccceEeccccccc----CccCCCCcChh
Confidence 7777665 55677889996 577778432 44599998754
No 111
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.64 E-value=1.1 Score=43.77 Aligned_cols=44 Identities=23% Similarity=0.480 Sum_probs=31.3
Q ss_pred CCcCccccCccCCCCeeE--EcCCCCccChhhHHHHHhcCCCCCCc
Q 023376 228 SLDCSICLESFTDGDELI--CLPCKHRFHSDCLDPWVRSCGDCPYC 271 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~--~LPCgH~FH~~CI~~WL~~~~tCPlC 271 (283)
-..|++|.-.+....... +-.|||.||+.|...|...+..|..|
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~ 351 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC 351 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence 456888877665443222 22499999999999998888777544
No 112
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.64 E-value=1.4 Score=43.52 Aligned_cols=37 Identities=35% Similarity=0.836 Sum_probs=31.0
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS 264 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~ 264 (283)
.....|-||.+.+.. .+..+.|||.||..|+...+..
T Consensus 68 ~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGT 104 (444)
T ss_pred CccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhh
Confidence 456889999999876 5556789999999999988875
No 113
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=76.32 E-value=1.7 Score=45.45 Aligned_cols=42 Identities=26% Similarity=0.623 Sum_probs=29.8
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCC
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPY 270 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPl 270 (283)
...|.+|-..+. |..+-.--|||.-|..|++.|+.....||.
T Consensus 779 ~~~CtVC~~vi~-G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~ 820 (839)
T KOG0269|consen 779 SAKCTVCDLVIR-GVDVWCQVCGHGGHDSHLKSWFFKASPCAK 820 (839)
T ss_pred hcCceeecceee-eeEeecccccccccHHHHHHHHhcCCCCcc
Confidence 346778855433 222211129999999999999999998877
No 114
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.92 E-value=0.91 Score=46.73 Aligned_cols=43 Identities=33% Similarity=0.708 Sum_probs=30.4
Q ss_pred CCcCccccCccCCCC-eeEEcCCCCccChhhHHHHHhcCCCCCCccc
Q 023376 228 SLDCSICLESFTDGD-ELICLPCKHRFHSDCLDPWVRSCGDCPYCRR 273 (283)
Q Consensus 228 ~~~C~ICle~~~~~~-~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~ 273 (283)
...|.||+..|.... .-+.|-|||..|..|+.... +.+|| |+.
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~scp-~~~ 54 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NASCP-TKR 54 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hccCC-CCc
Confidence 467999988886543 23345699999999997654 45677 543
No 115
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=73.70 E-value=2 Score=40.80 Aligned_cols=49 Identities=24% Similarity=0.510 Sum_probs=35.9
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc---CCCCCCcccc
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS---CGDCPYCRRN 274 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~---~~tCPlCR~~ 274 (283)
...+.|++--+.-.+......|.|||+.-.+-+...-++ ...||+|-..
T Consensus 334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~ 385 (396)
T COG5109 334 HSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEM 385 (396)
T ss_pred cceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcc
Confidence 346889987777665555567789999999998886554 3459999543
No 116
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.86 E-value=1.9 Score=45.33 Aligned_cols=45 Identities=27% Similarity=0.559 Sum_probs=33.4
Q ss_pred CCCCcCccccCccCC-C---CeeEEcCCCCccChhhHHHHHhcCCCCCCc
Q 023376 226 KTSLDCSICLESFTD-G---DELICLPCKHRFHSDCLDPWVRSCGDCPYC 271 (283)
Q Consensus 226 ~~~~~C~ICle~~~~-~---~~l~~LPCgH~FH~~CI~~WL~~~~tCPlC 271 (283)
.....|.-|.+.... + ..++.+-|||+||..|+.--..+++ |-.|
T Consensus 782 ~~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~ 830 (846)
T KOG2066|consen 782 SVEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIE 830 (846)
T ss_pred eehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChh
Confidence 345589999888762 2 4567788999999999987666554 6655
No 117
>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=70.35 E-value=3.2 Score=28.61 Aligned_cols=43 Identities=26% Similarity=0.563 Sum_probs=20.5
Q ss_pred CcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC---C--CCCCcccc
Q 023376 229 LDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC---G--DCPYCRRN 274 (283)
Q Consensus 229 ~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~---~--tCPlCR~~ 274 (283)
..|+|....+..+ ++...|.|.-|.+ +..||..+ + .||+|.++
T Consensus 3 L~CPls~~~i~~P--~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIP--VRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSE--EEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEeC--ccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 4689988887765 4445799986543 44565542 2 49999763
No 118
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=69.89 E-value=3.9 Score=39.01 Aligned_cols=51 Identities=29% Similarity=0.600 Sum_probs=38.0
Q ss_pred CCcCccccCccCCCCe-eEEcCCCCccChhhHHHHHhcCCCCCCcccceecC
Q 023376 228 SLDCSICLESFTDGDE-LICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVN 278 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~-l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~ 278 (283)
...|+||.+.....+. ..-.||++..|..|+..-...+..||.||.+....
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccccC
Confidence 4789999998743332 22224888888889888888899999999776544
No 119
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=68.89 E-value=4.2 Score=38.73 Aligned_cols=51 Identities=20% Similarity=0.524 Sum_probs=34.1
Q ss_pred CCCcCccccCccCC---------------CC-eeEEcCCCCccChhhHHHHHhc---------CCCCCCcccceec
Q 023376 227 TSLDCSICLESFTD---------------GD-ELICLPCKHRFHSDCLDPWVRS---------CGDCPYCRRNIVV 277 (283)
Q Consensus 227 ~~~~C~ICle~~~~---------------~~-~l~~LPCgH~FH~~CI~~WL~~---------~~tCPlCR~~l~~ 277 (283)
...+|+||+..-.. +. .-..-||||+--..-.+=|-+. +..||+|-..+.-
T Consensus 340 ~~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 340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAG 415 (429)
T ss_pred ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhcc
Confidence 46799999765210 00 1124589999888888888764 3459999776643
No 120
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.21 E-value=2.9 Score=39.22 Aligned_cols=40 Identities=25% Similarity=0.514 Sum_probs=30.9
Q ss_pred CCCCcCccccCccCCCCeeEEcC--CCCccChhhHHHHHhcCC
Q 023376 226 KTSLDCSICLESFTDGDELICLP--CKHRFHSDCLDPWVRSCG 266 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LP--CgH~FH~~CI~~WL~~~~ 266 (283)
.....|.+|.|.+++...+ +-| =.|.||.-|-.+-++.+.
T Consensus 266 ~apLcCTLC~ERLEDTHFV-QCPSVp~HKFCFPCSResIK~Qg 307 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFV-QCPSVPSHKFCFPCSRESIKQQG 307 (352)
T ss_pred CCceeehhhhhhhccCcee-ecCCCcccceecccCHHHHHhhc
Confidence 3457899999999887766 223 359999999999988743
No 121
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=64.19 E-value=5.8 Score=35.16 Aligned_cols=41 Identities=32% Similarity=0.819 Sum_probs=27.3
Q ss_pred CCCcCccccCc-----cCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 227 TSLDCSICLES-----FTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 227 ~~~~C~ICle~-----~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
..+.|-||-+. |......+.-.|+-+||..|... ..||-|-
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~-----~~CpkC~ 196 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK-----KSCPKCA 196 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC-----CCCCCcH
Confidence 46789999742 22222333334999999999652 6799994
No 122
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=63.92 E-value=3.7 Score=38.13 Aligned_cols=49 Identities=24% Similarity=0.582 Sum_probs=34.6
Q ss_pred CCcCccccCccCCCCeeEEc---C-CCCccChhhHHHHHhc---------CCCCCCccccee
Q 023376 228 SLDCSICLESFTDGDELICL---P-CKHRFHSDCLDPWVRS---------CGDCPYCRRNIV 276 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~L---P-CgH~FH~~CI~~WL~~---------~~tCPlCR~~l~ 276 (283)
..+|-||..+|.+.+..+.. | |.-++|..||..-+.. ...||.|+.-+.
T Consensus 182 ~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~ 243 (276)
T KOG3005|consen 182 NVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS 243 (276)
T ss_pred chhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence 36899999999554443222 2 8999999999984432 345999987543
No 123
>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 KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=61.58 E-value=6.1 Score=36.50 Aligned_cols=52 Identities=12% Similarity=0.170 Sum_probs=37.6
Q ss_pred CCCCcCccccCccCCCC-eeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCC
Q 023376 226 KTSLDCSICLESFTDGD-ELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNS 279 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~-~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~ 279 (283)
...+.|+|---+|.... .+...+|||+|-..-+++. ....|++|-+.+..++
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~d 161 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDD 161 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccC
Confidence 45688999766665443 3444579999999988874 3667999988766554
No 125
>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=60.45 E-value=4.8 Score=24.08 Aligned_cols=22 Identities=23% Similarity=0.662 Sum_probs=12.0
Q ss_pred cCccccCccCCCCeeEEcC-CCCcc
Q 023376 230 DCSICLESFTDGDELICLP-CKHRF 253 (283)
Q Consensus 230 ~C~ICle~~~~~~~l~~LP-CgH~F 253 (283)
.|+-|...+...... -| |||.|
T Consensus 2 ~CP~C~~~V~~~~~~--Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKF--CPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCc--CCCCCCCC
Confidence 467776665443322 24 77766
No 126
>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=58.77 E-value=7.3 Score=26.12 Aligned_cols=43 Identities=35% Similarity=0.841 Sum_probs=30.1
Q ss_pred cCccccCccCCCCeeEEcCCCCccChhhHHHHHhc------CCCCCCcc
Q 023376 230 DCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS------CGDCPYCR 272 (283)
Q Consensus 230 ~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~------~~tCPlCR 272 (283)
.|.||......+..+.--.|+-.||..|+..-... .-.||.|+
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 38899885555555554469999999999776542 23588775
No 127
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=57.14 E-value=10 Score=36.32 Aligned_cols=46 Identities=28% Similarity=0.497 Sum_probs=32.0
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
....|-.|.++.......+.-.|.+.||.+|=.-.=..-..||.|-
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcC
Confidence 4556999977777665555556999999999433323344699996
No 128
>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=55.27 E-value=6.6 Score=28.88 Aligned_cols=13 Identities=38% Similarity=1.027 Sum_probs=9.3
Q ss_pred ccChhhHHHHHhc
Q 023376 252 RFHSDCLDPWVRS 264 (283)
Q Consensus 252 ~FH~~CI~~WL~~ 264 (283)
-||..||..|+..
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3999999999864
No 129
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=54.93 E-value=5.2 Score=36.00 Aligned_cols=44 Identities=20% Similarity=0.628 Sum_probs=36.1
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
....|.+|-...-.+... -.|+-.+|..|+...+.....||-|-
T Consensus 180 nlk~Cn~Ch~LvIqg~rC--g~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 180 NLKNCNLCHCLVIQGIRC--GSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred HHHHHhHhHHHhheeecc--CcccchhhhHHHHHHhcccCcCCchh
Confidence 457899999887766433 26888899999999999999999994
No 130
>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=53.18 E-value=2.4 Score=39.49 Aligned_cols=48 Identities=19% Similarity=0.169 Sum_probs=21.8
Q ss_pred CCCCcCccccCccCCCCeeEEc--CCCCccChhhHHHHHhcCCCCCCccc
Q 023376 226 KTSLDCSICLESFTDGDELICL--PCKHRFHSDCLDPWVRSCGDCPYCRR 273 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~L--PCgH~FH~~CI~~WL~~~~tCPlCR~ 273 (283)
+....|+||=..-........- --.+.+|.-|-..|-.....||+|-.
T Consensus 170 w~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 170 WQRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN 219 (290)
T ss_dssp TT-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred ccCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence 4557999995543221111000 01467888899999888999999954
No 131
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.60 E-value=9 Score=36.24 Aligned_cols=15 Identities=20% Similarity=0.414 Sum_probs=12.2
Q ss_pred CCCcCccccCccCCC
Q 023376 227 TSLDCSICLESFTDG 241 (283)
Q Consensus 227 ~~~~C~ICle~~~~~ 241 (283)
...+|+||+....-+
T Consensus 6 ~~~eC~IC~nt~n~P 20 (324)
T KOG0824|consen 6 KKKECLICYNTGNCP 20 (324)
T ss_pred cCCcceeeeccCCcC
Confidence 467899999987766
No 132
>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=50.97 E-value=17 Score=22.20 Aligned_cols=36 Identities=19% Similarity=0.690 Sum_probs=23.5
Q ss_pred CccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccce
Q 023376 231 CSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 231 C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
|..|-..+...+... ..=+..||..|+ .|..|...|
T Consensus 2 C~~C~~~i~~~~~~~-~~~~~~~H~~Cf--------~C~~C~~~L 37 (39)
T smart00132 2 CAGCGKPIRGGELVL-RALGKVWHPECF--------KCSKCGKPL 37 (39)
T ss_pred ccccCCcccCCcEEE-EeCCccccccCC--------CCcccCCcC
Confidence 778888777653332 234678888874 577787665
No 133
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.49 E-value=12 Score=34.47 Aligned_cols=36 Identities=19% Similarity=0.227 Sum_probs=29.1
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS 264 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~ 264 (283)
+...-|+.||..+..+... |=||+|+.+||.+.+..
T Consensus 41 K~FdcCsLtLqPc~dPvit---~~GylfdrEaILe~ila 76 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCRDPVIT---PDGYLFDREAILEYILA 76 (303)
T ss_pred CCcceeeeecccccCCccC---CCCeeeeHHHHHHHHHH
Confidence 3456788999999887544 89999999999998653
No 134
>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=49.37 E-value=5.6 Score=38.93 Aligned_cols=50 Identities=20% Similarity=0.464 Sum_probs=0.0
Q ss_pred CCcCccccCccCC-------------C---CeeEEcCCCCccChhhHHHHHhc---------CCCCCCcccceec
Q 023376 228 SLDCSICLESFTD-------------G---DELICLPCKHRFHSDCLDPWVRS---------CGDCPYCRRNIVV 277 (283)
Q Consensus 228 ~~~C~ICle~~~~-------------~---~~l~~LPCgH~FH~~CI~~WL~~---------~~tCPlCR~~l~~ 277 (283)
..+|+||+..-.. + .....-||||+--....+-|-+. +..||+|-..|..
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g 402 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDG 402 (416)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccC
Confidence 6789999754211 0 01234589999989999999654 3459999877653
No 135
>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=47.98 E-value=9.8 Score=27.26 Aligned_cols=37 Identities=19% Similarity=0.323 Sum_probs=18.6
Q ss_pred CCCcCccccCccCCCCeeEEc-CCCCccChhhHHHHHh
Q 023376 227 TSLDCSICLESFTDGDELICL-PCKHRFHSDCLDPWVR 263 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~L-PCgH~FH~~CI~~WL~ 263 (283)
+...|.+|...|..-..--.- .||++||..|....+.
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~ 45 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIP 45 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEc
Confidence 457899999999653322122 3999999999876653
No 136
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.63 E-value=6.4 Score=37.19 Aligned_cols=48 Identities=29% Similarity=0.542 Sum_probs=39.3
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccce
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
.....|-||...+..+.... -|+|.|+..|...|....+.||-|+..+
T Consensus 103 ~~~~~~~~~~g~l~vpt~~q--g~w~qf~~~~p~~~~~~~~~~~d~~~~~ 150 (324)
T KOG0824|consen 103 QDHDICYICYGKLTVPTRIQ--GCWHQFCYVCPKSNFAMGNDCPDCRGKI 150 (324)
T ss_pred CCccceeeeeeeEEeccccc--CceeeeeecCCchhhhhhhccchhhcCc
Confidence 44677999988887765442 3999999999999999999999998754
No 137
>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=45.15 E-value=37 Score=24.20 Aligned_cols=49 Identities=22% Similarity=0.548 Sum_probs=31.7
Q ss_pred CcCccccCccCCCC-eeEEcCCCCccChhhHHHHHhcCCCCCCcccceecCC
Q 023376 229 LDCSICLESFTDGD-ELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVVNS 279 (283)
Q Consensus 229 ~~C~ICle~~~~~~-~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~~~ 279 (283)
..|-.|-.++.... ...+-.=-..||..|....| ++.||.|-..+....
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~RP 55 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVRRP 55 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccccCC
Confidence 34666766665444 22211212569999999877 678999988876543
No 138
>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=43.01 E-value=18 Score=24.75 Aligned_cols=35 Identities=23% Similarity=0.335 Sum_probs=24.2
Q ss_pred CcCccccCccCCCCeeEE-cCCCCccChhhHHHHHh
Q 023376 229 LDCSICLESFTDGDELIC-LPCKHRFHSDCLDPWVR 263 (283)
Q Consensus 229 ~~C~ICle~~~~~~~l~~-LPCgH~FH~~CI~~WL~ 263 (283)
..|.+|-..|..-..-.. -.||++||..|......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~ 38 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP 38 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence 468899877765332211 24999999999877654
No 139
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=42.61 E-value=8.5 Score=40.25 Aligned_cols=49 Identities=24% Similarity=0.504 Sum_probs=31.7
Q ss_pred CCcCccccCccCCCCe-----e--EEcCCCCccChhhHHHH----------HhcCCCCCCccccee
Q 023376 228 SLDCSICLESFTDGDE-----L--ICLPCKHRFHSDCLDPW----------VRSCGDCPYCRRNIV 276 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~-----l--~~LPCgH~FH~~CI~~W----------L~~~~tCPlCR~~l~ 276 (283)
...|.||.|.=.+.+. + -+-.|.-.||..|.... +.+-+.|-||+.-+.
T Consensus 117 nKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hfs 182 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFS 182 (900)
T ss_pred cceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHH
Confidence 3469999988444331 1 12238899999998654 122345999987653
No 140
>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=42.18 E-value=23 Score=27.47 Aligned_cols=38 Identities=24% Similarity=0.483 Sum_probs=30.9
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccceec
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNIVV 277 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l~~ 277 (283)
-..|.-|...+.--+.+ | |..|+..++.|..|+++++.
T Consensus 33 rS~C~~C~~~L~~~~lI---P---------i~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLI---P---------ILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCcCcCCCCcCcccccc---h---------HHHHHHhCCCCcccCCCCCh
Confidence 45799998888776665 4 77899999999999998764
No 141
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.44 E-value=26 Score=27.67 Aligned_cols=36 Identities=22% Similarity=0.501 Sum_probs=29.9
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS 264 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~ 264 (283)
...|.||-+.+.+|+.....+ .-..|++|+..-..+
T Consensus 6 ewkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~~~ 41 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESKRK 41 (103)
T ss_pred eeeEeeeCCEeeeccEEEEee-CCcchHHHHHHHHhc
Confidence 567999999999999888888 555799999876554
No 142
>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 PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=37.21 E-value=13 Score=25.54 Aligned_cols=38 Identities=29% Similarity=0.722 Sum_probs=20.3
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHh--cCCCCCCcccce
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVR--SCGDCPYCRRNI 275 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~--~~~tCPlCR~~l 275 (283)
.+.|+.|-+.+.... + +.| |...-.. +...||+|...+
T Consensus 2 ~f~CP~C~~~~~~~~-L----~~H-----~~~~H~~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGKGFSESS-L----VEH-----CEDEHRSESKNVVCPICSSRV 41 (54)
T ss_pred CcCCCCCCCccCHHH-H----HHH-----HHhHCcCCCCCccCCCchhhh
Confidence 467999988544322 2 222 2222222 234699997643
No 144
>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=37.15 E-value=11 Score=36.88 Aligned_cols=30 Identities=27% Similarity=0.620 Sum_probs=0.0
Q ss_pred eEEcCCCCccChhhHHHHHhc------CCCCCCccccee
Q 023376 244 LICLPCKHRFHSDCLDPWVRS------CGDCPYCRRNIV 276 (283)
Q Consensus 244 l~~LPCgH~FH~~CI~~WL~~------~~tCPlCR~~l~ 276 (283)
.+.|.|||++-. ..|-.. ...||+||..-+
T Consensus 304 ~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~g~ 339 (416)
T PF04710_consen 304 WVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQVGP 339 (416)
T ss_dssp ---------------------------------------
T ss_pred eeeccccceeee---cccccccccccccccCCCccccCC
Confidence 346689998765 457542 346999997543
No 145
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=36.93 E-value=16 Score=34.65 Aligned_cols=45 Identities=13% Similarity=0.344 Sum_probs=29.7
Q ss_pred CCCcCccccCccCCCCeeEEc--C--CCCccChhhHHHHHhcCCCCCCccc
Q 023376 227 TSLDCSICLESFTDGDELICL--P--CKHRFHSDCLDPWVRSCGDCPYCRR 273 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~L--P--CgH~FH~~CI~~WL~~~~tCPlCR~ 273 (283)
....|+||=..-... ++.+ . =.+.+|.-|-..|-.....||.|-.
T Consensus 186 ~~~~CPvCGs~P~~s--~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSS--VVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhh--eeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 467899996653211 0011 1 1255677799999888999999964
No 146
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.05 E-value=57 Score=26.49 Aligned_cols=45 Identities=31% Similarity=0.478 Sum_probs=32.0
Q ss_pred CCcCccccCccCCCCe-----------eEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 228 SLDCSICLESFTDGDE-----------LICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~-----------l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
...|--|+..|..+.. -.--.|.+.||.+|=.-|-..-..||-|-
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 3469999998865311 11224999999999777766667799995
No 147
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=33.68 E-value=7.5 Score=36.58 Aligned_cols=39 Identities=23% Similarity=0.477 Sum_probs=29.9
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcC
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSC 265 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~ 265 (283)
....|.||+++|..+.....+-|--+||..|+..|+...
T Consensus 213 ~~rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (288)
T KOG1729|consen 213 PIRVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTG 251 (288)
T ss_pred CceecHHHHHHHhcccccchhhccccccccccccccccc
Confidence 345999999999865444444555599999999999874
No 148
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.14 E-value=7.4 Score=36.00 Aligned_cols=47 Identities=23% Similarity=0.639 Sum_probs=36.2
Q ss_pred CCcCccccCccCCCC---eeEEcC--------CCCccChhhHHHHHhcC-CCCCCcccc
Q 023376 228 SLDCSICLESFTDGD---ELICLP--------CKHRFHSDCLDPWVRSC-GDCPYCRRN 274 (283)
Q Consensus 228 ~~~C~ICle~~~~~~---~l~~LP--------CgH~FH~~CI~~WL~~~-~tCPlCR~~ 274 (283)
...|.||...|...+ .-..+. |||..|..|+..-+... ..||.|+..
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 367999999988432 223455 99999999999998765 479999863
No 149
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.56 E-value=16 Score=36.23 Aligned_cols=37 Identities=22% Similarity=0.454 Sum_probs=27.2
Q ss_pred CCcCccccCccCCCCee-----EEcCCCCccChhhHHHHHhc
Q 023376 228 SLDCSICLESFTDGDEL-----ICLPCKHRFHSDCLDPWVRS 264 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l-----~~LPCgH~FH~~CI~~WL~~ 264 (283)
...|+.|.-.+...... ...+|.|.||+.|+..|...
T Consensus 226 tk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h 267 (444)
T KOG1815|consen 226 TKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH 267 (444)
T ss_pred CccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence 44599999888766522 12249999999998888765
No 150
>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=32.12 E-value=27 Score=23.66 Aligned_cols=14 Identities=36% Similarity=0.873 Sum_probs=6.2
Q ss_pred CCcCccccCccCCC
Q 023376 228 SLDCSICLESFTDG 241 (283)
Q Consensus 228 ~~~C~ICle~~~~~ 241 (283)
.+.|.+|-..+..+
T Consensus 26 Cf~C~~C~~~l~~~ 39 (58)
T PF00412_consen 26 CFKCSKCGKPLNDG 39 (58)
T ss_dssp TSBETTTTCBTTTS
T ss_pred ccccCCCCCccCCC
Confidence 44444444444433
No 151
>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=32.04 E-value=30 Score=24.10 Aligned_cols=42 Identities=33% Similarity=0.674 Sum_probs=18.2
Q ss_pred CccccCccCCCC------eeEEcC-CCCccChhhHHHHHhcCCCCCCcc
Q 023376 231 CSICLESFTDGD------ELICLP-CKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 231 C~ICle~~~~~~------~l~~LP-CgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
|--|+..|..+. ....-| |++.||.+|=.=.=+.--.||-|-
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 445555555542 122223 999999999322112234588883
No 152
>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=31.66 E-value=5.6 Score=29.62 Aligned_cols=39 Identities=18% Similarity=0.416 Sum_probs=19.0
Q ss_pred CcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCCCCCCcccce
Q 023376 229 LDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 229 ~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
..|++|..++... =++.+|..|-.. +.....||-|..+|
T Consensus 2 ~~CP~C~~~L~~~-------~~~~~C~~C~~~-~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQ-------GGHYHCEACQKD-YKKEAFCPDCGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEE-------TTEEEETTT--E-EEEEEE-TTT-SB-
T ss_pred CcCCCCCCccEEe-------CCEEECcccccc-ceecccCCCcccHH
Confidence 3588887764422 156677777654 34455688887765
No 153
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.37 E-value=21 Score=27.94 Aligned_cols=13 Identities=38% Similarity=1.020 Sum_probs=11.3
Q ss_pred ccChhhHHHHHhc
Q 023376 252 RFHSDCLDPWVRS 264 (283)
Q Consensus 252 ~FH~~CI~~WL~~ 264 (283)
-||..||..|+..
T Consensus 42 gFCRNCLs~Wy~e 54 (104)
T COG3492 42 GFCRNCLSNWYRE 54 (104)
T ss_pred HHHHHHHHHHHHH
Confidence 4999999999875
No 154
>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=30.07 E-value=18 Score=34.29 Aligned_cols=42 Identities=19% Similarity=0.301 Sum_probs=29.0
Q ss_pred CCCcCccccCccCCC--------CeeEEcCCCCccChhhHHHHHhcCCCCCCccc
Q 023376 227 TSLDCSICLESFTDG--------DELICLPCKHRFHSDCLDPWVRSCGDCPYCRR 273 (283)
Q Consensus 227 ~~~~C~ICle~~~~~--------~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR~ 273 (283)
....|+||-..-... +..+ +.+|.-|-..|-.....||.|-.
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~R-----yL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLR-----YLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCce-----EEEcCCCCCcccccCccCCCCCC
Confidence 355899996653211 1222 55667788999888999999965
No 155
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.02 E-value=34 Score=21.81 Aligned_cols=13 Identities=23% Similarity=0.644 Sum_probs=9.2
Q ss_pred cCccccCccCCCC
Q 023376 230 DCSICLESFTDGD 242 (283)
Q Consensus 230 ~C~ICle~~~~~~ 242 (283)
.|+=|...|..++
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 5777877776655
No 156
>PLN02189 cellulose synthase
Probab=28.97 E-value=50 Score=36.37 Aligned_cols=49 Identities=22% Similarity=0.560 Sum_probs=33.0
Q ss_pred CCCcCccccCccCCC---Ce-eEEcCCCCccChhhHHHHHhc--CCCCCCccccee
Q 023376 227 TSLDCSICLESFTDG---DE-LICLPCKHRFHSDCLDPWVRS--CGDCPYCRRNIV 276 (283)
Q Consensus 227 ~~~~C~ICle~~~~~---~~-l~~LPCgH~FH~~CI~~WL~~--~~tCPlCR~~l~ 276 (283)
....|.||-+++... +. +..--|+--.|..|. +.-++ ++.||-|++...
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCchh
Confidence 356899999997632 22 222238888999998 33333 667999988654
No 157
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=27.51 E-value=35 Score=23.48 Aligned_cols=9 Identities=56% Similarity=1.475 Sum_probs=6.5
Q ss_pred hcCCCCCCc
Q 023376 263 RSCGDCPYC 271 (283)
Q Consensus 263 ~~~~tCPlC 271 (283)
.....||+|
T Consensus 47 ~~~~~CP~C 55 (55)
T PF14311_consen 47 RRGKGCPYC 55 (55)
T ss_pred cCCCCCCCC
Confidence 446679988
No 158
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.90 E-value=25 Score=24.26 Aligned_cols=18 Identities=28% Similarity=0.728 Sum_probs=14.3
Q ss_pred eEEc-CCCCccChhhHHHH
Q 023376 244 LICL-PCKHRFHSDCLDPW 261 (283)
Q Consensus 244 l~~L-PCgH~FH~~CI~~W 261 (283)
.+.- .|++.||..|..+|
T Consensus 40 ~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 40 RVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred eeECCCCCCeECCCCCCcC
Confidence 3344 48999999999888
No 159
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.74 E-value=32 Score=36.03 Aligned_cols=42 Identities=14% Similarity=0.270 Sum_probs=30.0
Q ss_pred CCcCccccCccC-CCCeeEEcCCCCccChhhHHHHHhcCCCCCCcc
Q 023376 228 SLDCSICLESFT-DGDELICLPCKHRFHSDCLDPWVRSCGDCPYCR 272 (283)
Q Consensus 228 ~~~C~ICle~~~-~~~~l~~LPCgH~FH~~CI~~WL~~~~tCPlCR 272 (283)
...|.+|...-. +.+..+.+-|+-.||..| |+--.+.||+|-
T Consensus 654 ~r~C~vcq~pedse~~v~rt~~C~~~~C~~c---~~~~~~~~~vC~ 696 (717)
T KOG3726|consen 654 IRTCKVCQLPEDSETDVCRTTFCYTPYCVAC---SLDYASISEVCG 696 (717)
T ss_pred HHHHHHhcCCcCccccccCccccCCcchHhh---hhhhhccCcccC
Confidence 467899976533 233444556999999998 666788899993
No 160
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=26.59 E-value=37 Score=30.90 Aligned_cols=23 Identities=22% Similarity=0.524 Sum_probs=16.1
Q ss_pred cChhhHHHHHhcCCCCCCcccce
Q 023376 253 FHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 253 FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
-|..|-...=++-..||+|++.-
T Consensus 196 ~C~sC~qqIHRNAPiCPlCK~Ks 218 (230)
T PF10146_consen 196 TCQSCHQQIHRNAPICPLCKAKS 218 (230)
T ss_pred hhHhHHHHHhcCCCCCccccccc
Confidence 35566666656778899998753
No 161
>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=25.72 E-value=28 Score=23.98 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=5.4
Q ss_pred CCCCcccceec
Q 023376 267 DCPYCRRNIVV 277 (283)
Q Consensus 267 tCPlCR~~l~~ 277 (283)
.||+|..++..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 68999887754
No 162
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=25.64 E-value=68 Score=33.48 Aligned_cols=49 Identities=22% Similarity=0.516 Sum_probs=27.8
Q ss_pred CCCCcCccccCccCCCCeeEEcCCCCccChhhHHHHH-hc-C---C--CCCCcccceecCC
Q 023376 226 KTSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWV-RS-C---G--DCPYCRRNIVVNS 279 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL-~~-~---~--tCPlCR~~l~~~~ 279 (283)
.-...|+|+...+..+..- +.|+|+ .|.+.-+ .. + . .||+|.+.+..+.
T Consensus 304 ~vSL~CPl~~~Rm~~P~r~--~~CkHl---QcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~ 359 (636)
T KOG2169|consen 304 RVSLNCPLSKMRMSLPARG--HTCKHL---QCFDALSYLQMNEQKPTWRCPVCQKAAPFEG 359 (636)
T ss_pred eeEecCCcccceeecCCcc--cccccc---eecchhhhHHhccCCCeeeCccCCccccccc
Confidence 3457788887665543221 235554 5555433 22 1 1 3999988776654
No 163
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=25.47 E-value=50 Score=26.34 Aligned_cols=35 Identities=17% Similarity=0.366 Sum_probs=27.7
Q ss_pred CcCccccCccCCCCeeEEcCCCCccChhhHHHHHhc
Q 023376 229 LDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRS 264 (283)
Q Consensus 229 ~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~ 264 (283)
..|.||-..+..|+..+.++= -..|+.|+..=...
T Consensus 3 WkC~iCg~~I~~gqlFTF~~k-G~VH~~C~~~~~~~ 37 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKK-GPVHYECFREKASK 37 (101)
T ss_pred eEEEecCCeeeecceEEEecC-CcEeHHHHHHHHhh
Confidence 469999999999987766665 55799999876543
No 164
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=25.30 E-value=34 Score=24.60 Aligned_cols=14 Identities=29% Similarity=0.714 Sum_probs=10.4
Q ss_pred CCCCCCcccceecC
Q 023376 265 CGDCPYCRRNIVVN 278 (283)
Q Consensus 265 ~~tCPlCR~~l~~~ 278 (283)
...||+|..+....
T Consensus 39 ~p~CPlC~s~M~~~ 52 (59)
T PF14169_consen 39 EPVCPLCKSPMVSG 52 (59)
T ss_pred CccCCCcCCccccc
Confidence 35699999887654
No 165
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=25.17 E-value=55 Score=19.66 Aligned_cols=29 Identities=24% Similarity=0.661 Sum_probs=9.8
Q ss_pred cCccccCccCCCCeeEEcCCCCccChhhH
Q 023376 230 DCSICLESFTDGDELICLPCKHRFHSDCL 258 (283)
Q Consensus 230 ~C~ICle~~~~~~~l~~LPCgH~FH~~CI 258 (283)
.|.+|.........-.-..|.-.+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 47788777665333344458888888875
No 166
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=25.13 E-value=25 Score=40.04 Aligned_cols=49 Identities=33% Similarity=0.686 Sum_probs=38.5
Q ss_pred CCCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCC----CCCCcccce
Q 023376 227 TSLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCG----DCPYCRRNI 275 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~----tCPlCR~~l 275 (283)
....|.||.........+...-|--.||..|+.+-+..-. .||-|+..-
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 4578999999877766665555889999999999887643 599998754
No 167
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=24.98 E-value=62 Score=24.63 Aligned_cols=50 Identities=18% Similarity=0.425 Sum_probs=19.2
Q ss_pred CCCcCccccCccCCCC----eeEEcCCCCccChhhHHHHHhc-CCCCCCccccee
Q 023376 227 TSLDCSICLESFTDGD----ELICLPCKHRFHSDCLDPWVRS-CGDCPYCRRNIV 276 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~----~l~~LPCgH~FH~~CI~~WL~~-~~tCPlCR~~l~ 276 (283)
....|-||-+.+.... .+...-|+--.|..|..==.+. +..||-|+....
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 4578999988875432 2323348888888997543333 667999987653
No 168
>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=24.66 E-value=89 Score=24.81 Aligned_cols=24 Identities=29% Similarity=0.666 Sum_probs=19.0
Q ss_pred CCccChhhHHHHHhc---------CCCCCCccc
Q 023376 250 KHRFHSDCLDPWVRS---------CGDCPYCRR 273 (283)
Q Consensus 250 gH~FH~~CI~~WL~~---------~~tCPlCR~ 273 (283)
.=.||..||..++.. +-.||.||.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 677999999999764 224999986
No 169
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=24.20 E-value=62 Score=30.24 Aligned_cols=45 Identities=31% Similarity=0.481 Sum_probs=29.6
Q ss_pred CCCCcCccccCccCCCCeeEEcC--CCCccChhhHHHHH-hcCCCCCC
Q 023376 226 KTSLDCSICLESFTDGDELICLP--CKHRFHSDCLDPWV-RSCGDCPY 270 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~~l~~LP--CgH~FH~~CI~~WL-~~~~tCPl 270 (283)
+....|.||++...+|..-..|. =.=.-|..|+..|= ..+..||-
T Consensus 28 ~tLsfChiCfEl~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~pr 75 (285)
T PF06937_consen 28 ETLSFCHICFELSIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCPR 75 (285)
T ss_pred cceeecceeeccccccCccccccccccccchHHHHHHHHHHHcCCCCc
Confidence 45678999999887765332222 11135689999994 45778983
No 170
>PLN02436 cellulose synthase A
Probab=24.04 E-value=69 Score=35.46 Aligned_cols=49 Identities=22% Similarity=0.652 Sum_probs=33.1
Q ss_pred CCCcCccccCccCC---CCe-eEEcCCCCccChhhHHHHHhc--CCCCCCccccee
Q 023376 227 TSLDCSICLESFTD---GDE-LICLPCKHRFHSDCLDPWVRS--CGDCPYCRRNIV 276 (283)
Q Consensus 227 ~~~~C~ICle~~~~---~~~-l~~LPCgH~FH~~CI~~WL~~--~~tCPlCR~~l~ 276 (283)
....|-||-+++.. |+. +..--|+--.|..|.. .-++ ++.||-|++...
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye-yer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE-YERREGNQACPQCKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchhh-hhhhcCCccCcccCCchh
Confidence 45689999999753 332 2222388889999983 3333 667999998654
No 171
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=23.70 E-value=51 Score=25.67 Aligned_cols=33 Identities=36% Similarity=0.736 Sum_probs=22.8
Q ss_pred CCCcCccccCccCCCCeeEEcC--CCCccChhhHHHH
Q 023376 227 TSLDCSICLESFTDGDELICLP--CKHRFHSDCLDPW 261 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~l~~LP--CgH~FH~~CI~~W 261 (283)
....|.||... .|..+.--. |...||..|...+
T Consensus 54 ~~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 54 FKLKCSICGKS--GGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred cCCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHHC
Confidence 35689999887 343333222 8889999998653
No 172
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=22.61 E-value=44 Score=34.40 Aligned_cols=37 Identities=30% Similarity=0.454 Sum_probs=25.1
Q ss_pred CCCCcCccccCccCCCC-----e-----eEEcCCCCccChhhHHHHH
Q 023376 226 KTSLDCSICLESFTDGD-----E-----LICLPCKHRFHSDCLDPWV 262 (283)
Q Consensus 226 ~~~~~C~ICle~~~~~~-----~-----l~~LPCgH~FH~~CI~~WL 262 (283)
.....|+||.|.|..-- . .+.+-=|-+||..|+..--
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~ 557 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKR 557 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccchHH
Confidence 45788999999985311 0 1223358899999987643
No 173
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=22.34 E-value=1.6e+02 Score=30.17 Aligned_cols=33 Identities=21% Similarity=0.431 Sum_probs=20.1
Q ss_pred CCCcCccccCccCCCCe-eEEcCCCCccChhhHH
Q 023376 227 TSLDCSICLESFTDGDE-LICLPCKHRFHSDCLD 259 (283)
Q Consensus 227 ~~~~C~ICle~~~~~~~-l~~LPCgH~FH~~CI~ 259 (283)
....|-.|...|..-.. --.-.||-+||..|-.
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~cs~ 933 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCSC 933 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeeccccc
Confidence 34667778777642110 1112599999999953
No 174
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=22.24 E-value=45 Score=30.51 Aligned_cols=24 Identities=21% Similarity=0.540 Sum_probs=17.3
Q ss_pred ccChhhHHHHHhcCCCCCCcccce
Q 023376 252 RFHSDCLDPWVRSCGDCPYCRRNI 275 (283)
Q Consensus 252 ~FH~~CI~~WL~~~~tCPlCR~~l 275 (283)
..|..|-.+.-++-..||+|+..-
T Consensus 250 K~ClsChqqIHRNAPiCPlCKaKs 273 (286)
T KOG4451|consen 250 KVCLSCHQQIHRNAPICPLCKAKS 273 (286)
T ss_pred hHHHHHHHHHhcCCCCCcchhhcc
Confidence 345667666667778999998753
No 175
>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=22.07 E-value=68 Score=25.74 Aligned_cols=46 Identities=24% Similarity=0.544 Sum_probs=28.5
Q ss_pred CCCcCccccCccCC--CCeeEEcCCCCccChhhHHHHHhcCC--CCCCccc
Q 023376 227 TSLDCSICLESFTD--GDELICLPCKHRFHSDCLDPWVRSCG--DCPYCRR 273 (283)
Q Consensus 227 ~~~~C~ICle~~~~--~~~l~~LPCgH~FH~~CI~~WL~~~~--tCPlCR~ 273 (283)
....|.+|...|.. +......-|.|.+|..|-.. ..... .|-+|..
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 56789999987653 33444556999999999654 11122 3888754
No 176
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=21.24 E-value=53 Score=30.44 Aligned_cols=44 Identities=16% Similarity=0.144 Sum_probs=31.8
Q ss_pred CCcCccccCccCCCCeeEEcCCCCccChhhHHHHHhcCC--CCCCccc
Q 023376 228 SLDCSICLESFTDGDELICLPCKHRFHSDCLDPWVRSCG--DCPYCRR 273 (283)
Q Consensus 228 ~~~C~ICle~~~~~~~l~~LPCgH~FH~~CI~~WL~~~~--tCPlCR~ 273 (283)
...|+|=.-.+..+... -.|||+|-..-|.+.+.... .||+--+
T Consensus 176 s~rdPis~~~I~nPviS--kkC~HvydrDsI~~~l~~~~~i~CPv~gC 221 (262)
T KOG2979|consen 176 SNRDPISKKPIVNPVIS--KKCGHVYDRDSIMQILCDEITIRCPVLGC 221 (262)
T ss_pred cccCchhhhhhhchhhh--cCcCcchhhhhHHHHhccCceeecccccC
Confidence 46788876666665433 36999999999999987743 4776443
No 177
>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=20.91 E-value=55 Score=20.27 Aligned_cols=9 Identities=33% Similarity=0.663 Sum_probs=6.4
Q ss_pred CCCCCCccc
Q 023376 265 CGDCPYCRR 273 (283)
Q Consensus 265 ~~tCPlCR~ 273 (283)
...||+|..
T Consensus 17 ~~~CP~Cg~ 25 (33)
T cd00350 17 PWVCPVCGA 25 (33)
T ss_pred CCcCcCCCC
Confidence 347999965
No 178
>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=20.83 E-value=45 Score=23.94 Aligned_cols=16 Identities=25% Similarity=0.657 Sum_probs=11.5
Q ss_pred cCCCCCCcccceecCC
Q 023376 264 SCGDCPYCRRNIVVNS 279 (283)
Q Consensus 264 ~~~tCPlCR~~l~~~~ 279 (283)
.++.||+|-.+|+.+.
T Consensus 2 ~HkHC~~CG~~Ip~~~ 17 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDE 17 (59)
T ss_pred CCCcCCcCCCcCCcch
Confidence 3677888888877653
Done!